X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmol.java;h=8171f9da7e7d5d8aa7b2877708400fe0653217a9;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=962fe3cbf80e2fc4d93e85cc25a535866cb0e887;hpb=51d41d5951ea5865488d3f163b14d297cddd27b4;p=jalview.git
diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 962fe3c..8171f9d 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -1,51 +1,50 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.jmol;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+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 javax.xml.parsers.ParserConfigurationException;
+import javajs.awt.Dimension;
import org.jmol.api.JmolStatusListener;
import org.jmol.api.JmolViewer;
-import org.jmol.constant.EnumCallback;
-import org.jmol.constant.EnumStructure;
-import org.jmol.modelset.Chain;
+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 org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.io.AlignFile;
/**
* Import and process PDB files with Jmol
@@ -56,23 +55,20 @@ import jalview.io.AlignFile;
public class PDBFileWithJmol extends AlignFile implements
JmolStatusListener
{
-
- JmolApp jmolApp = null;
-
Viewer viewer = null;
- public PDBFileWithJmol(String inFile, String type)
- throws ExceptionUnmatchedClosingParentheses, IOException,
- ExceptionFileFormatOrSyntax, ParserConfigurationException,
- SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
- InterruptedException
+ public PDBFileWithJmol(String inFile, String type) throws IOException
{
super(inFile, type);
}
+ public PDBFileWithJmol(FileParse fp) throws IOException
+ {
+ super(fp);
+ }
+
public PDBFileWithJmol()
{
- // TODO Auto-generated constructor stub
}
/**
@@ -83,26 +79,16 @@ public class PDBFileWithJmol extends AlignFile implements
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(
- "Jmol version "
- + JmolViewer.getJmolVersion()
- + " is not compatible with this version of Jalview. Report this problem at issues.jalview.org",
- x);
+ throw new Error(MessageManager.formatMessage(
+ "error.jmol_version_not_compatible_with_jalview_version",
+ new String[] { JmolViewer.getJmolVersion() }), x);
}
}
return viewer;
@@ -128,120 +114,172 @@ public class PDBFileWithJmol extends AlignFile implements
* @see jalview.io.AlignFile#parse()
*/
@Override
- public void parse() throws IOException, ExceptionFileFormatOrSyntax,
- ParserConfigurationException, SAXException,
- ExceptionPermissionDenied, ExceptionLoadingFailed,
- InterruptedException, ExceptionUnmatchedClosingParentheses
+ public void parse() throws IOException
{
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];
- 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);
- 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);
- sq.addAlignmentAnnotation(ann);
- 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)
+ {
+ 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))
{
- if (len == 0)
+ 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);
}
}
@@ -288,7 +326,7 @@ public class PDBFileWithJmol extends AlignFile implements
* 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());
@@ -304,11 +342,16 @@ public class PDBFileWithJmol extends AlignFile implements
case MEASURE:
String mystatus = (String) data[3];
if (mystatus.indexOf("Picked") >= 0
- || mystatus.indexOf("Sequence") >= 0) // picking mode
+ || mystatus.indexOf("Sequence") >= 0)
+ {
+ // Picking mode
sendConsoleMessage(strInfo);
+ }
else if (mystatus.indexOf("Completed") >= 0)
+ {
sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
strInfo.length() - 1));
+ }
break;
case MESSAGE:
sendConsoleMessage(data == null ? null : strInfo);
@@ -321,13 +364,6 @@ public class PDBFileWithJmol extends AlignFile implements
}
}
- 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)
@@ -356,7 +392,7 @@ public class PDBFileWithJmol extends AlignFile implements
}
@Override
- public boolean notifyEnabled(EnumCallback callbackPick)
+ public boolean notifyEnabled(CBK callbackPick)
{
switch (callbackPick)
{
@@ -366,16 +402,9 @@ public class PDBFileWithJmol extends AlignFile implements
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
@@ -422,10 +451,15 @@ public class PDBFileWithJmol extends AlignFile implements
}
@Override
- public void resizeInnerPanel(String data)
+ public Dimension resizeInnerPanel(String data)
{
- // TODO Auto-generated method stub
+ return null;
+ }
+ @Override
+ public Map getJSpecViewProperty(String arg0)
+ {
+ return null;
}
}