JAL-2754 Sequence.findFeatures(fromCol, toCol)

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index dd7c24a..0055d0e 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -34,6 +34,7 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
+import java.util.ListIterator;
 import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
@@ -700,68 +701,6 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * {@inheritDoc}
-   */
-  @Override
-  public Range findPositions(int fromCol, int toCol)
-  {
-    /*
-     * count residues before fromCol
-     */
-    int j = 0;
-    int count = 0;
-    int seqlen = sequence.length;
-    while (j < fromCol && j < seqlen)
-    {
-      if (!Comparison.isGap(sequence[j]))
-      {
-        count++;
-      }
-      j++;
-    }
-
-    /*
-     * find first and last residues between fromCol and toCol
-     */
-    int firstPos = 0;
-    int lastPos = 0;
-    int firstPosCol = 0;
-    boolean foundFirst = false;
-    
-    while (j <= toCol && j < seqlen)
-    {
-      if (!Comparison.isGap(sequence[j]))
-      {
-        count++;
-        if (!foundFirst)
-        {
-          firstPos = count;
-          firstPosCol = j;
-          foundFirst = true;
-        }
-        lastPos = count;
-      }
-      j++;
-    }
-
-    if (firstPos == 0)
-    {
-      /*
-       * no residues in this range
-       */
-      return null;
-    }
-
-    /*
-     * adjust for sequence start coordinate
-     */
-    firstPos += start - 1;
-    lastPos += start - 1;
-
-    return new Range(firstPos, lastPos);
-  }
-
-  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -1505,13 +1444,55 @@ public class Sequence extends ASequence implements SequenceI
    * {@inheritDoc}
    */
   @Override
-  public List<SequenceFeature> findFeatures(int from, int to,
+  public List<SequenceFeature> findFeatures(int fromColumn, int toColumn,
           String... types)
   {
+    int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0
+    int endPos = findPosition(toColumn - 1);
+
+    List<SequenceFeature> result = new ArrayList<>();
     if (datasetSequence != null)
     {
-      return datasetSequence.findFeatures(from, to, types);
+      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
+              types);
     }
-    return sequenceFeatureStore.findFeatures(from, to, types);
+    else
+    {
+      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
+    }
+
+    /*
+     * if the start or end column is gapped, startPos or endPos may be to the 
+     * left or right, and we may have included adjacent or enclosing features;
+     * remove any that are not enclosing, non-contact features
+     */
+    if (endPos > this.end || Comparison.isGap(sequence[fromColumn - 1])
+            || Comparison.isGap(sequence[toColumn - 1]))
+    {
+      ListIterator<SequenceFeature> it = result.listIterator();
+      while (it.hasNext())
+      {
+        SequenceFeature sf = it.next();
+        int featureStartColumn = findIndex(sf.getBegin());
+        int featureEndColumn = findIndex(sf.getEnd());
+        boolean noOverlap = featureStartColumn > toColumn
+                        || featureEndColumn < fromColumn;
+
+        /*
+         * reject an 'enclosing' feature if it is actually a contact feature
+         */
+        if (sf.isContactFeature() && featureStartColumn < fromColumn
+                && featureEndColumn > toColumn)
+        {
+          noOverlap = true;
+        }
+        if (noOverlap)
+        {
+          it.remove();
+        }
+      }
+    }
+
+    return result;
   }
 }