Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / util / MappingUtils.java

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 25cb810..d60d4eb 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -20,12 +20,6 @@
  */
 package jalview.util;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewportI;
@@ -49,6 +43,12 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
 /**
  * Helper methods for manipulations involving sequence mappings.
  * 
@@ -364,6 +364,7 @@ public final class MappingUtils
        */
       int startResiduePos = selected.findPosition(firstUngappedPos);
       int endResiduePos = selected.findPosition(lastUngappedPos);
+
       for (SequenceI seq : mapTo.getAlignment().getSequences())
       {
         int mappedStartResidue = 0;
@@ -530,7 +531,7 @@ public final class MappingUtils
 
     if (colsel == null)
     {
-      return;
+      return; // mappedColumns;
     }
 
     char fromGapChar = mapFrom.getAlignment().getGapCharacter();
@@ -552,9 +553,10 @@ public final class MappingUtils
     while (regions.hasNext())
     {
       mapHiddenColumns(regions.next(), codonFrames, newHidden,
-              fromSequences, toSequences, fromGapChar);
+              fromSequences,
+              toSequences, fromGapChar);
     }
-    return;
+    return; // mappedColumns;
   }
 
   /**
@@ -1026,6 +1028,60 @@ public final class MappingUtils
       }
     }
   }
+  /**
+   * Adds the given range to a list of ranges. If the new range just extends
+   * existing ranges, the current endpoint is updated instead.
+   * 
+   * @param range
+   * @param addTo
+   */
+  public static void addRange(int[] range, List<int[]> addTo)
+  {
+    /*
+     * list is empty - add to it!
+     */
+    if (addTo.size() == 0)
+    {
+      addTo.add(range);
+      return;
+    }
+  
+    int[] last = addTo.get(addTo.size() - 1);
+    boolean lastForward = last[1] >= last[0];
+    boolean newForward = range[1] >= range[0];
+  
+    /*
+     * contiguous range in the same direction - just update endpoint
+     */
+    if (lastForward == newForward && last[1] == range[0])
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * next range starts at +1 in forward sense - update endpoint
+     */
+    if (lastForward && newForward && range[0] == last[1] + 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * next range starts at -1 in reverse sense - update endpoint
+     */
+    if (!lastForward && !newForward && range[0] == last[1] - 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * just add the new range
+     */
+    addTo.add(range);
+  }
 
   /**
    * Converts a list of {@code start-end} ranges to a single array of