More flexible sequence handling for reference data.

The test reference data framework now provides more flexible methods for
checking a sequence of values.  Added template methods and methods that
take iterators in addition to checking simple C-style arrays.
Also changed handling of compounds and vectors to make the output easier
to post-process.

Required regenerating the reference XML files.

Change-Id: Ib1806d6ee5e9b37165a3dc4b2e6f663088aeed07

diff --git a/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ResamplesAtDoubleBinWidth.xml b/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ResamplesAtDoubleBinWidth.xml
index b0566f10d0a633f62b89d31bd9cef1cc7b68bc45..8f2418499261957086c09c5587187afe61dac09d 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ResamplesAtDoubleBinWidth.xml
+++ b/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ResamplesAtDoubleBinWidth.xml
@@ -1,87 +1,87 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>3.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">2.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>4.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame4" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame4">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame5" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame5">
       <Real Name="X">3.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.000000</Real>
         <Real>3.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame6" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame6">
       <Real Name="X">4.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>3.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="ResampledHistogram" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="ResampledHistogram">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>3.000000</Real>
         <Real>1.414214</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>7.000000</Real>
         <Real>2.828427</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.000000</Real>
         <Real>3.162278</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ResamplesAtDoubleBinWidthWithIntegerBins.xml b/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ResamplesAtDoubleBinWidthWithIntegerBins.xml
index c21a28becad7d069b7e041d6fcd2333874879fb4..407c67c3e443ec71cf211be04b65a778d380382b 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ResamplesAtDoubleBinWidthWithIntegerBins.xml
+++ b/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ResamplesAtDoubleBinWidthWithIntegerBins.xml
@@ -1,95 +1,95 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>3.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">2.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>4.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame4" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame4">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame5" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame5">
       <Real Name="X">3.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.000000</Real>
         <Real>3.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame6" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame6">
       <Real Name="X">4.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>3.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="ResampledHistogram" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="ResampledHistogram">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>4.000000</Real>
         <Real>2.236068</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>6.000000</Real>
         <Real>2.236068</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">4.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>4.242640</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/AverageModuleTest_BasicTest.xml b/src/gromacs/analysisdata/tests/refdata/AverageModuleTest_BasicTest.xml
index aea230ca0c0b2ab288ebd8809b7fe825fd3fa065..cabe8addb2ef6c101d7d47a375c3464d446d3b16 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/AverageModuleTest_BasicTest.xml
+++ b/src/gromacs/analysisdata/tests/refdata/AverageModuleTest_BasicTest.xml
@@ -1,58 +1,58 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>1.000000</Real>
         <Real>1.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>2.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="Average" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="Average">
+    <DataFrame Name="Frame0">
       <Real Name="X">0.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>0.816497</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.666667</Real>
         <Real>0.471404</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>0.816497</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/AverageModuleTest_CanCustomizeXAxis.xml b/src/gromacs/analysisdata/tests/refdata/AverageModuleTest_CanCustomizeXAxis.xml
index 46260f94d39c06e9a21b7e0679dc4f7d965fb126..19e0bf289e34db64a8a442a92fac1b133dad52aa 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/AverageModuleTest_CanCustomizeXAxis.xml
+++ b/src/gromacs/analysisdata/tests/refdata/AverageModuleTest_CanCustomizeXAxis.xml
@@ -1,58 +1,58 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>1.000000</Real>
         <Real>1.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>2.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="Average" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="Average">
+    <DataFrame Name="Frame0">
       <Real Name="X">0.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>0.816497</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.666667</Real>
         <Real>0.471404</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">1.500000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.000000</Real>
         <Real>0.816497</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/BinAverageModuleTest_ComputesCorrectly.xml b/src/gromacs/analysisdata/tests/refdata/BinAverageModuleTest_ComputesCorrectly.xml
index 4b585ee83bb2e373235e081186da56a251ea17ea..a4dcc99f9452c612d67179f4cb4e3da8b5f24b9a 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/BinAverageModuleTest_ComputesCorrectly.xml
+++ b/src/gromacs/analysisdata/tests/refdata/BinAverageModuleTest_ComputesCorrectly.xml
@@ -1,97 +1,97 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.700000</Real>
         <Real>0.500000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.100000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.900000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.200000</Real>
         <Real>3.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>3.300000</Real>
         <Real>0.500000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.200000</Real>
         <Real>2.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="HistogramAverage" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="HistogramAverage">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>1.250000</Real>
         <Real>0.433013</Real>
         <Real>4.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>2.000000</Real>
         <Real>1.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">2.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>2.000000</Real>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/BinAverageModuleTest_ComputesCorrectlyWithAll.xml b/src/gromacs/analysisdata/tests/refdata/BinAverageModuleTest_ComputesCorrectlyWithAll.xml
index 15188a9f8326356a9f488fa68a5be12d1acf1b30..5b8c1ae86883ee866c3219183c933aba010abdb2 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/BinAverageModuleTest_ComputesCorrectlyWithAll.xml
+++ b/src/gromacs/analysisdata/tests/refdata/BinAverageModuleTest_ComputesCorrectlyWithAll.xml
@@ -1,97 +1,97 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.700000</Real>
         <Real>0.500000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.100000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.900000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.200000</Real>
         <Real>3.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>3.300000</Real>
         <Real>0.500000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.200000</Real>
         <Real>2.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="HistogramAverage" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="HistogramAverage">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>1.100000</Real>
         <Real>0.489898</Real>
         <Real>5.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>2.000000</Real>
         <Real>1.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">2.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">3</Int>
         <Real>1.250000</Real>
         <Real>0.750000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/SimpleHistogramModuleTest_ComputesCorrectly.xml b/src/gromacs/analysisdata/tests/refdata/SimpleHistogramModuleTest_ComputesCorrectly.xml
index b59421055ed9ceebd0dc8a0733918cf7d8bf943e..bcae99ff7982cf4fa3b72d7c4baf747b15ca0a73 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/SimpleHistogramModuleTest_ComputesCorrectly.xml
+++ b/src/gromacs/analysisdata/tests/refdata/SimpleHistogramModuleTest_ComputesCorrectly.xml
@@ -1,116 +1,116 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>0.700000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>1.100000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>2.300000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>2.900000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>1.300000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>2.200000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>3.300000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>1.200000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>1.300000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="Histogram" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="Histogram">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>1.000000</Real>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>1.000000</Real>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>2.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="HistogramAverage" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="HistogramAverage">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.333333</Real>
         <Real>0.471404</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.666667</Real>
         <Real>0.471404</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">2.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.333333</Real>
         <Real>0.471405</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/SimpleHistogramModuleTest_ComputesCorrectlyWithAll.xml b/src/gromacs/analysisdata/tests/refdata/SimpleHistogramModuleTest_ComputesCorrectlyWithAll.xml
index 817704c4af0cb139ec3b76c8c66139af770c257a..9424ffaec6a49a4d91487cd07c23e1c45da1cc00 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/SimpleHistogramModuleTest_ComputesCorrectlyWithAll.xml
+++ b/src/gromacs/analysisdata/tests/refdata/SimpleHistogramModuleTest_ComputesCorrectlyWithAll.xml
@@ -1,116 +1,116 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>0.700000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>1.100000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>2.300000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>2.900000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>1.300000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>2.200000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>3.300000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>1.200000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">1</Int>
         <Real>1.300000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="Histogram" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="Histogram">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>2.000000</Real>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>1.000000</Real>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>2.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="HistogramAverage" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="HistogramAverage">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.666667</Real>
         <Real>0.471405</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.666667</Real>
         <Real>0.471404</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">2.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.666667</Real>
         <Real>0.471404</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/WeightedHistogramModuleTest_ComputesCorrectly.xml b/src/gromacs/analysisdata/tests/refdata/WeightedHistogramModuleTest_ComputesCorrectly.xml
index ad055f33c34fea8d420a3a009da63931503b92f8..2907f31152571fcfbb3b585b2bf1bad0cf77f456 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/WeightedHistogramModuleTest_ComputesCorrectly.xml
+++ b/src/gromacs/analysisdata/tests/refdata/WeightedHistogramModuleTest_ComputesCorrectly.xml
@@ -1,125 +1,125 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.700000</Real>
         <Real>0.500000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.100000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.900000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.200000</Real>
         <Real>3.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>3.300000</Real>
         <Real>0.500000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.200000</Real>
         <Real>2.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="Histogram" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="Histogram">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>1.000000</Real>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>1.000000</Real>
         <Real>0.000000</Real>
         <Real>3.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>3.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="HistogramAverage" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="HistogramAverage">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.666667</Real>
         <Real>0.942809</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.333333</Real>
         <Real>1.247219</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">2.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.666667</Real>
         <Real>0.942809</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/analysisdata/tests/refdata/WeightedHistogramModuleTest_ComputesCorrectlyWithAll.xml b/src/gromacs/analysisdata/tests/refdata/WeightedHistogramModuleTest_ComputesCorrectlyWithAll.xml
index 65de6c81ff6986205fa00a91cb94a7e16df61fcd..1ad5f094b71aeb8f747850ce49b5115d596389ef 100644 (file)
--- a/src/gromacs/analysisdata/tests/refdata/WeightedHistogramModuleTest_ComputesCorrectlyWithAll.xml
+++ b/src/gromacs/analysisdata/tests/refdata/WeightedHistogramModuleTest_ComputesCorrectlyWithAll.xml
@@ -1,125 +1,125 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="InputData" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.700000</Real>
         <Real>0.500000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.100000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.900000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>2.200000</Real>
         <Real>3.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>3.300000</Real>
         <Real>0.500000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.200000</Real>
         <Real>2.000000</Real>
-      </Compound>
-      <Compound Name="Y" Subtype="SequenceReal">
+      </Sequence>
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.300000</Real>
         <Real>1.000000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="Histogram" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="Histogram">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>1.500000</Real>
         <Real>0.000000</Real>
         <Real>1.000000</Real>
         <Real>2.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">2.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>1.000000</Real>
         <Real>0.000000</Real>
         <Real>3.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">3.000000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">4</Int>
         <Real>3.000000</Real>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
         <Real>0.500000</Real>
-      </Compound>
-    </Compound>
-  </Compound>
-  <Compound Name="HistogramAverage" Subtype="AnalysisData">
-    <Compound Name="Frame0" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="HistogramAverage">
+    <DataFrame Name="Frame0">
       <Real Name="X">1.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.833333</Real>
         <Real>0.849837</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame1" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame1">
       <Real Name="X">1.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.000000</Real>
         <Real>0.000000</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame2" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame2">
       <Real Name="X">2.250000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>1.333333</Real>
         <Real>1.247219</Real>
-      </Compound>
-    </Compound>
-    <Compound Name="Frame3" Subtype="DataFrame">
+      </Sequence>
+    </DataFrame>
+    <DataFrame Name="Frame3">
       <Real Name="X">2.750000</Real>
-      <Compound Name="Y" Subtype="SequenceReal">
+      <Sequence Name="Y">
         <Int Name="Length">2</Int>
         <Real>0.833333</Real>
         <Real>0.849837</Real>
-      </Compound>
-    </Compound>
-  </Compound>
+      </Sequence>
+    </DataFrame>
+  </AnalysisData>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAllNone.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAllNone.xml
index bfb7ec3c98e0bbe3f788469af23e22a4915092c2..f5c443dbef97a92451fb878cef972cf5a5b4a4e9 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAllNone.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAllNone.xml
@@ -1,19 +1,19 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">all</String>
     <String Name="Name">all</String>
     <String Name="Text">all</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">none</String>
     <String Name="Name">none</String>
     <String Name="Text">none</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">10</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -25,11 +25,11 @@
       <Int>7</Int>
       <Int>8</Int>
       <Int>9</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">0</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesArithmeticExpressions.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesArithmeticExpressions.xml
index f2948acb237f9be1988105c29b98af3b1e013465..ed97a64326fea8a05a290efda1b3af2bf34f939f 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesArithmeticExpressions.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesArithmeticExpressions.xml
@@ -1,31 +1,31 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">x+1 &gt; 3</String>
     <String Name="Name">x+1 &gt; 3</String>
     <String Name="Text">x+1 &gt; 3</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">(y-1)^2 &lt;= 1</String>
     <String Name="Name">(y-1)^2 &lt;= 1</String>
     <String Name="Text">(y-1)^2 &lt;= 1</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">x+--1 &gt; 3</String>
     <String Name="Name">x+--1 &gt; 3</String>
     <String Name="Text">x+--1 &gt; 3</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection4Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection4Parse">
     <String Name="Input">-x+-1 &lt; -3</String>
     <String Name="Name">-x+-1 &lt; -3</String>
     <String Name="Text">-x+-1 &lt; -3</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -42,10 +42,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -62,10 +62,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -82,10 +82,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection4Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection4Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -102,10 +102,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">7</Int>
       <Int>8</Int>
       <Int>9</Int>
@@ -114,20 +114,48 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">7</Int>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>3.000000 2.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>3.000000 4.000000 0.000000</Vector>
-      <Vector>4.000000 1.000000 0.000000</Vector>
-      <Vector>4.000000 2.000000 0.000000</Vector>
-      <Vector>4.000000 3.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection2Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">8</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -137,21 +165,53 @@
       <Int>9</Int>
       <Int>12</Int>
       <Int>13</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">8</Int>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>3.000000 2.000000 0.000000</Vector>
-      <Vector>4.000000 1.000000 0.000000</Vector>
-      <Vector>4.000000 2.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection3Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">7</Int>
       <Int>8</Int>
       <Int>9</Int>
@@ -160,20 +220,48 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">7</Int>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>3.000000 2.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>3.000000 4.000000 0.000000</Vector>
-      <Vector>4.000000 1.000000 0.000000</Vector>
-      <Vector>4.000000 2.000000 0.000000</Vector>
-      <Vector>4.000000 3.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection4Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection4Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">7</Int>
       <Int>8</Int>
       <Int>9</Int>
@@ -182,16 +270,44 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">7</Int>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>3.000000 2.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>3.000000 4.000000 0.000000</Vector>
-      <Vector>4.000000 1.000000 0.000000</Vector>
-      <Vector>4.000000 2.000000 0.000000</Vector>
-      <Vector>4.000000 3.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomname.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomname.xml
index df5cf088398f73ad074b42798fb7502fe4c7f489..64558c59338e48fc40304a5187eae5173acf0b7c 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomname.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomname.xml
@@ -1,29 +1,29 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">name CB</String>
     <String Name="Name">name CB</String>
     <String Name="Text">name CB</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">name S1 S2</String>
     <String Name="Name">name S1 S2</String>
     <String Name="Text">name S1 S2</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">5</Int>
       <Int>0</Int>
       <Int>3</Int>
       <Int>6</Int>
       <Int>9</Int>
       <Int>12</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">10</Int>
       <Int>1</Int>
       <Int>2</Int>
@@ -35,6 +35,6 @@
       <Int>11</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomnr.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomnr.xml
index d0b8be0b5c53729e82a9a7c547bc1d749f6f4fb0..7cce2e024489851747eb5b9be858bfc676d43c98 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomnr.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomnr.xml
@@ -1,25 +1,25 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">atomnr 1 to 3 6 to 8</String>
     <String Name="Name">atomnr 1 to 3 6 to 8</String>
     <String Name="Text">atomnr 1 to 3 6 to 8</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">atomnr 4 2 5 to 7</String>
     <String Name="Name">atomnr 4 2 5 to 7</String>
