Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 4e07a08..fe95f4b 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -20,13 +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;
 import jalview.commands.CommandI;
@@ -46,6 +39,13 @@ 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.
  * 
@@ -546,7 +546,8 @@ public final class MappingUtils
     while (regions.hasNext())
     {
       mapHiddenColumns(regions.next(), codonFrames, newHidden,
-              fromSequences, toSequences, fromGapChar);
+              fromSequences,
+              toSequences, fromGapChar);
     }
     return; // mappedColumns;
   }
@@ -964,7 +965,7 @@ public final class MappingUtils
 
     int min = Math.min(range[0], range[1]);
     int max = Math.max(range[0], range[1]);
-
+  
     return (min <= queryRange[0] && max >= queryRange[0]
             && min <= queryRange[1] && max >= queryRange[1]);
   }
@@ -979,7 +980,8 @@ public final class MappingUtils
    *          a list of (single) [start, end] ranges
    * @return
    */
-  public static void removeEndPositions(int positions, List<int[]> ranges)
+  public static void removeEndPositions(int positions,
+          List<int[]> ranges)
   {
     int toRemove = positions;
     Iterator<int[]> it = new ReverseListIterator<>(ranges);
@@ -991,8 +993,8 @@ public final class MappingUtils
         /*
          * not coded for [start1, end1, start2, end2, ...]
          */
-        System.err.println(
-                "MappingUtils.removeEndPositions doesn't handle multiple  ranges");
+        System.err
+                .println("MappingUtils.removeEndPositions doesn't handle multiple  ranges");
         return;
       }
 
@@ -1002,8 +1004,8 @@ public final class MappingUtils
         /*
          * not coded for a reverse strand range (end < start)
          */
-        System.err.println(
-                "MappingUtils.removeEndPositions doesn't handle reverse strand");
+        System.err
+                .println("MappingUtils.removeEndPositions doesn't handle reverse strand");
         return;
       }
       if (length > toRemove)
@@ -1018,6 +1020,60 @@ 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