/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.io.*;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
+import jalview.analysis.AlignSeq;
+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()
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
- chains = new Vector();
-
- PDBChain tmpchain;
- String line=null;
- boolean modelFlag = false;
- boolean terFlag = false;
- String lastID = "";
+ chains = new Vector();
+ ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
+ PDBChain tmpchain;
+ String line = null;
+ boolean modelFlag = false;
+ boolean terFlag = false;
+ String lastID = "";
- int index = 0;
- String atomnam = null;
- try
- {
+ int index = 0;
+ String atomnam = null;
+ try
+ {
while ((line = nextLine()) != null)
{
if (line.indexOf("HEADER") == 0)
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
+ entry.setProperty(new Hashtable());
+ if (((PDBChain) chains.elementAt(i)).id != null)
+ {
+ entry.getProperty().put("CHAIN",
+ ((PDBChain) 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);
+ }
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
if (chainannot != null)
{
for (int ai = 0; ai < chainannot.length; ai++)
}
}
}
+ if (processSecondaryStructure)
+ {
+ 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)
+ {
+ 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");
- }
- catch (NumberFormatException ex)
+ throw new IOException(
+ MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
+ } catch (NumberFormatException ex)
{
- if (line!=null) {
+ if (line != null)
+ {
System.err.println("Couldn't read number from line:");
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
+ {
+ 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);
+ AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
+ }
+ } 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) }));
+ AlignSeq.replaceMatchingSeqsWith(seqs, annotations, 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)).setChainColours(Color.getHSBColor(
- 1.0f / (float) i, .4f, 1.0f));
+ 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;
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff