X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=8b089a22da302a9fe21a84496fa5e63655ed0f86;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=65d81799c8e8b779a515e3ff16b5dc9e704b7de2;hpb=3ef44bef1f825d26977dedd1608469712a87fe15;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 65d8179..8b089a2 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,9 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
+
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.List;
@@ -27,9 +30,6 @@ import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
 
-import jalview.analysis.AlignSeq;
-import jalview.util.StringUtils;
-
 /**
  * 
  * Implements the SequenceI interface for a char[] based sequence object.
@@ -37,7 +37,7 @@ import jalview.util.StringUtils;
  * @author $author$
  * @version $Revision$
  */
-public class Sequence implements SequenceI
+public class Sequence extends ASequence implements SequenceI
 {
   SequenceI datasetSequence;
 
@@ -90,20 +90,30 @@ public class Sequence implements SequenceI
    */
   public Sequence(String name, String sequence, int start, int end)
   {
-    this.name = name;
-    this.sequence = sequence.toCharArray();
-    this.start = start;
-    this.end = end;
-    parseId();
-    checkValidRange();
+    initSeqAndName(name, sequence.toCharArray(), start, end);
   }
 
   public Sequence(String name, char[] sequence, int start, int end)
   {
-    this.name = name;
-    this.sequence = sequence;
-    this.start = start;
-    this.end = end;
+    initSeqAndName(name, sequence, start, end);
+  }
+
+  /**
+   * Stage 1 constructor - assign name, sequence, and set start and end fields.
+   * start and end are updated values from name2 if it ends with /start-end
+   * 
+   * @param name2
+   * @param sequence2
+   * @param start2
+   * @param end2
+   */
+  protected void initSeqAndName(String name2, char[] sequence2, int start2,
+          int end2)
+  {
+    this.name = name2;
+    this.sequence = sequence2;
+    this.start = start2;
+    this.end = end2;
     parseId();
     checkValidRange();
   }
@@ -121,7 +131,7 @@ public class Sequence implements SequenceI
               .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
       name = "";
     }
-    // Does sequence have the /start-end signiature?
+    // Does sequence have the /start-end signature?
     if (limitrx.search(name))
     {
       name = limitrx.left();
@@ -196,7 +206,15 @@ public class Sequence implements SequenceI
    */
   public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
   {
-    this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+    initSeqFrom(seq, alAnnotation);
+
+  }
+
+  protected void initSeqFrom(SequenceI seq,
+          AlignmentAnnotation[] alAnnotation)
+  {
+    initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
+            seq.getEnd());
     description = seq.getDescription();
     if (seq.getSequenceFeatures() != null)
     {
@@ -241,9 +259,9 @@ public class Sequence implements SequenceI
         }
       }
     }
-    if (seq.getPDBId() != null)
+    if (seq.getAllPDBEntries() != null)
     {
-      Vector ids = seq.getPDBId();
+      Vector ids = seq.getAllPDBEntries();
       Enumeration e = ids.elements();
       while (e.hasMoreElements())
       {
@@ -355,19 +373,32 @@ public class Sequence implements SequenceI
     {
       pdbIds = new Vector<PDBEntry>();
     }
-    if (!pdbIds.contains(entry))
+    if (pdbIds.contains(entry))
+    {
+      updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
+    }
+    else
     {
       pdbIds.addElement(entry);
     }
   }
 
+  private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+  {
+    if (newEntry.getFile() != null)
+    {
+      oldEntry.setFile(newEntry.getFile());
+    }
+  }
+
   /**
    * DOCUMENT ME!
    * 
    * @param id
    *          DOCUMENT ME!
    */
-  public void setPDBId(Vector id)
+  @Override
+  public void setPDBId(Vector<PDBEntry> id)
   {
     pdbIds = id;
   }
@@ -377,7 +408,8 @@ public class Sequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getPDBId()
+  @Override
+  public Vector<PDBEntry> getAllPDBEntries()
   {
     return pdbIds;
   }
@@ -715,8 +747,7 @@ public class Sequence implements SequenceI
       {
         if (lastj != -1)
         {
-          map.add(new int[]
-          { lastj, j - 1 });
+          map.add(new int[] { lastj, j - 1 });
           lastj = -1;
         }
       }
@@ -724,8 +755,7 @@ public class Sequence implements SequenceI
     }
     if (lastj != -1)
     {
-      map.add(new int[]
-      { lastj, j - 1 });
+      map.add(new int[] { lastj, j - 1 });
       lastj = -1;
     }
     return map;
@@ -735,7 +765,7 @@ public class Sequence implements SequenceI
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
-    if (i >= sequence.length)
+    if (i >= sequence.length || i < 0)
     {
       return;
     }
@@ -923,7 +953,6 @@ public class Sequence implements SequenceI
             .toArray(new AlignmentAnnotation[annotation.size()]);
   }
 
-
   @Override
   public boolean hasAnnotation(AlignmentAnnotation ann)
   {
@@ -935,7 +964,7 @@ public class Sequence implements SequenceI
   {
     if (this.annotation == null)
     {
-      this.annotation = new Vector();
+      this.annotation = new Vector<AlignmentAnnotation>();
     }
     if (!this.annotation.contains(annotation))
     {
@@ -1024,7 +1053,7 @@ public class Sequence implements SequenceI
       // move database references onto dataset sequence
       datasetSequence.setDBRef(getDBRef());
       setDBRef(null);
-      datasetSequence.setPDBId(getPDBId());
+      datasetSequence.setPDBId(getAllPDBEntries());
       setPDBId(null);
       datasetSequence.updatePDBIds();
       if (annotation != null)
@@ -1175,8 +1204,7 @@ public class Sequence implements SequenceI
       for (int si = 0; si < sfs.length; si++)
       {
         SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
-                : new SequenceFeature[]
-                { new SequenceFeature(sfs[si]) };
+                : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
         if (sf != null && sf.length > 0)
         {
           for (int sfi = 0; sfi < sf.length; sfi++)
@@ -1188,9 +1216,9 @@ public class Sequence implements SequenceI
     }
 
     // transfer PDB entries
-    if (entry.getPDBId() != null)
+    if (entry.getAllPDBEntries() != null)
     {
-      Enumeration e = entry.getPDBId().elements();
+      Enumeration e = entry.getAllPDBEntries().elements();
       while (e.hasMoreElements())
       {
         PDBEntry pdb = (PDBEntry) e.nextElement();
@@ -1269,4 +1297,28 @@ public class Sequence implements SequenceI
     return result;
   }
 
+  public String toString()
+  {
+    return getDisplayId(false);
+  }
+
+  @Override
+  public PDBEntry getPDBEntry(String pdbIdStr)
+  {
+    if (getDatasetSequence() == null
+            || getDatasetSequence().getAllPDBEntries() == null)
+    {
+      return null;
+    }
+    List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+    for (PDBEntry entry : entries)
+    {
+      if (entry.getId().equalsIgnoreCase(pdbIdStr))
+      {
+        return entry;
+      }
+    }
+    return null;
+  }
+
 }