X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=58325fdc7791302b2c3bdfc38db3b94aed86e0a7;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=4ac247c9204f93257e4365bedc2cf8a988c19a1a;hpb=fd8ca94295a0f1fe8300112b90439d19f8cb683e;p=jalview.git
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 4ac247c..58325fd 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,27 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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 .
+ * 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 jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
-import jalview.api.SequenceStructureBinding;
-import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
@@ -29,9 +30,10 @@ 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.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
import java.awt.Color;
import java.awt.Container;
@@ -40,85 +42,50 @@ 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.List;
import java.util.Map;
import java.util.Vector;
+import javajs.awt.Dimension;
+
import org.jmol.adapter.smarter.SmarterJmolAdapter;
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, ComponentListener,
- StructureSelectionManagerProvider
-
+import org.jmol.c.CBK;
+import org.jmol.script.T;
+import org.jmol.viewer.JC;
+import org.jmol.viewer.Viewer;
+
+public abstract class JalviewJmolBinding extends AAStructureBindingModel
+ implements JmolStatusListener, JmolSelectionListener,
+ ComponentListener
{
- /**
- * set if Jmol state is being restored from some source - instructs binding
- * not to apply default display style when structure set is updated for first
- * 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
- */
- private boolean finishedInit = false;
-
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
boolean allChainsSelected = false;
- /**
+ /*
* when true, try to search the associated datamodel for sequences that are
* associated with any unknown structures in the Jmol view.
*/
private boolean associateNewStructs = false;
- Vector atomsPicked = new Vector();
+ Vector atomsPicked = new Vector();
- public Vector chainNames;
+ public Vector chainNames;
- Hashtable chainFile;
-
- /**
- * array of target chains for seuqences - tied to pdbentry and sequence[]
- */
- protected String[][] chains;
-
- boolean colourBySequence = true;
-
- StringBuffer eval = new StringBuffer();
+ Hashtable chainFile;
public String fileLoadingError;
- /**
+ /*
* the default or current model displayed if the model cannot be identified
* from the selection message
*/
int frameNo = 0;
- protected JmolPopup jmolpopup;
+ // protected JmolGenericPopup jmolpopup; // not used - remove?
String lastCommand;
@@ -131,37 +98,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
String[] modelFileNames = null;
- public PDBEntry[] pdbentry;
-
- /**
- * datasource protocol for access to PDBEntrylatest
- */
- String protocol = null;
-
StringBuffer resetLastRes = new StringBuffer();
- /**
- * sequences mapped to each pdbentry
- */
- public SequenceI[][] sequence;
-
- public StructureSelectionManager ssm;
-
- public JmolViewer viewer;
+ public Viewer viewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
String protocol)
{
- this.ssm = ssm;
- this.sequence = sequenceIs;
- this.chains = chains;
- this.pdbentry = pdbentry;
- this.protocol = protocol;
- if (chains == null)
- {
- this.chains = new String[pdbentry.length][];
- }
+ super(ssm, pdbentry, sequenceIs, chains, protocol);
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -172,10 +117,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
public JalviewJmolBinding(StructureSelectionManager ssm,
- JmolViewer viewer2)
+ SequenceI[][] seqs, Viewer theViewer)
{
- this.ssm = ssm;
- viewer = viewer2;
+ super(ssm, seqs);
+
+ viewer = theViewer;
viewer.setJmolStatusListener(this);
viewer.addSelectionListener(this);
}
@@ -188,30 +134,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
public String getViewerTitle()
{
- if (sequence == null || pdbentry == null || sequence.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());
-
- if (pdbentry[0].getProperty() != null)
- {
- if (pdbentry[0].getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry[0].getProperty().get("method"));
- }
- if (pdbentry[0].getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry[0].getProperty().get("chains"));
- }
- }
- return title.toString();
+ return getViewerTitle("Jmol", true);
}
/**
@@ -221,15 +144,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
* @param chainList
* list of chains to make visible
*/
- public void centerViewer(Vector chainList)
+ public void centerViewer(Vector chainList)
{
- StringBuffer cmd = new StringBuffer();
- String lbl;
+ StringBuilder cmd = new StringBuilder(128);
int mlength, p;
- for (int i = 0, iSize = chainList.size(); i < iSize; i++)
+ for (String lbl : chainList)
{
mlength = 0;
- lbl = (String) chainList.elementAt(i);
do
{
p = mlength;
@@ -237,18 +158,20 @@ public abstract class JalviewJmolBinding implements StructureListener,
} 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) + " /"
- + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
+ + (1 + getModelNum(chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
+ {
cmd.setLength(cmd.length() - 4);
+ }
evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
}
public void closeViewer()
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
+ viewer.acm.setModeMouse(JC.MOUSE_NONE);
// remove listeners for all structures in viewer
- ssm.removeStructureViewerListener(this, this.getPdbFile());
+ getSsm().removeStructureViewerListener(this, this.getPdbFile());
// and shut down jmol
viewer.evalStringQuiet("zap");
viewer.setJmolStatusListener(null);
@@ -257,12 +180,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
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;
@@ -314,51 +231,60 @@ public abstract class JalviewJmolBinding implements StructureListener,
public void superposeStructures(AlignmentI alignment, int refStructure,
ColumnSelection hiddenCols)
{
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[] { refStructure },
+ new ColumnSelection[] { hiddenCols });
}
+ /**
+ * Construct and send a command to align structures against a reference
+ * structure, based on one or more sequence alignments
+ *
+ * @param _alignment
+ * an array of alignments to process
+ * @param _refStructure
+ * an array of corresponding reference structures (index into pdb
+ * file array); if a negative value is passed, the first PDB file
+ * mapped to an alignment sequence is used as the reference for
+ * superposition
+ * @param _hiddenCols
+ * an array of corresponding hidden columns for each alignment
+ */
public void superposeStructures(AlignmentI[] _alignment,
int[] _refStructure, ColumnSelection[] _hiddenCols)
{
- assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
-
- String[] files = getPdbFile();
- // 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)
+ while (viewer.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException i)
{
- 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)
+ ;
+ }
+ String[] files = getPdbFile();
+ if (!waitForFileLoad(files))
{
- System.err.println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
return;
}
- StringBuffer selectioncom = new StringBuffer();
-
+ StringBuilder selectioncom = new StringBuilder(256);
+ // 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)
+ {
+ nSeconds = " 0.005 ";
+ }
+ else
+ {
+ nSeconds = " " + (2.0 / files.length) + " ";
+ // if (nSeconds).substring(0,5)+" ";
+ }
+ // 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++)
{
@@ -379,125 +305,78 @@ public abstract class JalviewJmolBinding implements StructureListener,
+ refStructure);
refStructure = -1;
}
- if (refStructure < -1)
- {
- refStructure = -1;
- }
- StringBuffer command = new StringBuffer();
+ /*
+ * 'matched' array will hold 'true' for visible alignment columns where
+ * all sequences have a residue with a mapping to the PDB structure
+ */
boolean matched[] = new boolean[alignment.getWidth()];
for (int m = 0; m < matched.length; m++)
{
-
matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
}
- 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++)
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
{
- 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;
-
- int lastPos = -1;
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
- {
- if (refStructure == -1)
- {
- refStructure = pdbfnum;
- }
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < matched.length; r++)
- {
- 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)))
- {
- // 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);
+ structures[f] = new SuperposeData(alignment.getWidth());
+ }
- 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)
- {
- targetC[pdbfnum] = "";
- }
- else
- {
- targetC[pdbfnum] = ":" + mapping[m].getChain();
- }
- chainNames[pdbfnum] = mapping[m].getPdbId()
- + targetC[pdbfnum];
- // move on to next pdb file
- s = sequence[pdbfnum].length;
- break;
- }
- }
- }
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
+ {
+ /*
+ * If no reference structure was specified, pick the first one that has
+ * a mapping in the alignment
+ */
+ refStructure = candidateRefStructure;
}
+
String[] selcom = new String[files.length];
int nmatched = 0;
- // generate select statements to select regions to superimpose structures
+ for (boolean b : matched)
+ {
+ if (b)
+ {
+ nmatched++;
+ }
+ }
+ if (nmatched < 4)
+ {
+ // TODO: bail out here because superposition illdefined?