     <String Name="Text">atomnr 4 2 5 to 7</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">atomnr &lt;= 5</String>
     <String Name="Name">atomnr &lt;= 5</String>
     <String Name="Text">atomnr &lt;= 5</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -27,26 +27,26 @@
       <Int>5</Int>
       <Int>6</Int>
       <Int>7</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">5</Int>
       <Int>1</Int>
       <Int>3</Int>
       <Int>4</Int>
       <Int>5</Int>
       <Int>6</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">5</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
       <Int>3</Int>
       <Int>4</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBasicBoolean.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBasicBoolean.xml
index a30c669793d33c091f5e219cb2ee8845c0285b4c..6f89bf8f25bc4895da0aa8b473a2260e2039d7cb 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBasicBoolean.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBasicBoolean.xml
@@ -1,34 +1,34 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">atomnr 1 to 5 and atomnr 2 to 7</String>
     <String Name="Name">atomnr 1 to 5 and atomnr 2 to 7</String>
     <String Name="Text">atomnr 1 to 5 and atomnr 2 to 7</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">atomnr 1 to 5 or not atomnr 3 to 8</String>
     <String Name="Name">atomnr 1 to 5 or not atomnr 3 to 8</String>
     <String Name="Text">atomnr 1 to 5 or not atomnr 3 to 8</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7</String>
     <String Name="Name">atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7</String>
     <String Name="Text">atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">4</Int>
       <Int>1</Int>
       <Int>2</Int>
       <Int>3</Int>
       <Int>4</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">7</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -37,14 +37,14 @@
       <Int>4</Int>
       <Int>8</Int>
       <Int>9</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">3</Int>
       <Int>2</Int>
       <Int>3</Int>
       <Int>4</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysis.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysis.xml
index 1a61687b228201192016af00eb2efa724302e381..b5b6e73e755049561426bb481e3b2e86a8055bf9 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysis.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysis.xml
@@ -1,64 +1,64 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">atomnr 1 to 5 and atomnr 2 to 7 and x &lt; 2</String>
     <String Name="Name">atomnr 1 to 5 and atomnr 2 to 7 and x &lt; 2</String>
     <String Name="Text">atomnr 1 to 5 and atomnr 2 to 7 and x &lt; 2</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">atomnr 1 to 5 and (atomnr 4 to 7 or x &lt; 2)</String>
     <String Name="Name">atomnr 1 to 5 and (atomnr 4 to 7 or x &lt; 2)</String>
     <String Name="Text">atomnr 1 to 5 and (atomnr 4 to 7 or x &lt; 2)</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">atomnr 1 to 5 and y &lt; 3 and (atomnr 4 to 7 or x &lt; 2)</String>
     <String Name="Name">atomnr 1 to 5 and y &lt; 3 and (atomnr 4 to 7 or x &lt; 2)</String>
     <String Name="Text">atomnr 1 to 5 and y &lt; 3 and (atomnr 4 to 7 or x &lt; 2)</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection4Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection4Parse">
     <String Name="Input">atomnr 1 to 5 and not (atomnr 4 to 7 or x &lt; 2)</String>
     <String Name="Name">atomnr 1 to 5 and not (atomnr 4 to 7 or x &lt; 2)</String>
     <String Name="Text">atomnr 1 to 5 and not (atomnr 4 to 7 or x &lt; 2)</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">4</Int>
       <Int>1</Int>
       <Int>2</Int>
       <Int>3</Int>
       <Int>4</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">5</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
       <Int>3</Int>
       <Int>4</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">5</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
       <Int>3</Int>
       <Int>4</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection4Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection4Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">3</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithMoreVariables.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithMoreVariables.xml
index 8a319a2a61c1d944867ef8fdb63df5409489332a..06a035077a54b7dc96fab2985b4f74a7528f9574 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithMoreVariables.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithMoreVariables.xml
@@ -1,52 +1,52 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Variable1Parse" Subtype="VariableParse">
+  <VariableParse Name="Variable1Parse">
     <String Name="Input">foo = atomnr 4 to 7</String>
-  </Compound>
-  <Compound Name="Variable2Parse" Subtype="VariableParse">
+  </VariableParse>
+  <VariableParse Name="Variable2Parse">
     <String Name="Input">bar = foo and x &lt; 2</String>
-  </Compound>
-  <Compound Name="Variable3Parse" Subtype="VariableParse">
+  </VariableParse>
+  <VariableParse Name="Variable3Parse">
     <String Name="Input">bar2 = foo and y &lt; 2</String>
-  </Compound>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  </VariableParse>
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">atomnr 1 to 4 and bar</String>
     <String Name="Name">atomnr 1 to 4 and bar</String>
     <String Name="Text">atomnr 1 to 4 and bar</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">atomnr 2 to 6 and y &lt; 3 and bar2</String>
     <String Name="Name">atomnr 2 to 6 and y &lt; 3 and bar2</String>
     <String Name="Text">atomnr 2 to 6 and y &lt; 3 and bar2</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">atomnr 6 to 10 and not foo</String>
     <String Name="Name">atomnr 6 to 10 and not foo</String>
     <String Name="Text">atomnr 6 to 10 and not foo</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">1</Int>
       <Int>3</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">3</Int>
       <Int>3</Int>
       <Int>4</Int>
       <Int>5</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">3</Int>
       <Int>7</Int>
       <Int>8</Int>
       <Int>9</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithVariables.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithVariables.xml
index a3c0f25388a48f49e46a1a01ebdc82db5c4f4dfb..568efdec64beff542679343e4b0695ed69faa770 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithVariables.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesBooleanStaticAnalysisWithVariables.xml
@@ -1,51 +1,51 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Variable1Parse" Subtype="VariableParse">
+  <VariableParse Name="Variable1Parse">
     <String Name="Input">foo = atomnr 4 to 7 or x &lt; 2</String>
-  </Compound>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  </VariableParse>
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">atomnr 1 to 4 and foo</String>
     <String Name="Name">atomnr 1 to 4 and foo</String>
     <String Name="Text">atomnr 1 to 4 and foo</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">atomnr 2 to 6 and y &lt; 3 and foo</String>
     <String Name="Name">atomnr 2 to 6 and y &lt; 3 and foo</String>
     <String Name="Text">atomnr 2 to 6 and y &lt; 3 and foo</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">atomnr 6 to 10 and not foo</String>
     <String Name="Name">atomnr 6 to 10 and not foo</String>
     <String Name="Text">atomnr 6 to 10 and not foo</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">4</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
       <Int>3</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">5</Int>
       <Int>1</Int>
       <Int>2</Int>
       <Int>3</Int>
       <Int>4</Int>
       <Int>5</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">3</Int>
       <Int>7</Int>
       <Int>8</Int>
       <Int>9</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesConstantPositions.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesConstantPositions.xml
index 407ad00ca40166cb44230056b955c27a8e6aa8e0..83b27049670a36eb02e4f0a8a3e528533e300fe1 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesConstantPositions.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesConstantPositions.xml
@@ -1,23 +1,27 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">[1, -2, 3.5]</String>
     <String Name="Name">[1, -2, 3.5]</String>
     <String Name="Text">[1, -2, 3.5]</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">0</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">0</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">1</Int>
-      <Vector>1.000000 -2.000000 3.500000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">-2.000000</Real>
+        <Real Name="Z">3.500000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesCoordinateKeywords.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesCoordinateKeywords.xml
index 038528c54d18a59ffd34d7cd7f3ba02929cab37a..e98f56f1ce2223916842ee0d062c55e2049fef7b 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesCoordinateKeywords.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesCoordinateKeywords.xml
@@ -1,25 +1,25 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">x &lt; 3</String>
     <String Name="Name">x &lt; 3</String>
     <String Name="Text">x &lt; 3</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">y &gt;= 3</String>
     <String Name="Name">y &gt;= 3</String>
     <String Name="Text">y &gt;= 3</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">x {-1 to 2}</String>
     <String Name="Name">x {-1 to 2}</String>
     <String Name="Text">x {-1 to 2}</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -36,10 +36,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -56,10 +56,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -76,10 +76,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">8</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -89,21 +89,53 @@
       <Int>5</Int>
       <Int>6</Int>
       <Int>7</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">8</Int>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection2Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">7</Int>
       <Int>2</Int>
       <Int>3</Int>
@@ -112,20 +144,48 @@
       <Int>10</Int>
       <Int>11</Int>
       <Int>14</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">7</Int>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>3.000000 4.000000 0.000000</Vector>
-      <Vector>4.000000 3.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection3Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">8</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -135,17 +195,49 @@
       <Int>5</Int>
       <Int>6</Int>
       <Int>7</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">8</Int>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesDistanceKeyword.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesDistanceKeyword.xml
index 0d5d97cf85d150625356bf078e765f0b51f0d5e6..42fa7b56f70c572ab21216f7ed545f9feee4bfd4 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesDistanceKeyword.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesDistanceKeyword.xml
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">distance from cog of resnr 1 &lt; 2</String>
     <String Name="Name">distance from cog of resnr 1 &lt; 2</String>
     <String Name="Text">distance from cog of resnr 1 &lt; 2</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -24,10 +24,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -35,15 +35,39 @@
       <Int>4</Int>
       <Int>5</Int>
       <Int>6</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">6</Int>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesMergeModifier.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesMergeModifier.xml
