/*
- * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
-import java.io.File;
-import java.net.URL;
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
-import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.io.File;
+import java.net.URL;
+import java.security.AccessControlException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
-import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
-import jalview.schemes.*;
-
-public abstract class JalviewJmolBinding implements StructureListener,
- JmolStatusListener, SequenceStructureBinding
-
+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.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;
- /**
- * state flag used to check if the Jmol viewer's paint method can be called
- */
- private boolean finishedInit=false;
-
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
boolean allChainsSelected = false;
- /**
+ /*
* when true, try to search the associated datamodel for sequences that are
* associated with any unknown structures in the Jmol view.
*/
private boolean associateNewStructs = false;
- Vector atomsPicked = new Vector();
+ Vector<String> atomsPicked = new Vector<String>();
- public Vector chainNames;
+ public Vector<String> chainNames;
- String[] chains;
-
- boolean colourBySequence = true;
-
- StringBuffer eval = new StringBuffer();
+ Hashtable<String, String> chainFile;
public String fileLoadingError;
- /**
+ /*
* the default or current model displayed if the model cannot be identified
* from the selection message
*/
int frameNo = 0;
- protected JmolPopup jmolpopup;
+ // protected JmolGenericPopup jmolpopup; // not used - remove?
String lastCommand;
boolean loadedInline;
- /**
- * current set of model filenames loaded in the Jmol instance
- */
- String[] modelFileNames = null;
-
- public PDBEntry[] pdbentry;
-
- /**
- * datasource protocol for access to PDBEntry
- */
- String protocol = null;
-
StringBuffer resetLastRes = new StringBuffer();
- public SequenceI[] sequence;
+ public Viewer viewer;
- StructureSelectionManager ssm;
-
- public JmolViewer viewer;
-
- public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[] seq,
- String[] chains, String protocol)
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
{
- this.sequence = seq;
- this.chains = chains;
- this.pdbentry = pdbentry;
- this.protocol = protocol;
-
+ super(ssm, pdbentry, sequenceIs, chains, protocol);
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
*/
}
+ public JalviewJmolBinding(StructureSelectionManager ssm,
+ SequenceI[][] seqs, Viewer theViewer)
+ {
+ super(ssm, seqs);
+
+ viewer = theViewer;
+ viewer.setJmolStatusListener(this);
+ viewer.addSelectionListener(this);
+ }
+
/**
- * construct a title string for the viewer window based on the data jalview knows about
- * @return
+ * construct a title string for the viewer window based on the data jalview
+ * knows about
+ *
+ * @return
*/
- public String getViewerTitle() {
- if (sequence==null || pdbentry==null || sequence.length<1 || pdbentry.length<1)
- {
- return("Jalview Jmol Window");
- }
- StringBuffer title = new StringBuffer(sequence[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();
+ public String getViewerTitle()
+ {
+ return getViewerTitle("Jmol", true);
}
/**
* @param chainList
* list of chains to make visible
*/
- public void centerViewer(Vector chainList)
+ public void centerViewer(Vector<String> 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;
mlength = lbl.indexOf(":", p);
} while (p < mlength && mlength < (lbl.length() - 2));
+ // TODO: lookup each pdb id and recover proper model number for it.