+ }
+
+ /*
+ * generate select statements to select regions to superimpose structures
+ */
{
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- String chainCd = targetC[pdbfnum];
+ String chainCd = ":" + structures[pdbfnum].chain;
int lpos = -1;
boolean run = false;
- StringBuffer molsel = new StringBuffer();
+ StringBuilder molsel = new StringBuilder();
molsel.append("{");
for (int r = 0; r < matched.length; r++)
{
if (matched[r])
{
- if (pdbfnum == 0)
- {
- nmatched++;
- }
- if (lpos != commonrpositions[pdbfnum][r] - 1)
+ int pdbResNo = structures[pdbfnum].pdbResNo[r];
+ if (lpos != pdbResNo - 1)
{
// discontinuity
if (lpos != -1)
{
molsel.append(lpos);
molsel.append(chainCd);
- // molsel.append("} {");
molsel.append("|");
}
+ run = false;
}
else
{
@@ -510,68 +389,78 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
run = true;
}
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
+ lpos = pdbResNo;
}
}
- // add final selection phrase
+ /*
+ * add final selection phrase
+ */
if (lpos != -1)
{
molsel.append(lpos);
molsel.append(chainCd);
molsel.append("}");
}
- 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)
+ 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("|");
+ }
+ }
+ else
{
- selectioncom.append("|");
+ selcom[pdbfnum] = null;
}
}
}
- // TODO: consider bailing if nmatched less than 4 because superposition
- // not
- // well defined.
- // TODO: refactor superposable position search (above) from jmol selection
- // construction (below)
+ StringBuilder command = new StringBuilder(256);
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- if (pdbfnum == refStructure)
+ if (pdbfnum == refStructure || selcom[pdbfnum] == null
+ || selcom[refStructure] == null)
{
continue;
}
command.append("echo ");
command.append("\"Superposing (");
- command.append(chainNames[pdbfnum]);
+ command.append(structures[pdbfnum].pdbId);
command.append(") against reference (");
- command.append(chainNames[refStructure]);
- command.append(")\";\ncompare ");
+ command.append(structures[refStructure].pdbId);
+ command.append(")\";\ncompare " + nSeconds);
command.append("{");
- command.append(1 + pdbfnum);
+ command.append(Integer.toString(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++)
- {
- command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
- }
+ command.append(Integer.toString(1 + refStructure));
+ // conformation=1 excludes alternate locations for CA (JAL-1757)
+ command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
+
+ // for (int s = 0; s < 2; s++)
+ // {
+ // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
+ // }
+ command.append(selcom[pdbfnum]);
+ command.append(selcom[refStructure]);
command.append(" ROTATE TRANSLATE;\n");
}
- 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());
+ if (selectioncom.length() > 0)
+ {
+ System.out.println("Select regions:\n" + selectioncom.toString());
+ evalStateCommand("select *; cartoons off; backbone; select ("
+ + selectioncom.toString() + "); cartoons; ");
+ // selcom.append("; ribbons; ");
+ String cmdString = command.toString();
+ System.out.println("Superimpose command(s):\n" + cmdString);
+
+ evalStateCommand(cmdString);
+ }
}
if (selectioncom.length() > 0)
{// finally, mark all regions that were superposed.
@@ -602,12 +491,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
* using the getFeatureRenderer() and getSequenceRenderer() renderers but only
* if colourBySequence is enabled.
