X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=c075bf58bf9f4de18153ea7a346e5ab110ae459d;hb=c38d37887ae51d63942ac4321f6769308188ed6b;hp=80cc8af16df0f3009d9ff28d6f4ba41c7bdd617c;hpb=b3d9ad42a4cc73a11a1478d8735dfe66a88a2953;p=jalview.git
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 80cc8af..eee48df 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,141 +1,89 @@
/*
- * 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 ($$Version-Rel$$)
+ * 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 java.awt.Container;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
import java.io.File;
import java.net.URL;
-import java.util.*;
-import java.applet.Applet;
-import java.awt.*;
-import java.awt.event.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+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.c.CBK;
+import org.jmol.viewer.Viewer;
+
+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 org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
-import jalview.schemes.*;
-
-public abstract class JalviewJmolBinding implements StructureListener,
- JmolStatusListener, SequenceStructureBinding, JmolSelectionListener
-
+import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import javajs.util.BS;
+
+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;
+ private String lastMessage;
- /**
- * 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;
-
- /**
- * array of target chains for seuqences - tied to pdbentry and sequence[]
- */
- protected String[][] chains;
-
- boolean colourBySequence = true;
-
- StringBuffer eval = new StringBuffer();
-
- public String fileLoadingError;
+ private Vector atomsPicked = new Vector<>();
- /**
- * the default or current model displayed if the model cannot be identified
- * from the selection message
- */
- int frameNo = 0;
-
- protected JmolPopup jmolpopup;
-
- String lastCommand;
+ private String lastCommand;
- String lastMessage;
-
- boolean loadedInline;
-
- /**
- * current set of model filenames loaded in the Jmol instance
- */
- String[] modelFileNames = null;
+ private boolean loadedInline;
- public PDBEntry[] pdbentry;
-
- /**
- * datasource protocol for access to PDBEntry
- */
- String protocol = null;
-
- StringBuffer resetLastRes = new StringBuffer();
-
- /**
- * sequences mapped to each pdbentry
- */
- public SequenceI[][] sequence;
+ private StringBuffer resetLastRes = new StringBuffer();
- StructureSelectionManager ssm;
+ public Viewer jmolViewer;
- public JmolViewer viewer;
-
- public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
- String[][] chains, String protocol)
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- 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);
+ setStructureCommands(new JmolCommands());
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -145,11 +93,15 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
}
- public JalviewJmolBinding(JmolViewer viewer2)
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ SequenceI[][] seqs, Viewer theViewer)
{
- viewer = viewer2;
- viewer.setJmolStatusListener(this);
- viewer.addSelectionListener(this);
+ super(ssm, seqs);
+
+ jmolViewer = theViewer;
+ jmolViewer.setJmolStatusListener(this);
+ jmolViewer.addSelectionListener(this);
+ setStructureCommands(new JmolCommands());
}
/**
@@ -160,434 +112,35 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
public String getViewerTitle()
{
- if (sequence == null || pdbentry == null || sequence.length < 1
- || pdbentry.length < 1)
- {
- return ("Jalview Jmol Window");
- }
- 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();
- }
-
- /**
- * prepare the view for a given set of models/chains. chainList contains
- * strings of the form 'pdbfilename:Chaincode'
- *
- * @param chainList
- * list of chains to make visible
- */
- public void centerViewer(Vector chainList)
- {
- StringBuffer cmd = new StringBuffer();
- String lbl;
- int mlength, p;
- for (int i = 0, iSize = chainList.size(); i < iSize; i++)
- {
- mlength = 0;
- lbl = (String) chainList.elementAt(i);
- do
- {
- p = mlength;
- mlength = lbl.indexOf(":", p);
- } while (p < mlength && mlength < (lbl.length() - 2));
- cmd.append(":" + lbl.substring(mlength + 1) + " /"
- + getModelNum(lbl.substring(0, mlength)) + " or ");
- }
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
- evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
+ return getViewerTitle("Jmol", true);
}
- public void closeViewer()
+ private String jmolScript(String script)
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- // remove listeners for all structures in viewer
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, this.getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- lastCommand = null;
- viewer = null;
- }
+ Cache.log.debug(">>Jmol>> " + script);
+ String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+ Cache.log.debug("< executeCommand(StructureCommandI command,
+ boolean getReply)
{
- superposeStructures(alignment, -1, null);
- }
-
- /**
- * 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)
- */
- public void superposeStructures(AlignmentI alignment, int refStructure)
- {
- superposeStructures(alignment, refStructure, null);
