X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=8ee22964da54980984e13c3f151dda1b403f81ad;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=f8fe17b5fb200e56091903842bfb30245aaf4895;hpb=4de8dbdccf508589bec18d9a8af5799531c5807b;p=jalview.git
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index f8fe17b..8ee2296 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,46 +1,63 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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 jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
+import jalview.api.StructureSelectionManagerProvider;
+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.security.AccessControlException;
+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 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, JmolSelectionListener
+ JmolStatusListener, SequenceStructureBinding,
+ JmolSelectionListener, ComponentListener,
+ StructureSelectionManagerProvider
{
/**
@@ -49,6 +66,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
* time.
*/
private boolean loadingFromArchive = false;
+
+ /**
+ * second flag to indicate if the jmol viewer should ignore sequence colouring
+ * events from the structure manager because the GUI is still setting up
+ */
+ private boolean loadingFinished = true;
/**
* state flag used to check if the Jmol viewer's paint method can be called
@@ -77,6 +100,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
public Vector chainNames;
+ Hashtable chainFile;
+
/**
* array of target chains for seuqences - tied to pdbentry and sequence[]
*/
@@ -110,7 +135,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
public PDBEntry[] pdbentry;
/**
- * datasource protocol for access to PDBEntry
+ * datasource protocol for access to PDBEntrylatest
*/
String protocol = null;
@@ -121,13 +146,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
public SequenceI[][] sequence;
- StructureSelectionManager ssm;
+ public StructureSelectionManager ssm;
public JmolViewer viewer;
- public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- String[][] chains, String protocol)
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
{
+ this.ssm = ssm;
this.sequence = sequenceIs;
this.chains = chains;
this.pdbentry = pdbentry;
@@ -145,8 +172,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
}
- public JalviewJmolBinding(JmolViewer viewer2)
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ JmolViewer viewer2)
{
+ this.ssm = ssm;
viewer = viewer2;
viewer.setJmolStatusListener(this);
viewer.addSelectionListener(this);
@@ -161,10 +190,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
public String getViewerTitle()
{
if (sequence == null || pdbentry == null || sequence.length < 1
- || pdbentry.length < 1)
+ || pdbentry.length < 1 || sequence[0].length < 1)
{
return ("Jalview Jmol Window");
}
+ // TODO: give a more informative title when multiple structures are
+ // displayed.
StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
+ pdbentry[0].getId());
@@ -205,8 +236,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
p = mlength;
mlength = lbl.indexOf(":", p);
} while (p < mlength && mlength < (lbl.length() - 2));
+ // TODO: lookup each pdb id and recover proper model number for it.
cmd.append(":" + lbl.substring(mlength + 1) + " /"
- + getModelNum(lbl.substring(0, mlength)) + " or ");
+ + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
cmd.setLength(cmd.length() - 4);
@@ -217,18 +249,27 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
// remove listeners for all structures in viewer
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, this.getPdbFile());
+ ssm.removeStructureViewerListener(this, this.getPdbFile());
// and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
lastCommand = null;
viewer = null;
+ releaseUIResources();
}
+ /**
+ * called by JalviewJmolbinding after closeViewer is called - release any
+ * resources and references so they can be garbage collected.
