Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 96747e4..2f1da7f 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -155,8 +155,8 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (name == null)
     {
-      System.err
-              .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+      System.err.println(
+              "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
       name = "";
     }
     // Does sequence have the /start-end signature?
@@ -723,7 +723,10 @@ public class Sequence extends ASequence implements SequenceI
    */
   protected void updateCursor(int residuePos, int column, int startColumn)
   {
-    int endColumn = cursor == null ? 0 : cursor.lastColumnPosition;
+    /*
+     * preserve end residue column provided cursor was valid
+     */
+    int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
     if (residuePos == this.end)
     {
       endColumn = column;
@@ -981,6 +984,53 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
+   * {@inheritDoc}
+   */
+  @Override
+  public Range findPositions(int fromColumn, int toColumn)
+  {
+    if (toColumn < fromColumn || fromColumn < 1)
+    {
+      return null;
+    }
+
+    /*
+     * find the first non-gapped position, if any
+     */
+    int firstPosition = 0;
+    int col = fromColumn - 1;
+    int length = sequence.length;
+    while (col < length && col < toColumn)
+    {
+      if (!Comparison.isGap(sequence[col]))
+      {
+        firstPosition = findPosition(col++);
+        break;
+      }
+      col++;
+    }
+
+    if (firstPosition == 0)
+    {
+      return null;
+    }
+
+    /*
+     * find the last non-gapped position
+     */
+    int lastPosition = firstPosition;
+    while (col < length && col < toColumn)
+    {
+      if (!Comparison.isGap(sequence[col++]))
+      {
+        lastPosition++;
+      }
+    }
+
+    return new Range(firstPosition, lastPosition);
+  }
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -1314,8 +1364,9 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public AlignmentAnnotation[] getAnnotation()
   {
-    return annotation == null ? null : annotation
-            .toArray(new AlignmentAnnotation[annotation.size()]);
+    return annotation == null ? null
+            : annotation
+                    .toArray(new AlignmentAnnotation[annotation.size()]);
   }
 
   @Override
@@ -1427,8 +1478,9 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (datasetSequence == null)
     {
-      Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, getSequenceAsString()),
+      Sequence dsseq = new Sequence(getName(),
+              AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                      getSequenceAsString()),
               getStart(), getEnd());
 
       datasetSequence = dsseq;
@@ -1570,7 +1622,7 @@ public class Sequence extends ASequence implements SequenceI
       List<SequenceFeature> sfs = entry.getSequenceFeatures();
       for (SequenceFeature feature : sfs)
       {
-        SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+       SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
                 : new SequenceFeature[] { new SequenceFeature(feature) };
         if (sf != null)
         {
@@ -1727,8 +1779,8 @@ public class Sequence extends ASequence implements SequenceI
           }
         }
         // whilst it looks like it is a primary ref, we also sanity check type
-        if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
-                DBRefUtils.getCanonicalName(ref.getSource())))
+        if (DBRefUtils.getCanonicalName(DBRefSource.PDB)
+                .equals(DBRefUtils.getCanonicalName(ref.getSource())))
         {
           // PDB dbrefs imply there should be a PDBEntry associated
           // TODO: tighten PDB dbrefs
@@ -1764,52 +1816,45 @@ public class Sequence extends ASequence implements SequenceI
           String... types)
   {
     int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0
-    int endPos = findPosition(toColumn - 1);
-    // to trace / debug behaviour:
-    // System.out
-    // .println(String
-    // .format("%s.findFeatures columns [%d-%d] positions [%d-%d] leaves cursor %s",
-    // getName(), fromColumn, toColumn, startPos,
-    // endPos, cursor));
-    List<SequenceFeature> result = new ArrayList<>();
-    if (datasetSequence != null)
-    {
-      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
-              types);
-    }
-    else
-    {
-      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
-    }
+    int endPos = fromColumn == toColumn ? startPos
+            : findPosition(toColumn - 1);
+
+    List<SequenceFeature> result = getFeatures().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;
+     * if end column is gapped, endPos may be to the 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]))
+    if (endPos > this.end || 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)
+        int sfBegin = sf.getBegin();
+        int sfEnd = sf.getEnd();
+        int featureStartColumn = findIndex(sfBegin);
+        if (featureStartColumn > toColumn)
         {
-          noOverlap = true;
+          it.remove();
         }
-        if (noOverlap)
+        else if (featureStartColumn < fromColumn)
         {
-          it.remove();
+          int featureEndColumn = sfEnd == sfBegin ? featureStartColumn
+                  : findIndex(sfEnd);
+          if (featureEndColumn < fromColumn)
+          {
+            it.remove();
+          }
+          else if (featureEndColumn > toColumn && sf.isContactFeature())
+          {
+            /*
+             * remove an enclosing feature if it is a contact feature
+             */
+            it.remove();
+          }
         }
       }
     }