/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.SequenceI;
import jalview.io.AlignFile;
import jalview.io.FileParse;
+import jalview.schemes.ResidueProperties;
import jalview.util.MessageManager;
import java.io.IOException;
import java.util.Hashtable;
import java.util.Map;
+import javajs.awt.Dimension;
+
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
-import org.jmol.constant.EnumCallback;
+import org.jmol.c.CBK;
import org.jmol.modelset.Group;
import org.jmol.modelset.Model;
import org.jmol.modelset.ModelSet;
-import org.jmol.modelset.Polymer;
+import org.jmol.modelsetbio.BioModel;
import org.jmol.modelsetbio.BioPolymer;
import org.jmol.viewer.Viewer;
-import org.openscience.jmol.app.JmolApp;
/**
* Import and process PDB files with Jmol
public class PDBFileWithJmol extends AlignFile implements
JmolStatusListener
{
-
- JmolApp jmolApp = null;
-
Viewer viewer = null;
public PDBFileWithJmol(String inFile, String type) throws IOException
public PDBFileWithJmol()
{
- // TODO Auto-generated constructor stub
}
/**
private Viewer getJmolData()
{
if (viewer == null)
- { // note that -o -n -x are all implied
- jmolApp = new JmolApp();
- jmolApp.isDataOnly = true;
- jmolApp.haveConsole = false;
- jmolApp.haveDisplay = false;
- jmolApp.exitUponCompletion = true;
+ {
try
{
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, jmolApp.commandOptions, this);
- viewer.setScreenDimension(jmolApp.startupWidth,
- jmolApp.startupHeight);
- jmolApp.startViewer(viewer, null);
+ null, "-x -o -n", this);
} catch (ClassCastException x)
{
- throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
- x);
+ throw new Error(MessageManager.formatMessage(
+ "error.jmol_version_not_compatible_with_jalview_version",
+ new String[] { JmolViewer.getJmolVersion() }), x);
}
}
return viewer;
Viewer jmd = getJmolData();
jmd.openReader(getDataName(), getDataName(), getReader());
waitForScript(jmd);
- if (jmd.getModelCount() > 0)
+
+ if (jmd.ms.mc > 0)
{
- ModelSet ms = jmd.getModelSet();
- String structs = ms.calculateStructures(null, true, false, true);
+ ModelSet ms = jmd.ms;
+ // Jmol 14.2 added third argument doReport = false
+ ms.calculateStructures(null, true, false, false, true);
// System.out.println("Structs\n"+structs);
- for (Model model : ms.getModels())
+ Group group = null;
+ int modelIndex = -1;
+ for (Model model : ms.am)
{
- for (int _bp = 0, _bpc = model.getBioPolymerCount(); _bp < _bpc; _bp++)
+ modelIndex++;
+ for (BioPolymer bp : ((BioModel) model).bioPolymers)
{
- Polymer bp = model.getBioPolymer(_bp);
- if (bp instanceof BioPolymer)
+ int lastChainId = 0; // int value of character e.g. 65 for A
+ String lastChainIdAlpha = "";
+
+ int[] groups = bp.getLeadAtomIndices();
+ char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
+ int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
+
+ do
{
- BioPolymer biopoly = (BioPolymer) bp;
- char _lastChainId = 0;
- int[] groups = biopoly.getLeadAtomIndices();
- Group[] bpgrp = biopoly.getGroups();
- char seq[] = new char[groups.length], secstr[] = new char[groups.length], secstrcode[] = new char[groups.length];
- int groupc = 0, len = 0, firstrnum = 1, lastrnum = 0;
- do
+ if (groupc >= groups.length
+ || ms.at[groups[groupc]].group.chain.chainID != lastChainId)