index 9108a2172458134f0ee08a8af8a834e773212ad7..1a85139a6168b4fe02387d599d73399482f4573b 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesMergeModifier.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesMergeModifier.xml
@@ -1,19 +1,19 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">name S2 merge name S1</String>
     <String Name="Name">name S2 merge name S1</String>
     <String Name="Text">name S2 merge name S1</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">name S2 merge name S1 merge name CB</String>
     <String Name="Name">name S2 merge name S1 merge name CB</String>
     <String Name="Text">name S2 merge name S1 merge name CB</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">10</Int>
       <Int>2</Int>
       <Int>1</Int>
@@ -25,10 +25,10 @@
       <Int>10</Int>
       <Int>14</Int>
       <Int>13</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>2</Int>
       <Int>1</Int>
@@ -45,10 +45,10 @@
       <Int>14</Int>
       <Int>13</Int>
       <Int>12</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">10</Int>
       <Int>2</Int>
       <Int>1</Int>
@@ -60,23 +60,63 @@
       <Int>10</Int>
       <Int>14</Int>
       <Int>13</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">10</Int>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>4.000000 3.000000 0.000000</Vector>
-      <Vector>4.000000 2.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection2Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>2</Int>
       <Int>1</Int>
@@ -93,24 +133,84 @@
       <Int>14</Int>
       <Int>13</Int>
       <Int>12</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">15</Int>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>1.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-      <Vector>3.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>3.000000 2.000000 0.000000</Vector>
-      <Vector>4.000000 3.000000 0.000000</Vector>
-      <Vector>4.000000 2.000000 0.000000</Vector>
-      <Vector>4.000000 1.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesMinDistanceKeyword.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesMinDistanceKeyword.xml
index eacce2d990440bbb14883202bbbb718580f97b47..e8c1458e00980800a7890bcf20ea373cfb5fb6fa 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesMinDistanceKeyword.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesMinDistanceKeyword.xml
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">mindistance from resnr 1 &lt; 2</String>
     <String Name="Name">mindistance from resnr 1 &lt; 2</String>
     <String Name="Text">mindistance from resnr 1 &lt; 2</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -24,10 +24,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">8</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -37,17 +37,49 @@
       <Int>5</Int>
       <Int>6</Int>
       <Int>7</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">8</Int>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPermuteModifier.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPermuteModifier.xml
index fb59f6371ab9aeff68f3a520c9aa2cb7781d7de1..2eb312e097cc9021c4dee8ffeb59962ab5a44eba 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPermuteModifier.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPermuteModifier.xml
@@ -1,25 +1,25 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">all permute 3 1 2</String>
     <String Name="Name">all permute 3 1 2</String>
     <String Name="Text">all permute 3 1 2</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">res_cog of resnr 1 to 4 permute 2 1</String>
     <String Name="Name">res_cog of resnr 1 to 4 permute 2 1</String>
     <String Name="Text">res_cog of resnr 1 to 4 permute 2 1</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">name CB S1 and res_cog x &lt; 3 permute 2 1</String>
     <String Name="Name">name CB S1 and res_cog x &lt; 3 permute 2 1</String>
     <String Name="Text">name CB S1 and res_cog x &lt; 3 permute 2 1</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>1</Int>
       <Int>2</Int>
@@ -36,8 +36,8 @@
       <Int>13</Int>
       <Int>14</Int>
       <Int>12</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">16</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -55,10 +55,10 @@
       <Int>13</Int>
       <Int>14</Int>
       <Int>15</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">12</Int>
       <Int>3</Int>
       <Int>4</Int>
@@ -72,18 +72,18 @@
       <Int>6</Int>
       <Int>7</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">5</Int>
       <Int>0</Int>
       <Int>3</Int>
       <Int>6</Int>
       <Int>9</Int>
       <Int>12</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">10</Int>
       <Int>1</Int>
       <Int>0</Int>
@@ -95,8 +95,8 @@
       <Int>9</Int>
       <Int>13</Int>
       <Int>12</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">11</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -109,10 +109,10 @@
       <Int>8</Int>
       <Int>9</Int>
       <Int>10</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>1</Int>
       <Int>2</Int>
@@ -129,8 +129,8 @@
       <Int>13</Int>
       <Int>14</Int>
       <Int>12</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">16</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -148,28 +148,88 @@
       <Int>13</Int>
       <Int>14</Int>
       <Int>15</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">15</Int>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>3.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 2.000000 0.000000</Vector>
-      <Vector>4.000000 2.000000 0.000000</Vector>
-      <Vector>4.000000 3.000000 0.000000</Vector>
-      <Vector>4.000000 1.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection2Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">12</Int>
       <Int>3</Int>
       <Int>4</Int>
@@ -183,25 +243,41 @@
       <Int>6</Int>
       <Int>7</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">5</Int>
       <Int>0</Int>
       <Int>3</Int>
       <Int>6</Int>
       <Int>9</Int>
       <Int>12</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">4</Int>
-      <Vector>1.666667 2.333333 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>2.333333 2.666667 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.666667</Real>
+        <Real Name="Y">2.333333</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.333333</Real>
+        <Real Name="Y">2.666667</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection3Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>1</Int>
       <Int>0</Int>
@@ -209,8 +285,8 @@
       <Int>3</Int>
       <Int>7</Int>
       <Int>6</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">7</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -219,15 +295,39 @@
       <Int>4</Int>
       <Int>5</Int>
       <Int>6</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">6</Int>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>1.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPlusModifier.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPlusModifier.xml
index 3c8cee01e7992e18ff355c368cfe0d356db013fb..31e361e50a6b86a36eef91feffdbe76759df6b3d 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPlusModifier.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPlusModifier.xml
@@ -1,19 +1,19 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">name S2 plus name S1</String>
     <String Name="Name">name S2 plus name S1</String>
     <String Name="Text">name S2 plus name S1</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3</String>
     <String Name="Name">res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3</String>
     <String Name="Text">res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">10</Int>
       <Int>2</Int>
       <Int>5</Int>
@@ -25,8 +25,8 @@
       <Int>7</Int>
       <Int>10</Int>
       <Int>13</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">11</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -39,10 +39,10 @@
       <Int>8</Int>
       <Int>9</Int>
       <Int>10</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">9</Int>
       <Int>3</Int>
       <Int>4</Int>
@@ -53,17 +53,17 @@
       <Int>6</Int>
       <Int>7</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">4</Int>
       <Int>0</Int>
       <Int>3</Int>
       <Int>6</Int>
       <Int>9</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">10</Int>
       <Int>2</Int>
       <Int>5</Int>
@@ -75,8 +75,8 @@
       <Int>7</Int>
       <Int>10</Int>
       <Int>13</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">11</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -89,23 +89,63 @@
       <Int>8</Int>
       <Int>9</Int>
       <Int>10</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">10</Int>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>3.000000 4.000000 0.000000</Vector>
-      <Vector>4.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 3.000000 0.000000</Vector>
-      <Vector>4.000000 2.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">4.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection2Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">9</Int>
       <Int>3</Int>
       <Int>4</Int>
@@ -116,19 +156,31 @@
       <Int>6</Int>
       <Int>7</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">4</Int>
       <Int>0</Int>
       <Int>3</Int>
       <Int>6</Int>
       <Int>9</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">3</Int>
-      <Vector>1.666667 2.333333 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>2.333333 2.666667 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.666667</Real>
+        <Real Name="Y">2.333333</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.333333</Real>
+        <Real Name="Y">2.666667</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPositionKeywords.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPositionKeywords.xml
index 88572dc7b8202c8ec07d3290c24e3d2093f0858d..00bf5ce312fc128943087f46fb226ce8792596b1 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPositionKeywords.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesPositionKeywords.xml
@@ -1,37 +1,37 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">cog of resnr 1 3</String>
     <String Name="Name">cog of resnr 1 3</String>
     <String Name="Text">cog of resnr 1 3</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">res_cog of name CB and resnr 1 3</String>
     <String Name="Name">res_cog of name CB and resnr 1 3</String>
     <String Name="Text">res_cog of name CB and resnr 1 3</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection3Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection3Parse">
     <String Name="Input">whole_res_cog of name CB and resnr 1 3</String>
     <String Name="Name">whole_res_cog of name CB and resnr 1 3</String>
     <String Name="Text">whole_res_cog of name CB and resnr 1 3</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection4Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection4Parse">
     <String Name="Input">part_res_cog of x &lt; 3</String>
     <String Name="Name">part_res_cog of x &lt; 3</String>
     <String Name="Text">part_res_cog of x &lt; 3</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection5Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection5Parse">
     <String Name="Input">dyn_res_cog of x &lt; 3</String>
     <String Name="Name">dyn_res_cog of x &lt; 3</String>
     <String Name="Text">dyn_res_cog of x &lt; 3</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -39,41 +39,41 @@
       <Int>6</Int>
       <Int>7</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">2</Int>
       <Int>0</Int>
       <Int>6</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">2</Int>
       <Int>0</Int>
       <Int>6</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">3</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection3Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">2</Int>
