*/
package MCview;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
+import jalview.io.StructureFile;
import jalview.util.MessageManager;
-import java.awt.Color;
import java.io.IOException;
-import java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
-public class PDBfile extends jalview.io.AlignFile
+public class PDBfile extends StructureFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
- public Vector<PDBChain> chains;
-
- public String id;
-
- /**
- * set to true to add derived sequence annotations (temp factor read from
- * file, or computed secondary structure) to the alignment
- */
- private boolean visibleChainAnnotation = false;
-
- /*
- * Set true to predict secondary structure (using JMol for protein, Annotate3D
- * for RNA)
- */
- private boolean predictSecondaryStructure = true;
-
- /*
- * Set true (with predictSecondaryStructure=true) to predict secondary
- * structure using an external service (currently Annotate3D for RNA only)
- */
- private boolean externalSecondaryStructure = false;
-
public PDBfile(boolean addAlignmentAnnotations,
boolean predictSecondaryStructure, boolean externalSecStr)
{
super();
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+ externalSecStr);
}
- public PDBfile(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- String file, String protocol) throws IOException
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String dataObject, String protocol)
+ throws IOException
{
- super(false, file, protocol);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ super(false, dataObject, protocol);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
- public PDBfile(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- FileParse source) throws IOException
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse source) throws IOException
{
super(false, source);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
doParse();
}
@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<PDBChain>();
+ setChains(new Vector<PDBChain>());
List<SequenceI> rna = new ArrayList<SequenceI>();
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
}
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 (PDBChain chain : chains)
+ for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
if (isRNA(chainseq))
}
if (predictSecondaryStructure)
{
- predictSecondaryStructure(rna, prot);
+ addSecondaryStructure(rna, prot);
}
} catch (OutOfMemoryError er)
{
}
/**
- * Predict secondary structure for RNA and/or protein sequences and add as
- * annotations
- *
- * @param rnaSequences
- * @param proteinSequences
- */
- protected void predictSecondaryStructure(List<SequenceI> rnaSequences,
- List<SequenceI> proteinSequences)
- {
- /*
- * Currently using Annotate3D for RNA, but only if the 'use external
- * prediction' flag is set
- */
- if (externalSecondaryStructure && rnaSequences.size() > 0)
- {
- try
- {
- processPdbFileWithAnnotate3d(rnaSequences);
- } catch (Exception x)
- {
- System.err.println("Exceptions when dealing with RNA in pdb file");
- x.printStackTrace();
-
- }
- }
-
- /*
- * Currently using JMol PDB parser for peptide
- */
- if (proteinSequences.size() > 0)
- {
- try
- {
- processPdbFileWithJmol(proteinSequences);
- } catch (Exception x)
- {
- System.err
- .println("Exceptions from Jmol when processing data in pdb file");
- x.printStackTrace();
- }
- }
- }
-
- /**
* Process a parsed chain to construct and return a Sequence, and add it to
* the list of sequences parsed.