+ */
+ protected abstract void releaseUIResources();
+
public void colourByChain()
{
colourBySequence = false;
+ // TODO: colour by chain should colour each chain distinctly across all
+ // visible models
+ // TODO: http://issues.jalview.org/browse/JAL-628
evalStateCommand("select *;color chain");
}
@@ -264,195 +305,311 @@ public abstract class JalviewJmolBinding implements StructureListener,
/**
* superpose the structures associated with sequences in the alignment
* according to their corresponding positions. ded)
+ *
* @param refStructure
* - select which pdb file to use as reference (default is -1 - the
* first structure in the alignment)
- * @param hiddenCols TODO
+ * @param hiddenCols
+ * TODO
*/
- public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols)
+ public void superposeStructures(AlignmentI alignment, int refStructure,
+ ColumnSelection hiddenCols)
{
+ superposeStructures(new AlignmentI[]
+ { alignment }, new int[]
+ { refStructure }, new ColumnSelection[]
+ { hiddenCols });
+ }
+
+ public void superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, ColumnSelection[] _hiddenCols)
+ {
+ assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+
String[] files = getPdbFile();
- if (refStructure>=files.length)
+ // check to see if we are still waiting for Jmol files
+ long starttime=System.currentTimeMillis();
+ boolean waiting=true;
+ do {
+ waiting=false;
+ for (String file:files)
+ {
+ try {
+ // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
+ // every possible exception
+ StructureMapping[] sm = ssm.getMapping(file);
+ if (sm == null || sm.length == 0)
+ {
+ waiting = true;
+ }
+ } catch (Exception x)
+ {
+ waiting = true;
+ } catch (Error q)
+ {
+ waiting = true;
+ }
+ }
+ // we wait around for a reasonable time before we give up
+ } while (waiting && System.currentTimeMillis()<(10000+1000*files.length+starttime));
+ if (waiting)
{
- System.err.println("Invalid reference structure value "+refStructure);
- refStructure= -1;
+ System.err.println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
+ return;
}
- if (refStructure<-1)
+ StringBuffer selectioncom = new StringBuffer();
+ // In principle - nSeconds specifies the speed of animation for each
+ // superposition - but is seems to behave weirdly, so we don't specify it.
+ String nSeconds = " ";
+ if (files.length > 10)
{
- refStructure=-1;
+ nSeconds = " 0.00001 ";
}
- StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer();
-
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
+ else
{
-
- matched[m] = (hiddenCols!=null) ? hiddenCols.isVisible(m) : true;
+ nSeconds = " " + (2.0 / files.length) + " ";
+ // if (nSeconds).substring(0,5)+" ";
}
-
- int commonrpositions[][] = new int[files.length][alignment.getWidth()];
- String isel[] = new String[files.length];
- // reference structure - all others are superposed in it
- String[] targetC = new String[files.length];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ // see JAL-1345 - should really automatically turn off the animation for
+ // large numbers of structures, but Jmol doesn't seem to allow that.
+ nSeconds = " ";
+ // union of all aligned positions are collected together.
+ for (int a = 0; a < _alignment.length; a++)
{
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ int refStructure = _refStructure[a];
+ AlignmentI alignment = _alignment[a];
+ ColumnSelection hiddenCols = _hiddenCols[a];
+ if (a > 0
+ && selectioncom.length() > 0
+ && !selectioncom.substring(selectioncom.length() - 1).equals(
+ "|"))
+ {
+ selectioncom.append("|");
+ }
+ // process this alignment
+ if (refStructure >= files.length)
+ {
+ System.err.println("Invalid reference structure value "
+ + refStructure);
+ refStructure = -1;
+ }
+ if (refStructure < -1)
+ {
+ refStructure = -1;
+ }
+ StringBuffer command = new StringBuffer();
- if (mapping == null || mapping.length < 1)
- continue;
+ boolean matched[] = new boolean[alignment.getWidth()];
+ for (int m = 0; m < matched.length; m++)
+ {
+
+ matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ }
- int lastPos = -1;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
+ int commonrpositions[][] = new int[files.length][alignment.getWidth()];
+ String isel[] = new String[files.length];
+ // reference structure - all others are superposed in it
+ String[] targetC = new String[files.length];
+ String[] chainNames = new String[files.length];
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- for (int sp, m = 0; m < mapping.length; m++)
+ 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)
+ {
+ throw new Error("Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016");
+ }
+ int lastPos = -1;
+ for (int s = 0; s < sequence[pdbfnum].length; s++)
{
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ for (int sp, m = 0; m < mapping.length; m++)
