X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=1ceabd19fc0fb7c1c8a58ccda26a0070701c65bf;hb=b8c8a9017c9abd4cd0b2d685d34a3c4b7982d7ac;hp=cb3b59bc8c5672bbeae69119967938db155e472f;hpb=6f87f39822deb287831e26e273ceb9df8d9cc882;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index cb3b59b..1ceabd1 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.gui.IProgressIndicator; import jalview.io.DataSourceType; import jalview.io.StructureFile; import jalview.schemes.ColourSchemeI; @@ -43,12 +44,12 @@ import java.awt.event.ComponentEvent; import java.awt.event.ComponentListener; import java.io.File; import java.net.URL; -import java.security.AccessControlException; import java.util.ArrayList; import java.util.BitSet; import java.util.Hashtable; import java.util.List; import java.util.Map; +import java.util.StringTokenizer; import java.util.Vector; import org.jmol.adapter.smarter.SmarterJmolAdapter; @@ -64,6 +65,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel implements JmolStatusListener, JmolSelectionListener, ComponentListener { + private String lastMessage; + boolean allChainsSelected = false; /* @@ -72,7 +75,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ private boolean associateNewStructs = false; - Vector atomsPicked = new Vector(); + Vector atomsPicked = new Vector<>(); private List chainNames; @@ -88,8 +91,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String lastCommand; - String lastMessage; - boolean loadedInline; StringBuffer resetLastRes = new StringBuffer(); @@ -477,6 +478,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel lastCommand = command; } + Thread colourby = null; /** * Sends a set of colour commands to the structure viewer * @@ -484,15 +486,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ @Override protected void colourBySequence( - StructureMappingcommandSet[] colourBySequenceCommands) + final StructureMappingcommandSet[] colourBySequenceCommands) { - for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) + if (colourby != null) { - for (String cbyseq : cpdbbyseq.commands) + colourby.interrupt(); + colourby = null; + } + colourby = new Thread(new Runnable() + { + @Override + public void run() { - executeWhenReady(cbyseq); + for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) + { + for (String cbyseq : cpdbbyseq.commands) + { + executeWhenReady(cbyseq); + } + } } - } + }); + colourby.start(); } /** @@ -599,78 +614,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ private int _modelFileNameMap[]; - // //////////////////////////////// - // /StructureListener - // @Override - public synchronized String[] getPdbFilex() - { - if (viewer == null) - { - return new String[0]; - } - if (modelFileNames == null) - { - List mset = new ArrayList(); - _modelFileNameMap = new int[viewer.ms.mc]; - String m = viewer.ms.getModelFileName(0); - if (m != null) - { - String filePath = m; - try - { - filePath = new File(m).getAbsolutePath(); - } catch (AccessControlException x) - { - // usually not allowed to do this in applet - System.err.println( - "jmolBinding: Using local file string from Jmol: " + m); - } - if (filePath.indexOf("/file:") != -1) - { - // applet path with docroot - discard as format won't match pdbfile - filePath = m; - } - mset.add(filePath); - _modelFileNameMap[0] = 0; // filename index for first model is always 0. - } - int j = 1; - for (int i = 1; i < viewer.ms.mc; i++) - { - m = viewer.ms.getModelFileName(i); - String filePath = m; - if (m != null) - { - try - { - filePath = new File(m).getAbsolutePath(); - } catch (AccessControlException x) - { - // usually not allowed to do this in applet, so keep raw handle - // System.err.println("jmolBinding: Using local file string from - // Jmol: "+m); - } - } - - /* - * add this model unless it is read from a structure file we have - * already seen (example: 2MJW is an NMR structure with 10 models) - */ - if (!mset.contains(filePath)) - { - mset.add(filePath); - _modelFileNameMap[j] = i; // record the model index for the filename - j++; - } - } - modelFileNames = mset.toArray(new String[mset.size()]); - } - return modelFileNames; - } - @Override public synchronized String[] getStructureFiles() { - List mset = new ArrayList(); + List mset = new ArrayList<>(); if (viewer == null) { return new String[0]; @@ -807,7 +754,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel viewer.openStringInline(string); } - public void mouseOverStructure(int atomIndex, String strInfo) + protected void mouseOverStructure(int atomIndex, final String strInfo) { int pdbResNum; int alocsep = strInfo.indexOf("^"); @@ -861,34 +808,63 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel try { // recover PDB filename for the model hovered over. - int _mp = _modelFileNameMap.length - 1, - mnumber = new Integer(mdlId).intValue() - 1; - while (mnumber < _modelFileNameMap[_mp]) + int mnumber = Integer.valueOf(mdlId).intValue() - 1; + if (_modelFileNameMap != null) { - _mp--; + int _mp = _modelFileNameMap.length - 1; + + while (mnumber < _modelFileNameMap[_mp]) + { + _mp--; + } + pdbfilename = modelFileNames[_mp]; } - pdbfilename = modelFileNames[_mp]; - if (pdbfilename == null) + else { - pdbfilename = new File(viewer.ms.getModelFileName(mnumber)) - .getAbsolutePath(); - } + if (mnumber >= 0 && mnumber < modelFileNames.length) + { + pdbfilename = modelFileNames[mnumber]; + } + if (pdbfilename == null) + { + pdbfilename = new File(viewer.ms.getModelFileName(mnumber)) + .getAbsolutePath(); + } + } } catch (Exception e) { } - ; } - if (lastMessage == null || !lastMessage.equals(strInfo)) + + /* + * highlight position on alignment(s); if some text is returned, + * show this as a second line on the structure hover tooltip + */ + String label = getSsm().mouseOverStructure(pdbResNum, chainId, + pdbfilename); + if (label != null) { - getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename); + // change comma to pipe separator (newline token for Jmol) + label = label.replace(',', '|'); + StringTokenizer toks = new StringTokenizer(strInfo, " "); + StringBuilder sb = new StringBuilder(); + sb.append("select ").append(String.valueOf(pdbResNum)).append(":") + .append(chainId).append("/1"); + sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ") + .append(toks.nextToken()); + sb.append("|").append(label).append("\""); + evalStateCommand(sb.toString()); } - - lastMessage = strInfo; } public void notifyAtomHovered(int atomIndex, String strInfo, String data) { + if (strInfo.equals(lastMessage)) + { + return; + } + lastMessage = strInfo; if (data != null) { System.err.println("Ignoring additional hover info: " + data @@ -975,9 +951,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); // also highlight in alignment - notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - break; + // deliberate fall through case HOVER: notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]); @@ -1062,8 +1036,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel fileLoadingError = null; String[] oldmodels = modelFileNames; modelFileNames = null; - chainNames = new ArrayList(); - chainFile = new Hashtable(); + chainNames = new ArrayList<>(); + chainFile = new Hashtable<>(); boolean notifyLoaded = false; String[] modelfilenames = getStructureFiles(); // first check if we've lost any structures @@ -1129,7 +1103,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // see JAL-623 - need method of matching pasted data up { pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], - pdbfile, DataSourceType.PASTE); + pdbfile, DataSourceType.PASTE, + getIProgressIndicator()); getPdbEntry(modelnum).setFile("INLINE" + pdb.getId()); matches = true; foundEntry = true; @@ -1161,7 +1136,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } // Explicitly map to the filename used by Jmol ; pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], - fileName, protocol); + fileName, protocol, getIProgressIndicator()); // pdbentry[pe].getFile(), protocol); } @@ -1229,6 +1204,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return chainNames; } + protected IProgressIndicator getIProgressIndicator() + { + return null; + } + public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) { notifyAtomPicked(iatom, strMeasure, null);