       <Int>0</Int>
       <Int>6</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">3</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection4Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection4Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -90,8 +90,8 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">6</Int>
       <Int>0</Int>
       <Int>3</Int>
@@ -99,10 +99,10 @@
       <Int>9</Int>
       <Int>12</Int>
       <Int>15</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection5Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection5Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -119,8 +119,8 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">6</Int>
       <Int>0</Int>
       <Int>3</Int>
@@ -128,10 +128,10 @@
       <Int>9</Int>
       <Int>12</Int>
       <Int>15</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -139,55 +139,75 @@
       <Int>6</Int>
       <Int>7</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">2</Int>
       <Int>0</Int>
       <Int>6</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">1</Int>
-      <Vector>1.666667 2.333333 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.666667</Real>
+        <Real Name="Y">2.333333</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection2Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">2</Int>
       <Int>0</Int>
       <Int>6</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">3</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">2</Int>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection3Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection3Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">2</Int>
       <Int>0</Int>
       <Int>6</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">3</Int>
       <Int>0</Int>
       <Int>1</Int>
       <Int>2</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">2</Int>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>2.333333 2.666667 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection4Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.333333</Real>
+        <Real Name="Y">2.666667</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection4Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">8</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -197,23 +217,35 @@
       <Int>5</Int>
       <Int>6</Int>
       <Int>7</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">4</Int>
       <Int>0</Int>
       <Int>3</Int>
       <Int>6</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">3</Int>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.666667 2.333333 0.000000</Vector>
-      <Vector>2.333333 2.666667 0.000000</Vector>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection5Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.666667</Real>
+        <Real Name="Y">2.333333</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.333333</Real>
+        <Real Name="Y">2.666667</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
+  <SelectionFrame Name="Selection5Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">8</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -223,19 +255,31 @@
       <Int>5</Int>
       <Int>6</Int>
       <Int>7</Int>
-    </Compound>
-    <Compound Name="PositionBlocks" Subtype="SequenceInteger">
+    </Sequence>
+    <Sequence Name="PositionBlocks">
       <Int Name="Length">4</Int>
       <Int>0</Int>
       <Int>3</Int>
       <Int>6</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">3</Int>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.666667 2.333333 0.000000</Vector>
-      <Vector>2.000000 3.500000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.666667</Real>
+        <Real Name="Y">2.333333</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.500000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesRegexMatching.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesRegexMatching.xml
index a8a8540abab2e0dc69c06f1caa7814b7345c8e04..2f863067e8cc00de43be1be24141a96c0d555835 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesRegexMatching.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesRegexMatching.xml
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">resname "R[BD]"</String>
     <String Name="Name">resname "R[BD]"</String>
     <String Name="Text">resname "R[BD]"</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>3</Int>
       <Int>4</Int>
@@ -15,6 +15,6 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResname.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResname.xml
index bbaa1f9b3ddec96d5dcb1f3472f2d20fd9a2d7f5..bb20c401fec264090584dece7f26fee2c000888b 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResname.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResname.xml
@@ -1,19 +1,19 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">resname RA</String>
     <String Name="Name">resname RA</String>
     <String Name="Text">resname RA</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">resname RB RC</String>
     <String Name="Name">resname RB RC</String>
     <String Name="Text">resname RB RC</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -21,10 +21,10 @@
       <Int>6</Int>
       <Int>7</Int>
       <Int>8</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>3</Int>
       <Int>4</Int>
@@ -32,6 +32,6 @@
       <Int>9</Int>
       <Int>10</Int>
       <Int>11</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResnr.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResnr.xml
index e983090677683c062db0ac556f83eae0c354c5ce..a4441d10c074cebfcc1bdfcd648e2ad5227d1427 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResnr.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResnr.xml
@@ -1,19 +1,19 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">resnr 1 2 5</String>
     <String Name="Name">resnr 1 2 5</String>
     <String Name="Text">resnr 1 2 5</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection2Parse" Subtype="SelectionParse">
+  </SelectionParse>
+  <SelectionParse Name="Selection2Parse">
     <String Name="Input">resnr 4 to 3</String>
     <String Name="Name">resnr 4 to 3</String>
     <String Name="Text">resnr 4 to 3</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">9</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -24,10 +24,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection2Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionCompile Name="Selection2Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">6</Int>
       <Int>6</Int>
       <Int>7</Int>
@@ -35,6 +35,6 @@
       <Int>9</Int>
       <Int>10</Int>
       <Int>11</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesSameResidue.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesSameResidue.xml
index 5469fdf8fabd4a6eecf677b531e3b7181593f18a..9120c75393b2b649255582301cc700382227ee2a 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesSameResidue.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesSameResidue.xml
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">same residue as atomnr 1 4 12</String>
     <String Name="Name">same residue as atomnr 1 4 12</String>
     <String Name="Text">same residue as atomnr 1 4 12</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">9</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -18,6 +18,6 @@
       <Int>9</Int>
       <Int>10</Int>
       <Int>11</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesSameResidueName.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesSameResidueName.xml
index e3b07c45992bca82043709c0d985c51967ececdb..6e0c6b5aba2a50c822da0a7ca368becba1bf7591 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesSameResidueName.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesSameResidueName.xml
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">same resname as atomnr 1 14</String>
     <String Name="Name">same resname as atomnr 1 14</String>
     <String Name="Text">same resname as atomnr 1 14</String>
     <Bool Name="Dynamic">false</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">9</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -18,6 +18,6 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
+    </Sequence>
+  </SelectionCompile>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesWithinConstantPositions.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesWithinConstantPositions.xml
index 7277310ab4d9674545c4590cea2ba0274767e603..5d608cda00ca5f0b2b3e2f5ea412c7b0dc4f4c3c 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesWithinConstantPositions.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesWithinConstantPositions.xml
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">within 1 of [2, 1, 0]</String>
     <String Name="Name">within 1 of [2, 1, 0]</String>
     <String Name="Text">within 1 of [2, 1, 0]</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -24,22 +24,38 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">4</Int>
       <Int>0</Int>
       <Int>4</Int>
       <Int>5</Int>
       <Int>8</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">4</Int>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesWithinKeyword.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesWithinKeyword.xml
index 0b3a3e0f3907b5231ec14520d103c25696a0d823..572e38bb1d68af2089254bdd3a3a4f02a683cfa2 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesWithinKeyword.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesWithinKeyword.xml
@@ -1,13 +1,13 @@
 <?xml version="1.0"?>
 <ReferenceData>
-  <Compound Name="Selection1Parse" Subtype="SelectionParse">
+  <SelectionParse Name="Selection1Parse">
     <String Name="Input">within 1 of resnr 2</String>
     <String Name="Name">within 1 of resnr 2</String>
     <String Name="Text">within 1 of resnr 2</String>
     <Bool Name="Dynamic">true</Bool>
-  </Compound>
-  <Compound Name="Selection1Compile" Subtype="SelectionCompile">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+  </SelectionParse>
+  <SelectionCompile Name="Selection1Compile">
+    <Sequence Name="Atoms">
       <Int Name="Length">15</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -24,10 +24,10 @@
       <Int>12</Int>
       <Int>13</Int>
       <Int>14</Int>
-    </Compound>
-  </Compound>
-  <Compound Name="Selection1Frame1" Subtype="SelectionFrame">
-    <Compound Name="Atoms" Subtype="SequenceInteger">
+    </Sequence>
+  </SelectionCompile>
+  <SelectionFrame Name="Selection1Frame1">
+    <Sequence Name="Atoms">
       <Int Name="Length">10</Int>
       <Int>0</Int>
       <Int>1</Int>
@@ -39,19 +39,59 @@
       <Int>7</Int>
       <Int>8</Int>
       <Int>9</Int>
-    </Compound>
-    <Compound Name="Positions" Subtype="SequenceVector">
+    </Sequence>
+    <Sequence Name="Positions">
       <Int Name="Length">10</Int>
-      <Vector>1.000000 1.000000 0.000000</Vector>
-      <Vector>1.000000 2.000000 0.000000</Vector>
-      <Vector>1.000000 3.000000 0.000000</Vector>
-      <Vector>1.000000 4.000000 0.000000</Vector>
-      <Vector>2.000000 1.000000 0.000000</Vector>
-      <Vector>2.000000 2.000000 0.000000</Vector>
-      <Vector>2.000000 3.000000 0.000000</Vector>
-      <Vector>2.000000 4.000000 0.000000</Vector>
-      <Vector>3.000000 1.000000 0.000000</Vector>
-      <Vector>3.000000 2.000000 0.000000</Vector>
-    </Compound>
-  </Compound>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">3.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.000000</Real>
+        <Real Name="Y">4.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">1.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.000000</Real>
+        <Real Name="Y">2.000000</Real>
+        <Real Name="Z">0.000000</Real>
+      </Vector>
+    </Sequence>
+  </SelectionFrame>
 </ReferenceData>

