/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*/
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.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 IOException
+ boolean processSecondaryStructure = true;
+
+ boolean externalSecondaryStructure = false;
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, boolean externalSecStr)
+ {
+ super();
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ }
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, boolean externalSecStr,
+ String file, String protocol) throws IOException
{
- super(inFile, inType);
+ super(false, file, protocol);
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ doParse();
}
- public PDBfile(FileParse source) throws IOException
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, boolean externalSecStr,
+ FileParse source) throws IOException
{
- super(source);
+ super(false, source);
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ doParse();
}
public String print()
}
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());
- if (((PDBChain) chains.elementAt(i)).id != null)
+ if (chains.elementAt(i).id != null)
{
- entry.getProperty().put("CHAIN",
- ((PDBChain) chains.elementAt(i)).id);
+ entry.getProperty().put("CHAIN", chains.elementAt(i).id);
}
if (inFile != null)
{
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)
- {
- System.err
- .println("Exceptions when dealing with RNA in pdb file");
- x.printStackTrace();
-
- }
- ;
- if (prot.size() > 0)
- try
- {
- processPdbFileWithJmol(prot);
- } catch (Exception x)
+ if (processSecondaryStructure)
+ {
+ if (externalSecondaryStructure && rna.size() > 0)
{
- System.err
- .println("Exceptions when dealing with RNA in pdb file");
- x.printStackTrace();
+ try
+ {
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+ }
}
- ;
- if (prot.size() > 0)
- try
+ ;
+ if (prot.size() > 0)
{
- processPdbFileWithJmol(prot);
- } catch (Exception x)
- {
- System.err
- .println("Exceptions when dealing with RNA in pdb file");
- x.printStackTrace();
+ 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));
+ }
+
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
+ {
+ return alan.getCalcId() != null
+ && calcIdPrefix.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
+ }
+
+ 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 markCalcIds()
+ {
+ for (SequenceI sq : seqs)
+ {
+ if (sq.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : sq.getAnnotation())
+ {
+ String oldId = aa.getCalcId();
+ if (oldId == null)
+ {
+ oldId = "";
+ }
+ aa.setCalcId(calcIdPrefix);
+ aa.setProperty("PDBID", id);
+ aa.setProperty("oldCalcId", oldId);
+ }
+ }
+ }
}
private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
{ Alignment.class }).invoke(jmf, al);
- replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ 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
{
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)
+ 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 (((AlignmentAnnotation) annotations.get(ap)).sequenceRef == sp)
- {
- if (inspos == -1)
- {
- inspos = ap;
- }
- annotations.remove(ap);
- }
- else
+ if (sq.getDatasetSequence().getPDBId() != null)
{
- ap++;
+ sq.getDatasetSequence().getPDBId().clear();
}
}
- if (sq.getAnnotation() != null)
+ else
{
- annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ if (sq.getPDBId() != null)
+ {
+ sq.getPDBId().clear();
+ }
}
}
+ replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
}
+ } catch (ClassNotFoundException x)
+ {
+ // ignore classnotfounds - occurs in applet
}
+ ;
}
/**
{
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));
}
}
git://source.jalview.org / jalview.git / blobdiff