{
- if (groupc >= groups.length
- || ms.atoms[groups[groupc]].getChainID() != _lastChainId)
+ /*
+ * on change of chain (or at end), construct the sequence and
+ * secondary structure annotation for the last chain
+ */
+ if (len > 0)
{
- if (len > 0)
+ boolean isNa = bp.isNucleic();
+ // normalise sequence from Jmol to jalview
+ int[] cinds = isNa ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex;
+ int nonGap = isNa ? ResidueProperties.maxNucleotideIndex
+ : ResidueProperties.maxProteinIndex;
+ char ngc = 'X';
+ char newseq[] = new char[len];
+ Annotation asecstr[] = new Annotation[len + firstrnum - 1];
+ for (int p = 0; p < len; p++)
{
- char newseq[] = new char[len];
- System.arraycopy(seq, 0, newseq, 0, len);
- Annotation asecstr[] = new Annotation[len+firstrnum-1];
- for (int p = 0; p < len; p++)
+ newseq[p] = cinds[seq[p]] == nonGap ? ngc : seq[p];
+ if (secstr[p] >= 'A' && secstr[p] <= 'z')
{
- if (secstr[p] >= 'A' && secstr[p] <= 'z')
+ try
{
asecstr[p] = new Annotation("" + secstr[p], null,
secstrcode[p], Float.NaN);
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // skip - patch for JAL-1836
}
}
- SequenceI sq = new Sequence("" + getDataName() + "|"
- + model.getModelTitle() + "|" + _lastChainId,
- newseq, firstrnum, lastrnum);
- PDBEntry pdbe = new PDBEntry();
- pdbe.setFile(getDataName());
- pdbe.setId(getDataName());
- sq.addPDBId(pdbe);
- pdbe.setProperty(new Hashtable());
- pdbe.getProperty().put("CHAIN", "" + _lastChainId);
- // JAL-1533
- // Need to put the number of models for this polymer somewhere for Chimera/others to grab
- // pdbe.getProperty().put("PDBMODELS", biopoly.)
- seqs.add(sq);
- if (!(biopoly.isDna() || biopoly.isRna()))
+ }
+ String modelTitle = (String) ms
+ .getInfo(modelIndex, "title");
+ SequenceI sq = new Sequence("" + getDataName() + "|"
+ + modelTitle + "|" + lastChainIdAlpha, newseq,
+ firstrnum, lastrnum);
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setFile(getDataName());
+ pdbe.setId(getDataName());
+ pdbe.setProperty(new Hashtable());
+ // pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+ pdbe.setChainCode(lastChainIdAlpha);
+ sq.addPDBId(pdbe);
+ // JAL-1533
+ // Need to put the number of models for this polymer somewhere
+ // for Chimera/others to grab
+ // pdbe.getProperty().put("PDBMODELS", biopoly.)
+ seqs.add(sq);
+ if (!isNa)
+ {
+ String mt = modelTitle == null ? getDataName()
+ : modelTitle;
+ if (lastChainId >= ' ')
{
- AlignmentAnnotation ann = new AlignmentAnnotation(
- "Secondary Structure",
- "Secondary Structure from PDB File", asecstr);
- ann.belowAlignment=true;
- ann.visible=true;
- ann.autoCalculated=false;
- ann.setCalcId(getClass().getName());
- sq.addAlignmentAnnotation(ann);
- ann.adjustForAlignment();
- ann.validateRangeAndDisplay();
- annotations.add(ann);
+ mt += lastChainIdAlpha;
}
+ AlignmentAnnotation ann = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure for "
+ + mt, asecstr);
+ ann.belowAlignment = true;
+ ann.visible = true;
+ ann.autoCalculated = false;
+ ann.setCalcId(getClass().getName());
+ sq.addAlignmentAnnotation(ann);
+ ann.adjustForAlignment();
+ ann.validateRangeAndDisplay();
+ annotations.add(ann);
}
- len = 0;
- firstrnum = 1;
- lastrnum = 0;
}
