/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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 MCview;
import java.awt.*;
-import javax.xml.parsers.ParserConfigurationException;
-
-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.analysis.AlignSeq;
import jalview.datamodel.*;
-import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
-import jalview.io.RnamlFile;
-import jalview.ws.jws1.Annotate3D;
public class PDBfile extends jalview.io.AlignFile
{
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBfile(String inFile, String inType) throws IOException
{
super(inFile, inType);
}
- public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBfile(FileParse source) throws IOException
{
super(source);
}
return null;
}
- public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public void parse() throws IOException
{
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
chains = new Vector();
- ArrayList<SequenceI> rna=new ArrayList<SequenceI>();
+ ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
PDBEntry entry = new PDBEntry();
entry.setId(id);
entry.setProperty(new Hashtable());
- entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+ if (((PDBChain)chains.elementAt(i)).id!=null) {
+ entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+ }
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
if(isRNA(chainseq)==true)
{
rna.add(chainseq);
+ } else {
+ prot.add(chainseq);
}
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
}
if (rna.size()>0)
try {
- String path =inFile.getPath();
- System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D();
- AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
- if (al!=null && al.getHeight()>0)
- {
- ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
- ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
- for (SequenceI sq:rna)
- {
- SequenceI bestm=null;
- AlignSeq bestaseq=null;
- int bestscore=0;
- for (SequenceI msq:al.getSequences())
- {
- AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, AlignSeq.DNA);
- if (bestm==null || aseq.getMaxScore()>bestscore)
- {
- bestscore=aseq.getMaxScore();
- bestaseq= aseq;
- bestm=msq;
- }
- }
- System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
- matches.add(bestm);
- aligns.add(bestaseq);
- al.deleteSequence(bestm);
- }
- for (int p=0,pSize=seqs.size();p<pSize;p++)
- {
- SequenceI sq,sp=seqs.get(p);
- int q;
- if ((q=rna.indexOf(sp))>-1)
- {
- seqs.set(p, sq=matches.get(q));
- sq.setName(sp.getName());
- sq.setDescription(sp.getDescription());
- sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
- //sq.setSequenceFeatures(sp.getSequenceFeatures());
- int inspos=-1;
- for (int ap=0;ap<annotations.size();)
- {
- if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
- if (inspos==-1)
- {
- inspos=ap;
- }
- annotations.remove(ap);
- } else {
- ap++;
- }
- }
- annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
- }
- }
- }
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
} catch (Exception x)
{
System.err.println("Exceptions when dealing with RNA in pdb file");
}
}
}
-
+ private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+ {
+ try {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl!=null)
+ {
+ Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
+ cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
+ replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ } catch (ClassNotFoundException q)
+ {}
+ }
+ private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
+// System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service
+ try {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl!=null)
+ {
+ // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
+ Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(new Object[] {});
+ AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)}));
+ replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ }
+ } catch (ClassNotFoundException x)
+ {
+ //ignore classnotfounds - occurs in applet
+ };
+ }
+ private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+ {
+ if (al!=null && al.getHeight()>0)
+ {
+ ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+ ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+
+ for (SequenceI sq:ochains)
+ {
+ SequenceI bestm=null;
+ AlignSeq bestaseq=null;
+ int bestscore=0;
+ for (SequenceI msq:al.getSequences())
+ {
+ AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
+ if (bestm==null || aseq.getMaxScore()>bestscore)
+ {
+ bestscore=aseq.getMaxScore();
+ bestaseq= aseq;
+ bestm=msq;
+ }
+ }
+ System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
+ matches.add(bestm);
+ aligns.add(bestaseq);
+ al.deleteSequence(bestm);
+ }
+ for (int p=0,pSize=seqs.size();p<pSize;p++)
+ {
+ SequenceI sq,sp=seqs.get(p);
+ int q;
+ if ((q=ochains.indexOf(sp))>-1)
+ {
+ seqs.set(p, sq=matches.get(q));
+ sq.setName(sp.getName());
+ sq.setDescription(sp.getDescription());
+ sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
+ int inspos=-1;
+ for (int ap=0;ap<annotations.size();)
+ {
+ if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
+ if (inspos==-1)
+ {
+ inspos=ap;
+ }
+ annotations.remove(ap);
+ } else {
+ ap++;
+ }
+ }
+ if (sq.getAnnotation()!=null) {
+ annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ }
+ }
/**
* make a friendly ID string.
*
git://source.jalview.org / jalview.git / blobdiff