X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=8436b48eef8a8811416955a1b257feaf77cb6dcf;hb=bc97c1d6107222987fc31af58ba390c5425dcdda;hp=289d340260858586e695f5bfd6d036b6f13bcc0e;hpb=0e8ea80cb031f3bb9cf8f979fe138bf68dbc2446;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 289d340..8436b48 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -29,6 +29,7 @@ import java.util.BitSet; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import javax.swing.SwingUtilities; @@ -39,8 +40,9 @@ import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; import jalview.datamodel.MappedFeatures; import jalview.datamodel.PDBEntry; @@ -59,6 +61,7 @@ import jalview.structure.AtomSpec; import jalview.structure.AtomSpecModel; import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsI; +import jalview.structure.StructureCommandsI.AtomSpecType; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; @@ -67,9 +70,9 @@ import jalview.util.MessageManager; /** * - * A base class to hold common function for protein structure model binding. - * Initial version created by refactoring JMol and Chimera binding models, but - * other structure viewers could in principle be accommodated in future. + * A base class to hold common function for 3D structure model binding. Initial + * version created by refactoring JMol and Chimera binding models, but other + * structure viewers could in principle be accommodated in future. * * @author gmcarstairs * @@ -89,6 +92,9 @@ public abstract class AAStructureBindingModel public String chain = ""; + /** + * is the mapped sequence not protein ? + */ public boolean isRna; /* @@ -165,6 +171,9 @@ public abstract class AAStructureBindingModel protected boolean colourBySequence = true; + /** + * true if all sequences appear to be nucleotide + */ private boolean nucleotide; private boolean finishedInit = false; @@ -713,7 +722,7 @@ public abstract class AAStructureBindingModel structures[pdbfnum].chain = chain; } structures[pdbfnum].pdbId = mapping.getPdbId(); - structures[pdbfnum].isRna = theSequence.getRNA() != null; + structures[pdbfnum].isRna = !theSequence.isProtein(); /* * move on to next pdb file (ignore sequences for other chains @@ -862,21 +871,39 @@ public abstract class AAStructureBindingModel { AlignmentI alignment = view.getAlignment(); HiddenColumns hiddenCols = alignment.getHiddenColumns(); - /* * 'matched' bit i will be set for visible alignment columns i where * all sequences have a residue with a mapping to their PDB structure */ - BitSet matched = new BitSet(); final int width = alignment.getWidth(); - for (int m = 0; m < width; m++) + BitSet matched = new BitSet(); + ColumnSelection cs = view.getAlignViewport().getColumnSelection(); + // restrict to active column selection, if there is one + if (cs != null && cs.hasSelectedColumns() + && cs.getSelected().size() >= 4) + { + for (int s : cs.getSelected()) + { + if (hiddenCols == null) + { + matched.set(s); + } + else + { + matched.set(hiddenCols.visibleToAbsoluteColumn(s)); + } + } + } + else { - if (hiddenCols == null || hiddenCols.isVisible(m)) + for (int m = 0; m < width; m++) { - matched.set(m); + if (hiddenCols == null || hiddenCols.isVisible(m)) + { + matched.set(m); + } } } - AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length]; for (int f = 0; f < files.length; f++) { @@ -916,6 +943,11 @@ public abstract class AAStructureBindingModel // todo better way to ensure synchronous than setting getReply true!! executeCommands(commandGenerator.showBackbone(), true, null); + AtomSpecType backbone = structures[refStructure].isRna + ? AtomSpecType.PHOSPHATE + : AtomSpecType.ALPHA; + List models = new ArrayList(); + models.add(refAtoms); /* * superpose each (other) structure to the reference in turn */ @@ -925,20 +957,24 @@ public abstract class AAStructureBindingModel { AtomSpecModel atomSpec = getAtomSpec(structures[i], matched); List commands = commandGenerator - .superposeStructures(refAtoms, atomSpec); + .superposeStructures(refAtoms, atomSpec, backbone); List replies = executeCommands(commands, true, null); for (String reply : replies) { // return this error (Chimera only) to the user - if (reply.toLowerCase().contains("unequal numbers of atoms")) + if (reply.toLowerCase(Locale.ROOT) + .contains("unequal numbers of atoms")) { error += "; " + reply; } } + models.add(atomSpec); } } + List finalView = commandGenerator + .centerViewOn(models); + executeCommands(finalView, false, "Centered on Superposition"); } - return error; } @@ -1072,7 +1108,10 @@ public abstract class AAStructureBindingModel * executed. *

* If a reply is wanted, the execution is done synchronously (waits), - * otherwise it is done in a separate thread (doesn't wait). + * otherwise it is done in a separate thread (doesn't wait). WARNING: if you + * are sending commands that need to execute before later calls to + * executeCommand (e.g. mouseovers, which clean up after previous ones) then + * set getReply true to ensure that commands are not executed out of order. * * @param getReply * @param msg @@ -1216,8 +1255,7 @@ public abstract class AAStructureBindingModel } /** - * Returns the FeatureRenderer for the given alignment view, or null if - * feature display is turned off in the view. + * Returns the FeatureRenderer for the given alignment view * * @param avp * @return @@ -1230,9 +1268,7 @@ public abstract class AAStructureBindingModel { return null; } - return ap.getAlignViewport().isShowSequenceFeatures() - ? ap.getFeatureRenderer() - : null; + return ap.getFeatureRenderer(); } protected void setStructureCommands(StructureCommandsI cmd) @@ -1267,6 +1303,12 @@ public abstract class AAStructureBindingModel @Override public void updateColours(Object source) { + if (getViewer() == null) + { + // can happen if a viewer was not instantiated or cleaned up and is still + // registered - mostly during tests + return; + } AlignmentViewPanel ap = (AlignmentViewPanel) source; // ignore events from panels not used to colour this view if (!getViewer().isUsedForColourBy(ap)) @@ -1494,7 +1536,7 @@ public abstract class AAStructureBindingModel saveSession(f); } catch (IOException e) { - Cache.log.error(String.format("Error saving %s session: %s", prefix, + Console.error(String.format("Error saving %s session: %s", prefix, e.toString())); }