cmd.append(":" + lbl.substring(mlength + 1) + " /"
- + getModelNum(lbl.substring(0, mlength)) + " or ");
+ + (1 + getModelNum(chainFile.get(lbl))) + " or ");
}
if (cmd.length() > 0)
+ {
cmd.setLength(cmd.length() - 4);
- evalStateCommand("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
+ }
+ 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
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, this.getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- lastCommand=null;
+ getSsm().removeStructureViewerListener(this, this.getPdbFile());
+ viewer.dispose();
+ lastCommand = null;
viewer = null;
+ releaseUIResources();
}
public void colourByChain()
{
colourBySequence = false;
+ // TODO: colour by chain should colour each chain distinctly across all
+ // visible models
+ // TODO: http://issues.jalview.org/browse/JAL-628
evalStateCommand("select *;color chain");
}
*/
public void superposeStructures(AlignmentI alignment)
{
+ 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)
+ {
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[] { refStructure },
+ new ColumnSelection[] { hiddenCols });
+ }
+
+ /**
+ * Construct and send a command to align structures against a reference
+ * structure, based on one or more sequence alignments
+ *
+ * @param _alignment
+ * an array of alignments to process
+ * @param _refStructure
+ * an array of corresponding reference structures (index into pdb
+ * file array); if a negative value is passed, the first PDB file
+ * mapped to an alignment sequence is used as the reference for
+ * superposition
+ * @param _hiddenCols
+ * an array of corresponding hidden columns for each alignment
+ */
+ public void superposeStructures(AlignmentI[] _alignment,
+ int[] _refStructure, ColumnSelection[] _hiddenCols)
+ {
+ while (viewer.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException i)
+ {
+ }
+ }
+
+ /*
+ * get the distinct structure files modelled
+ * (a file with multiple chains may map to multiple sequences)
+ */
String[] files = getPdbFile();
+ if (!waitForFileLoad(files))
+ {
+ return;
+ }
- StringBuffer command = new StringBuffer();
- boolean matched[] = new boolean[alignment.getWidth()];
- String commonpositions[][] = new String[files.length][alignment
- .getWidth()];
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ 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)
{
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+ 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(
+ "|"))
+ {
+ selectioncom.append("|");
+ }
+ // process this alignment
+ if (refStructure >= files.length)
+ {
+ System.err.println("Invalid reference structure value "
+ + refStructure);
+ refStructure = -1;
+ }
+
+ /*
+ * 'matched' array will hold 'true' for visible alignment columns where
+ * all sequences have a residue with a mapping to the PDB structure
+ */
+ // TODO could use a BitSet for matched
+ boolean matched[] = new boolean[alignment.getWidth()];
+ for (int m = 0; m < matched.length; m++)
+ {
+ matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+ }
+
+ SuperposeData[] structures = new SuperposeData[files.length];
+ for (int f = 0; f < files.length; f++)
+ {
+ structures[f] = new SuperposeData(alignment.getWidth());
+ }
- if (mapping == null || mapping.length < 1)
- continue;
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ int candidateRefStructure = findSuperposableResidues(alignment,
+ matched, structures);
+ if (refStructure < 0)
+ {
+ /*
+ * If no reference structure was specified, pick the first one that has
+ * a mapping in the alignment
+ */
+ refStructure = candidateRefStructure;
+ }
- int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ String[] selcom = new String[files.length];
+ int nmatched = 0;
+ for (boolean b : matched)
{
- for (int sp, m = 0; m < mapping.length; m++)
+ if (b)
{
- if (mapping[m].getSequence() == sequence[s]
- && (sp = alignment.findIndex(sequence[s])) > -1)
+ nmatched++;
+ }
+ }
+ if (nmatched < 4)
+ {
+ // TODO: bail out here because superposition illdefined?
+ }
+
+ /*
+ * 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 = ":" + structures[pdbfnum].chain;
+ int lpos = -1;
+ boolean run = false;
+ StringBuilder molsel = new StringBuilder();
+ molsel.append("{");
+ for (int r = 0; r < matched.length; r++)
{
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
+ if (matched[r])
{
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ int pdbResNo = structures[pdbfnum].pdbResNo[r];
+ if (lpos != pdbResNo - 1)
{
- matched[r] = false; // exclude from common set
- continue;
+ // discontinuity
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("|");
+ }
+ run = false;
}
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- commonpositions[m][r] = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/" + (pdbfnum + 1) + ".1";
+ else
+ {
+ // continuous run - and lpos >-1
+ if (!run)
+ {
+ // at the beginning, so add dash
+ molsel.append(lpos);
+ molsel.append("-");
+ }
+ run = true;
+ }
+ lpos = pdbResNo;
}
- break;
+ }
+ /*
+ * add final selection phrase
+ */
+ if (lpos != -1)
+ {
+ molsel.append(lpos);
+ molsel.append(chainCd);
+ molsel.append("}");
+ }
+ if (molsel.length() > 1)
+ {
+ selcom[pdbfnum] = molsel.toString();
+ selectioncom.append("((");
+ selectioncom.append(selcom[pdbfnum].substring(1,
+ selcom[pdbfnum].length() - 1));
+ selectioncom.append(" )& ");
+ selectioncom.append(pdbfnum + 1);
+ selectioncom.append(".1)");
+ if (pdbfnum < files.length - 1)
+ {
+ selectioncom.append("|");
+ }
+ }
+ else
+ {
+ selcom[pdbfnum] = null;
}
}
}
- }
- command.append("select ");
- // form the matched pair selection strings
- String sep = "";
- for (int r = 0; r < matched.length; r++)
- {
- if (matched[r])
+ StringBuilder command = new StringBuilder(256);
+ // command.append("set spinFps 10;\n");
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- command.append(sep);
- command.append("(");
- for (int s = 0; s < commonpositions.length; s++)
+ if (pdbfnum == refStructure || selcom[pdbfnum] == null
+ || selcom[refStructure] == null)
{
- if (s > 0)
- {
- command.append(" | ");
- }
- command.append(commonpositions[s][r]);
+ continue;
}
- command.append(")");
- sep = " | ";
+ command.append("echo ");
+ command.append("\"Superposing (");
+ command.append(structures[pdbfnum].pdbId);
+ command.append(") against reference (");
+ command.append(structures[refStructure].pdbId);
+ command.append(")\";\ncompare " + nSeconds);
+ command.append("{");
+ command.append(Integer.toString(1 + pdbfnum));
+ command.append(".1} {");
+ 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");
+ }
+ 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);
}
}
- evalStateCommand(command.toString());
+ if (selectioncom.length() > 0)
+ {// finally, mark all regions that were superposed.
