/*
- * 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 ($$Version-Rel$$)
+ * 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 MCview;
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-
-
import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
-import jalview.ws.jws1.Annotate3D;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
public class PDBfile extends jalview.io.AlignFile
{
- public Vector chains;
+ public Vector<PDBChain> chains;
public String id;
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws Exception
+ boolean processSecondaryStructure = true;
+
+ boolean externalSecondaryStructure = false;
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, boolean externalSecStr)
{
- super(inFile, inType);
+ super();
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
}
- public PDBfile(FileParse source) throws Exception
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, boolean externalSecStr,
+ String file, String protocol) throws IOException
{
- super(source);
+ super(false, file, protocol);
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ doParse();
+ }
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, boolean externalSecStr,
+ FileParse source) throws IOException
+ {
+ super(false, source);
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ doParse();
}
public String print()
return null;
}
- public void parse() throws Exception
+ 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>(), prot=new ArrayList<SequenceI>();
+ ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
}
for (int i = 0; i < chains.size(); i++)
{
- SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
+ SequenceI dataset = chains.elementAt(i).sequence;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
entry.setProperty(new Hashtable());
- entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+ if (chains.elementAt(i).id != null)
+ {
+ entry.getProperty().put("CHAIN", chains.elementAt(i).id);
+ }
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
// maintain reference to
// dataset
seqs.addElement(chainseq);
- if(isRNA(chainseq)==true)
- {
- rna.add(chainseq);
- } else {
- prot.add(chainseq);
- }
-
+ if (isRNA(chainseq) == true)
+ {
+ rna.add(chainseq);
+ }
+ else
+ {
+ prot.add(chainseq);
+ }
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
- if (chainannot != null)
+
+ if (chainannot != null && VisibleChainAnnotation)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
-
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
- if (rna.size()>0)
- try {
- processPdbFileWithAnnotate3d(rna);
- } catch (Exception x)
+ if (processSecondaryStructure)
{
- 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 (externalSecondaryStructure && rna.size() > 0)
+ {
+ try
+ {
+ 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 from Jmol when processing data in pdb file");
+ x.printStackTrace();
+
+ }
+ }
+ }
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException("Out of memory loading PDB File");
+ throw new IOException(
+ MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
} catch (NumberFormatException ex)
{
if (line != null)
System.err.println(line);
}
}
+ markCalcIds();
+ }
+
+ private static String calcIdPrefix = "JalviewPDB";
+
+ public static boolean isCalcIdHandled(String calcId)
+ {
+ return calcId != null && (calcIdPrefix.equals(calcId));
}
- private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
{
-// System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D();
- AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
- replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ return alan.getCalcId() != null
+ && calcIdPrefix.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
}
- private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
-// System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D();
- AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
- replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+
+ public static String relocateCalcId(String calcId,
+ Hashtable<String, String> alreadyLoadedPDB) throws Exception
+ {
+ int s = calcIdPrefix.length(), end = calcId.indexOf(calcIdPrefix, s);
+ String between = calcId.substring(s, end - 1);
+ return calcIdPrefix + alreadyLoadedPDB.get(between) + ":"
+ + calcId.substring(end);
}
- private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+
+ private void markCalcIds()
{
- if (al!=null && al.getHeight()>0)
+ for (SequenceI sq : seqs)
{
- ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
- ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
-
- for (SequenceI sq:ochains)
+ if (sq.getAnnotation() != null)
{
- SequenceI bestm=null;
- AlignSeq bestaseq=null;
- int bestscore=0;
- for (SequenceI msq:al.getSequences())
+ for (AlignmentAnnotation aa : sq.getAnnotation())
{
- AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
- if (bestm==null || aseq.getMaxScore()>bestscore)
+ String oldId = aa.getCalcId();
+ if (oldId == null)
{
- bestscore=aseq.getMaxScore();
- bestaseq= aseq;
- bestm=msq;
+ oldId = "";
}
+ aa.setCalcId(calcIdPrefix);
+ aa.setProperty("PDBID", id);
+ aa.setProperty("oldCalcId", oldId);
}
- 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++)
+ }
+ }
+
+ 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);
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ sq.getDatasetSequence().getPDBId().clear();
+ }
+ else
+ {
+ sq.getPDBId().clear();
+ }
+ }
+ replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
+ }
+ } catch (ClassNotFoundException q)
+ {
+ }
+ }
+
+ private void replaceAndUpdateChains(ArrayList<SequenceI> prot,
+ AlignmentI al, String pep, boolean b)
+ {
+ List<List<? extends Object>> replaced = AlignSeq
+ .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
+ false);
+ for (PDBChain ch : chains)
+ {
+ int p = 0;
+ for (SequenceI sq : (List<SequenceI>) replaced.get(0))
+ {
+ p++;
+ if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
+ {
+ p = -p;
+ break;
+ }
+ }
+ if (p < 0)
+ {
+ p = -p - 1;
+ // set shadow entry for chains
+ ch.shadow = (SequenceI) replaced.get(1).get(p);
+ ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
+ .getMappingFromS1(false);
+ }
+ }
+ }
+
+ 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)
{
- SequenceI sq,sp=seqs.get(p);
- int q;
- if ((q=ochains.indexOf(sp))>-1)
+ // 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) }));
+ for (SequenceI sq : al.getSequences())
{
- 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 (sq.getDatasetSequence() != null)
+ {
+ if (sq.getDatasetSequence().getPDBId() != null)
+ {
+ sq.getDatasetSequence().getPDBId().clear();
+ }
+ }
+ else
{
- if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
- if (inspos==-1)
- {
- inspos=ap;
- }
- annotations.remove(ap);
- } else {
- ap++;
+ if (sq.getPDBId() != null)
+ {
+ sq.getPDBId().clear();
}
}
- annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
}
+ replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
}
+ } catch (ClassNotFoundException x)
+ {
+ // ignore classnotfounds - occurs in applet
}
+ ;
}
+
/**
* make a friendly ID string.
*
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).makeResidueList();
+ chains.elementAt(i).makeResidueList(VisibleChainAnnotation);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
+ chains.elementAt(i).makeCaBondList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- if (((PDBChain) chains.elementAt(i)).id.equals(id))
+ if (chains.elementAt(i).id.equals(id))
{
- return (PDBChain) chains.elementAt(i);
+ return chains.elementAt(i);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChargeColours();
+ chains.elementAt(i).setChargeColours();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+ chains.elementAt(i).setChainColours(cs);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
- 1.0f / (float) i, .4f, 1.0f));
+ chains.elementAt(i).setChainColours(
+ Color.getHSBColor(1.0f / i, .4f, 1.0f));
}
}
+
public boolean isRNA(SequenceI seqs)
{
- for (int i=0;i<seqs.getLength();i++){
- if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
- {
- return false;
- }
- }
-
- return true;
-
-
+ for (int i = 0; i < seqs.getLength(); i++)
+ {
+ if ((seqs.getCharAt(i) != 'A') && (seqs.getCharAt(i) != 'C')
+ && (seqs.getCharAt(i) != 'G') && (seqs.getCharAt(i) != 'U'))
+ {
+ return false;
+ }
+ }
+
+ return true;
+
}
}
git://source.jalview.org / jalview.git / blobdiff