*
* @param chain
* @return
*/
- protected SequenceI postProcessChain(PDBChain chain)
- {
- SequenceI pdbSequence = chain.sequence;
- pdbSequence.setName(id + "|" + pdbSequence.getName());
- PDBEntry entry = new PDBEntry();
- entry.setId(id);
- entry.setType(PDBEntry.Type.PDB);
- entry.setProperty(new Hashtable());
- if (chain.id != null)
- {
- // entry.getProperty().put("CHAIN", chains.elementAt(i).id);
- entry.setChainCode(String.valueOf(chain.id));
- }
- if (inFile != null)
- {
- entry.setFile(inFile.getAbsolutePath());
- }
- else
- {
- // TODO: decide if we should dump the datasource to disk
- entry.setFile(getDataName());
- }
-
- DBRefEntry sourceDBRef = new DBRefEntry();
- sourceDBRef.setAccessionId(id);
- sourceDBRef.setSource(DBRefSource.PDB);
- sourceDBRef.setStartRes(pdbSequence.getStart());
- sourceDBRef.setEndRes(pdbSequence.getEnd());
-
- // PDBChain objects maintain reference to dataset
- SequenceI chainseq = pdbSequence.deriveSequence();
- chainseq.setSourceDBRef(sourceDBRef);
- chainseq.addPDBId(entry);
- chainseq.addDBRef(sourceDBRef);
-
- seqs.addElement(chainseq);
-
- AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
- if (chainannot != null && visibleChainAnnotation)
- {
- for (int ai = 0; ai < chainannot.length; ai++)
- {
- chainannot[ai].visible = visibleChainAnnotation;
- annotations.addElement(chainannot[ai]);
- }
- }
- return chainseq;
- }
public static boolean isCalcIdHandled(String calcId)
{
oldId = "";
}
aa.setCalcId(CALC_ID_PREFIX);
- aa.setProperty("PDBID", id);
+ aa.setProperty("PDBID", getId());
aa.setProperty("oldCalcId", oldId);
}
}
}
}
- private void processPdbFileWithJmol(List<SequenceI> prot)
- throws Exception
- {
- try
- {
- Class cl = Class.forName("jalview.ext.jmol.JmolParser");
- if (cl != null)
- {
- final Constructor constructor = cl
- .getConstructor(new Class[] { FileParse.class });
- final Object[] args = new Object[] { new FileParse(getDataName(),
- type) };
- Object jmf = constructor.newInstance(args);
- AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
- "getSeqsAsArray", new Class[] {}).invoke(jmf));
- cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
- .invoke(jmf, al);
- for (SequenceI sq : al.getSequences())
- {
- if (sq.getDatasetSequence() != null)
- {
- sq.getDatasetSequence().getAllPDBEntries().clear();
- }
- else
- {
- sq.getAllPDBEntries().clear();
- }
- }
- replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
- }
- } catch (ClassNotFoundException q)
- {
- }
- }
-
- private void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
- String pep, boolean b)
- {
- List<List<? extends Object>> replaced = AlignSeq
- .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
- false);
- for (PDBChain ch : chains)
- {
- int p = 0;
- for (SequenceI sq : (List<SequenceI>) replaced.get(0))
- {
- p++;
- if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
- {
- p = -p;
- break;
- }
- }
- if (p < 0)
- {
- p = -p - 1;
- // set shadow entry for chains
- ch.shadow = (SequenceI) replaced.get(1).get(p);
- ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
- .getMappingFromS1(false);
- }
- }
- }
-
- private void processPdbFileWithAnnotate3d(List<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) }));
- for (SequenceI sq : al.getSequences())
- {
- if (sq.getDatasetSequence() != null)
- {
- if (sq.getDatasetSequence().getAllPDBEntries() != null)
- {
- sq.getDatasetSequence().getAllPDBEntries().clear();
- }
- }
- else
- {
- if (sq.getAllPDBEntries() != null)
- {
- sq.getAllPDBEntries().clear();
- }
- }
- }
- replaceAndUpdateChains(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++)
- {
- chains.elementAt(i).makeResidueList(visibleChainAnnotation);
- }
- }
-
- public void makeCaBondList()
- {
- for (int i = 0; i < chains.size(); i++)
- {
- chains.elementAt(i).makeCaBondList();
- }
- }
-
- public PDBChain findChain(String id)
- {
- for (int i = 0; i < chains.size(); i++)
- {
- if (chains.elementAt(i).id.equals(id))
- {
- return chains.elementAt(i);
- }
- }
-
- return null;
- }
-
- public void setChargeColours()
- {
- for (int i = 0; i < chains.size(); i++)
- {
- chains.elementAt(i).setChargeColours();
- }
- }
-
- public void setColours(jalview.schemes.ColourSchemeI cs)
- {
- for (int i = 0; i < chains.size(); i++)
- {
- chains.elementAt(i).setChainColours(cs);
- }
- }
-
- public void setChainColours()
- {
- for (int i = 0; i < chains.size(); i++)
- {
- // divide by zero --> infinity --> 255 ;-)
- chains.elementAt(i).setChainColours(
- Color.getHSBColor(1.0f / i, .4f, 1.0f));
- }
- }
-
- public static boolean isRNA(SequenceI seq)
- {
- for (char c : seq.getSequence())
- {
- if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
- {
- return false;
- }
- }
-
- return true;
-
- }
}
git://source.jalview.org / jalview.git / blobdiff