*/
- public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ public void colourBySequence(AlignmentViewPanel alignmentv)
{
- if (!colourBySequence || !loadingFinished)
+ boolean showFeatures = alignmentv.getAlignViewport()
+ .isShowSequenceFeatures();
+ if (!colourBySequence || !isLoadingFinished())
+ {
return;
- if (ssm == null)
+ }
+ if (getSsm() == null)
{
return;
}
@@ -622,23 +514,37 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands
- .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
- alignment))
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ files, sr, fr, alignment))
+ {
for (String cbyseq : cpdbbyseq.commands)
{
- evalStateCommand(cbyseq);
+ executeWhenReady(cbyseq);
}
+ }
}
- public boolean isColourBySequence()
+ /**
+ * @param files
+ * @param sr
+ * @param fr
+ * @param alignment
+ * @return
+ */
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
{
- return colourBySequence;
+ return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, fr, alignment);
}
- public void setColourBySequence(boolean colourBySequence)
+ /**
+ * @param command
+ */
+ protected void executeWhenReady(String command)
{
- this.colourBySequence = colourBySequence;
+ evalStateCommand(command);
}
public void createImage(String file, String type, int quality)
@@ -678,9 +584,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
String pdbfile)
{
if (getModelNum(pdbfile) < 0)
+ {
return null;
+ }
// TODO: verify atomIndex is selecting correct model.
- return new Color(viewer.getAtomArgb(atomIndex));
+ // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
+ int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
+ return new Color(colour);
}
/**
@@ -711,7 +621,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
for (int i = 0; i < mfn.length; i++)
{
if (mfn[i].equalsIgnoreCase(modelFileName))
+ {
return i;
+ }
}
return -1;
}
@@ -725,6 +637,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
// ////////////////////////////////
// /StructureListener
+ @Override
public synchronized String[] getPdbFile()
{
if (viewer == null)
@@ -733,26 +646,34 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
if (modelFileNames == null)
{
-
- String mset[] = new String[viewer.getModelCount()];
+ String mset[] = new String[viewer.ms.mc];
_modelFileNameMap = new int[mset.length];
- int j = 1;
- String m = viewer.getModelFileName(0);
+ String m = viewer.ms.getModelFileName(0);
if (m != null)
{
+ mset[0] = m;
try
{
mset[0] = new File(m).getAbsolutePath();
} catch (AccessControlException x)
{
- // usually not allowed to do this in applet, so keep raw handle
+ // usually not allowed to do this in applet
+ System.err
+ .println("jmolBinding: Using local file string from Jmol: "
+ + m);
+ }
+ if (mset[0].indexOf("/file:") != -1)
+ {
+ // applet path with docroot - discard as format won't match pdbfile
mset[0] = m;
- // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
}
+ _modelFileNameMap[0] = 0; // filename index for first model is always 0.
}
+ int j = 1;
for (int i = 1; i < mset.length; i++)
{
- m = viewer.getModelFileName(i);
+ m = viewer.ms.getModelFileName(i);
+ mset[j] = m;
if (m != null)
{
try
@@ -761,7 +682,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
} 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);
}
}
@@ -782,7 +702,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
/**
* map from string to applet
*/
- public Map getRegistryInfo()
+ @Override
+ public Map getRegistryInfo()
{
// TODO Auto-generated method stub
return null;
@@ -804,7 +725,24 @@ public abstract class JalviewJmolBinding implements StructureListener,
public void handlePopupMenu(int x, int y)
{
- jmolpopup.show(x, y);
+ // jmolpopup.show(x, y);
+ // jmolpopup.jpiShow(x, y);
+ }
+
+ /**
+ * Highlight zero, one or more atoms on the structure
+ */
+ @Override
+ public void highlightAtoms(List atoms)
+ {
+ if (atoms != null)
+ {
+ for (AtomSpec atom : atoms)
+ {
+ highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ }
+ }
}
// jmol/ssm only
@@ -818,12 +756,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
// look up file model number for this pdbfile
int mdlNum = 0;
- String fn;
// may need to adjust for URLencoding here - we don't worry about that yet.