{
- if (refStructure == -1)
- {
- refStructure = pdbfnum;
- }
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < matched.length; r++)
+ if (mapping[m].getSequence() == sequence[pdbfnum][s]
+ && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
{
- if (!matched[r])
+ if (refStructure == -1)
{
- continue;
+ refStructure = pdbfnum;
}
- matched[r] = false; // assume this is not a good site
- if (r >= asp.getLength())
+ SequenceI asp = alignment.getSequenceAt(sp);
+ for (int r = 0; r < matched.length; r++)
{
- continue;
- }
+ if (!matched[r])
+ {
+ continue;
+ }
+ matched[r] = false; // assume this is not a good site
+ if (r >= asp.getLength())
+ {
+ continue;
+ }
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ {
+ // no mapping to gaps in sequence
+ continue;
+ }
+ int t = asp.findPosition(r); // sequence position
+ int apos = mapping[m].getAtomNum(t);
+ int pos = mapping[m].getPDBResNum(t);
+
+ if (pos < 1 || pos == lastPos)
+ {
+ // can't align unmapped sequence
+ continue;
+ }
+ matched[r] = true; // this is a good ite
+ lastPos = pos;
+ // just record this residue position
+ commonrpositions[pdbfnum][r] = pos;
+ }
+ // create model selection suffix
+ isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
+ if (mapping[m].getChain() == null
+ || mapping[m].getChain().trim().length() == 0)
{
- // no mapping to gaps in sequence
- continue;
+ targetC[pdbfnum] = "";
}
- int t = asp.findPosition(r); // sequence position
- int apos = mapping[m].getAtomNum(t);
- int pos = mapping[m].getPDBResNum(t);
-
- if (pos < 1 || pos == lastPos)
+ else
{
- // can't align unmapped sequence
- continue;
+ targetC[pdbfnum] = ":" + mapping[m].getChain();
}
- matched[r] = true; // this is a good ite
- lastPos = pos;
- // just record this residue position
- commonrpositions[pdbfnum][r] = pos;
- }
- // create model selection suffix
- isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
- if (mapping[m].getChain() == null
- || mapping[m].getChain().trim().length() == 0)
- {
- targetC[pdbfnum] = "";
+ chainNames[pdbfnum] = mapping[m].getPdbId()
+ + targetC[pdbfnum];
+ // move on to next pdb file
+ s = sequence[pdbfnum].length;
+ break;
}
- else
- {
- targetC[pdbfnum] = ":" + mapping[m].getChain();
- }
- // move on to next pdb file
- s = sequence[pdbfnum].length;
- break;
}
}
}
- }
- String[] selcom = new String[files.length];
- // generate select statements to select regions to superimpose structures
- {
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+
+ // TODO: consider bailing if nmatched less than 4 because superposition
+ // not
+ // well defined.
+ // TODO: refactor superposable position search (above) from jmol selection
+ // construction (below)
+
+ String[] selcom = new String[files.length];
+ int nmatched = 0;
+ // generate select statements to select regions to superimpose structures
{
- String chainCd = targetC[pdbfnum];
- int lpos = -1;
- boolean run = false;
- StringBuffer molsel = new StringBuffer();
- molsel.append("{");
- for (int r = 0; r < matched.length; r++)
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- if (matched[r])
+ String chainCd = targetC[pdbfnum];
+ int lpos = -1;
+ boolean run = false;
+ StringBuffer molsel = new StringBuffer();
+ molsel.append("{");
+ for (int r = 0; r < matched.length; r++)
{
-
- if (lpos != commonrpositions[pdbfnum][r] - 1)
+ if (matched[r])
{
- // discontinuity
- if (lpos != -1)
+ if (pdbfnum == 0)
{
- molsel.append(lpos);
- molsel.append(chainCd);
- // molsel.append("} {");
- molsel.append("|");
+ nmatched++;
}
- }
- else
- {
- // continuous run - and lpos >-1
- if (!run)
+ if (lpos != commonrpositions[pdbfnum][r] - 1)
{
- // at the beginning, so add dash
- molsel.append(lpos);
- molsel.append("-");
+ // discontinuity
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ // molsel.append("} {");
+ molsel.append("|");
+ }
}
- run = true;
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
+ {
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
+ }
+ run = true;
+ }
+ lpos = commonrpositions[pdbfnum][r];
+ // molsel.append(lpos);
+ }
+ }
+ // add final selection phrase
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("}");
+ }
+ if (molsel.length() > 1)
+ {
+ selcom[pdbfnum] = molsel.toString();
+ selectioncom.append("((");
+ selectioncom.append(selcom[pdbfnum].substring(1,
+ selcom[pdbfnum].length() - 1));
+ selectioncom.append(" )& ");
+ selectioncom.append(pdbfnum + 1);
+ selectioncom.append(".1)");
+ if (pdbfnum < files.length - 1)
+ {
+ selectioncom.append("|");
}
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
+ } else {
+ selcom[pdbfnum] = null;
}
}
- // add final selection phrase
- if (lpos != -1)
+ }
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ if (pdbfnum == refStructure || selcom[pdbfnum]==null || selcom[refStructure]==null)
