X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=6b623a1e2d43e31c55256097388ed7117b6f7728;hb=5022579ec6cc4eecfabd9df69e0fb039e3186a0a;hp=d4c2d7faf0405bc7180a89aeb87f58cb9e898cc4;hpb=6d7ab37f37b09174ec61fee301aed6057ef86605;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index d4c2d7f..6b623a1 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,39 +1,64 @@
+/*
+ * 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.
+ *  
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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.util.Hashtable;
+import java.lang.reflect.Constructor;
 import java.util.List;
 import java.util.Vector;
 
-import MCview.PDBChain;
+import mc_view.PDBChain;
 
 public abstract class StructureFile extends AlignFile
 {
-
   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)
    */
@@ -41,9 +66,12 @@ public abstract class StructureFile extends AlignFile
 
   private Vector<PDBChain> chains;
 
-  public StructureFile(String inFile, String type) throws IOException
+  private boolean pdbIdAvailable;
+
+  public StructureFile(Object inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public StructureFile(FileParse fp) throws IOException
@@ -51,10 +79,29 @@ public abstract class StructureFile extends AlignFile
     super(fp);
   }
 
-  public StructureFile(boolean parseImmediately, String inFile, String type)
-          throws IOException
+  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
+            .isProcessSecondaryStructure();
+    this.externalSecondaryStructure = StructureImportSettings
+            .isExternalSecondaryStructure();
+
+  }
+
+  public StructureFile(boolean parseImmediately, Object dataObject,
+          DataSourceType sourceType) throws IOException
   {
-    super(parseImmediately, inFile, type);
+    super(parseImmediately, dataObject, sourceType);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -72,11 +119,11 @@ public abstract class StructureFile extends AlignFile
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
-    entry.setType(PDBEntry.Type.PDB);
-    entry.setProperty(new Hashtable());
+    entry.setFakedPDBId(!isPPDBIdAvailable());
+    entry.setType(getStructureFileType());
     if (chain.id != null)
     {
-      entry.setChainCode(String.valueOf(chain.id));
+      entry.setChainCode(chain.id);
     }
     if (inFile != null)
     {
@@ -90,17 +137,13 @@ public abstract class StructureFile extends AlignFile
     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);
-
+    // TODO: specify version for 'PDB' database ref if it is read from a file.
+    // TODO: decide if jalview.io should be creating primary refs!
+    sourceDBRef.setVersion("");
+    pdbSequence.addPDBId(entry);
+    pdbSequence.addDBRef(sourceDBRef);
+    SequenceI chainseq = pdbSequence;
     seqs.addElement(chainseq);
-
     AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
 
     if (chainannot != null && visibleChainAnnotation)
@@ -114,6 +157,27 @@ public abstract class StructureFile extends AlignFile
     return chainseq;
   }
 
+  /**
+   * filetype of structure file - default is PDB
+   */
+  String structureFileType = PDBEntry.Type.PDB.toString();
+
+  protected void setStructureFileType(String structureFileType)
+  {
+    this.structureFileType = structureFileType;
+  }
+
+  /**
+   * filetype of last file processed
+   * 
+   * @return
+   */
+  public String getStructureFileType()
+  {
+    return structureFileType;
+  }
+
+  @SuppressWarnings({ "unchecked", "rawtypes" })
   protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
           throws Exception
   {
@@ -128,11 +192,13 @@ public abstract class StructureFile extends AlignFile
       {
         // 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) }));
+        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(), dataSourceType) }));
         for (SequenceI sq : al.getSequences())
         {
           if (sq.getDatasetSequence() != null)
@@ -158,8 +224,8 @@ public abstract class StructureFile extends AlignFile
     }
   }
 
-  protected void replaceAndUpdateChains(List<SequenceI> prot,
-          AlignmentI al,
+  @SuppressWarnings("unchecked")
+  protected void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
           String pep, boolean b)
   {
     List<List<? extends Object>> replaced = AlignSeq
@@ -188,16 +254,112 @@ public abstract class StructureFile extends AlignFile
     }
   }
 
-  public PDBChain findChain(String id) throws Exception
+  /**
+   * 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[]
+                { FileParse.class });
+        final Object[] args = new Object[] {
+            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);
+  }
+
+  /**
+   * Answers the first PDBChain found matching the given id, or null if none is
+   * found
+   * 
+   * @param id
+   * @return
+   */
+  public PDBChain findChain(String id)
   {
     for (PDBChain chain : getChains())
     {
-      if (chain.id.equalsIgnoreCase(id))
+      if (chain.id.equals(id))
       {
         return chain;
       }
     }
-    throw new Exception("PDB chain not Found!");
+    return null;
   }
 
   public void makeResidueList()
@@ -243,8 +405,10 @@ public abstract class StructureFile extends AlignFile
 
   public static boolean isRNA(SequenceI seq)
   {
-    for (char c : seq.getSequence())
+    int length = seq.getLength();
+    for (int i = 0; i < length; i++)
     {
+      char c = seq.getCharAt(i);
       if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
       {
         return false;
@@ -257,7 +421,8 @@ public abstract class StructureFile extends AlignFile
    * make a friendly ID string.
    * 
    * @param dataName
-   * @return truncated dataName to after last '/'
+   * @return truncated dataName to after last '/' and pruned .extension if
+   *         present
    */
   protected String safeName(String dataName)
   {
@@ -266,6 +431,10 @@ public abstract class StructureFile extends AlignFile
     {
       dataName = dataName.substring(p + 1);
     }
+    if (dataName.indexOf(".") > -1)
+    {
+      dataName = dataName.substring(0, dataName.lastIndexOf("."));
+    }
     return dataName;
   }
 
@@ -288,4 +457,49 @@ public abstract class StructureFile extends AlignFile
   {
     this.chains = chains;
   }
+
+  public Type getDbRefType()
+  {
+    return dbRefType;
+  }
+
+  public void setDbRefType(String dbRefType)
+  {
+    this.dbRefType = Type.getType(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();
+  }
+
+  /**
+   * Answers true if the structure file has a PDBId
+   * 
+   * @return
+   */
+  public boolean isPPDBIdAvailable()
+  {
+    return pdbIdAvailable;
+  }
+
+  public void setPDBIdAvailable(boolean pdbIdAvailable)
+  {
+    this.pdbIdAvailable = pdbIdAvailable;
+  }
 }