- }
-
- /**
- * 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
- */
- public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols)
- {
- String[] files = getPdbFile();
- if (refStructure>=files.length)
- {
- System.err.println("Invalid reference structure value "+refStructure);
- refStructure= -1;
- }
- if (refStructure<-1)
- {
- refStructure=-1;
- }
- StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer();
-
- 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];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ if (command == null)
{
- 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 (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();
- }
- // 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++)
- {
- 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 (matched[r])
- {
-
- if (lpos != commonrpositions[pdbfnum][r] - 1)
- {
- // discontinuity
- if (lpos != -1)
- {
- molsel.append(lpos);
- molsel.append(chainCd);
- // molsel.append("} {");
- molsel.append("|");
- }
- }
- 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("}");
- }
- 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 -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(command.toString());
- }
-
- public boolean isColourBySequence()
- {
- return colourBySequence;
- }
-
- public void setColourBySequence(boolean colourBySequence)
- {
- 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;
+ lastCommand = cmd;
+ return null;
}
public void createImage(String file, String type, int quality)
@@ -595,6 +148,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
System.out.println("JMOL CREATE IMAGE");
}
+ @Override
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
@@ -602,6 +156,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
return null;
}
+ @Override
public String eval(String strEval)
{
// System.out.println(strEval);
@@ -612,181 +167,158 @@ 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;
}
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (getModelNum(pdbfile) < 0)
- return null;
- // TODO: verify atomIndex is selecting correct model.
- return new Color(viewer.getAtomArgb(atomIndex));
- }
-
- /**
- * returns the current featureRenderer that should be used to colour the
- * structures
- *
- * @return
- */
- public abstract FeatureRenderer getFeatureRenderer();
-
/**
- * 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.
+ * 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.
*/
- public abstract void refreshPdbEntries();
+ private int _modelFileNameMap[];
- private int getModelNum(String modelFileName)
+ @Override
+ public synchronized String[] getStructureFiles()
{
- String[] mfn = getPdbFile();
- if (mfn == null)
- {
- return -1;
- }
- for (int i = 0; i < mfn.length; i++)
+ if (jmolViewer == null)
{
- if (mfn[i].equalsIgnoreCase(modelFileName))
- return i;
+ return new String[0];
}
- return -1;
- }
- // ////////////////////////////////
- // /StructureListener
- public synchronized String[] getPdbFile()
- {
if (modelFileNames == null)
{
- String mset[] = new String[viewer.getModelCount()];
- int j=1;
- mset[0] = viewer.getModelFileName(0);
- for (int i = 1; i < mset.length; i++)
+ int modelCount = jmolViewer.ms.mc;
+ String filePath = null;
+ List mset = new ArrayList<>();
+ for (int i = 0; i < modelCount; ++i)
{
- // skip any additional models in the same file (NMR structures)
- if (!(mset[j] = viewer.getModelFileName(i)).equals(mset[j-1]))
+ /*
+ * defensive check for null as getModelFileName can return null
+ * even when model count ms.mc is > 0
+ */
+ filePath = jmolViewer.ms.getModelFileName(i);
+ if (filePath != null && !mset.contains(filePath))
{
- j++;
+ mset.add(filePath);
}
}
- modelFileNames = new String[j];
- System.arraycopy(mset, 0, modelFileNames, 0, j);
+ if (!mset.isEmpty())
+ {
+ 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
- *
- * @return
- */
- public abstract SequenceRenderer getSequenceRenderer();
-
// ///////////////////////////////
// JmolStatusListener
public void handlePopupMenu(int x, int y)
{
- jmolpopup.show(x, y);
+ // jmolpopup.show(x, y);
+ // jmolpopup.jpiShow(x, y);
}
- // jmol/ssm only
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
+ /**
+ * Highlight zero, one or more atoms on the structure
+ */
+ @Override
+ public void highlightAtoms(List atoms)
{
- if (modelFileNames == null)
+ if (atoms != null)
{
- return;
+ if (resetLastRes.length() > 0)
+ {
+ jmolScript(resetLastRes.toString());
+ resetLastRes.setLength(0);
+ }
+ for (AtomSpec atom : atoms)
+ {
+ highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ }
}
+ }
- // 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)
+ // jmol/ssm only
+ public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
+ {
+ String modelId = getModelIdForFile(pdbfile);
+ if (modelId.isEmpty())
{
return;
}
jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum); // +modelNum
- eval.append(":");
- resetLastRes.append(":");
+ StringBuilder selection = new StringBuilder(32);
+ StringBuilder cmd = new StringBuilder(64);
+ selection.append("select ").append(String.valueOf(pdbResNum));
+ selection.append(":");
if (!chain.equals(" "))