+ if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
+ {
+ selectioncom.setLength(selectioncom.length() - 1);
+ }
+ // 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());
+ }
}
- public void evalStateCommand(String command) {
+ public void evalStateCommand(String command)
+ {
jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(command))
{
- viewer.evalStringQuiet(command+"\n");
+ viewer.evalStringQuiet(command + "\n");
}
jmolHistory(true);
lastCommand = command;
}
+
/**
* colour any structures associated with sequences in the given alignment
* using the getFeatureRenderer() and getSequenceRenderer() renderers but only
* if colourBySequence is enabled.
*/
- public void colourBySequence(boolean showFeatures, AlignmentI alignment)
+ public void colourBySequence(AlignmentViewPanel alignmentv)
{
- if (!colourBySequence)
+ boolean showFeatures = alignmentv.getAlignViewport()
+ .isShowSequenceFeatures();
+ if (!colourBySequence || !isLoadingFinished())
+ {
return;
- if (ssm==null)
+ }
+ if (getSsm() == null)
{
return;
}
String[] files = getPdbFile();
- SequenceRenderer sr = getSequenceRenderer();
+
+ SequenceRenderer sr = getSequenceRenderer(alignmentv);
FeatureRenderer fr = null;
if (showFeatures)
{
- fr = getFeatureRenderer();
+ fr = getFeatureRenderer(alignmentv);
}
+ AlignmentI alignment = alignmentv.getAlignment();
- StringBuffer command = new StringBuffer();
-
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ files, sr, fr, alignment))
{
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
- int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
+ for (String cbyseq : cpdbbyseq.commands)
{
- for (int sp, m = 0; m < mapping.length; m++)
- {
- if (mapping[m].getSequence() == sequence[s]
- && (sp = alignment.findIndex(sequence[s])) > -1)
- {
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[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;
- }
- }
+ executeWhenReady(cbyseq);
}
}
- evalStateCommand(command.toString());
}
- public boolean isColourBySequence()
- {
- return colourBySequence;
- }
-
- public void setColourBySequence(boolean colourBySequence)
+ /**
+ * @param files
+ * @param sr
+ * @param fr
+ * @param alignment
+ * @return
+ */
+ protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ String[] files, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
{
- this.colourBySequence = colourBySequence;
+ return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, fr, alignment);
}
- StringBuffer condenseCommand(String command, int pos)
+ /**
+ * @param command
+ */
+ protected void executeWhenReady(String command)
{
-
- 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;
+ evalStateCommand(command);
}
public void createImage(String file, String type, int quality)
System.out.println("JMOL CREATE IMAGE");
}
+ @Override
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
return null;
}
+ @Override
public String eval(String strEval)
{
// System.out.println(strEval);
// End StructureListener
// //////////////////////////
+ @Override
public float[][] functionXY(String functionName, int x, int y)
{
return null;
}
+ @Override
public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
{
// TODO Auto-generated method stub
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();
+ 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.
+ */
+ public abstract void refreshPdbEntries();
private int getModelNum(String modelFileName)
{
for (int i = 0; i < mfn.length; i++)
{
if (mfn[i].equalsIgnoreCase(modelFileName))
+ {
return i;
+ }
}
return -1;
}
+ /**
+ * map between index of model filename returned from getPdbFile and the first
+ * index of models from this file in the viewer. Note - this is not trimmed -
+ * use getPdbFile to get number of unique models.
