*/
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.Vector;
public class PDBfile extends jalview.io.AlignFile
{
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws IOException
+ boolean processSecondaryStructure=true;
+
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure)
{
- super(inFile, inType);
+ super();
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
}
- public PDBfile(FileParse source) throws IOException
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, String file, String protocol) throws IOException
{
- super(source);
+ super(false, file, protocol);
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ doParse();
+ }
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, FileParse source) throws IOException
+ {
+ super(false, source);
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ doParse();
}
public String print()
{
for (int ai = 0; ai < chainannot.length; ai++)
{
-
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
+ if (processSecondaryStructure)
+ {
if (rna.size() > 0)
+ {
try
{
processPdbFileWithAnnotate3d(rna);
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");
+ .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(MessageManager.getString("exception.outofmemory_loading_pdb_file"));
+ throw new IOException(
+ MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
} catch (NumberFormatException ex)
{
if (line != null)
System.err.println(line);
}
}
+ markCalcIds();
}
+ public static boolean isCalcIdForFile(String calcId, String pdbFile)
+ {
+ return (calcId != null && calcId.startsWith("JalviewPDB:" + pdbFile
+ + ":JalviewPDB:"));
+ }
+ private void markCalcIds()
+ {
+ for (SequenceI sq : seqs)
+ {
+ for (AlignmentAnnotation aa : sq.getAnnotation())
+ {
+ String oldId = aa.getCalcId();
+ if (oldId == null)
+ {
+ oldId = "";
+ }
+ aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
+ }
+ }
+ }
private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
throws Exception
{
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
{ Alignment.class }).invoke(jmf, al);
- replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
}
} catch (ClassNotFoundException q)
{
new Class[]
{ FileParse.class }).invoke(annotate3d, new Object[]
{ new FileParse(getDataName(), type) }));
- replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
}
} catch (ClassNotFoundException x)
{
;
}
- 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.
*
for (int i = 0; i < chains.size(); i++)
{
((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
- 1.0f / (float) i, .4f, 1.0f));
+ 1.0f / i, .4f, 1.0f));
}
}
git://source.jalview.org / jalview.git / blobdiff