{
- molsel.append(lpos);
- molsel.append(chainCd);
- molsel.append("}");
+ continue;
}
- selcom[pdbfnum] = molsel.toString();
- selectioncom.append("((");
- selectioncom.append(selcom[pdbfnum].substring(1, selcom[pdbfnum].length()-1));
- selectioncom.append(" )& ");
- selectioncom.append(pdbfnum+1);
- selectioncom.append(".1)");
- if (pdbfnum 0)
{
- continue;
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ evalStateCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ");
+ // selcom.append("; ribbons; ");
+ System.out
+ .println("Superimpose command(s):\n" + command.toString());
+
+ evalStateCommand(command.toString());
}
- command.append("compare ");
- command.append("{");
- command.append(1 + pdbfnum);
- command.append(".1} {");
- command.append(1 + refStructure);
- command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
-
- // form the matched pair strings
- String sep = "";
- for (int s = 0; s < 2; s++)
+ }
+ if (selectioncom.length() > 0)
+ {// finally, mark all regions that were superposed.
+ if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
{
- command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ selectioncom.setLength(selectioncom.length() - 1);
}
- command.append(" ROTATE TRANSLATE;\n");
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ evalStateCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ");
+ // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
}
- System.out.println("Select regions:\n" + selectioncom.toString());
- evalStateCommand("select *; cartoons off; backbone; select ("+selectioncom.toString()+"); cartoons; ");
- // selcom.append("; ribbons; ");
- System.out.println("Superimpose command(s):\n" + command.toString());
-
- evalStateCommand(command.toString());
-
- // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
}
public void evalStateCommand(String command)
@@ -471,87 +628,33 @@ public abstract class JalviewJmolBinding implements StructureListener,
* using the getFeatureRenderer() and getSequenceRenderer() renderers but only
* if colourBySequence is enabled.
*/
- public void colourBySequence(boolean showFeatures, AlignmentI alignment)
+ public void colourBySequence(boolean showFeatures,
+ jalview.api.AlignmentViewPanel alignmentv)
{
- if (!colourBySequence)
+ if (!colourBySequence || !loadingFinished)
return;
if (ssm == null)
{
return;
}
String[] files = getPdbFile();
- SequenceRenderer sr = getSequenceRenderer();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
FeatureRenderer fr = null;
if (showFeatures)
{
- fr = getFeatureRenderer();
+ fr = getFeatureRenderer(alignmentv);
}
+ AlignmentI alignment = alignmentv.getAlignment();
- StringBuffer command = new StringBuffer();
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
- int lastPos = -1;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands
+ .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
+ alignment))
+ for (String cbyseq : cpdbbyseq.commands)
{
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
- if (command.toString().endsWith(newSelcom))
- {
- command = condenseCommand(command.toString(), pos);
- continue;
- }
- // TODO: deal with case when buffer is too large for Jmol to parse
- // - execute command and flush
-
- command.append(";select " + pos);
- command.append(newSelcom);
- }
- break;
- }
- }
+ evalStateCommand(cbyseq);
}
- }
- evalStateCommand(command.toString());
}
public boolean isColourBySequence()
@@ -564,30 +667,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
this.colourBySequence = colourBySequence;
}
- StringBuffer condenseCommand(String command, int pos)
- {
-
- StringBuffer sb = new StringBuffer(command.substring(0,
- command.lastIndexOf("select") + 7));
-
- command = command.substring(sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
- {
- start = command.substring(0, command.indexOf(":"));
- }
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
public void createImage(String file, String type, int quality)
{
System.out.println("JMOL CREATE IMAGE");
@@ -634,9 +713,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
* returns the current featureRenderer that should be used to colour the
* structures
*
+ * @param alignment
+ *
* @return
*/
- public abstract FeatureRenderer getFeatureRenderer();
+ public abstract FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment);
/**
* instruct the Jalview binding to update the pdbentries vector if necessary
@@ -660,18 +742,65 @@ public abstract class JalviewJmolBinding implements StructureListener,
return -1;
}
+ /**
+ * map between index of model filename returned from getPdbFile and the first
+ * index of models from this file in the viewer. Note - this is not trimmed -
+ * use getPdbFile to get number of unique models.