{
- eval.append(chain);
- resetLastRes.append(chain);
+ selection.append(chain);
}
- {
- eval.append(" /" + (mdlNum + 1));
- resetLastRes.append("/" + (mdlNum + 1));
- }
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
+ selection.append(" /").append(modelId);
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + " and not hetero; spacefill 0;");
+ cmd.append(selection).append(";wireframe 100;").append(selection)
+ .append(" and not hetero;").append("spacefill 200;select none");
- eval.append("spacefill 200;select none");
+ resetLastRes.append(selection).append(";wireframe 0;").append(selection)
+ .append(" and not hetero; spacefill 0;");
- viewer.evalStringQuiet(eval.toString());
+ jmolScript(cmd.toString());
jmolHistory(true);
-
}
- boolean debug = true;
+ private boolean debug = true;
private void jmolHistory(boolean enable)
{
- viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
+ jmolScript("History " + ((debug || enable) ? "on" : "off"));
}
public void loadInline(String string)
{
loadedInline = true;
- viewer.openStringInline(string);
+ // 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);
+ jmolViewer.openStringInline(string);
}
- public void mouseOverStructure(int atomIndex, String strInfo)
+ protected void mouseOverStructure(int atomIndex, final String strInfo)
{
int pdbResNum;
+ int alocsep = strInfo.indexOf("^");
int mdlSep = strInfo.indexOf("/");
int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
@@ -799,47 +331,100 @@ 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)
+ {
chainId = strInfo.substring(strInfo.indexOf(":") + 1,
strInfo.indexOf("."));
+ }
else
{
chainId = " ";
}
- String pdbfilename = modelFileNames[frameNo]; // default is first or current
- // model
+ String pdbfilename = modelFileNames[0]; // default is first model
if (mdlSep > -1)
{
if (chainSeparator1 == -1)
{
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.
- pdbfilename = viewer
- .getModelFileName(new Integer(mdlId).intValue() - 1);
+ int mnumber = Integer.valueOf(mdlId).intValue() - 1;
+ if (_modelFileNameMap != null)
+ {
+ int _mp = _modelFileNameMap.length - 1;
+
+ while (mnumber < _modelFileNameMap[_mp])
+ {
+ _mp--;
+ }
+ pdbfilename = modelFileNames[_mp];
+ }
+ else
+ {
+ if (mnumber >= 0 && mnumber < modelFileNames.length)
+ {
+ pdbfilename = modelFileNames[mnumber];
+ }
+
+ if (pdbfilename == null)
+ {
+ pdbfilename = new File(jmolViewer.ms.getModelFileName(mnumber))
+ .getAbsolutePath();
+ }
+ }
} catch (Exception e)
{
}
- ;
}
- if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
- lastMessage = strInfo;
+ /*
+ * highlight position on alignment(s); if some text is returned,
+ * show this as a second line on the structure hover tooltip
+ */
+ String label = getSsm().mouseOverStructure(pdbResNum, chainId,
+ pdbfilename);
+ if (label != null)
+ {
+ // change comma to pipe separator (newline token for Jmol)
+ label = label.replace(',', '|');
+ StringTokenizer toks = new StringTokenizer(strInfo, " ");
+ StringBuilder sb = new StringBuilder();
+ sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
+ .append(chainId).append("/1");
+ sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
+ .append(toks.nextToken());
+ sb.append("|").append(label).append("\"");
+ executeCommand(new StructureCommand(sb.toString()), false);
+ }
}
public void notifyAtomHovered(int atomIndex, String strInfo, String data)
{
+ if (strInfo.equals(lastMessage))
+ {
+ return;
+ }
+ lastMessage = strInfo;
if (data != null)
{
System.err.println("Ignoring additional hover info: " + data
@@ -854,11 +439,12 @@ 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
- * structure viewer, MCView
+ * structure viewer, mc_view
*/
if (strData != null)
{
@@ -867,13 +453,17 @@ 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)
{
@@ -885,12 +475,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
if (!atomsPicked.contains(picked))
{
- viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
+ jmolScript("select " + picked + ";label %n %r:%c");
atomsPicked.addElement(picked);
}
else
{
- viewer.evalString("select " + picked + ";label off");
+ jmolViewer.evalString("select " + picked + ";label off");
atomsPicked.removeElement(picked);
}
jmolHistory(true);
@@ -904,51 +494,52 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
- public void notifyCallback(int type, Object[] data)
+ @Override
+ public void notifyCallback(CBK 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:
+ // deliberate fall through
+ 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:
- sendConsoleMessage((data == null) ? ((String) null)
- : (String) data[1]);
+ 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());
+ System.err.println(
+ "Unhandled callback " + type + " " + data[1].toString());
break;
}
} catch (Exception e)
@@ -958,26 +549,33 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
}
- public boolean notifyEnabled(int callbackPick)
+ @Override
+ public boolean notifyEnabled(CBK 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:
+ default:
+ return false;
}
- 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,
@@ -989,16 +587,22 @@ 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.
