X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=97e11eb05db197b43cb7ce699922e845e76aaf73;hb=331cf6c6db133ff63d426b8ab6ad6aed8f0e33c5;hp=d4c2d7faf0405bc7180a89aeb87f58cb9e898cc4;hpb=6d7ab37f37b09174ec61fee301aed6057ef86605;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index d4c2d7f..97e11eb 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,15 +1,19 @@
 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.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;
@@ -21,19 +25,21 @@ public abstract class StructureFile extends AlignFile
 
   private String id;
 
+  private String 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)
    */
@@ -51,10 +57,29 @@ public abstract class StructureFile extends AlignFile
     super(fp);
   }
 
-  public StructureFile(boolean parseImmediately, String inFile, String type)
+  public void addSettings(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
+  {
+    this.visibleChainAnnotation = addAlignmentAnnotations;
+    this.predictSecondaryStructure = predictSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
+  }
+
+  public void xferSettings()
+  {
+    this.visibleChainAnnotation = StructureImportSettings
+            .isVisibleChainAnnotation();
+    this.predictSecondaryStructure = StructureImportSettings
+            .isPredictSecondaryStructure();
+    this.externalSecondaryStructure = StructureImportSettings
+            .isExternalSecondaryStructure();
+
+  }
+
+  public StructureFile(boolean parseImmediately, String dataObject, String type)
           throws IOException
   {
-    super(parseImmediately, inFile, type);
+    super(parseImmediately, dataObject, type);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -66,13 +91,14 @@ public abstract class StructureFile extends AlignFile
   {
   }
 
+  @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)
     {
@@ -92,15 +118,11 @@ public abstract class StructureFile extends AlignFile
     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)
@@ -114,6 +136,7 @@ public abstract class StructureFile extends AlignFile
     return chainseq;
   }
 
+  @SuppressWarnings({ "unchecked", "rawtypes" })
   protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
           throws Exception
   {
@@ -158,9 +181,9 @@ public abstract class StructureFile extends AlignFile
     }
   }
 
+  @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,
@@ -188,11 +211,100 @@ public abstract class StructureFile extends AlignFile
     }
   }
 
+  /**
+   * 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(), type) };
+
+        StructureImportSettings.setShowSeqFeatures(false);
+        StructureImportSettings.setVisibleChainAnnotation(false);
+        StructureImportSettings
+                .setPredictSecondaryStructure(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;
       }
@@ -288,4 +400,29 @@ public abstract class StructureFile extends AlignFile
   {
     this.chains = chains;
   }
+
+  public String getDbRefType()
+  {
+    return dbRefType;
+  }
+
+  public void setDbRefType(String 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();
+  }
 }