+ */
+ private int _modelFileNameMap[];
+
// ////////////////////////////////
// /StructureListener
- public String[] getPdbFile()
+ public synchronized String[] getPdbFile()
{
+ if (viewer == null)
+ {
+ return new String[0];
+ }
if (modelFileNames == null)
{
+
String mset[] = new String[viewer.getModelCount()];
- for (int i = 0; i < mset.length; i++)
+ _modelFileNameMap = new int[mset.length];
+ int j = 1;
+ String m = viewer.getModelFileName(0);
+ if (m != null)
{
- mset[i] = viewer.getModelFileName(i);
+ try
+ {
+ mset[0] = new File(m).getAbsolutePath();
+ } catch (AccessControlException x)
+ {
+ // usually not allowed to do this in applet, so keep raw handle
+ mset[0] = m;
+ // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
+ }
}
- modelFileNames = mset;
+ for (int i = 1; i < mset.length; i++)
+ {
+ m = viewer.getModelFileName(i);
+ if (m != null)
+ {
+ try
+ {
+ mset[j] = new File(m).getAbsolutePath();
+ } catch (AccessControlException x)
+ {
+ // usually not allowed to do this in applet, so keep raw handle
+ mset[j] = m;
+ // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
+ }
+ }
+ _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]
+ : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
+ {
+ j++;
+ }
+ }
+ modelFileNames = new String[j];
+ System.arraycopy(mset, 0, modelFileNames, 0, j);
}
return modelFileNames;
}
@@ -689,9 +818,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
* returns the current sequenceRenderer that should be used to colour the
* structures
*
+ * @param alignment
+ *
* @return
*/
- public abstract SequenceRenderer getSequenceRenderer();
+ public abstract SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment);
// ///////////////////////////////
// JmolStatusListener
@@ -772,12 +904,21 @@ public abstract class JalviewJmolBinding implements StructureListener,
public void loadInline(String string)
{
loadedInline = true;
+ // TODO: re JAL-623
+ // viewer.loadInline(strModel, isAppend);
+ // could do this:
+ // construct fake fullPathName and fileName so we can identify the file
+ // later.
+ // Then, construct pass a reader for the string to Jmol.
+ // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+ // fileName, null, reader, false, null, null, 0);
viewer.openStringInline(string);
}
public void mouseOverStructure(int atomIndex, String strInfo)
{
int pdbResNum;
+ int alocsep = strInfo.indexOf("^");
int mdlSep = strInfo.indexOf("/");
int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
@@ -790,9 +931,18 @@ public abstract class JalviewJmolBinding implements StructureListener,
chainSeparator = mdlSep;
}
}
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
+ // handle insertion codes
+ if (alocsep != -1)
+ {
+ pdbResNum = Integer.parseInt(strInfo.substring(
+ strInfo.indexOf("]") + 1, alocsep));
+ }
+ else
+ {
+ pdbResNum = Integer.parseInt(strInfo.substring(
+ strInfo.indexOf("]") + 1, chainSeparator));
+ }
String chainId;
if (strInfo.indexOf(":") > -1)
@@ -816,8 +966,19 @@ 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)
{
}
@@ -895,48 +1056,48 @@ 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 JmolConstants.CALLBACK_CLICK:
+ case MEASURE:
+ case CLICK:
default:
System.err.println("Unhandled callback " + type + " "
+ data[1].toString());
@@ -949,28 +1110,39 @@ 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;
}
+ // incremented every time a load notification is successfully handled -
+ // lightweight mechanism for other threads to detect when they can start
+ // referrring to new structures.