- if (groupc < groups.length)
+ len = 0;
+ firstrnum = 1;
+ lastrnum = 0;
+ }
+ if (groupc < groups.length)
+ {
+ group = ms.at[groups[groupc]].group;
+ if (len == 0)
{
- if (len == 0)
+ firstrnum = group.getResno();
+ lastChainId = group.chain.chainID;
+ lastChainIdAlpha = group.chain.getIDStr();
+ }
+ else
+ {
+ lastrnum = group.getResno();
+ }
+ seq[len] = group.getGroup1();
+
+ /*
+ * JAL-1828 replace a modified amino acid with its standard
+ * equivalent (e.g. MSE with MET->M) to maximise sequence matching
+ */
+ String threeLetterCode = group.getGroup3();
+ String canonical = ResidueProperties
+ .getCanonicalAminoAcid(threeLetterCode);
+ if (canonical != null
+ && !canonical.equalsIgnoreCase(threeLetterCode))
+ {
+ seq[len] = ResidueProperties
+ .getSingleCharacterCode(canonical);
+ }
+ switch (group.getProteinStructureSubType())
+ {
+ case HELIX310:
+ if (secstr[len] == 0)
{
- firstrnum = bpgrp[groupc].getResno();
- _lastChainId = bpgrp[groupc].getChainID();
+ secstr[len] = '3';
}
- else
+ case HELIXALPHA:
+ if (secstr[len] == 0)
{
- lastrnum = bpgrp[groupc].getResno();
+ secstr[len] = 'H';
}
- seq[len] = bpgrp[groupc].getGroup1();
- switch (bpgrp[groupc].getProteinStructureSubType())
+ case HELIXPI:
+ if (secstr[len] == 0)
{
- case HELIX_310:
- if (secstr[len] == 0)
- {
- secstr[len] = '3';
- }
- case HELIX_ALPHA:
- if (secstr[len] == 0)
- {
- secstr[len] = 'H';
- }
- case HELIX_PI:
- if (secstr[len] == 0)
- {
- secstr[len] = 'P';
- }
- case HELIX:
- if (secstr[len] == 0)
- {
- secstr[len] = 'H';
- }
- secstrcode[len] = 'H';
- break;
- case SHEET:
- secstr[len] = 'E';
- secstrcode[len] = 'E';
- break;
- default:
- secstr[len] = 0;
- secstrcode[len] = 0;
+ secstr[len] = 'P';
+ }
+ case HELIX:
+ if (secstr[len] == 0)
+ {
+ secstr[len] = 'H';
}
- len++;
+ secstrcode[len] = 'H';
+ break;
+ case SHEET:
+ secstr[len] = 'E';
+ secstrcode[len] = 'E';
+ break;
+ default:
+ secstr[len] = 0;
+ secstrcode[len] = 0;
}
- } while (groupc++ < groups.length);
-
- }
+ len++;
+ }
+ } while (groupc++ < groups.length);
}
}
* System.err.println("Squashed Jmol callback handler error:");
* e.printStackTrace(); } }
*/
- public void notifyCallback(EnumCallback type, Object[] data)
+ public void notifyCallback(CBK type, Object[] data)
{
String strInfo = (data == null || data[1] == null ? null : data[1]
.toString());
}
}
- private void notifyFileLoaded(String string, String string2,
- String string3, String string4, int intValue)
- {
- // TODO Auto-generated method stub
-
- }
-
String lastConsoleEcho = "";
private void sendConsoleEcho(String string)
}
@Override
- public boolean notifyEnabled(EnumCallback callbackPick)
+ public boolean notifyEnabled(CBK callbackPick)
{
switch (callbackPick)
{
case LOADSTRUCT:
case ERROR:
return true;
- case MEASURE:
- case PICK:
- case HOVER:
- case RESIZE:
- case SYNC:
- case CLICK:
- case ANIMFRAME:
- case MINIMIZATION:
+ default:
+ return false;
}
- return false;
}
@Override
}
@Override
- public void resizeInnerPanel(String data)
+ public Dimension resizeInnerPanel(String data)
{
- // TODO Auto-generated method stub
+ return null;
+ }
+ @Override
+ public Map<String, Object> getJSpecViewProperty(String arg0)
+ {
+ return null;
}
}
git://source.jalview.org / jalview.git / blobdiff