X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=88322785ee9fbce68679087362a8bbfcaa40fe6c;hb=3f53fef393541cb63beb8766a4f3922b8c420579;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..8832278 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,37 +1,42 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
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 jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Container;
@@ -40,8 +45,10 @@ import java.awt.event.ComponentListener;
import java.io.File;
import java.net.URL;
import java.security.AccessControlException;
-import java.util.Enumeration;
+import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Hashtable;
+import java.util.List;
import java.util.Map;
import java.util.Vector;
@@ -50,75 +57,35 @@ 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.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();
-
- public Vector chainNames;
-
- Hashtable chainFile;
-
- /**
- * array of target chains for seuqences - tied to pdbentry and sequence[]
- */
- protected String[][] chains;
-
- boolean colourBySequence = true;
+ Vector atomsPicked = new Vector<>();
- StringBuffer eval = new StringBuffer();
+ private List chainNames;
- public String fileLoadingError;
+ Hashtable chainFile;
- /**
+ /*
* 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;
@@ -126,42 +93,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
boolean loadedInline;
- /**
- * current set of model filenames loaded in the Jmol instance
- */
- 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)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType 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, protocol);
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -172,10 +112,11 @@ 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 +129,7 @@ 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 +139,13 @@ 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;
@@ -237,32 +153,26 @@ 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);
// remove listeners for all structures in viewer
- ssm.removeStructureViewerListener(this, this.getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
+ viewer.dispose();
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();
-
+ @Override
public void colourByChain()
{
colourBySequence = false;
@@ -272,6 +182,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
evalStateCommand("select *;color chain");
}
+ @Override
public void colourByCharge()
{
colourBySequence = false;
@@ -312,266 +223,233 @@ public abstract class JalviewJmolBinding implements StructureListener,
* TODO
*/
public void superposeStructures(AlignmentI alignment, int refStructure,
- ColumnSelection hiddenCols)
+ HiddenColumns hiddenCols)
{
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[]
+ { refStructure }, new HiddenColumns[] { hiddenCols });
}
- public void superposeStructures(AlignmentI[] _alignment,
- int[] _refStructure, ColumnSelection[] _hiddenCols)
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public String superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, HiddenColumns[] _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)
+ }
+
+ /*
+ * get the distinct structure files modelled
+ * (a file with multiple chains may map to multiple sequences)
+ */
+ String[] files = getStructureFiles();
+ if (!waitForFileLoad(files))
{
- System.err.println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
- return;
+ return null;
}
- 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++)
{
int refStructure = _refStructure[a];
AlignmentI alignment = _alignment[a];
- ColumnSelection hiddenCols = _hiddenCols[a];
- if (a > 0
- && selectioncom.length() > 0
- && !selectioncom.substring(selectioncom.length() - 1).equals(
- "|"))
+ HiddenColumns 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);
+ System.err.println(
+ "Invalid reference structure value " + refStructure);
refStructure = -1;
}
- if (refStructure < -1)
+
+ /*
+ * 'matched' bit j will be set for visible alignment columns j where
+ * all sequences have a residue with a mapping to the PDB structure
+ */
+ BitSet matched = new BitSet();
+ for (int m = 0; m < alignment.getWidth(); m++)
{
- refStructure = -1;
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
- StringBuffer command = new StringBuffer();
- boolean matched[] = new boolean[alignment.getWidth()];
- for (int m = 0; m < matched.length; m++)
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
{
-
- matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ structures[f] = new SuperposeData(alignment.getWidth());
}
- 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++)
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
{
- 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);
-
- 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;
- }
- }
- }
+ /*
+ * 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
+ int nmatched = matched.cardinality();
+ if (nmatched < 4)
{
+ return (MessageManager.formatMessage("label.insufficient_residues",
+ nmatched));
+ }
+
+ /*
+ * generate select statements to select regions to superimpose structures
+ */
+ {
+ // TODO extract method to construct selection statements
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++)
+
+ int nextColumnMatch = matched.nextSetBit(0);
+ while (nextColumnMatch != -1)
{
- if (matched[r])
+ int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch];
+ if (lpos != pdbResNo - 1)
{
- if (pdbfnum == 0)
+ // discontinuity
+ if (lpos != -1)
{
- nmatched++;
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("|");
}
- if (lpos != commonrpositions[pdbfnum][r] - 1)
- {
- // discontinuity
- if (lpos != -1)
- {
- molsel.append(lpos);
- molsel.append(chainCd);
- // molsel.append("} {");
- molsel.append("|");
- }
- }
- else
+ run = false;
+ }
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
{
- // continuous run - and lpos >-1
- if (!run)
- {
- // at the beginning, so add dash
- molsel.append(lpos);
- molsel.append("-");
- }
- run = true;
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
}
- lpos = commonrpositions[pdbfnum][r];
- // molsel.append(lpos);
+ run = true;
}
+ lpos = pdbResNo;
+ nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
}
- // 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)
{
- selectioncom.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)
+ {
+ selectioncom.append("|");
+ }
+ }
+ else
+ {
+ 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);
+ // command.append("set spinFps 10;\n");
+
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)
+ {
+ // TODO is performing selectioncom redundant here? is done later on
+ // 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.