+ private long loadNotifiesHandled = 0;
+
+ public long getLoadNotifiesHandled()
+ {
+ return loadNotifiesHandled;
+ }
+
public void notifyFileLoaded(String fullPathName, String fileName2,
String modelName, String errorMsg, int modelParts)
{
@@ -980,6 +1152,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
refreshGUI();
return;
}
+ // TODO: deal sensibly with models loaded inLine:
+ // modelName will be null, as will fullPathName.
+
// the rest of this routine ignores the arguments, and simply interrogates
// the Jmol view to find out what structures it contains, and adds them to
// the structure selection manager.
@@ -987,9 +1162,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
String[] oldmodels = modelFileNames;
modelFileNames = null;
chainNames = new Vector();
+ chainFile = new Hashtable();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
- ssm = StructureSelectionManager.getStructureSelectionManager();
// first check if we've lost any structures
if (oldmodels != null && oldmodels.length > 0)
{
@@ -1029,102 +1204,123 @@ public abstract class JalviewJmolBinding implements StructureListener,
for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
{
String fileName = modelfilenames[modelnum];
- if (fileName != null)
+ boolean foundEntry = false;
+ MCview.PDBfile pdb = null;
+ String pdbfile = null, pdbfhash = null;
+ // model was probably loaded inline - so check the pdb file hashcode
+ if (loadedInline)
+ {
+ // calculate essential attributes for the pdb data imported inline.
+ // prolly need to resolve modelnumber properly - for now just use our
+ // 'best guess'
+ pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ + ".0", "PDB");
+ pdbfhash = "" + pdbfile.hashCode();
+ }
+ if (pdbentry != null)
{
- boolean foundEntry = false;
- // search pdbentries and sequences to find correct pdbentry and
- // sequence[] pair for this filename
- if (pdbentry != null)
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
+ for (int pe = 0; pe < pdbentry.length; pe++)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ boolean matches = false;
+ if (fileName == null)
{
- if (pdbentry[pe].getFile().equals(fileName))
+ if (false)
+ // see JAL-623 - need method of matching pasted data up
{
+ pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,
+ AppletFormatAdapter.PASTE);
+ pdbentry[modelnum].setFile("INLINE" + pdb.id);
+ matches = true;
foundEntry = true;
- MCview.PDBfile pdb;
- if (loadedInline)
- {
- // TODO: replace with getData ?
- pdb = ssm.setMapping(sequence[pe], chains[pe],
- pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
- pdbentry[pe].setFile("INLINE" + pdb.id);
- }
- else
+ }
+ }
+ else
+ {
+ 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
+ // this
+ // needs
+ // to be tested. See mantis bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+ String protocol = AppletFormatAdapter.URL;
+ try
{
- // TODO: Jmol can in principle retrieve from CLASSLOADER but
- // this
- // needs
- // to be tested. See mantis bug
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- String protocol = AppletFormatAdapter.URL;
- try
- {
- File fl = new java.io.File(pdbentry[pe].getFile());
- if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
+ if (fl.exists())
{
+ protocol = AppletFormatAdapter.FILE;
}
- ;
- pdb = ssm.setMapping(sequence[pe], chains[pe],
- pdbentry[pe].getFile(), protocol);
-
- }
-
- pdbentry[pe].setId(pdb.id);
-
- for (int i = 0; i < pdb.chains.size(); i++)
+ } catch (Exception e)
+ {
+ } catch (Error e)
{
- chainNames.addElement(new String(pdb.id + ":"
- + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
}
- notifyLoaded = true;
+ // Explicitly map to the filename used by Jmol ;
+ pdb = ssm.setMapping(sequence[pe], chains[pe], fileName,
+ protocol);
+ // pdbentry[pe].getFile(), protocol);
+
+ }
+ }
+ if (matches)
+ {
+ // add an entry for every chain in the model
+ for (int i = 0; i < pdb.chains.size(); i++)
+ {
+ String chid = new String(pdb.id + ":"
+ + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);
+ chainFile.put(chid, fileName);
+ chainNames.addElement(chid);
}
+ notifyLoaded = true;
}
}
- if (!foundEntry && associateNewStructs)
- {
- // this is a foreign pdb file that jalview doesn't know about - add
- // it to the dataset and try to find a home - either on a matching
- // sequence or as a new sequence.
- String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
- "PDB");
- // parse pdb file into a chain, etc.