diff --git a/src/testutils/refdata-impl.h b/src/testutils/refdata-impl.h
index 7c9dd7b81b02305f261d955e7128966b5f25b653..422e6753e5c6d81e8c8a94f61a7a56bc0990c103 100644 (file)
--- a/src/testutils/refdata-impl.h
+++ b/src/testutils/refdata-impl.h
@@ -91,18 +91,13 @@ class TestReferenceData::Impl
 class TestReferenceChecker::Impl
 {
     public:
-        static const xmlChar * const cCompoundNodeName;
         static const xmlChar * const cBooleanNodeName;
         static const xmlChar * const cStringNodeName;
         static const xmlChar * const cIntegerNodeName;
         static const xmlChar * const cRealNodeName;
-        static const xmlChar * const cVectorIntegerNodeName;
-        static const xmlChar * const cVectorRealNodeName;
         static const xmlChar * const cIdAttrName;
-        static const xmlChar * const cCompoundTypeAttrName;
-        static const char * const cSequenceIntegerType;
-        static const char * const cSequenceRealType;
-        static const char * const cSequenceVectorType;
+        static const char * const cVectorType;
+        static const char * const cSequenceType;
         static const char * const cSequenceLengthName;
 
         //! Creates a checker that does nothing.

diff --git a/src/testutils/refdata.cpp b/src/testutils/refdata.cpp
index 873bf3f2f527c8abc6c4f8569bb47b4a62f96f1d..7314b7988f29febbe3893f5f66fadc70d42ea8f5 100644 (file)
--- a/src/testutils/refdata.cpp
+++ b/src/testutils/refdata.cpp
@@ -90,8 +90,6 @@ const xmlChar * const TestReferenceData::Impl::cXmlVersion =
     (const xmlChar *)"1.0";
 const xmlChar * const TestReferenceData::Impl::cRootNodeName =
     (const xmlChar *)"ReferenceData";
-const xmlChar * const TestReferenceChecker::Impl::cCompoundNodeName =
-    (const xmlChar *)"Compound";
 const xmlChar * const TestReferenceChecker::Impl::cBooleanNodeName =
     (const xmlChar *)"Bool";
 const xmlChar * const TestReferenceChecker::Impl::cStringNodeName =
@@ -100,20 +98,12 @@ const xmlChar * const TestReferenceChecker::Impl::cIntegerNodeName  =
     (const xmlChar *)"Int";
 const xmlChar * const TestReferenceChecker::Impl::cRealNodeName =
     (const xmlChar *)"Real";
-const xmlChar * const TestReferenceChecker::Impl::cVectorIntegerNodeName =
-    (const xmlChar *)"Vector";
-const xmlChar * const TestReferenceChecker::Impl::cVectorRealNodeName =
-    (const xmlChar *)"Vector";
 const xmlChar * const TestReferenceChecker::Impl::cIdAttrName =
     (const xmlChar *)"Name";
-const xmlChar * const TestReferenceChecker::Impl::cCompoundTypeAttrName =
-    (const xmlChar *)"Subtype";
-const char * const TestReferenceChecker::Impl::cSequenceIntegerType =
-    "SequenceInteger";
-const char * const TestReferenceChecker::Impl::cSequenceRealType =
-    "SequenceReal";
-const char * const TestReferenceChecker::Impl::cSequenceVectorType =
-    "SequenceVector";
+const char * const TestReferenceChecker::Impl::cVectorType =
+    "Vector";
+const char * const TestReferenceChecker::Impl::cSequenceType =
+    "Sequence";
 const char * const TestReferenceChecker::Impl::cSequenceLengthName =
     "Length";
 
