X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;fp=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=8818bf1711925f8c812149820d50327c586e8e89;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=26a67bcef78492695883449627d5e6d92f1089ab;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java index 26a67bc..8818bf1 100644 --- a/test/jalview/structures/models/AAStructureBindingModelTest.java +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -57,6 +57,7 @@ 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; @@ -126,7 +127,7 @@ public class AAStructureBindingModelTest // 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( @@ -135,38 +136,38 @@ public class AAStructureBindingModelTest // 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( StructureSelectionManager.getStructureSelectionManager(null), 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 atoms) { } - + @Override - public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) + public SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment) { return null; } @@ -197,6 +198,7 @@ public class AAStructureBindingModelTest assertEquals(chains[0][0], "A"); assertEquals(chains[0][1], "B"); } + AAStructureBindingModel testee; AlignmentI al = null; @@ -243,11 +245,11 @@ public class AAStructureBindingModelTest * @param pdbFiles * @param seqs * @param ssm - * @param alignPanel + * @param alignPanel */ protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles, - SequenceI[][] seqs, - StructureSelectionManager ssm, AlignmentViewPanel avp) + SequenceI[][] seqs, StructureSelectionManager ssm, + AlignmentViewPanel avp) { AAStructureBindingModel model = new AAStructureBindingModel(ssm, pdbFiles, seqs, null) @@ -279,12 +281,10 @@ public class AAStructureBindingModelTest } @Override - public SequenceRenderer getSequenceRenderer( - AlignmentViewPanel avp) + public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp) { return avp == null ? null - : new jalview.gui.SequenceRenderer( - avp.getAlignViewport()); + : new jalview.gui.SequenceRenderer(avp.getAlignViewport()); } @Override @@ -331,10 +331,12 @@ public class AAStructureBindingModelTest /* * 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 @@ -346,8 +348,8 @@ public class AAStructureBindingModelTest matched.set(i); } - int refStructure = testee - .findSuperposableResidues(al, matched, structs); + int refStructure = testee.findSuperposableResidues(al, matched, + structs); assertEquals(refStructure, 0); @@ -379,10 +381,12 @@ public class AAStructureBindingModelTest @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 @@ -397,8 +401,8 @@ public class AAStructureBindingModelTest // 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); @@ -436,7 +440,7 @@ public class AAStructureBindingModelTest 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 */ @@ -462,7 +466,7 @@ public class AAStructureBindingModelTest Map 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 @@ -470,7 +474,8 @@ public class AAStructureBindingModelTest 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 @@ -478,7 +483,8 @@ public class AAStructureBindingModelTest 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 @@ -486,7 +492,8 @@ public class AAStructureBindingModelTest 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) @@ -495,7 +502,8 @@ public class AAStructureBindingModelTest 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 @@ -503,7 +511,7 @@ public class AAStructureBindingModelTest 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