*/
package jalview.structures.models;
+import static org.testng.Assert.assertFalse;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
import jalview.api.AlignmentViewPanel;
import jalview.api.SequenceRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
+import jalview.io.FileFormats;
import jalview.schemes.ColourSchemeI;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel.SuperposeData;
import java.awt.Color;
+import java.io.IOException;
import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
+ "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
+ "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
+ /**
+ * Multichain PDB with identical sequences imported - Binding should correctly
+ * recover chain mappings for each derived sequence
+ */
+ private static final String PDB_4_MC = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
+ + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
+ + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
+ + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
+ + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
+ + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n"
+ + "ATOM 1030 CA MET B 1 18.869 -7.572 3.432 1.00 31.52 C \n"
+ + "ATOM 1038 CA LYS B 2 19.182 -10.025 6.313 1.00 26.41 C \n"
+ + "ATOM 1047 CA LYS B 3 17.107 -12.963 7.534 1.00 19.71 C \n"
+ + "ATOM 1056 CA LEU B 4 16.142 -13.579 11.164 1.00 14.81 C \n"
+ + "ATOM 1064 CA GLN B 5 14.648 -17.005 11.785 1.00 13.38 C \n";
+
+ // TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
+
+ @Test(groups= {"Functional"})
+ public void testImportPDBPreservesChainMappings() throws IOException
+ {
+ AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
+ PDB_4_MC, DataSourceType.PASTE, FileFormats.getInstance()
+ .forName(jalview.io.FileFormat.PDB.toString()));
+ // ideally, we would match on the actual data for the 'File' handle for
+ // pasted files,
+ // see JAL-623 - pasting is still not correctly handled...
+ PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB,
+ "Paste");
+ AAStructureBindingModel binder = new AAStructureBindingModel(
+ new StructureSelectionManager(), new PDBEntry[]
+ { importedPDB },
+ new SequenceI[][]
+ { importedAl.getSequencesArray() }, null)
+ {
+
+ @Override
+ public void updateColours(Object source)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String[] getStructureFiles()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String superposeStructures(AlignmentI[] alignments,
+ int[] structureIndices, HiddenColumns[] hiddenCols)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setBackgroundColour(Color col)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void highlightAtoms(List<AtomSpec> atoms)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected String[] getColourBySequenceCommands(String[] files,
+ AlignmentViewPanel avp)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected void colourBySequence(String[] colourBySequenceCommands)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void colourByCharge()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void colourByChain()
+ {
+ // TODO Auto-generated method stub
+
+ }
+ };
+ String[][] chains = binder.getChains();
+ assertFalse(chains == null || chains[0] == null,
+ "No chains discovered by binding");
+ assertEquals(2, chains[0].length);
+ assertEquals("A", chains[0][0]);
+ assertEquals("B", chains[0][1]);
+ }
AAStructureBindingModel testee;
AlignmentI al = null;
StructureSelectionManager ssm = new StructureSelectionManager();
ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
- DataSourceType.PASTE);
+ DataSourceType.PASTE, null);
testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
{
@Override
- public String[] getPdbFile()
+ public String[] getStructureFiles()
{
return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
}
}
@Override
- public List<String> getChainNames()
- {
- return null;
- }
-
- @Override
public void setJalviewColourScheme(ColourSchemeI cs)
{
}
@Override
public String superposeStructures(AlignmentI[] als, int[] alm,
- ColumnSelection[] alc)
+ HiddenColumns[] alc)
{
return null;
}
}
@Override
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel avp)
+ protected String[] getColourBySequenceCommands(
+ String[] files, AlignmentViewPanel avp)
{
return null;
}
}
@Override
- protected void colourBySequence(
- StructureMappingcommandSet[] colourBySequenceCommands)
+ protected void colourBySequence(String[] colourBySequenceCommands)
{
}
}
@Override
- protected FeatureRenderer getFeatureRenderer(
+ public FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
return null;
/*
* create a data bean to hold data per structure file
*/
- SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
+ SuperposeData[] structs = new SuperposeData[testee.getStructureFiles().length];
for (int i = 0; i < structs.length; i++)
{
structs[i] = testee.new SuperposeData(al.getWidth());
git://source.jalview.org / jalview.git / blobdiff