X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=37e327889a68feab439f4eb97c9016cec0a41576;hb=5143fe21d91fa16c40be42cc0923be0d6f2f6536;hp=895b2307a2281bb23ab23b1b32022bb091ca269f;hpb=0e5e2bec7c3518eab6df87070b23164b135af828;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 895b230..37e3278 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -445,7 +445,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public Vector<PDBEntry> getAllPDBEntries()
   {
-    return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
+    return pdbIds == null ? new Vector<>() : pdbIds;
   }
 
   /**
@@ -658,10 +658,10 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Sets the sequence description, and also parses out any special formats of
+   * interest
    * 
    * @param desc
-   *          DOCUMENT ME!
    */
   @Override
   public void setDescription(String desc)
@@ -669,10 +669,67 @@ public class Sequence extends ASequence implements SequenceI
     this.description = desc;
   }
 
+  @Override
+  public void setGeneLoci(String speciesId, String assemblyId,
+          String chromosomeId, MapList map)
+  {
+    addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME
+            + ":" + chromosomeId, new Mapping(map)));
+  }
+
   /**
-   * DOCUMENT ME!
+   * Returns the gene loci mapping for the sequence (may be null)
    * 
-   * @return DOCUMENT ME!
+   * @return
+   */
+  @Override
+  public GeneLociI getGeneLoci()
+  {
+    DBRefEntry[] refs = getDBRefs();
+    if (refs != null)
+    {
+      for (final DBRefEntry ref : refs)
+      {
+        if (ref.isChromosome())
+        {
+          return new GeneLociI()
+          {
+            @Override
+            public String getSpeciesId()
+            {
+              return ref.getSource();
+            }
+
+            @Override
+            public String getAssemblyId()
+            {
+              return ref.getVersion();
+            }
+
+            @Override
+            public String getChromosomeId()
+            {
+              // strip off "chromosome:" prefix to chrId
+              return ref.getAccessionId().substring(
+                      DBRefEntry.CHROMOSOME.length() + 1);
+            }
+
+            @Override
+            public MapList getMap()
+            {
+              return ref.getMap().getMap();
+            }
+          };
+        }
+      }
+    }
+    return null;
+  }
+
+  /**
+   * Answers the description
+   * 
+   * @return
    */
   @Override
   public String getDescription()
@@ -758,7 +815,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param curs
    * @return
    */
-  protected int findIndex(int pos, SequenceCursor curs)
+  protected int findIndex(final int pos, SequenceCursor curs)
   {
     if (!isValidCursor(curs))
     {
@@ -784,10 +841,15 @@ public class Sequence extends ASequence implements SequenceI
     while (newPos != pos)
     {
       col += delta; // shift one column left or right
-      if (col < 0 || col == sequence.length)
+      if (col < 0)
       {
         break;
       }
+      if (col == sequence.length)
+      {
+        col--; // return last column if we failed to reach pos
+        break;
+      }
       if (!Comparison.isGap(sequence[col]))
       {
         newPos += delta;
@@ -795,7 +857,14 @@ public class Sequence extends ASequence implements SequenceI
     }
 
     col++; // convert back to base 1
-    updateCursor(pos, col, curs.firstColumnPosition);
+
+    /*
+     * only update cursor if we found the target position
+     */
+    if (newPos == pos)
+    {
+      updateCursor(pos, col, curs.firstColumnPosition);
+    }
 
     return col;
   }
@@ -1000,7 +1069,7 @@ public class Sequence extends ASequence implements SequenceI
    * {@inheritDoc}
    */
   @Override
-  public Range findPositions(int fromColumn, int toColumn)
+  public ContiguousI findPositions(int fromColumn, int toColumn)
   {
     if (toColumn < fromColumn || fromColumn < 1)
     {
@@ -1946,4 +2015,53 @@ public class Sequence extends ASequence implements SequenceI
 
     return newSequence.toString();
   }
+
+  @Override
+  public int firstResidueOutsideIterator(Iterator<int[]> regions)
+  {
+    int start = 0;
+
+    if (!regions.hasNext())
+    {
+      return findIndex(getStart()) - 1;
+    }
+
+    // Simply walk along the sequence whilst watching for region
+    // boundaries
+    int hideStart = getLength();
+    int hideEnd = -1;
+    boolean foundStart = false;
+
+    // step through the non-gapped positions of the sequence
+    for (int i = getStart(); i <= getEnd() && (!foundStart); i++)
+    {
+      // get alignment position of this residue in the sequence
+      int p = findIndex(i) - 1;
+
+      // update region start/end
+      while (hideEnd < p && regions.hasNext())
+      {
+        int[] region = regions.next();
+        hideStart = region[0];
+        hideEnd = region[1];
+      }
+      if (hideEnd < p)
+      {
+        hideStart = getLength();
+      }
+      // update boundary for sequence
+      if (p < hideStart)
+      {
+        start = p;
+        foundStart = true;
+      }
+    }
+
+    if (foundStart)
+    {
+      return start;
+    }
+    // otherwise, sequence was completely hidden
+    return 0;
+  }
 }