/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 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.*;
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
-import jalview.datamodel.*;
-
-public class PDBfile
- extends jalview.io.AlignFile
+public class PDBfile extends jalview.io.AlignFile
{
public Vector chains;
+
public String id;
/**
* set to true to add chain alignment annotation as visible annotation.
*/
- boolean VisibleChainAnnotation=false;
- public PDBfile(String inFile, String inType)
- throws IOException
+ boolean VisibleChainAnnotation = false;
+
+ boolean processSecondaryStructure=true;
+
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure)
+ {
+ super();
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ }
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, String file, String protocol) throws IOException
+ {
+ super(false, file, protocol);
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ doParse();
+ }
+
+ public PDBfile(boolean visibleChainAnnotation,
+ boolean processSecondaryStructure, FileParse source) throws IOException
{
- super(inFile, inType);
+ super(false, source);
+ VisibleChainAnnotation = visibleChainAnnotation;
+ this.processSecondaryStructure = processSecondaryStructure;
+ doParse();
}
public String print()
return null;
}
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
- // TODO set the filename sensibly
- id = (inFile==null) ? "PDBFILE" : inFile.getName();
- try
- {
- chains = new Vector();
+ // 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)
{
- id = line.substring(62, 67).trim();
- continue;
+ if (line.length() > 62)
+ {
+ 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)
break;
}
if (line.indexOf("ATOM") == 0
- || (line.indexOf("HETATM") == 0 && !terFlag)
- )
+ || (line.indexOf("HETATM") == 0 && !terFlag))
{
terFlag = false;
- //Jalview is only interested in CA bonds????
- if (!line.substring(12, 15).trim().equals("CA"))
+ // Jalview is only interested in CA bonds????
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
{
continue;
}
tmpchain = findChain(tmpatom.chain);
if (tmpchain != null)
{
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
tmpchain.atoms.addElement(tmpatom);
}
else
chains.addElement(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
+ lastID = tmpatom.resNumIns.trim();
}
index++;
}
}
for (int i = 0; i < chains.size(); i++)
{
- SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
- sequence;
+ 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)
+ {
+ entry.getProperty().put("CHAIN",
+ ((PDBChain) chains.elementAt(i)).id);
+ }
if (inFile != null)
{
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
+ 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();
- if (chainannot!=null)
+
+ if (chainannot != null)
{
- for (int ai=0; ai<chainannot.length; ai++)
+ for (int ai = 0; ai < chainannot.length; ai++)
{
- chainannot[ai].visible=VisibleChainAnnotation;
+ chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
- }
- catch (OutOfMemoryError er)
+ 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");
+ throw new IOException(
+ MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
+ } catch (NumberFormatException ex)
+ {
+ if (line != null)
+ {
+ System.err.println("Couldn't read number from line:");
+ System.err.println(line);
+ }
+ }
+ markCalcIds();
+ }
+
+ private static String calcIdPrefix = "JalviewPDB:";
+
+ public static boolean isCalcIdHandled(String calcId)
+ {
+ return calcId != null
+ && (calcId.startsWith(calcIdPrefix) && calcId.indexOf(
+ calcIdPrefix,
+ calcIdPrefix.length() + 1) > -1);
+ }
+ public static boolean isCalcIdForFile(String calcId, String pdbFile)
+ {
+ return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile
+ + ":" + calcIdPrefix));
+ }
+
+ 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)
+ {
+ 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
+ }
+ ;
+ }
+
+ /**
+ * 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 makeResidueList()
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).makeResidueList();
+ ((PDBChain) chains.elementAt(i)).makeResidueList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).makeCaBondList();
+ ((PDBChain) chains.elementAt(i)).makeCaBondList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
+ if (((PDBChain) chains.elementAt(i)).id.equals(id))
{
return (PDBChain) chains.elementAt(i);
}
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).setChargeColours();
+ ((PDBChain) chains.elementAt(i)).setChargeColours();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
+ ((PDBChain) 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)
- );
+ ((PDBChain) 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;
+
}
}