- // locate best match for pdb in associated views and add mapping to
- // ssm
- // if properly registered then
- notifyLoaded = true;
+ }
+ if (!foundEntry && associateNewStructs)
+ {
+ // this is a foreign pdb file that jalview doesn't know about - add
+ // it to the dataset and try to find a home - either on a matching
+ // sequence or as a new sequence.
+ String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+ "PDB");
+ // parse pdb file into a chain, etc.
+ // locate best match for pdb in associated views and add mapping to
+ // ssm
+ // if properly registered then
+ notifyLoaded = true;
- }
}
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
if (jmolpopup != null)
{
- jmolpopup.updateComputedMenus();
+ // potential for deadlock here:
+ // jmolpopup.updateComputedMenus();
}
if (!isLoadingFromArchive())
{
viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
- setLoadingFromArchive(false);
// register ourselves as a listener and notify the gui that it needs to
// update itself.
ssm.addStructureViewerListener(this);
if (notifyLoaded)
{
- FeatureRenderer fr = getFeatureRenderer();
+ FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
fr.featuresAdded();
}
refreshGUI();
+ loadNotifiesHandled++;
}
+ setLoadingFromArchive(false);
}
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
@@ -1216,6 +1412,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
public abstract void refreshGUI();
/**
+ * called to show or hide the associated console window container.
+ *
+ * @param show
+ */
+ public abstract void showConsole(boolean show);
+
+ /**
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
@@ -1225,24 +1428,99 @@ public abstract class JalviewJmolBinding implements StructureListener,
* @param codeBase
* @param commandOptions
*/
- public void allocateViewer(Component renderPanel, boolean jmolfileio,
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
String htmlName, URL documentBase, URL codeBase,
String commandOptions)
{
+ allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+ codeBase, commandOptions, null, null);
+ }
+
+ /**
+ *
+ * @param renderPanel
+ * @param jmolfileio
+ * - when true will initialise jmol's file IO system (should be false
+ * in applet context)
+ * @param htmlName
+ * @param documentBase
+ * @param codeBase
+ * @param commandOptions
+ * @param consolePanel
+ * - panel to contain Jmol console
+ * @param buttonsToShow
+ * - buttons to show on the console, in ordr
+ */
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions, final Container consolePanel,
+ String buttonsToShow)
+ {
+ if (commandOptions == null)
+ {
+ commandOptions = "";
+ }
viewer = JmolViewer.allocateViewer(renderPanel,
(jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
+
+ console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+ if (consolePanel != null)
+ {
+ consolePanel.addComponentListener(this);
+
+ }
+
+ }
+
+ protected abstract JmolAppConsoleInterface createJmolConsole(
+ JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+
+ protected org.jmol.api.JmolAppConsoleInterface console = null;
+
+ public void componentResized(ComponentEvent e)
+ {
+
+ }
+
+ public void componentMoved(ComponentEvent e)
+ {
+
+ }
+
+ public void componentShown(ComponentEvent e)
+ {
+ showConsole(true);
+ }
+
+ public void componentHidden(ComponentEvent e)
+ {
+ showConsole(false);
}
public void setLoadingFromArchive(boolean loadingFromArchive)
{
this.loadingFromArchive = loadingFromArchive;
}
-
+
+ /**
+ *
+ * @return true if Jmol is still restoring state or loading is still going on (see setFinsihedLoadingFromArchive)
+ */
public boolean isLoadingFromArchive()
{
- return loadingFromArchive;
+ return loadingFromArchive && !loadingFinished;
+ }
+
+ /**
+ * modify flag which controls if sequence colouring events are honoured by the binding.
+ * Should be true for normal operation
+ * @param finishedLoading
+ */
+ public void setFinishedLoadingFromArchive(boolean finishedLoading)
+ {
+ loadingFinished = finishedLoading;
}
public void setBackgroundColour(java.awt.Color col)
@@ -1252,4 +1530,160 @@ public abstract class JalviewJmolBinding implements StructureListener,
+ col.getGreen() + "," + col.getBlue() + "];");
jmolHistory(true);
}
+
+ /**
+ * add structures and any known sequence associations
+ *
+ * @returns the pdb entries added to the current set.
