import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormats;
+import jalview.io.FileLoader;
import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import junit.extensions.PA;
// TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
- @Test(groups= {"Functional"})
+ @Test(groups = { "Functional" })
public void testImportPDBPreservesChainMappings() throws IOException
{
AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
// 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");
+ 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)
{
}
-
+
@Override
public void releaseReferences(Object svl)
{
}
-
+
@Override
public String[] getStructureFiles()
{
return null;
}
-
+
@Override
public void highlightAtoms(List<AtomSpec> atoms)
{
}
-
+
@Override
- public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
{
return null;
}
assertEquals(chains[0][0], "A");
assertEquals(chains[0][1], "B");
}
+
AAStructureBindingModel testee;
AlignmentI al = null;
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
DataSourceType.PASTE, null);
- testee = newBindingModel(pdbFiles, seqs, ssm);
+ testee = newBindingModel(pdbFiles, seqs, ssm, null);
}
/**
* @param pdbFiles
* @param seqs
* @param ssm
+ * @param alignPanel
*/
protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
- SequenceI[][] seqs,
- StructureSelectionManager ssm)
+ SequenceI[][] seqs, StructureSelectionManager ssm,
+ AlignmentViewPanel avp)
{
AAStructureBindingModel model = new AAStructureBindingModel(ssm,
pdbFiles, seqs, null)
@Override
public String[] getStructureFiles()
{
- return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
+ String[] files = new String[getPdbCount()];
+ for (int i = 0; i < this.getPdbCount(); i++)
+ {
+ files[i] = getPdbEntry(i).getFile();
+ }
+ return files;
}
@Override
}
@Override
- public SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
{
- return null;
+ return avp == null ? null
+ : new jalview.gui.SequenceRenderer(avp.getAlignViewport());
}
@Override
/*
* create a data bean to hold data per structure file
*/
- AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee.getStructureFiles().length];
+ AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee
+ .getStructureFiles().length];
for (int i = 0; i < structs.length; i++)
{
- structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
+ structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
+ "0");
}
/*
* initialise BitSet of 'superposable columns' to true (would be false for
matched.set(i);
}
- int refStructure = testee
- .findSuperposableResidues(al, matched, structs);
+ int refStructure = testee.findSuperposableResidues(al, matched,
+ structs);
assertEquals(refStructure, 0);
@Test(groups = { "Functional" })
public void testFindSuperposableResidues_hiddenColumn()
{
- AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al.getHeight()];
+ AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al
+ .getHeight()];
for (int i = 0; i < structs.length; i++)
{
- structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
+ structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
+ "0");
}
/*
* initialise BitSet of 'superposable columns' to true (would be false for
// treat column 5 of the alignment as hidden
matched.clear(4);
- int refStructure = testee
- .findSuperposableResidues(al, matched, structs);
+ int refStructure = testee.findSuperposableResidues(al, matched,
+ structs);
assertEquals(refStructure, 0);
* load these sequences, coloured by Strand propensity,
* with columns 2-4 hidden
*/
- SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
- SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
- AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
- AlignFrame af = new AlignFrame(al, 800, 500);
+ String fasta = ">seq1\nMHRSQSSSGG\n>seq2\nMVRSNGGSSS";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
+ DataSourceType.PASTE);
+ AlignmentI al = af.getViewport().getAlignment();
af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
ColumnSelection cs = new ColumnSelection();
cs.addElement(2);
cs.addElement(4);
af.getViewport().setColumnSelection(cs);
af.hideSelColumns_actionPerformed(null);
- SequenceRenderer sr = new jalview.gui.SequenceRenderer(
- af.getViewport());
+ SequenceI seq1 = al.getSequenceAt(0);
+ SequenceI seq2 = al.getSequenceAt(1);
SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
- String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
PDBEntry[] pdbFiles = new PDBEntry[2];
pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
StructureSelectionManager ssm = new StructureSelectionManager();
-
+
/*
* map residues 1-10 to residues 21-30 (atoms 105-150) in structures
*/
"B", map, null);
ssm.addStructureMapping(sm2);
- AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm);
+ AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm,
+ af.alignPanel);
/*
* method under test builds a map of structures residues by colour
* verify the map holds what it should
*/
- Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, files,
- seqs, sr, af.alignPanel);
+ Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, seqs,
+ af.alignPanel);
ChimeraCommands helper = new ChimeraCommands();
-
+
/*
* M colour is #82827d (see strand.html help page)
* sequence residue 1 mapped to structure residue 21
Color mColor = new Color(0x82827d);
AtomSpecModel atomSpec = colours.get(mColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:21.A|#1:21.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
+ "#0:21.A|#1:21.B");
/*
* H colour is #60609f, seq1.2 mapped to structure 0 residue 22
Color hColor = new Color(0x60609f);
atomSpec = colours.get(hColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:22.A");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
+ "#0:22.A");
/*
* V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
Color vColor = new Color(0xffff00);
atomSpec = colours.get(vColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#1:22.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
+ "#1:22.B");
/*
* hidden columns are Gray (128, 128, 128)
Color gray = new Color(128, 128, 128);
atomSpec = colours.get(gray);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false), "#0:23-25.A|#1:23-25.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
+ "#0:23-25.A|#1:23-25.B");
/*
* S and G are both coloured #4949b6, structure residues 26-30
Color sgColour = new Color(0x4949b6);
atomSpec = colours.get(sgColour);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, false),
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
"#0:26-30.A|#1:26-30.B");
}
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff