/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package MCview;
-import java.io.*;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
+import jalview.io.StructureFile;
import jalview.util.MessageManager;
-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;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
- boolean processSecondaryStructure=true;
-
+public class PDBfile extends StructureFile
+{
+ private static String CALC_ID_PREFIX = "JalviewPDB";
- public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure)
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr)
{
super();
- VisibleChainAnnotation = visibleChainAnnotation;
- this.processSecondaryStructure = processSecondaryStructure;
+ addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+ externalSecStr);
}
- public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure, String file, String protocol) throws IOException
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String dataObject, String protocol)
+ throws IOException
{
- super(false, file, protocol);
- VisibleChainAnnotation = visibleChainAnnotation;
- this.processSecondaryStructure = processSecondaryStructure;
+ super(false, dataObject, protocol);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
- public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure, FileParse source) throws IOException
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse source) throws IOException
{
super(false, source);
- VisibleChainAnnotation = visibleChainAnnotation;
- this.processSecondaryStructure = processSecondaryStructure;
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
+ @Override
public String print()
{
return null;
}
+ @Override
public void parse() throws IOException
{
+ setDbRefType(DBRefSource.PDB);
// TODO set the filename sensibly - try using data source name.
- id = safeName(getDataName());
+ setId(safeName(getDataName()));
- chains = new Vector();
- ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
+ setChains(new Vector<PDBChain>());
+ List<SequenceI> rna = new ArrayList<SequenceI>();
+ List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
boolean terFlag = false;
String lastID = "";
- int index = 0;
+ int indexx = 0;
String atomnam = null;
try
{
}
if (tid.length() > 0)
{
- id = tid;
+ setId(tid);
}
continue;
}
}
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();
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);
- 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
- seqs.addElement(chainseq);
- if (isRNA(chainseq) == true)
+ SequenceI chainseq = postProcessChain(chain);
+ if (isRNA(chainseq))
{
rna.add(chainseq);
}
{
prot.add(chainseq);
}
-
- AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
- if (chainannot != null)
- {
- for (int ai = 0; ai < chainannot.length; ai++)
- {
-
- chainannot[ai].visible = VisibleChainAnnotation;
- annotations.addElement(chainannot[ai]);
- }
- }
}
- if (processSecondaryStructure)
+ if (predictSecondaryStructure)
{
- 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();
-
- }
+ addSecondaryStructure(rna, prot);
}
} catch (OutOfMemoryError er)
{
System.err.println(line);
}
}
- }
-
- 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
- }
- ;
+ 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)
- {
- int p = 0;
- while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
- {
- dataName = dataName.substring(p + 1);
- }
- return dataName;
- }
- public void makeResidueList()
+ public static boolean isCalcIdHandled(String calcId)
{
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).makeResidueList();
- }
+ return calcId != null && (CALC_ID_PREFIX.equals(calcId));
}
- public void makeCaBondList()
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
{
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
- }
+ return alan.getCalcId() != null
+ && CALC_ID_PREFIX.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
}
- public PDBChain findChain(String id)
+ public static String relocateCalcId(String calcId,
+ Hashtable<String, String> alreadyLoadedPDB) throws Exception
{
- for (int i = 0; i < chains.size(); i++)
- {
- if (((PDBChain) chains.elementAt(i)).id.equals(id))
- {
- return (PDBChain) chains.elementAt(i);
- }
- }
-
- return null;
+ 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 void setChargeColours()
+ private void markCalcIds()
{
- for (int i = 0; i < chains.size(); i++)
+ for (SequenceI sq : seqs)
{
- ((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'))
+ if (sq.getAnnotation() != null)
{
- return false;
+ 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 true;
-
}
+
}
git://source.jalview.org / jalview.git / blobdiff