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new Vector();
boolean notifyLoaded = false;
- String[] modelfilenames = getPdbFile();
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ String[] modelfilenames = getStructureFiles();
+ if (modelfilenames == null)
+ {
+ // Jmol is still loading files!
+ return;
+ }
// first check if we've lost any structures
if (oldmodels != null && oldmodels.length > 0)
{
@@ -1031,109 +635,127 @@ 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();
for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
{
String fileName = modelfilenames[modelnum];
- if (fileName != null)
+ boolean foundEntry = false;
+ 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 = jmolViewer.getData(
+ "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
+ }
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
+ for (int pe = 0; pe < getPdbCount(); pe++)
{
- boolean foundEntry = false;
- // search pdbentries and sequences to find correct pdbentry and
- // sequence[] pair for this filename
- if (pdbentry != null)
+ boolean matches = false;
+ addSequence(pe, getSequence()[pe]);
+ if (fileName == null)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ if (false)
+ // see JAL-623 - need method of matching pasted data up
{
- if (pdbentry[pe].getFile().equals(fileName))
+ pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
+ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
+ getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
+ matches = true;
+ foundEntry = true;
+ }
+ }
+ else
+ {
+ File fl = new File(getPdbEntry(pe).getFile());
+ matches = fl.equals(new File(fileName));
+ if (matches)
+ {
+ 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;
- MCview.PDBfile pdb;
- if (loadedInline)
+ if (fl.exists())
{
- // TODO: replace with getData ?
- pdb = ssm.setMapping(sequence[pe], chains[pe],
- pdbentry[pe].getFile(), AppletFormatAdapter.PASTE);
- pdbentry[pe].setFile("INLINE" + pdb.id);
+ protocol = DataSourceType.FILE;
}
- else
- {
- // 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)
- {
- }
- ;
- 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++)
- {
- chainNames.addElement(new String(pdb.id + ":"
- + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
- }
- notifyLoaded = true;
+ } 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 (!foundEntry && associateNewStructs)
+ if (matches)
{
- // 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
+ stashFoundChains(pdb, fileName);
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 = jmolViewer.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();
- }
+ // if (jmolpopup != null)
+ // {
+ // // potential for deadlock here:
+ // // jmolpopup.updateComputedMenus();
+ // }
if (!isLoadingFromArchive())
{
- viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ jmolScript(
+ "model *; 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);
+ getSsm().addStructureViewerListener(this);
if (notifyLoaded)
{
- FeatureRenderer fr = getFeatureRenderer();
+ FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
fr.featuresAdded();
}
refreshGUI();
+ loadNotifiesHandled++;
}
+ setLoadingFromArchive(false);
+ }
+
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return null;
}
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
@@ -1166,6 +788,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
*/
public abstract void sendConsoleMessage(String strStatus);
+ @Override
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
@@ -1174,40 +797,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
}
- 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())
- {
- 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() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- }
-
- evalStateCommand(command.toString());
- jmolHistory(true);
- }
-
public void showHelp()
{
- showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+ showUrl("http://wiki.jmol.org"
+ // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
+ , "jmolHelp");
}
/**
@@ -1218,13 +812,22 @@ public abstract class JalviewJmolBinding implements StructureListener,
public abstract void showUrl(String url, String target);
/**
- * called when the binding thinks the UI needs to be refreshed after a Jmol
- * state change. this could be because structures were loaded, or because an
- * error has occured.
+ * called to show or hide the associated console window container.
+ *
+ * @param show
*/
- public abstract void refreshGUI();
+ public abstract void showConsole(boolean show);
+
+ public static Viewer getJmolData(JmolParser jmolParser)
+ {
+ return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null,
+ "-x -o -n", jmolParser);
+ }
/**
+ *
+ *
+ *
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
@@ -1234,169 +837,191 @@ 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)
{
- viewer = JmolViewer.allocateViewer(renderPanel,
- (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
- + ((Object) this).toString(), documentBase, codeBase,
- commandOptions, this);
+ allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+ codeBase, commandOptions, null, null);
}
- public void setLoadingFromArchive(boolean loadingFromArchive)
+ /**
+ *
+ * @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 order
+ */
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions, final Container consolePanel,
+ String buttonsToShow)
{
- this.loadingFromArchive = loadingFromArchive;
- }
- public boolean isLoadingFromArchive()
- {
- return loadingFromArchive;
+ System.err.println("Allocating Jmol Viewer: " + commandOptions);
+
+ if (commandOptions == null)
+ {
+ commandOptions = "";
+ }
+ jmolViewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
+ (jmolfileio ? new SmarterJmolAdapter() : null),
+ htmlName + ((Object) this).toString(), documentBase, codeBase,
+ commandOptions, this);
+
+ jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener
+
+ try
+ {
+ console = createJmolConsole(consolePanel, buttonsToShow);
+ } catch (Throwable e)
+ {
+ System.err.println("Could not create Jmol application console. "
+ + e.getMessage());
+ e.printStackTrace();
+ }
+ if (consolePanel != null)
+ {
+ consolePanel.addComponentListener(this);
+
+ }
+
}
- public void setBackgroundColour(java.awt.Color col)
+ protected abstract JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow);
+
+ // BH 2018 -- Jmol console is not working due to problems with styled
+ // documents.
+
+ protected org.jmol.api.JmolAppConsoleInterface console = null;
+
+ @Override
+ public int[] resizeInnerPanel(String data)
{
- jmolHistory(false);
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- jmolHistory(true);
+ // 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++)
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentShown(ComponentEvent e)
+ {
+ showConsole(true);
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentHidden(ComponentEvent e)
+ {
+ showConsole(false);
+ }
+
+ @Override
+ protected String getModelIdForFile(String pdbFile)
+ {
+ if (modelFileNames == null)
{
- if (!s.contains(seq[i]))
- {
- s.addElement(seq[i]);
- if (tchain != null && i < tchain.length)
- {
- c.addElement(tchain[i] == null ? nullChain : tchain[i]);
- }
- }
+ return "";
}
- SequenceI[] tmp = new SequenceI[s.size()];
- s.copyInto(tmp);
- sequence[pe] = tmp;
- if (c.size() > 0)
+ for (int i = 0; i < modelFileNames.length; i++)
{
- String[] tch = new String[c.size()];
- c.copyInto(tch);
- for (int i = 0; i < tch.length; i++)
+ if (modelFileNames[i].equalsIgnoreCase(pdbFile))
{
- if (tch[i] == nullChain)
- {
- tch[i] = null;
- }
+ return String.valueOf(i + 1);
}
- chains[pe] = tch;
- }
- else
- {
- chains[pe] = null;
}
+ return "";
+ }
+
+ @Override
+ protected ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
+ }
+
+ @Override
+ protected String getModelId(int pdbfnum, String file)
+ {
+ return String.valueOf(pdbfnum + 1);
+ }
+
+ /**
+ * Returns ".spt" - the Jmol session file extension
+ *
+ * @return
+ * @see https://chemapps.stolaf.edu/jmol/docs/#writemodel
+ */
+ @Override
+ public String getSessionFileExtension()
+ {
+ return ".spt";
+ }
+
+ @Override
+ public void selectionChanged(BS arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
+ {
+ return new jalview.gui.SequenceRenderer(avp.getAlignViewport());
+ }
+
+ @Override
+ public String getHelpURL()
+ {
+ return "http://wiki.jmol.org"; // BH 2018
}
}