while (mdlNum < modelFileNames.length
&& !pdbfile.equals(modelFileNames[mdlNum]))
{
- // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);
mdlNum++;
}
if (mdlNum == modelFileNames.length)
@@ -839,31 +775,31 @@ public abstract class JalviewJmolBinding implements StructureListener,
viewer.evalStringQuiet(resetLastRes.toString());
}
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
+ StringBuilder cmd = new StringBuilder(64);
+ cmd.append("select " + pdbResNum); // +modelNum
resetLastRes.setLength(0);
resetLastRes.append("select " + pdbResNum); // +modelNum
- eval.append(":");
+ cmd.append(":");
resetLastRes.append(":");
if (!chain.equals(" "))
{
- eval.append(chain);
+ cmd.append(chain);
resetLastRes.append(chain);
}
{
- eval.append(" /" + (mdlNum + 1));
+ cmd.append(" /" + (mdlNum + 1));
resetLastRes.append("/" + (mdlNum + 1));
}
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
+ cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
+ " and not hetero; spacefill 0;");
- eval.append("spacefill 200;select none");
+ cmd.append("spacefill 200;select none");
- viewer.evalStringQuiet(eval.toString());
+ viewer.evalStringQuiet(cmd.toString());
jmolHistory(true);
}
@@ -920,8 +856,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
String chainId;
if (strInfo.indexOf(":") > -1)
+ {
chainId = strInfo.substring(strInfo.indexOf(":") + 1,
strInfo.indexOf("."));
+ }
else
{
chainId = " ";
@@ -949,7 +887,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
pdbfilename = modelFileNames[_mp];
if (pdbfilename == null)
{
- pdbfilename = new File(viewer.getModelFileName(mnumber))
+ pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
.getAbsolutePath();
}
@@ -959,7 +897,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
;
}
if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ {
+ getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ }
lastMessage = strInfo;
}
@@ -993,13 +933,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
int chainSeparator = strInfo.indexOf(":");
int p = 0;
if (chainSeparator == -1)
+ {
chainSeparator = strInfo.indexOf(".");
+ }
String picked = strInfo.substring(strInfo.indexOf("]") + 1,
chainSeparator);
String mdlString = "";
if ((p = strInfo.indexOf(":")) > -1)
- picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+ {
+ picked += strInfo.substring(p, strInfo.indexOf("."));
+ }
if ((p = strInfo.indexOf("/")) > -1)
{
@@ -1031,7 +975,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
@Override
- public void notifyCallback(EnumCallback type, Object[] data)
+ public void notifyCallback(CBK type, Object[] data)
{
try
{
@@ -1085,7 +1029,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
@Override
- public boolean notifyEnabled(EnumCallback callbackPick)
+ public boolean notifyEnabled(CBK callbackPick)
{
switch (callbackPick)
{
@@ -1098,13 +1042,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
case HOVER:
case ERROR:
return true;
- case RESIZE:
- case SYNC:
- case CLICK:
- case ANIMFRAME:
- case MINIMIZATION:
+ default:
+ return false;
}
- return false;
}
// incremented every time a load notification is successfully handled -
@@ -1135,8 +1075,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new Vector();
- chainFile = new Hashtable();
+ chainNames = new Vector();
+ chainFile = new Hashtable();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
// first check if we've lost any structures
@@ -1171,7 +1111,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
// deregister the Jmol instance for these structures - we'll add
// ourselves again at the end for the current structure set.
- ssm.removeStructureViewerListener(this, oldmfn);
+ getSsm().removeStructureViewerListener(this, oldmfn);
}
}
refreshPdbEntries();
@@ -1180,7 +1120,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
MCview.PDBfile pdb = null;
- String pdbfile = null, pdbfhash = null;
+ String pdbfile = null;
// model was probably loaded inline - so check the pdb file hashcode
if (loadedInline)
{
@@ -1189,72 +1129,69 @@ public abstract class JalviewJmolBinding implements StructureListener,
// 'best guess'
pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ ".0", "PDB");
- pdbfhash = "" + pdbfile.hashCode();
}
- if (pdbentry != null)
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
+ for (int pe = 0; pe < getPdbCount(); pe++)
{
- // search pdbentries and sequences to find correct pdbentry for this
- // model
- for (int pe = 0; pe < pdbentry.length; pe++)
+ boolean matches = false;
+ if (fileName == null)
{
- boolean matches = false;
- if (fileName == null)
+ if (false)
+ // see JAL-623 - need method of matching pasted data up
{
- 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;
- }
+ pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
+ pdbfile, AppletFormatAdapter.PASTE);
+ getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
+ matches = true;
+ foundEntry = true;
}
- else