@@ -579,11 +457,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
selectioncom.setLength(selectioncom.length() - 1);
}
- System.out.println("Select regions:\n" + selectioncom.toString());
+ // 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());
+ // evalStateCommand("select *; backbone; select "+selcom.toString()+";
+ // cartoons; center "+selcom.toString());
}
+
+ return null;
}
public void evalStateCommand(String command)
@@ -597,48 +478,58 @@ public abstract class JalviewJmolBinding implements StructureListener,
lastCommand = command;
}
+ Thread colourby = null;
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Sends a set of colour commands to the structure viewer
+ *
+ * @param colourBySequenceCommands
*/
- public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ @Override
+ protected void colourBySequence(
+ final StructureMappingcommandSet[] colourBySequenceCommands)
{
- if (!colourBySequence || !loadingFinished)
- return;
- if (ssm == null)
+ if (colourby != null)
{
- return;
+ colourby.interrupt();
+ colourby = null;
}
- String[] files = getPdbFile();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
- FeatureRenderer fr = null;
- if (showFeatures)
+ colourby = new Thread(new Runnable()
{
- fr = getFeatureRenderer(alignmentv);
- }
- AlignmentI alignment = alignmentv.getAlignment();
-
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands
- .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
- alignment))
- for (String cbyseq : cpdbbyseq.commands)
+ @Override
+ public void run()
{
- evalStateCommand(cbyseq);
+ for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+ {
+ for (String cbyseq : cpdbbyseq.commands)
+ {
+ executeWhenReady(cbyseq);
+ }
+ }
}
+ });
+ colourby.start();
}
- public boolean isColourBySequence()
+ /**
+ * @param files
+ * @param sr
+ * @param viewPanel
+ * @return
+ */
+ @Override
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
{
- return colourBySequence;
+ return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, viewPanel);
}
- 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)
@@ -646,6 +537,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
System.out.println("JMOL CREATE IMAGE");
}
+ @Override
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
@@ -653,6 +545,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
return null;
}
+ @Override
public String eval(String strEval)
{
// System.out.println(strEval);
@@ -663,12 +556,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
// End StructureListener
// //////////////////////////
+ @Override
public float[][] functionXY(String functionName, int x, int y)
{
return null;
}
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ @Override
+ public float[][][] functionXYZ(String functionName, int nx, int ny,
+ int nz)
{
// TODO Auto-generated method stub
return null;
@@ -678,23 +574,16 @@ 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);
}
/**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment);
-
- /**
* instruct the Jalview binding to update the pdbentries vector if necessary
* prior to matching the jmol view's contents to the list of structure files
* Jalview knows about.
