X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=f5558559b37e5f6dbeb3dac62d4e06ed490d3681;hb=b83eff8c672cede0305da3c76823dab414749dde;hp=eaeed9cdcf980e58e96c793653969fb17a04f4df;hpb=d943fcd0dc04fd4974344eddd13902c89fb595b2;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index eaeed9c..f555855 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -34,6 +34,7 @@ import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.Enumeration;
+import java.util.Iterator;
 import java.util.List;
 import java.util.ListIterator;
 import java.util.Vector;
@@ -405,7 +406,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (pdbIds == null)
     {
-      pdbIds = new Vector<PDBEntry>();
+      pdbIds = new Vector<>();
       pdbIds.add(entry);
       return true;
     }
@@ -441,7 +442,7 @@ 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;
   }
 
   /**
@@ -654,10 +655,10 @@ 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)
@@ -665,10 +666,67 @@ 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()
@@ -755,7 +813,7 @@ 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))
     {
@@ -780,10 +838,15 @@ 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;
@@ -791,7 +854,14 @@ 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;
   }
@@ -1068,6 +1138,27 @@ public class Sequence extends ASequence implements SequenceI
     return map;
   }
 
+  /**
+   * Build a bitset corresponding to sequence gaps
+   * 
+   * @return a BitSet where set values correspond to gaps in the sequence
+   */
+  @Override
+  public BitSet gapBitset()
+  {
+    BitSet gaps = new BitSet(sequence.length);
+    int j = 0;
+    while (j < sequence.length)
+    {
+      if (jalview.util.Comparison.isGap(sequence[j]))
+      {
+        gaps.set(j);
+      }
+      j++;
+    }
+    return gaps;
+  }
+
   @Override
   public int[] findPositionMap()
   {
@@ -1091,7 +1182,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public List<int[]> getInsertions()
   {
-    ArrayList<int[]> map = new ArrayList<int[]>();
+    ArrayList<int[]> map = new ArrayList<>();
     int lastj = -1, j = 0;
     int pos = start;
     int seqlen = sequence.length;
@@ -1403,7 +1494,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (this.annotation == null)
     {
-      this.annotation = new Vector<AlignmentAnnotation>();
+      this.annotation = new Vector<>();
     }
     if (!this.annotation.contains(annotation))
     {
@@ -1570,7 +1661,7 @@ public class Sequence extends ASequence implements SequenceI
       return null;
     }
 
-    Vector<AlignmentAnnotation> subset = new Vector<AlignmentAnnotation>();
+    Vector<AlignmentAnnotation> subset = new Vector<>();
     Enumeration<AlignmentAnnotation> e = annotation.elements();
     while (e.hasMoreElements())
     {
@@ -1704,7 +1795,7 @@ public class Sequence extends ASequence implements SequenceI
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)
   {
-    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
@@ -1760,7 +1851,7 @@ public class Sequence extends ASequence implements SequenceI
     }
     synchronized (dbrefs)
     {
-      List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+      List<DBRefEntry> primaries = new ArrayList<>();
       DBRefEntry[] tmp = new DBRefEntry[1];
       for (DBRefEntry ref : dbrefs)
       {
@@ -1911,4 +2002,73 @@ public class Sequence extends ASequence implements SequenceI
 
     return count;
   }
+
+  @Override
+  public String getSequenceStringFromIterator(Iterator<int[]> it)
+  {
+    StringBuilder newSequence = new StringBuilder();
+    while (it.hasNext())
+    {
+      int[] block = it.next();
+      if (it.hasNext())
+      {
+        newSequence.append(getSequence(block[0], block[1] + 1));
+      }
+      else
+      {
+        newSequence.append(getSequence(block[0], block[1]));
+      }
+    }
+
+    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;
+  }
 }