/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * 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.
+ *
+ * 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/>.
+ * 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.io.FileParse;
+import jalview.util.MessageManager;
-import java.io.*;
+public class PDBfile extends jalview.io.AlignFile
+{
+ public Vector chains;
-import java.util.*;
-import java.awt.Color;
+ public String id;
+ /**
+ * set to true to add chain alignment annotation as visible annotation.
+ */
+ boolean VisibleChainAnnotation = false;
-public class PDBfile extends jalview.io.AlignFile {
- public Vector chains;
- public String id;
+ public PDBfile(String inFile, String inType) throws IOException
+ {
+ super(inFile, inType);
+ }
- public PDBfile(String inFile, String inType) throws IOException
- {
- super(inFile, inType);
- }
+ public PDBfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
- public String print()
- {
- return null;
- }
+ public String print()
+ {
+ return null;
+ }
- public void parse() throws IOException
- {
- try{
- chains = new Vector();
+ public void parse() throws IOException
+ {
+ // TODO set the filename sensibly - try using data source name.
+ id = safeName(getDataName());
- PDBChain tmpchain;
- String line;
- boolean modelFlag = false;
- boolean terFlag = false;
+ 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;
- while ( (line = nextLine()) != null)
+ int index = 0;
+ String atomnam = null;
+ try
+ {
+ while ((line = nextLine()) != null)
+ {
+ if (line.indexOf("HEADER") == 0)
{
- if (line.indexOf("HEADER") == 0)
+ if (line.length() > 62)
{
- id = line.substring(62, 67).trim();
+ String tid;
+ if (line.length() > 67)
+ {
+ tid = line.substring(62, 67).trim();
+ }
+ else
+ {
+ tid = line.substring(62).trim();
+ }
+ if (tid.length() > 0)
+ {
+ id = tid;
+ }
continue;
}
- // Were we to do anything with SEQRES - we start it here
- if (line.indexOf("SEQRES") == 0) {
- }
-
- if (line.indexOf("MODEL") == 0)
- modelFlag = true;
-
- if (line.indexOf("TER") == 0)
- terFlag = true;
-
- if (modelFlag && line.indexOf("ENDMDL") == 0)
- break;
- if (line.indexOf("ATOM") == 0
- || (line.indexOf("HETATM") == 0 && !terFlag)
- )
+ }
+ // Were we to do anything with SEQRES - we start it here
+ if (line.indexOf("SEQRES") == 0)
+ {
+ }
+
+ if (line.indexOf("MODEL") == 0)
+ {
+ modelFlag = true;
+ }
+
+ if (line.indexOf("TER") == 0)
+ {
+ terFlag = true;
+ }
+
+ if (modelFlag && line.indexOf("ENDMDL") == 0)
+ {
+ break;
+ }
+ if (line.indexOf("ATOM") == 0
+ || (line.indexOf("HETATM") == 0 && !terFlag))
+ {
+ terFlag = false;
+
+ // Jalview is only interested in CA bonds????
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
{
- terFlag = false;
+ continue;
+ }
- //Jalview is only interested in CA bonds????
- if (!line.substring(12, 15).trim().equals("CA"))
+ Atom tmpatom = new Atom(line);
+ tmpchain = findChain(tmpatom.chain);
+ if (tmpchain != null)
+ {
+ if (tmpatom.resNumIns.trim().equals(lastID))
{
+ // phosphorylated protein - seen both CA and P..
continue;
}
-
- Atom tmpatom = new Atom(line);
- tmpchain = findChain(tmpatom.chain);
- if (tmpchain != null)
- {
- tmpchain.atoms.addElement(tmpatom);
- }
- else
- {
- tmpchain = new PDBChain(tmpatom.chain);
- chains.addElement(tmpchain);
- tmpchain.atoms.addElement(tmpatom);
- }
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ else
+ {
+ tmpchain = new PDBChain(id, tmpatom.chain);
+ chains.addElement(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
}
- index++;
+ lastID = tmpatom.resNumIns.trim();
}
+ index++;
+ }
- makeResidueList();
- makeCaBondList();
+ makeResidueList();
+ makeCaBondList();
- if (id == null)
+ if (id == null)
+ {
+ id = inFile.getName();
+ }
+ for (int i = 0; i < chains.size(); i++)
+ {
+ SequenceI dataset = ((PDBChain) 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)
{
- id = inFile.getName();
+ entry.getProperty().put("CHAIN",
+ ((PDBChain) chains.elementAt(i)).id);
}
- for (int i = 0; i < chains.size(); i++)
+ if (inFile != null)
{
- SequenceI seq = ( (PDBChain) chains.elementAt(i)).
- sequence;
- seq.setName(id + "|" + seq.getName());
- Sequence dataset = new Sequence(seq.
- getName(),
- seq.getSequence().toString(),
- seq.getStart(), seq.getEnd());
- dataset.setSequenceFeatures(seq.getSequenceFeatures());
- PDBEntry entry = new PDBEntry();
- entry.setId(id);
- if (inFile != null)
- entry.setFile(inFile.getAbsolutePath());
+ entry.setFile(inFile.getAbsolutePath());
+ }
+ else
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
+ dataset.addPDBId(entry);
+ SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+ // maintain reference to
+ // dataset
+ seqs.addElement(chainseq);
+ if (isRNA(chainseq) == true)
+ {
+ rna.add(chainseq);
+ }
+ else
+ {
+ prot.add(chainseq);
+ }
+
+ AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
- seq.setDatasetSequence(dataset);
- dataset.addPDBId(entry);
+ if (chainannot != null)
+ {
+ 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();
- getSeqs().addElement(seq);
}
- }catch(OutOfMemoryError er)
+ ;
+ 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");
+ x.printStackTrace();
+
+ }
+ ;
+ } catch (OutOfMemoryError er)
+ {
+ System.out.println("OUT OF MEMORY LOADING PDB FILE");
+ throw new IOException(MessageManager.getString("exception.outofmemory_loading_pdb_file"));
+ } catch (NumberFormatException ex)
+ {
+ if (line != null)
{
- System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException("Out of memory loading PDB File");
+ System.err.println("Couldn't read number from line:");
+ System.err.println(line);
}
}
+ }
- public void makeResidueList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeResidueList();
- }
+ 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)
+ {
}
+ }
- public void makeCaBondList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
- }
+ 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>();
- public PDBChain findChain(String id) {
- for (int i = 0; i < chains.size(); i++) {
- if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
- return (PDBChain) chains.elementAt(i);
+ 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()));
+ }
}
+ }
+ }
+ }
- return null;
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int p = 0;
+ while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
+ {
+ dataName = dataName.substring(p + 1);
}
+ return dataName;
+ }
- public void setChargeColours() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setChargeColours();
- }
+ public void makeResidueList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).makeResidueList();
}
+ }
- public void setColours(jalview.schemes.ColourSchemeI cs) {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setChainColours(cs);
- }
+ public void makeCaBondList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).makeCaBondList();
}
+ }
- public void setChainColours()
+ public PDBChain findChain(String id)
+ {
+ for (int i = 0; i < chains.size(); i++)
{
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).setChainColours(
- Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
- );
- }
+ if (((PDBChain) chains.elementAt(i)).id.equals(id))
+ {
+ return (PDBChain) chains.elementAt(i);
+ }
+ }
+
+ return null;
+ }
+
+ public void setChargeColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChargeColours();
+ }
+ }
+
+ public void setColours(jalview.schemes.ColourSchemeI cs)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+ }
+ }
+
+ public void setChainColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+ 1.0f / (float) 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