@@ -431,21 +421,14 @@ TestReferenceChecker TestReferenceChecker::checkCompound(const char *type, const
     {
         return TestReferenceChecker(new Impl(isWriteMode()));
     }
-    xmlNodePtr newNode = _impl->findOrCreateNode(Impl::cCompoundNodeName, id);
+    const xmlChar *xmlNodeName = reinterpret_cast<const xmlChar *>(type);
+    xmlNodePtr newNode = _impl->findOrCreateNode(xmlNodeName, id);
     if (newNode == NULL)
     {
         GMX_RELEASE_ASSERT(!isWriteMode(), "Node creation failed without exception");
         ADD_FAILURE() << "Reference data item not found";
         return TestReferenceChecker(new Impl(isWriteMode()));
     }
-    if (isWriteMode())
-    {
-        if (xmlNewProp(newNode, Impl::cCompoundTypeAttrName,
-                       reinterpret_cast<const xmlChar *>(type)) == NULL)
-        {
-            GMX_THROW(TestException("XML property creation failed"));
-        }
-    }
     return TestReferenceChecker(
             new Impl(_impl->appendPath(id), newNode, isWriteMode()));
 }
@@ -553,146 +536,37 @@ void TestReferenceChecker::checkReal(double value, const char *id)
 
 void TestReferenceChecker::checkVector(const int value[3], const char *id)
 {
-    if (_impl->shouldIgnore())
-    {
-        return;
-    }
-    SCOPED_TRACE(_impl->traceString(id));
-    bool bFound = false;
-    char strValue[50];
-    snprintf(strValue, 50, "%d %d %d", value[0], value[1], value[2]);
-    std::string refStrValue =
-        _impl->processItem(Impl::cVectorIntegerNodeName, id, strValue, &bFound);
-    if (bFound)
-    {
-        EXPECT_EQ(refStrValue, strValue);
-    }
+    TestReferenceChecker compound(checkCompound(Impl::cVectorType, id));
+    compound.checkInteger(value[0], "X");
+    compound.checkInteger(value[1], "Y");
+    compound.checkInteger(value[2], "Z");
 }
 
 
 void TestReferenceChecker::checkVector(const float value[3], const char *id)
 {
-    if (_impl->shouldIgnore())
-    {
-        return;
-    }
-    SCOPED_TRACE(_impl->traceString(id));
-    bool bFound = false;
-    char strValue[50];
-    snprintf(strValue, 50, "%f %f %f", value[0], value[1], value[2]);
-    std::string refStrValue =
-        _impl->processItem(Impl::cVectorRealNodeName, id, strValue, &bFound);
-    if (bFound)
-    {
-        float refX, refY, refZ;
-        int count = std::sscanf(refStrValue.c_str(), " %g %g %g", &refX, &refY, &refZ);
-        if (count != 3)
-        {
-            GMX_THROW(TestException("Corrupt reference vector data"));
-        }
-        EXPECT_NEAR(refX, value[0], 0.0001);
-        EXPECT_NEAR(refY, value[1], 0.0001);
-        EXPECT_NEAR(refZ, value[2], 0.0001);
-    }
+    TestReferenceChecker compound(checkCompound(Impl::cVectorType, id));
+    compound.checkReal(value[0], "X");
+    compound.checkReal(value[1], "Y");
+    compound.checkReal(value[2], "Z");
 }
 
 
 void TestReferenceChecker::checkVector(const double value[3], const char *id)
 {
-    if (_impl->shouldIgnore())
-    {
-        return;
-    }
-    SCOPED_TRACE(_impl->traceString(id));
-    bool bFound = false;
-    char strValue[50];
-    snprintf(strValue, 50, "%f %f %f", value[0], value[1], value[2]);
-    std::string refStrValue =
-        _impl->processItem(Impl::cVectorRealNodeName, id, strValue, &bFound);
-    if (bFound)
-    {
-        double refX, refY, refZ;
-        int count = std::sscanf(refStrValue.c_str(), " %lg %lg %lg", &refX, &refY, &refZ);
-        if (count != 3)
-        {
-            GMX_THROW(TestException("Corrupt reference vector data"));
-        }
-        EXPECT_NEAR(refX, value[0], 0.0001);
-        EXPECT_NEAR(refY, value[1], 0.0001);
-        EXPECT_NEAR(refZ, value[2], 0.0001);
-    }
-}
-
-
-void TestReferenceChecker::checkSequenceArray(size_t length, const int *values,
-                                              const char *id)
-{
-    TestReferenceChecker compound(checkCompound(Impl::cSequenceIntegerType, id));
-    compound.checkInteger(static_cast<int>(length), Impl::cSequenceLengthName);
-    for (size_t i = 0; i < length; ++i)
-    {
-        compound.checkInteger(values[i], NULL);
-    }
-}
-
-
-void TestReferenceChecker::checkSequenceArray(size_t length, const float *values,
-                                              const char *id)
-{
-    TestReferenceChecker compound(checkCompound(Impl::cSequenceRealType, id));
-    compound.checkInteger(static_cast<int>(length), Impl::cSequenceLengthName);
-    for (size_t i = 0; i < length; ++i)
-    {
-        compound.checkFloat(values[i], NULL);
-    }
-}
-
-
-void TestReferenceChecker::checkSequenceArray(size_t length, const double *values,
-                                              const char *id)
-{
-    TestReferenceChecker compound(checkCompound(Impl::cSequenceRealType, id));
-    compound.checkInteger(static_cast<int>(length), Impl::cSequenceLengthName);
-    for (size_t i = 0; i < length; ++i)
-    {
-        compound.checkDouble(values[i], NULL);
-    }
-}
-
-
-void TestReferenceChecker::checkSequenceArray(size_t length, const int values[][3],
-                                              const char *id)
-{
-    TestReferenceChecker compound(checkCompound(Impl::cSequenceVectorType, id));
-    compound.checkInteger(static_cast<int>(length), Impl::cSequenceLengthName);
-    for (size_t i = 0; i < length; ++i)
-    {
-        compound.checkVector(values[i], NULL);
-    }
+    TestReferenceChecker compound(checkCompound(Impl::cVectorType, id));
+    compound.checkReal(value[0], "X");
+    compound.checkReal(value[1], "Y");
+    compound.checkReal(value[2], "Z");
 }
 
 
-void TestReferenceChecker::checkSequenceArray(size_t length, const float values[][3],
-                                              const char *id)
+TestReferenceChecker
+TestReferenceChecker::checkSequenceCompound(const char *id, size_t length)
 {
-    TestReferenceChecker compound(checkCompound(Impl::cSequenceVectorType, id));
+    TestReferenceChecker compound(checkCompound(Impl::cSequenceType, id));
     compound.checkInteger(static_cast<int>(length), Impl::cSequenceLengthName);
-    for (size_t i = 0; i < length; ++i)
-    {
-        compound.checkVector(values[i], NULL);
-    }
-}
-
-
-void TestReferenceChecker::checkSequenceArray(size_t length, const double values[][3],
-                                             const char *id)
-{
-    TestReferenceChecker compound(checkCompound(Impl::cSequenceVectorType, id));
-    compound.checkInteger(static_cast<int>(length), Impl::cSequenceLengthName);
-    for (size_t i = 0; i < length; ++i)
-    {
-        compound.checkVector(values[i], NULL);
-    }
+    return compound;
 }
 
 } // namespace test

diff --git a/src/testutils/refdata.h b/src/testutils/refdata.h
index 39187a0f338b1af71f748f36c060a2e2a6914af9..188315c9855efeca609d3d99cc56fd559f7ac966 100644 (file)
--- a/src/testutils/refdata.h
+++ b/src/testutils/refdata.h
@@ -39,6 +39,7 @@
 #ifndef GMX_TESTUTILS_REFDATA_H
 #define GMX_TESTUTILS_REFDATA_H
 
+#include <iterator>
 #include <string>
 
 namespace gmx
@@ -293,24 +294,164 @@ class TestReferenceChecker
         void checkVector(const float value[3], const char *id);
         //! Check a vector of three double-precision floating point values.
         void checkVector(const double value[3], const char *id);
-        //! Check an arbitrary-length sequence of integer values.
-        void checkSequenceArray(size_t length, const int *values,
-                                const char *id);
-        //! Check an arbitrary-length sequence of floating-point values.
-        void checkSequenceArray(size_t length, const float *values,
-                                const char *id);
-        //! Check an arbitrary-length sequence of floating-point values.
-        void checkSequenceArray(size_t length, const double *values,
-                                const char *id);
-        //! Check an arbitrary-length sequence of integer vector values.
-        void checkSequenceArray(size_t length, const int values[][3],
-                                const char *id);
-        //! Check an arbitrary-length sequence of floating-point vector values.
-        void checkSequenceArray(size_t length, const float values[][3],
-                                const char *id);
-        //! Check an arbitrary-length sequence of floating-point vector values.
-        void checkSequenceArray(size_t length, const double values[][3],
-                                const char *id);
+
+        /*! \name Overloaded versions of simple checker methods
+         *
+         * These methods provide overloads under a single name for all the
+         * methods checkBoolean(), checkString(), checkReal() and checkVector().
+         * They are provided mainly to allow template implementations (such as
+         * checkSequence()).  Typically callers should use the individually
+         * named versions for greater clarity.
+         * \{
+         */
+        //! Check a single boolean value.
+        void checkValue(bool value, const char *id)
+        {
+            checkBoolean(value, id);
+        }
+        //! Check a single string value.
+        void checkValue(const char *value, const char *id)
+        {
+            checkString(value, id);
+        }
+        //! Check a single string value.
+        void checkValue(const std::string &value, const char *id)
+        {
+            checkString(value, id);
+        }
+        //! Check a single integer value.
+        void checkValue(int value, const char *id)
+        {
+            checkInteger(value, id);
+        }
+        //! Check a single single-precision floating point value.
+        void checkValue(float value, const char *id)
+        {
+            checkFloat(value, id);
+        }
+        //! Check a single double-precision floating point value.
+        void checkValue(double value, const char *id)
+        {
+            checkDouble(value, id);
+        }
+        //! Check a vector of three integer values.
+        void checkValue(const int value[3], const char *id)
+        {
+            checkVector(value, id);
+        }
+        //! Check a vector of three single-precision floating point values.
+        void checkValue(const float value[3], const char *id)
+        {
+            checkVector(value, id);
+        }
+        //! Check a vector of three double-precision floating point values.
+        void checkValue(const double value[3], const char *id)
+        {
+            checkVector(value, id);
+        }
+        /*!\}*/
+
+        /*! \brief
+         * Generic method to check a sequence of simple values.
+         *
+         * \tparam Iterator  Input iterator that allows multiple (two) passes.
+         *      Value type must be one of those accepted by checkValue(), or
+         *      implicitly convertible to one.
+         * \param[in] begin  Iterator to the start of the range to check.
+         * \param[in] end    Iterator to the end of the range to check.
+         * \param[in] id     Unique identifier for the sequence among its
+         *                   siblings.
+         */
+        template <class Iterator>
+        void checkSequence(Iterator begin, Iterator end, const char *id)
+        {
+            typename std::iterator_traits<Iterator>::difference_type length
+                = std::distance(begin, end);
+            TestReferenceChecker compound(checkSequenceCompound(id, length));
+            for (Iterator i = begin; i != end; ++i)
+            {
+                compound.checkValue(*i, NULL);
+            }
+        }
+        /*! \brief
+         * Generic method to check a sequence of custom values.
+         *
+         * \tparam Iterator    Input iterator that allows multiple (two) passes.
+         * \tparam ItemChecker Functor to check an individual value. Signature
+         *      void(TestReferenceChecker *, const T &), where T is the value
+         *      type of \p Iterator.
+         * \param[in] begin  Iterator to the start of the range to check.
+         * \param[in] end    Iterator to the end of the range to check.
+         * \param[in] id     Unique identifier for the sequence among its
+         *                   siblings.
+         * \param[in] checkItem  Functor to check an individual item.
+         *
+         * This method creates a compound checker \c compound within which all
+         * values of the sequence are checked.  Calls checkItem(&compound, *i)
+         * with that compound for each iterator \c i in the range [begin, end).
+         * \p checkItem should use check*() methods in the passed checker to
+         * check the each value.
+         *
+         * This method can be used to check a sequence made of compound types.
+         * Typically \p checkItem will create a compound within the passed
+         * checker to check different aspects of the passed in value.
+         */
+        template <class Iterator, class ItemChecker>
+        void checkSequence(Iterator begin, Iterator end, const char *id,
+                           ItemChecker checkItem)
+        {
+            typename std::iterator_traits<Iterator>::difference_type length
+                = std::distance(begin, end);
+            TestReferenceChecker compound(checkSequenceCompound(id, length));
+            for (Iterator i = begin; i != end; ++i)
+            {
+                checkItem(&compound, *i);
+            }
+        }
+        /*! \brief
+         * Check an array of values.
+         *
+         * \tparam T  Type of values to check. Should be one of those accepted
+         *      by checkValue(), or implicitly convertible to one.
+         *
+         * \param[in] length  Number of values to check.
+         * \param[in] values  Pointer to the first value to check.
+         * \param[in] id     Unique identifier for the sequence among its
+         *                   siblings.
+         *
+         * This is a convenience method that delegates all work to
+         * checkSequence().
+         */
+        template <typename T>
+        void checkSequenceArray(size_t length, const T *values, const char *id)
+        {
+            checkSequence(values, values + length, id);
+        }
+        /*! \brief
+         * Convenience method for checking that a sequence is empty.
+         *
+         * \param[in] id     Unique identifier for the sequence among its
+         *                   siblings.
+         *
+         * This method provides a convenient solution for a case where there is
+         * implicitly a sequence to be checked, but there is no pointer
+         * available to the values since the sequence is empty.
+         * Since this method does not require the type of the values, it can be
+         * used in such cases easily.
+         */
+        void checkEmptySequence(const char *id);
+        /*! \brief
+         * Initializes a compound for a sequence of items.
+         *
+         * \param[in] id     Unique identifier for the sequence among its
+         *                   siblings.
+         * \param[in] length Number of items that will be in the sequence.
+         * \returns   Checker to use for comparison within the sequence.
+         *
+         * This method can be used to check custom sequences where
+         * checkSequence() is not appropriate.
+         */
+        TestReferenceChecker checkSequenceCompound(const char *id, size_t length);
 
     private:
         class Impl;