JAL-2541 revised cut with features (work in progress)

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 2f1da7f..b758d51 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -44,10 +44,7 @@ import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
  * 
- * Implements the SequenceI interface for a char[] based sequence object.
- * 
- * @author $author$
- * @version $Revision$
+ * Implements the SequenceI interface for a char[] based sequence object
  */
 public class Sequence extends ASequence implements SequenceI
 {
@@ -1901,4 +1898,75 @@ public class Sequence extends ASequence implements SequenceI
 
     return count;
   }
+
+  @Override
+  public List<SequenceFeature[]> adjustFeatures(int fromColumn, int toColumn)
+  {
+    List<SequenceFeature[]> amended = new ArrayList<>();
+
+    if (toColumn < fromColumn)
+    {
+      return amended;
+    }
+
+    synchronized (sequenceFeatureStore)
+    {
+      /*
+       * get features that overlap or span the cut region
+       */
+      List<SequenceFeature> overlaps = findFeatures(fromColumn, toColumn);
+      int cutWidth = toColumn - fromColumn + 1;
+
+      /*
+       * get features that strictly follow the cut region,
+       *  and shift them left by the width of the cut
+       */
+      List<SequenceFeature> follow = findFeatures(toColumn + 1,
+              Integer.MAX_VALUE);
+      follow.removeAll(overlaps);
+      for (SequenceFeature sf : follow)
+      {
+        SequenceFeature copy = new SequenceFeature(sf, sf.getBegin()
+                - cutWidth, sf.getEnd() - cutWidth, sf.getFeatureGroup(),
+                sf.getScore());
+        deleteFeature(sf);
+        addSequenceFeature(copy);
+      }
+
+      /*
+       * adjust start-end of overlapping features, and delete if enclosed by
+       * the cut, or a partially overlapping contact feature
+       */
+      for (SequenceFeature sf : overlaps)
+      {
+        // TODO recode to compute newBegin, newEnd, isDelete
+        // then perform the action
+        int sfBegin = sf.getBegin();
+        int sfEnd = sf.getEnd();
+        int startCol = findIndex(sfBegin);
+        int endCol = findIndex(sfEnd);
+        if (startCol >= fromColumn && endCol <= toColumn)
+        {
+          // within cut region - delete feature
+          deleteFeature(sf);
+          amended.add(new SequenceFeature[] { sf, null });
+          continue;
+        }
+        if (startCol < fromColumn && endCol > toColumn)
+        {
+          // feature spans cut region - shift end left
+          SequenceFeature copy = new SequenceFeature(sf, sf.getBegin(),
+                  sf.getEnd() - cutWidth, sf.getFeatureGroup(),
+                  sf.getScore());
+          deleteFeature(sf);
+          addSequenceFeature(copy);
+          amended.add(new SequenceFeature[] { sf, copy });
+          continue;
+        }
+        // todo partial overlap - delete if contact feature
+      }
+    }
+
+    return amended;
+  }
 }