X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=7f949c78c97048588bab395d73697bb6d6da7bfd;hb=6909336c10f55ddf2813b983b0eb0fe79488c971;hp=1299ddcff5be60e7b19c0a9635b54e5e5eb438c4;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 1299ddc..7f949c7 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -17,32 +17,40 @@ */ package jalview.ext.jmol; -import java.io.File; -import java.net.URL; -import java.util.*; -import java.applet.Applet; -import java.awt.*; -import java.awt.event.*; - -import javax.swing.JPanel; - import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.SequenceStructureBinding; import jalview.api.StructureSelectionManagerProvider; -import jalview.datamodel.*; -import jalview.structure.*; -import jalview.io.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; + +import java.awt.Color; +import java.awt.Container; +import java.awt.event.ComponentEvent; +import java.awt.event.ComponentListener; +import java.io.File; +import java.net.URL; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Map; +import java.util.Vector; -import org.jmol.api.*; import org.jmol.adapter.smarter.SmarterJmolAdapter; - -import org.jmol.popup.*; -import org.jmol.viewer.JmolConstants; -import org.jmol.viewer.Viewer; - -import jalview.schemes.*; +import org.jmol.api.JmolAppConsoleInterface; +import org.jmol.api.JmolSelectionListener; +import org.jmol.api.JmolStatusListener; +import org.jmol.api.JmolViewer; +import org.jmol.constant.EnumCallback; +import org.jmol.popup.JmolPopup; public abstract class JalviewJmolBinding implements StructureListener, JmolStatusListener, SequenceStructureBinding, @@ -349,7 +357,7 @@ public abstract class JalviewJmolBinding implements StructureListener, for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - + // RACE CONDITION - getMapping only returns Jmol loaded filenames once Jmol callback has completed. if (mapping == null || mapping.length < 1) continue; @@ -682,10 +690,17 @@ public abstract class JalviewJmolBinding implements StructureListener, String mset[] = new String[viewer.getModelCount()]; _modelFileNameMap = new int[mset.length]; int j = 1; - mset[0] = viewer.getModelFileName(0); + String m=viewer.getModelFileName(0); + if (m!=null) + { + mset[0] = new File(m).getAbsolutePath(); + } for (int i = 1; i < mset.length; i++) { - mset[j] = viewer.getModelFileName(i); + m=viewer.getModelFileName(i); + if (m!=null) { + mset[j] = new File(m).getAbsolutePath(); + } _modelFileNameMap[j] = i; // record the model index for the filename // skip any additional models in the same file (NMR structures) if ((mset[j] == null ? mset[j] != mset[j - 1] @@ -861,8 +876,17 @@ public abstract class JalviewJmolBinding implements StructureListener, try { // recover PDB filename for the model hovered over. - pdbfilename = viewer - .getModelFileName(new Integer(mdlId).intValue() - 1); + int _mp=_modelFileNameMap.length-1, + mnumber=new Integer(mdlId).intValue() - 1; + while(mnumber<_modelFileNameMap[_mp]) + { + _mp--; + } + pdbfilename = modelFileNames[_mp]; + if (pdbfilename==null) {pdbfilename=new File(viewer + .getModelFileName(mnumber)).getAbsolutePath(); + } + } catch (Exception e) { } @@ -940,47 +964,48 @@ public abstract class JalviewJmolBinding implements StructureListener, } - public void notifyCallback(int type, Object[] data) + @Override + public void notifyCallback(EnumCallback type, Object[] data) { try { switch (type) { - case JmolConstants.CALLBACK_LOADSTRUCT: + case LOADSTRUCT: notifyFileLoaded((String) data[1], (String) data[2], (String) data[3], (String) data[4], ((Integer) data[5]).intValue()); break; - case JmolConstants.CALLBACK_PICK: + case PICK: notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); // also highlight in alignment - case JmolConstants.CALLBACK_HOVER: + case HOVER: notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); break; - case JmolConstants.CALLBACK_SCRIPT: + case SCRIPT: notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue()); break; - case JmolConstants.CALLBACK_ECHO: + case ECHO: sendConsoleEcho((String) data[1]); break; - case JmolConstants.CALLBACK_MESSAGE: + case MESSAGE: sendConsoleMessage((data == null) ? ((String) null) : (String) data[1]); break; - case JmolConstants.CALLBACK_ERROR: + case ERROR: // System.err.println("Ignoring error callback."); break; - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_RESIZE: + case SYNC: + case RESIZE: refreshGUI(); break; - case JmolConstants.CALLBACK_MEASURE: + case MEASURE: - case JmolConstants.CALLBACK_CLICK: + case CLICK: default: System.err.println("Unhandled callback " + type + " " + data[1].toString()); @@ -993,24 +1018,25 @@ public abstract class JalviewJmolBinding implements StructureListener, } } - public boolean notifyEnabled(int callbackPick) + @Override + public boolean notifyEnabled(EnumCallback callbackPick) { switch (callbackPick) { - case JmolConstants.CALLBACK_ECHO: - case JmolConstants.CALLBACK_LOADSTRUCT: - case JmolConstants.CALLBACK_MEASURE: - case JmolConstants.CALLBACK_MESSAGE: - case JmolConstants.CALLBACK_PICK: - case JmolConstants.CALLBACK_SCRIPT: - case JmolConstants.CALLBACK_HOVER: - case JmolConstants.CALLBACK_ERROR: + case ECHO: + case LOADSTRUCT: + case MEASURE: + case MESSAGE: + case PICK: + case SCRIPT: + case HOVER: + case ERROR: return true; - case JmolConstants.CALLBACK_RESIZE: - case JmolConstants.CALLBACK_SYNC: - case JmolConstants.CALLBACK_CLICK: - case JmolConstants.CALLBACK_ANIMFRAME: - case JmolConstants.CALLBACK_MINIMIZATION: + case RESIZE: + case SYNC: + case CLICK: + case ANIMFRAME: + case MINIMIZATION: } return false; } @@ -1120,7 +1146,8 @@ public abstract class JalviewJmolBinding implements StructureListener, } else { - if (matches = pdbentry[pe].getFile().equals(fileName)) + File fl; + if (matches = (fl=new File(pdbentry[pe].getFile())).equals(new File(fileName))) { foundEntry = true; // TODO: Jmol can in principle retrieve from CLASSLOADER but @@ -1131,7 +1158,6 @@ public abstract class JalviewJmolBinding implements StructureListener, String protocol = AppletFormatAdapter.URL; try { - File fl = new java.io.File(pdbentry[pe].getFile()); if (fl.exists()) { protocol = AppletFormatAdapter.FILE; @@ -1141,9 +1167,10 @@ public abstract class JalviewJmolBinding implements StructureListener, } catch (Error e) { } - ; + //Explicitly map to the filename used by Jmol ; pdb = ssm.setMapping(sequence[pe], chains[pe], - pdbentry[pe].getFile(), protocol); + fileName, protocol); + //pdbentry[pe].getFile(), protocol); } } @@ -1154,7 +1181,7 @@ public abstract class JalviewJmolBinding implements StructureListener, { String chid = new String(pdb.id + ":" + ((MCview.PDBChain) pdb.chains.elementAt(i)).id); - chainFile.put(chid, pdbentry[pe].getFile()); + chainFile.put(chid, fileName); chainNames.addElement(chid); } notifyLoaded = true; @@ -1542,5 +1569,10 @@ public abstract class JalviewJmolBinding implements StructureListener, { return ssm.printMapping(pdbfile); } - + @Override + public void resizeInnerPanel(String data) + { + // Jalview doesn't honour resize panel requests + + } }