Merge remote-tracking branch 'origin/releases/Release_2_10_3_Branch'

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 96b0757..15d1378 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -77,11 +77,6 @@ public class Sequence extends ASequence implements SequenceI
    */
   Vector<AlignmentAnnotation> annotation;
 
-  /**
-   * The index of the sequence in a MSA
-   */
-  int index = -1;
-
   private SequenceFeaturesI sequenceFeatureStore;
 
   /*
@@ -1165,7 +1160,7 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public void deleteChars(int i, int j)
+  public void deleteChars(final int i, final int j)
   {
     int newstart = start, newend = end;
     if (i >= sequence.length || i < 0)
@@ -1177,62 +1172,75 @@ public class Sequence extends ASequence implements SequenceI
     boolean createNewDs = false;
     // TODO: take a (second look) at the dataset creation validation method for
     // the very large sequence case
-    int eindex = -1, sindex = -1;
-    boolean ecalc = false, scalc = false;
+    int startIndex = findIndex(start) - 1;
+    int endIndex = findIndex(end) - 1;
+    int startDeleteColumn = -1; // for dataset sequence deletions
+    int deleteCount = 0;
+
     for (int s = i; s < j; s++)
     {
-      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      if (Comparison.isGap(sequence[s]))
+      {
+        continue;
+      }
+      deleteCount++;
+      if (startDeleteColumn == -1)
+      {
+        startDeleteColumn = findPosition(s) - start;
+      }
+      if (createNewDs)
+      {
+        newend--;
+      }
+      else
       {
-        if (createNewDs)
+        if (startIndex == s)
         {
-          newend--;
+          /*
+           * deleting characters from start of sequence; new start is the
+           * sequence position of the next column (position to the right
+           * if the column position is gapped)
+           */
+          newstart = findPosition(j);
+          break;
         }
         else
         {
-          if (!scalc)
+          if (endIndex < j)
           {
-            sindex = findIndex(start) - 1;
-            scalc = true;
-          }
-          if (sindex == s)
-          {
-            // delete characters including start of sequence
-            newstart = findPosition(j);
-            break; // don't need to search for any more residue characters.
+            /*
+             * deleting characters at end of sequence; new end is the sequence
+             * position of the column before the deletion; subtract 1 if this is
+             * gapped since findPosition returns the next sequence position
+             */
+            newend = findPosition(i - 1);
+            if (Comparison.isGap(sequence[i - 1]))
+            {
+              newend--;
+            }
+            break;
           }
           else
           {
-            // delete characters after start.
-            if (!ecalc)
-            {
-              eindex = findIndex(end) - 1;
-              ecalc = true;
-            }
-            if (eindex < j)
-            {
-              // delete characters at end of sequence
-              newend = findPosition(i - 1);
-              break; // don't need to search for any more residue characters.
-            }
-            else
-            {
-              createNewDs = true;
-              newend--; // decrease end position by one for the deleted residue
-              // and search further
-            }
+            createNewDs = true;
+            newend--;
           }
         }
       }
     }
-    // deletion occured in the middle of the sequence
+
     if (createNewDs && this.datasetSequence != null)
     {
-      // construct a new sequence
+      /*
+       * if deletion occured in the middle of the sequence,
+       * construct a new dataset sequence and delete the residues
+       * that were deleted from the aligned sequence
+       */
       Sequence ds = new Sequence(datasetSequence);
+      ds.deleteChars(startDeleteColumn, startDeleteColumn + deleteCount);
+      datasetSequence = ds;
       // TODO: remove any non-inheritable properties ?
       // TODO: create a sequence mapping (since there is a relation here ?)
-      ds.deleteChars(i, j);
-      datasetSequence = ds;
     }
     start = newstart;
     end = newend;
@@ -1682,30 +1690,6 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-  /**
-   * @return The index (zero-based) on this sequence in the MSA. It returns
-   *         {@code -1} if this information is not available.
-   */
-  @Override
-  public int getIndex()
-  {
-    return index;
-  }
-
-  /**
-   * Defines the position of this sequence in the MSA. Use the value {@code -1}
-   * if this information is undefined.
-   * 
-   * @param The
-   *          position for this sequence. This value is zero-based (zero for
-   *          this first sequence)
-   */
-  @Override
-  public void setIndex(int value)
-  {
-    index = value;
-  }
-
   @Override
   public void setRNA(RNA r)
   {