+ */
+ private int _modelFileNameMap[];
+
// ////////////////////////////////
// /StructureListener
- public String[] getPdbFile()
+ @Override
+ public synchronized String[] getPdbFile()
{
+ if (viewer == null)
+ {
+ return new String[0];
+ }
if (modelFileNames == null)
{
- String mset[] = new String[viewer.getModelCount()];
- for (int i = 0; i < mset.length; i++)
+ List<String> mset = new ArrayList<String>();
+ _modelFileNameMap = new int[viewer.ms.mc];
+ String m = viewer.ms.getModelFileName(0);
+ if (m != null)
{
- mset[i] = viewer.getModelFileName(i);
+ String filePath = m;
+ try
+ {
+ filePath = new File(m).getAbsolutePath();
+ } catch (AccessControlException x)
+ {
+ // usually not allowed to do this in applet
+ System.err
+ .println("jmolBinding: Using local file string from Jmol: "
+ + m);
+ }
+ if (filePath.indexOf("/file:") != -1)
+ {
+ // applet path with docroot - discard as format won't match pdbfile
+ filePath = m;
+ }
+ mset.add(filePath);
+ _modelFileNameMap[0] = 0; // filename index for first model is always 0.
}
- modelFileNames = mset;
+ int j = 1;
+ for (int i = 1; i < viewer.ms.mc; i++)
+ {
+ m = viewer.ms.getModelFileName(i);
+ String filePath = m;
+ if (m != null)
+ {
+ try
+ {
+ filePath = new File(m).getAbsolutePath();
+ } catch (AccessControlException x)
+ {
+ // usually not allowed to do this in applet, so keep raw handle
+ // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
+ }
+ }
+
+ /*
+ * add this model unless it is read from a structure file we have
+ * already seen (example: 2MJW is an NMR structure with 10 models)
+ */
+ if (!mset.contains(filePath))
+ {
+ mset.add(filePath);
+ _modelFileNameMap[j] = i; // record the model index for the filename
+ j++;
+ }
+ }
+ modelFileNames = mset.toArray(new String[mset.size()]);
}
return modelFileNames;
}
- public Hashtable getRegistryInfo()
+ /**
+ * map from string to applet
+ */
+ @Override
+ public Map<String, Object> 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();
+ 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<AtomSpec> 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
// 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)
}
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);
}
public void loadInline(String string)
{
loadedInline = true;
+ // TODO: re JAL-623
+ // viewer.loadInline(strModel, isAppend);
+ // could do this:
+ // construct fake fullPathName and fileName so we can identify the file
+ // later.
+ // Then, construct pass a reader for the string to Jmol.
+ // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+ // fileName, null, reader, false, null, null, 0);
viewer.openStringInline(string);
}
public void mouseOverStructure(int atomIndex, String strInfo)
{
int pdbResNum;
+ int alocsep = strInfo.indexOf("^");
int mdlSep = strInfo.indexOf("/");
int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
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("."));
+ {
+ chainId = strInfo.substring(strInfo.indexOf(":") + 1,
+ strInfo.indexOf("."));
+ }
else
{
chainId = " ";
try
{
// recover PDB filename for the model hovered over.
- pdbfilename = viewer
- .getModelFileName(new Integer(mdlId).intValue() - 1);
+ int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
+ .intValue() - 1;
+ while (mnumber < _modelFileNameMap[_mp])
+ {
+ _mp--;
+ }
+ pdbfilename = modelFileNames[_mp];
+ if (pdbfilename == null)
+ {
+ pdbfilename = new File(viewer.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;
}
{
if (data != null)
{
- System.err.println("Ignoring additional hover info: " + data+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+ System.err.println("Ignoring additional hover info: " + data
+ + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
}
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)
{
jmolHistory(true);
// TODO: in application this happens
//
-//if (scriptWindow != null)
-// {
-// scriptWindow.sendConsoleMessage(strInfo);
-// scriptWindow.sendConsoleMessage("\n");
-// }
-
+ // if (scriptWindow != null)
+ // {
+ // scriptWindow.sendConsoleMessage(strInfo);
+ // scriptWindow.sendConsoleMessage("\n");
+ // }
}
- 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());
+ (String) data[3], (String) data[4],
+ ((Integer) data[5]).intValue());
break;
- case JmolConstants.CALLBACK_PICK:
+ case PICK:
notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
// also highlight in alignment
- case JmolConstants.CALLBACK_HOVER:
+ case HOVER:
notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
break;
- case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String) data[2], ((Integer) data[3])
- .intValue());
+ case SCRIPT:
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
break;
- case JmolConstants.CALLBACK_ECHO:
+ case ECHO:
sendConsoleEcho((String) data[1]);
break;
- case JmolConstants.CALLBACK_MESSAGE:
+ case MESSAGE:
sendConsoleMessage((data == null) ? ((String) null)
: (String) data[1]);
break;
- case JmolConstants.CALLBACK_ERROR:
+ case ERROR:
// System.err.println("Ignoring error callback.");
break;
- case JmolConstants.CALLBACK_SYNC:
- case JmolConstants.CALLBACK_RESIZE:
- updateUI();
+ 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)
}
}
- 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,
if (errorMsg != null)
{
fileLoadingError = errorMsg;
- updateUI();
+ 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();
+ chainNames = new Vector<String>();
+ chainFile = new Hashtable<String, String>();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
- ssm = StructureSelectionManager.getStructureSelectionManager();
// first check if we've lost any structures
- if (oldmodels!=null && oldmodels.length>0)
+ if (oldmodels != null && oldmodels.length > 0)
{
- int oldm=0;
- for (int i=0;i<oldmodels.length;i++)
+ int oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
{
- for (int n=0;n<modelfilenames.length; n++)
+ for (int n = 0; n < modelfilenames.length; n++)
{
- if (modelfilenames[n]==oldmodels[i])
+ if (modelfilenames[n] == oldmodels[i])
{
- oldmodels[i]=null;
+ oldmodels[i] = null;
break;
}
}
- if (oldmodels[i]!=null)
+ if (oldmodels[i] != null)
{
oldm++;
}
}
- if (oldm>0)
+ if (oldm > 0)
{
String[] oldmfn = new String[oldm];
- oldm=0;
- for (int i=0;i<oldmodels.length; i++)
+ oldm = 0;
+ for (int i = 0; i < oldmodels.length; i++)
{
- if (oldmodels[i]!=null) {
+ if (oldmodels[i] != null)
+ {
oldmfn[oldm++] = oldmodels[i];
}
}
- // deregister the Jmol instance for these structures - we'll add
- // ourselves again at the end for the current structure set.
- ssm.removeStructureViewerListener(this, oldmfn);
+ // deregister the Jmol instance for these structures - we'll add
+ // ourselves again at the end for the current structure set.
+ 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)
{
- // search pdbentries and sequences to find correct pdbentry and
- // sequence[] pair for this filename
- if (pdbentry != null)
+ // 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");
+ }
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
+ for (int pe = 0; pe < getPdbCount(); pe++)
+ {
+ boolean matches = false;
+ if (fileName == null)
+ {
+ if (false)
+ // see JAL-623 - need method of matching pasted data up
+ {
+ pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
+ pdbfile, AppletFormatAdapter.PASTE);
+ getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
+ matches = true;
+ foundEntry = true;
+ }
+ }
+ else
{
- boolean foundEntry = false;
- for (int pe = 0; pe < pdbentry.length; pe++)
+ File fl = new File(getPdbEntry(pe).getFile());
+ matches = fl.equals(new File(fileName));
+ if (matches)
{
- if (pdbentry[pe].getFile().equals(fileName))
+ foundEntry = true;
+ // TODO: Jmol can in principle retrieve from CLASSLOADER but
+ // this
+ // needs
+ // to be tested. See mantis bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+ String protocol = AppletFormatAdapter.URL;
+ try
{
- foundEntry = true;
- MCview.PDBfile pdb;
- if (loadedInline)
- {
- // TODO: replace with getData ?
- pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
- .getFile(), AppletFormatAdapter.PASTE);
- pdbentry[pe].setFile("INLINE" + pdb.id);
- }
- else
+ if (fl.exists())
{
- // 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, chains, pdbentry[pe]
- .getFile(), protocol);
-
+ protocol = AppletFormatAdapter.FILE;
}
-
- 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);
+ // pdbentry[pe].getFile(), protocol);
+
}
- if (!foundEntry && associateNewStructs)
+ }
+ if (matches)
+ {
+ // add an entry for every chain in the model
+ for (int i = 0; i < pdb.getChains().size(); i++)
{
- // this is a foreign pdb file that jalview doesn't know about - add
- // it
- // to the dataset
- // and try to find a home - either on a matching sequence or as a
- // new
- // sequence.
- String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
- "PDB");
- // parse pdb file into a chain, etc.
