Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 6bffcae..dc0fe88 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -35,6 +35,7 @@ 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;
@@ -1142,6 +1143,27 @@ 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()
   {
@@ -2060,4 +2082,73 @@ 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;
+  }
 }