@@ -703,7 +592,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
private int getModelNum(String modelFileName)
{
- String[] mfn = getPdbFile();
+ String[] mfn = getStructureFiles();
if (mfn == null)
{
return -1;
@@ -711,7 +600,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
for (int i = 0; i < mfn.length; i++)
{
if (mfn[i].equalsIgnoreCase(modelFileName))
+ {
return i;
+ }
}
return -1;
}
@@ -725,7 +616,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
// ////////////////////////////////
// /StructureListener
- public synchronized String[] getPdbFile()
+ // @Override
+ public synchronized String[] getPdbFilex()
{
if (viewer == null)
{
@@ -733,78 +625,128 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
if (modelFileNames == null)
{
-
- String mset[] = new String[viewer.getModelCount()];
- _modelFileNameMap = new int[mset.length];
- int j = 1;
- String m = viewer.getModelFileName(0);
+ List mset = new ArrayList<>();
+ _modelFileNameMap = new int[viewer.ms.mc];
+ String m = viewer.ms.getModelFileName(0);
if (m != null)
{
+ String filePath = m;
try
{
- mset[0] = new File(m).getAbsolutePath();
+ filePath = 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);
+ // 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.
}
- for (int i = 1; i < mset.length; i++)
+ int j = 1;
+ for (int i = 1; i < viewer.ms.mc; i++)
{
- m = viewer.getModelFileName(i);
+ m = viewer.ms.getModelFileName(i);
+ String filePath = m;
if (m != null)
{
try
{
- mset[j] = new File(m).getAbsolutePath();
+ filePath = 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);
+ // 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]))))
+
+ /*
+ * 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 = new String[j];
- System.arraycopy(mset, 0, modelFileNames, 0, j);
+ modelFileNames = mset.toArray(new String[mset.size()]);
}
return modelFileNames;
}
+ @Override
+ public synchronized String[] getStructureFiles()
+ {
+ List mset = new ArrayList<>();
+ if (viewer == null)
+ {
+ return new String[0];
+ }
+
+ if (modelFileNames == null)
+ {
+ int modelCount = viewer.ms.mc;
+ String filePath = null;
+ for (int i = 0; i < modelCount; ++i)
+ {
+ filePath = viewer.ms.getModelFileName(i);
+ if (!mset.contains(filePath))
+ {
+ mset.add(filePath);
+ }
+ }
+ modelFileNames = mset.toArray(new String[mset.size()]);
+ }
+
+ return modelFileNames;
+ }
+
/**
* map from string to applet
*/
- public Map getRegistryInfo()
+ @Override
+ public Map getRegistryInfo()
{
// TODO Auto-generated method stub
return null;
}
- /**
- * returns the current sequenceRenderer that should be used to colour the
- * structures
- *
- * @param alignment
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment);
-
// ///////////////////////////////
// JmolStatusListener
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)
+ {
+ if (resetLastRes.length() > 0)
+ {
+ viewer.evalStringQuiet(resetLastRes.toString());
+ resetLastRes.setLength(0);
+ }
+ for (AtomSpec atom : atoms)
+ {
+ highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ }
+ }
}
// jmol/ssm only
@@ -818,12 +760,10 @@ 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)
@@ -832,38 +772,31 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- 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);
}
@@ -908,20 +841,22 @@ public abstract class JalviewJmolBinding implements StructureListener,
// handle insertion codes
if (alocsep != -1)
{
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, alocsep));
+ pdbResNum = Integer.parseInt(
+ strInfo.substring(strInfo.indexOf("]") + 1, alocsep));
}
else
{
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
+ pdbResNum = Integer.parseInt(
+ strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator));
}
String chainId;
if (strInfo.indexOf(":") > -1)
+ {
chainId = strInfo.substring(strInfo.indexOf(":") + 1,
strInfo.indexOf("."));
+ }
else
{
chainId = " ";
@@ -935,31 +870,45 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
chainSeparator1 = strInfo.indexOf(".", mdlSep);
}
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
- chainSeparator1) : strInfo.substring(mdlSep + 1);
+ String mdlId = (chainSeparator1 > -1)
+ ? strInfo.substring(mdlSep + 1, chainSeparator1)
+ : strInfo.substring(mdlSep + 1);
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 = new Integer(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.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))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ {
+ getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+ }
lastMessage = strInfo;
}
@@ -980,7 +929,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
* } }
*/
- public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
+ public void notifyAtomPicked(int atomIndex, String strInfo,
+ String strData)
{
/**
* this implements the toggle label behaviour copied from the original
@@ -993,13 +943,17 @@ 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 +985,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