+ */
+ public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+ SequenceI[][] seq, String[][] chns)
+ {
+ int pe = -1;
+ Vector v = new Vector();
+ Vector rtn = new Vector();
+ for (int i = 0; i < pdbentry.length; i++)
+ {
+ v.addElement(pdbentry[i]);
+ }
+ for (int i = 0; i < pdbe.length; i++)
+ {
+ int r = v.indexOf(pdbe[i]);
+ if (r == -1 || r >= pdbentry.length)
+ {
+ rtn.addElement(new int[]
+ { v.size(), i });
+ v.addElement(pdbe[i]);
+ }
+ else
+ {
+ // just make sure the sequence/chain entries are all up to date
+ addSequenceAndChain(r, seq[i], chns[i]);
+ }
+ }
+ pdbe = new PDBEntry[v.size()];
+ v.copyInto(pdbe);
+ pdbentry = pdbe;
+ if (rtn.size() > 0)
+ {
+ // expand the tied seuqence[] and string[] arrays
+ SequenceI[][] sqs = new SequenceI[pdbentry.length][];
+ String[][] sch = new String[pdbentry.length][];
+ System.arraycopy(sequence, 0, sqs, 0, sequence.length);
+ System.arraycopy(chains, 0, sch, 0, this.chains.length);
+ sequence = sqs;
+ chains = sch;
+ pdbe = new PDBEntry[rtn.size()];
+ for (int r = 0; r < pdbe.length; r++)
+ {
+ int[] stri = ((int[]) rtn.elementAt(r));
+ // record the pdb file as a new addition
+ pdbe[r] = pdbentry[stri[0]];
+ // and add the new sequence/chain entries
+ addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
+ }
+ }
+ else
+ {
+ pdbe = null;
+ }
+ return pdbe;
+ }
+
+ public void addSequence(int pe, SequenceI[] seq)
+ {
+ // add sequences to the pe'th pdbentry's seuqence set.
+ addSequenceAndChain(pe, seq, null);
+ }
+
+ private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ {
+ if (pe < 0 || pe >= pdbentry.length)
+ {
+ throw new Error(
+ "Implementation error - no corresponding pdbentry (for index "
+ + pe + ") to add sequences mappings to");
+ }
+ final String nullChain = "TheNullChain";
+ Vector s = new Vector();
+ Vector c = new Vector();
+ if (chains == null)
+ {
+ chains = new String[pdbentry.length][];
+ }
+ if (sequence[pe] != null)
+ {
+ for (int i = 0; i < sequence[pe].length; i++)
+ {
+ s.addElement(sequence[pe][i]);
+ if (chains[pe] != null)
+ {
+ if (i < chains[pe].length)
+ {
+ c.addElement(chains[pe][i]);
+ }
+ else
+ {
+ c.addElement(nullChain);
+ }
+ }
+ else
+ {
+ if (tchain != null && tchain.length > 0)
+ {
+ c.addElement(nullChain);
+ }
+ }
+ }
+ }
+ for (int i = 0; i < seq.length; i++)
+ {
+ if (!s.contains(seq[i]))
+ {
+ s.addElement(seq[i]);
+ if (tchain != null && i < tchain.length)
+ {
+ c.addElement(tchain[i] == null ? nullChain : tchain[i]);
+ }
+ }
+ }
+ SequenceI[] tmp = new SequenceI[s.size()];
+ s.copyInto(tmp);
+ sequence[pe] = tmp;
+ if (c.size() > 0)
+ {
+ String[] tch = new String[c.size()];
+ c.copyInto(tch);
+ for (int i = 0; i < tch.length; i++)
+ {
+ if (tch[i] == nullChain)
+ {
+ tch[i] = null;
+ }
+ }
+ chains[pe] = tch;
+ }
+ else
+ {
+ chains[pe] = null;
+ }
+ }
+
+ /**
+ *
+ * @param pdbfile
+ * @return text report of alignment between pdbfile and any associated
+ * alignment sequences
+ */
+ public String printMapping(String pdbfile)
+ {
+ return ssm.printMapping(pdbfile);
+ }
+
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // Jalview doesn't honour resize panel requests
+
+ }
}