+ }
+ else
+ {
+ File fl = new File(getPdbEntry(pe).getFile());
+ matches = fl.equals(new File(fileName));
+ if (matches)
{
- 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
{
- 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
- {
- if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
+ if (fl.exists())
{
+ protocol = AppletFormatAdapter.FILE;
}
- // Explicitly map to the filename used by Jmol ;
- pdb = ssm.setMapping(sequence[pe], chains[pe], fileName,
- protocol);
- // pdbentry[pe].getFile(), protocol);
-
+ } catch (Exception e)
+ {
+ } catch (Error e)
+ {
}
+ // Explicitly map to the filename used by Jmol ;
+ pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
+ fileName, protocol);
+ // pdbentry[pe].getFile(), protocol);
+
}
- if (matches)
+ }
+ if (matches)
+ {
+ // add an entry for every chain in the model
+ for (int i = 0; i < pdb.chains.size(); i++)
{
- // 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;
+ String chid = new String(pdb.id + ":"
+ + 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
@@ -1272,18 +1209,18 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
- if (jmolpopup != null)
- {
- // potential for deadlock here:
- // jmolpopup.updateComputedMenus();
- }
+ // if (jmolpopup != null)
+ // {
+ // // potential for deadlock here:
+ // // jmolpopup.updateComputedMenus();
+ // }
if (!isLoadingFromArchive())
{
- viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ viewer.evalStringQuiet("model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
- ssm.addStructureViewerListener(this);
+ getSsm().addStructureViewerListener(this);
if (notifyLoaded)
{
FeatureRenderer fr = getFeatureRenderer(null);
@@ -1340,24 +1277,18 @@ public abstract class JalviewJmolBinding implements StructureListener,
colourBySequence = false;
if (cs == null)
+ {
return;
+ }
- String res;
- int index;
- Color col;
jmolHistory(false);
- // TODO: Switch between nucleotide or aa selection expressions
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
+ StringBuilder command = new StringBuilder(128);
+ command.append("select *;color white;");
+ List residueSet = ResidueProperties.getResidues(isNucleotide(),
+ false);
+ for (String res : residueSet)
{
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
+ Color col = cs.findColour(res.charAt(0));
command.append("select " + res + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
}
@@ -1434,12 +1365,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
commandOptions = "";
}
- viewer = JmolViewer.allocateViewer(renderPanel,
+ viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
(jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
- console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+ viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+
+ console = createJmolConsole(consolePanel, buttonsToShow);
if (consolePanel != null)
{
consolePanel.addComponentListener(this);
@@ -1449,54 +1382,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
protected abstract JmolAppConsoleInterface createJmolConsole(
- JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+ 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 && !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)
{
jmolHistory(false);
@@ -1505,159 +1394,64 @@ public abstract class JalviewJmolBinding implements StructureListener,
jmolHistory(true);
}
+ @Override
+ public Dimension resizeInnerPanel(String data)
+ {
+ // Jalview doesn't honour resize panel requests
+ return null;
+ }
+
/**
- * 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)
+ protected void closeConsole()
{
- 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++)
+ if (console != null)
{
- int r = v.indexOf(pdbe[i]);
- if (r == -1 || r >= pdbentry.length)
+ try
{
- rtn.addElement(new int[]
- { v.size(), i });
- v.addElement(pdbe[i]);
- }
- else
+ console.setVisible(false);
+ } catch (Error e)
{
- // 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++)
+ } catch (Exception x)
{
- 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]]);
}
+ ;
+ console = null;
}
- else
- {
- pdbe = null;
- }
- return pdbe;
}
- public void addSequence(int pe, SequenceI[] seq)
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentMoved(ComponentEvent e)
{
- // add sequences to the pe'th pdbentry's seuqence set.
- addSequenceAndChain(pe, seq, null);
}
- private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentResized(ComponentEvent e)
{
- 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
+ * ComponentListener method
*/
- public String printMapping(String pdbfile)
+ @Override
+ public void componentShown(ComponentEvent e)
{
- return ssm.printMapping(pdbfile);
+ showConsole(true);
}
+ /**
+ * ComponentListener method
+ */
@Override
- public void resizeInnerPanel(String data)
+ public void componentHidden(ComponentEvent e)
{
- // Jalview doesn't honour resize panel requests
-
+ showConsole(false);
}
}