@Override
- public void notifyCallback(EnumCallback type, Object[] data)
+ public void notifyCallback(CBK type, Object[] data)
{
try
{
@@ -1047,6 +1001,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
// also highlight in alignment
+ // deliberate fall through
case HOVER:
notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
@@ -1059,8 +1014,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
sendConsoleEcho((String) data[1]);
break;
case MESSAGE:
- sendConsoleMessage((data == null) ? ((String) null)
- : (String) data[1]);
+ sendConsoleMessage(
+ (data == null) ? ((String) null) : (String) data[1]);
break;
case ERROR:
// System.err.println("Ignoring error callback.");
@@ -1073,8 +1028,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
case CLICK:
default:
- System.err.println("Unhandled callback " + type + " "
- + data[1].toString());
+ System.err.println(
+ "Unhandled callback " + type + " " + data[1].toString());
break;
}
} catch (Exception e)
@@ -1085,7 +1040,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
@Override
- public boolean notifyEnabled(EnumCallback callbackPick)
+ public boolean notifyEnabled(CBK callbackPick)
{
switch (callbackPick)
{
@@ -1098,13 +1053,9 @@ 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 -
@@ -1135,10 +1086,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new Vector();
- chainFile = new Hashtable();
+ chainNames = new ArrayList<>();
+ chainFile = new Hashtable<>();
boolean notifyLoaded = false;
- String[] modelfilenames = getPdbFile();
+ String[] modelfilenames = getStructureFiles();
// first check if we've lost any structures
if (oldmodels != null && oldmodels.length > 0)
{
@@ -1171,7 +1122,7 @@ 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();
@@ -1179,82 +1130,81 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
- MCview.PDBfile pdb = null;
- String pdbfile = null, pdbfhash = null;
+ StructureFile pdb = null;
+ String pdbfile = 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();
+ pdbfile = viewer.getData(
+ "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
}
- 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;
+ addSequence(pe, getSequence()[pe]);
+ 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, DataSourceType.PASTE,
+ getIProgressIndicator());
+ getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
+ 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
+ DataSourceType protocol = DataSourceType.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 = DataSourceType.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, getIProgressIndicator());
+ // pdbentry[pe].getFile(), protocol);
+
}
- if (matches)
+ }
+ if (matches)
+ {
+ // add an entry for every chain in the model
+ for (int i = 0; i < pdb.getChains().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.getId() + ":" + pdb.getChains().elementAt(i).id);
+ chainFile.put(chid, fileName);
+ chainNames.add(chid);
}
+ notifyLoaded = true;
}
}
+
if (!foundEntry && associateNewStructs)
{
// this is a foreign pdb file that jalview doesn't know about - add
@@ -1272,18 +1222,19 @@ 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);
@@ -1297,6 +1248,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
setLoadingFromArchive(false);
}
+ @Override
+ public List getChainNames()
+ {
+ return chainNames;
+ }
+
+ protected abstract IProgressIndicator getIProgressIndicator();
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
@@ -1327,6 +1286,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
public abstract void sendConsoleMessage(String strStatus);
+ @Override
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
@@ -1335,30 +1295,28 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
+ @Override
public void setJalviewColourScheme(ColourSchemeI cs)
{
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 resName : residueSet)
{
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
- command.append("select " + res + ";color[" + col.getRed() + ","
+ char res = resName.length() == 3
+ ? ResidueProperties.getSingleCharacterCode(resName)
+ : resName.charAt(0);
+ Color col = cs.findColour(res, 0, null, null, 0f);
+ command.append("select " + resName + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
}
@@ -1434,12 +1392,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
{
commandOptions = "";
}
- viewer = JmolViewer.allocateViewer(renderPanel,
- (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
- + ((Object) this).toString(), documentBase, codeBase,
+ 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 +1409,11 @@ 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;
- }
-
+ @Override
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
@@ -1505,159 +1422,64 @@ public abstract class JalviewJmolBinding implements StructureListener,
jmolHistory(true);
}
+ @Override
+ public int[] 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);
}
}