package jalview.io;
import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
+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.PDBEntry.Type;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureImportSettings;
import java.awt.Color;
import java.io.IOException;
+import java.lang.reflect.Constructor;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
private String id;
+ private PDBEntry.Type dbRefType;
+
/**
* set to true to add derived sequence annotations (temp factor read from
* file, or computed secondary structure) to the alignment
*/
protected boolean visibleChainAnnotation = false;
- /*
+ /**
* Set true to predict secondary structure (using JMol for protein, Annotate3D
* for RNA)
*/
- protected boolean predictSecondaryStructure = true;
+ protected boolean predictSecondaryStructure = false;
- /*
+ /**
* Set true (with predictSecondaryStructure=true) to predict secondary
* structure using an external service (currently Annotate3D for RNA only)
*/
private Vector<PDBChain> chains;
- public StructureFile(String inFile, String type) throws IOException
+ public StructureFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
public StructureFile(FileParse fp) throws IOException
super(fp);
}
- public StructureFile(boolean parseImmediately, String inFile, String type)
- throws IOException
+ public void addSettings(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr)
{
- super(parseImmediately, inFile, type);
+ this.visibleChainAnnotation = addAlignmentAnnotations;
+ this.predictSecondaryStructure = predictSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ }
+
+ public void xferSettings()
+ {
+ this.visibleChainAnnotation = StructureImportSettings
+ .isVisibleChainAnnotation();
+ this.predictSecondaryStructure = StructureImportSettings
+ .isProcessSecondaryStructure();
+ this.externalSecondaryStructure = StructureImportSettings
+ .isExternalSecondaryStructure();
+
+ }
+
+ public StructureFile(boolean parseImmediately, String dataObject,
+ DataSourceType sourceType) throws IOException
+ {
+ super(parseImmediately, dataObject, sourceType);
}
public StructureFile(boolean a, FileParse fp) throws IOException
{
}
+ @SuppressWarnings("rawtypes")
protected SequenceI postProcessChain(PDBChain chain)
{
SequenceI pdbSequence = chain.sequence;
pdbSequence.setName(getId() + "|" + pdbSequence.getName());
PDBEntry entry = new PDBEntry();
entry.setId(getId());
- entry.setType(PDBEntry.Type.PDB);
+ entry.setType(this.dbRefType);
entry.setProperty(new Hashtable());
if (chain.id != null)
{
DBRefEntry sourceDBRef = new DBRefEntry();
sourceDBRef.setAccessionId(getId());
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);
-
+ pdbSequence.setSourceDBRef(sourceDBRef);
+ pdbSequence.addPDBId(entry);
+ pdbSequence.addDBRef(sourceDBRef);
+ SequenceI chainseq = pdbSequence;
seqs.addElement(chainseq);
-
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
if (chainannot != null && visibleChainAnnotation)
return chainseq;
}
+ @SuppressWarnings({ "unchecked", "rawtypes" })
protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
throws Exception
{
new Object[] {});
AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
new Class[] { FileParse.class }).invoke(annotate3d,
- new Object[] { new FileParse(getDataName(), type) }));
+ new Object[] { new FileParse(getDataName(), dataSourceType) }));
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
}
}
+ @SuppressWarnings("unchecked")
protected void replaceAndUpdateChains(List<SequenceI> prot,
- AlignmentI al,
- String pep, boolean b)
+ AlignmentI al, String pep, boolean b)
{
List<List<? extends Object>> replaced = AlignSeq
.replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
}
}
+ /**
+ * Predict secondary structure for RNA and/or protein sequences and add as
+ * annotations
+ *
+ * @param rnaSequences
+ * @param proteinSequences
+ */
+ protected void addSecondaryStructure(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
+ {
+ processWithJmolParser(proteinSequences);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions from Jmol when processing data in pdb file");
+ x.printStackTrace();
+ }
+ }
+ }
+
+ @SuppressWarnings({ "unchecked", "rawtypes" })
+ private void processWithJmolParser(List<SequenceI> prot) throws Exception
+ {
+ try
+ {
+
+ Class cl = Class.forName("jalview.ext.jmol.JmolParser");
+ if (cl != null)
+ {
+ final Constructor constructor = cl.getConstructor(new Class[] {
+ boolean.class, boolean.class, boolean.class, FileParse.class });
+ final Object[] args = new Object[] { visibleChainAnnotation,
+ predictSecondaryStructure, externalSecondaryStructure,
+ new FileParse(getDataName(), dataSourceType) };
+
+ StructureImportSettings.setShowSeqFeatures(false);
+ StructureImportSettings.setVisibleChainAnnotation(false);
+ StructureImportSettings
+ .setProcessSecondaryStructure(predictSecondaryStructure);
+ StructureImportSettings
+ .setExternalSecondaryStructure(externalSecondaryStructure);
+ 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)
+ {
+ }
+ StructureImportSettings.setShowSeqFeatures(true);
+ }
+
public PDBChain findChain(String id) throws Exception
{
for (PDBChain chain : getChains())
{
- if (chain.id.equalsIgnoreCase(id))
+ if (chain.id.equals(id))
{
return chain;
}
{
this.chains = chains;
}
+
+ public Type getDbRefType()
+ {
+ return dbRefType;
+ }
+
+ public void setDbRefType(String dbRefType)
+ {
+ this.dbRefType = Type.valueOf(dbRefType);
+ }
+
+ public void setDbRefType(Type dbRefType)
+ {
+ this.dbRefType = dbRefType;
+ }
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>ResNums or insertions features visible</li>
+ * <li>insertions features coloured red</li>
+ * <li>ResNum features coloured by label</li>
+ * <li>Insertions displayed above (on top of) ResNums</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new PDBFeatureSettings();
+ }
}
git://source.jalview.org / jalview.git / blobdiff