X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=ebc52aaf0aa0643410590de2c330fd5611782160;hb=39b4859e1a1b011af5d06058461db4d075acb578;hp=fe2851a6510036e1f7a8426fdaae39308b191f8a;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index fe2851a..ebc52aa 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,84 +1,94 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
-import jalview.io.RnamlFile;
-import jalview.ws.jws1.Annotate3D;
+import jalview.io.StructureFile;
+import jalview.util.MessageManager;
-public class PDBfile extends jalview.io.AlignFile
-{
- public Vector chains;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
- public String id;
+public class PDBfile extends StructureFile
+{
+ private static String CALC_ID_PREFIX = "JalviewPDB";
- /**
- * set to true to add chain alignment annotation as visible annotation.
- */
- boolean VisibleChainAnnotation = false;
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr)
+ {
+ super();
+ addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+ externalSecStr);
+ }
- public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String dataObject,
+ DataSourceType sourceType) throws IOException
{
- super(inFile, inType);
+ super(false, dataObject, sourceType);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
}
- public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse source) throws IOException
{
- super(source);
+ super(false, source);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
}
- public String print()
+ @Override
+ public String print(SequenceI[] seqs, boolean jvSuffix)
{
return null;
}
- public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ @Override
+ public void parse() throws IOException
{
+ setDbRefType(DBRefSource.PDB);
// TODO set the filename sensibly - try using data source name.
- id = safeName(getDataName());
-
- chains = new Vector();
+ setId(safeName(getDataName()));
- PDBChain tmpchain;
- String line=null;
- boolean modelFlag = false;
- boolean terFlag = false;
- String lastID = "";
+ setChains(new Vector());
+ List rna = new ArrayList();
+ List prot = new ArrayList();
+ PDBChain tmpchain;
+ String line = null;
+ boolean modelFlag = false;
+ boolean terFlag = false;
+ String lastID = "";
- int index = 0;
- String atomnam = null;
- try
- {
+ int indexx = 0;
+ String atomnam = null;
+ try
+ {
while ((line = nextLine()) != null)
{
if (line.indexOf("HEADER") == 0)
@@ -96,7 +106,7 @@ public class PDBfile extends jalview.io.AlignFile
}
if (tid.length() > 0)
{
- id = tid;
+ setId(tid);
}
continue;
}
@@ -133,20 +143,19 @@ public class PDBfile extends jalview.io.AlignFile
}
Atom tmpatom = new Atom(line);
- tmpchain = findChain(tmpatom.chain);
- if (tmpchain != null)
+ try
{
+ tmpchain = findChain(tmpatom.chain);
if (tmpatom.resNumIns.trim().equals(lastID))
{
// phosphorylated protein - seen both CA and P..
continue;
}
tmpchain.atoms.addElement(tmpatom);
- }
- else
+ } catch (Exception e)
{
- tmpchain = new PDBChain(id, tmpatom.chain);
- chains.addElement(tmpchain);
+ tmpchain = new PDBChain(getId(), tmpatom.chain);
+ getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
lastID = tmpatom.resNumIns.trim();
@@ -157,160 +166,92 @@ public class PDBfile extends jalview.io.AlignFile
makeResidueList();
makeCaBondList();
- if (id == null)
+ if (getId() == null)
{
- id = inFile.getName();
+ setId(inFile.getName());
}
- for (int i = 0; i < chains.size(); i++)
+ for (PDBChain chain : getChains())
{
- SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
- dataset.setName(id + "|" + dataset.getName());
- PDBEntry entry = new PDBEntry();
- entry.setId(id);
- if (inFile != null)
+ SequenceI chainseq = postProcessChain(chain);
+ if (isRNA(chainseq))
{
- entry.setFile(inFile.getAbsolutePath());
+ rna.add(chainseq);
}
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)
- {
- String path =inFile.getPath();
- System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D(path);
- System.out.println(id);
- //BufferedWriter r = an3d.getReader();
-
- // BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
-
- //String str;
- // while ((str = in.readLine()) != null) {
- // System.out.println(str);
- // System.out.println("toto");
-
- // }
- //String type = "File";
- //RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
- System.out.println("Create rnamfile object");
- //rnaml.parse("temp");
- //this.annotations =rnaml.getAnnot();
-
- }
-
- AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
- if (chainannot != null)
- {
- for (int ai = 0; ai < chainannot.length; ai++)
- {
-
- chainannot[ai].visible = VisibleChainAnnotation;
- annotations.addElement(chainannot[ai]);
- }
+ prot.add(chainseq);
}
}
+ if (predictSecondaryStructure)
+ {
+ addSecondaryStructure(rna, prot);
+ }
} 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();
}
/**
- * make a friendly ID string.
+ * Process a parsed chain to construct and return a Sequence, and add it to
+ * the list of sequences parsed.
*
- * @param dataName
- * @return truncated dataName to after last '/'
+ * @param chain
+ * @return
*/
- private String safeName(String dataName)
+
+ public static boolean isCalcIdHandled(String calcId)
{
- int p = 0;
- while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
- {
- dataName = dataName.substring(p + 1);
- }
- return dataName;
+ return calcId != null && (CALC_ID_PREFIX.equals(calcId));
}
- public void makeResidueList()
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
{
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).makeResidueList();
- }
+ return alan.getCalcId() != null
+ && CALC_ID_PREFIX.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
}
- public void makeCaBondList()
+ public static String relocateCalcId(String calcId,
+ Hashtable alreadyLoadedPDB) throws Exception
{
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
- }
+ int s = CALC_ID_PREFIX.length(),
+ end = calcId.indexOf(CALC_ID_PREFIX, s);
+ String between = calcId.substring(s, end - 1);
+ return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+ + calcId.substring(end);
}
- public PDBChain findChain(String id)
+ private void markCalcIds()
{
- for (int i = 0; i < chains.size(); i++)
+ for (SequenceI sq : seqs)
{
- if (((PDBChain) chains.elementAt(i)).id.equals(id))
+ if (sq.getAnnotation() != null)
{
- return (PDBChain) chains.elementAt(i);
+ for (AlignmentAnnotation aa : sq.getAnnotation())
+ {
+ String oldId = aa.getCalcId();
+ if (oldId == null)
+ {
+ oldId = "";
+ }
+ aa.setCalcId(CALC_ID_PREFIX);
+ aa.setProperty("PDBID", getId());
+ aa.setProperty("oldCalcId", oldId);
+ }
}
}
-
- 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