/*
-* 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 2.8.0b1)
+ * 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.datamodel.*;
+import jalview.io.FileParse;
-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());
+
+ chains = new Vector();
- PDBChain tmpchain;
- String line;
- boolean modelFlag = false;
- boolean terFlag = false;
+ 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(id,tmpatom.chain);
- chains.addElement(tmpchain);
- tmpchain.atoms.addElement(tmpatom);
- }
+ tmpchain.atoms.addElement(tmpatom);
}
- index++;
+ else
+ {
+ tmpchain = new PDBChain(id, tmpatom.chain);
+ chains.addElement(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ 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);
+ if (inFile != null)
{
- id = inFile.getName();
+ entry.setFile(inFile.getAbsolutePath());
}
- for (int i = 0; i < chains.size(); i++)
+ else
{
- SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
- sequence;
- dataset.setName(id + "|" + dataset.getName());
- PDBEntry entry = new PDBEntry();
- entry.setId(id);
- if (inFile != null)
- entry.setFile(inFile.getAbsolutePath());
- dataset.addPDBId(entry);
- getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
}
- }catch(OutOfMemoryError er)
+ dataset.addPDBId(entry);
+ SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+ // maintain reference to
+ // dataset
+ seqs.addElement(chainseq);
+ AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+ if (chainannot != null)
+ {
+ for (int ai = 0; ai < chainannot.length; ai++)
+ {
+ chainannot[ai].visible = VisibleChainAnnotation;
+ annotations.addElement(chainannot[ai]);
+ }
+ }
+ }
+ } catch (OutOfMemoryError er)
+ {
+ System.out.println("OUT OF MEMORY LOADING PDB FILE");
+ throw new IOException("Out of memory 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();
- }
+ /**
+ * 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 makeCaBondList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
- }
+ public void makeResidueList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).makeResidueList();
}
+ }
- 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);
- }
- }
+ public void makeCaBondList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).makeCaBondList();
+ }
+ }
- return null;
+ 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);
+ }
}
- public void setChargeColours() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setChargeColours();
- }
+ 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 setColours(jalview.schemes.ColourSchemeI cs)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChainColours(cs);
}
+ }
- public void setChainColours()
+ public void setChainColours()
+ {
+ 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)
- );
- }
+ ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+ 1.0f / (float) i, .4f, 1.0f));
}
+ }
}
git://source.jalview.org / jalview.git / blobdiff