- // locate best match for pdb in associated views and add mapping to
- // ssm
- // if properly registered then
- notifyLoaded = true;
+ String chid = new String(pdb.getId() + ":"
+ + pdb.getChains().elementAt(i).id);
+ chainFile.put(chid, fileName);
+ chainNames.addElement(chid);
}
+ notifyLoaded = true;
}
}
+
+ if (!foundEntry && associateNewStructs)
+ {
+ // this is a foreign pdb file that jalview doesn't know about - add
+ // it to the dataset and try to find a home - either on a matching
+ // sequence or as a new sequence.
+ String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+ "PDB");
+ // parse pdb file into a chain, etc.
+ // locate best match for pdb in associated views and add mapping to
+ // ssm
+ // if properly registered then
+ notifyLoaded = true;
+
+ }
}
// FILE LOADED OK
// so finally, update the jmol bits and pieces
- 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");
}
- 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();
- if (fr!=null)
+ FeatureRenderer fr = getFeatureRenderer(null);
+ if (fr != null)
{
fr.featuresAdded();
}
- updateUI();
+ refreshGUI();
+ loadNotifiesHandled++;
}
+ setLoadingFromArchive(false);
}
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
notifyAtomPicked(iatom, strMeasure, null);
}
- public abstract void notifyScriptTermination(String strStatus, int msWalltime);
+ public abstract void notifyScriptTermination(String strStatus,
+ int msWalltime);
/**
* display a message echoed from the jmol viewer
*/
public abstract void sendConsoleMessage(String strStatus);
+ @Override
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
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<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
+ false);
+ for (String res : residueSet)
{
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
+ Color col = cs.findColour(res.charAt(0));
command.append("select " + res + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
}
* state change. this could be because structures were loaded, or because an
* error has occured.
*/
- public abstract void updateUI();
+ public abstract void refreshGUI();
- public void allocateViewer(Component renderPanel, String htmlName,
- URL documentBase, URL codeBase, String commandOptions)
- {
- viewer = JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter(), htmlName+((Object) this).toString(), documentBase, codeBase,
- commandOptions, this);
- }
+ /**
+ * called to show or hide the associated console window container.
+ *
+ * @param show
+ */
+ public abstract void showConsole(boolean show);
- 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
+ */
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions)
{
- this.loadingFromArchive = loadingFromArchive;
+ allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+ codeBase, commandOptions, null, null);
}
- public boolean isLoadingFromArchive()
+ /**
+ *
+ * @param renderPanel
+ * @param jmolfileio
+ * - when true will initialise jmol's file IO system (should be false
+ * in applet context)
+ * @param htmlName
+ * @param documentBase
+ * @param codeBase
+ * @param commandOptions
+ * @param consolePanel
+ * - panel to contain Jmol console
+ * @param buttonsToShow
+ * - buttons to show on the console, in ordr
+ */
+ public void allocateViewer(Container renderPanel, boolean jmolfileio,
+ String htmlName, URL documentBase, URL codeBase,
+ String commandOptions, final Container consolePanel,
+ String buttonsToShow)
{
- return loadingFromArchive;
+ if (commandOptions == null)
+ {
+ commandOptions = "";
+ }
+ viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
+ (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+ + ((Object) this).toString(), documentBase, codeBase,
+ commandOptions, this);
+
+ viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+
+ console = createJmolConsole(consolePanel, buttonsToShow);
+ if (consolePanel != null)
+ {
+ consolePanel.addComponentListener(this);
+
+ }
+
}
+
+ protected abstract JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow);
+
+ protected org.jmol.api.JmolAppConsoleInterface console = null;
+
public void setBackgroundColour(java.awt.Color col)
{
jmolHistory(false);
+ col.getGreen() + "," + col.getBlue() + "];");
jmolHistory(true);
}
+
+ @Override
+ public int[] resizeInnerPanel(String data)
+ {
+ // Jalview doesn't honour resize panel requests
+ return null;
+ }
+
+ /**
+ *
+ */
+ protected void closeConsole()
+ {
+ if (console != null)
+ {
+ try
+ {
+ console.setVisible(false);
+ } catch (Error e)
+ {
+ } catch (Exception x)
+ {
+ }
+ ;
+ console = null;
+ }
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentMoved(ComponentEvent e)
+ {
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentResized(ComponentEvent e)
+ {
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentShown(ComponentEvent e)
+ {
+ showConsole(true);
+ }
+
+ /**
+ * ComponentListener method
+ */
+ @Override
+ public void componentHidden(ComponentEvent e)
+ {
+ showConsole(false);
+ }
}
git://source.jalview.org / jalview.git / blobdiff