JAL-2989 support value display names for Option or Parameters combo boxes

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

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 3ce0bb3..60054f1 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -77,8 +77,8 @@ public class MapList
    */
   public MapList()
   {
-    fromShifts = new ArrayList<int[]>();
-    toShifts = new ArrayList<int[]>();
+    fromShifts = new ArrayList<>();
+    toShifts = new ArrayList<>();
   }
 
   /**
@@ -116,8 +116,17 @@ public class MapList
   {
     int hashCode = 31 * fromRatio;
     hashCode = 31 * hashCode + toRatio;
-    hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
-    hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+    for (int[] shift : fromShifts)
+    {
+      hashCode = 31 * hashCode + shift[0];
+      hashCode = 31 * hashCode + shift[1];
+    }
+    for (int[] shift : toShifts)
+    {
+      hashCode = 31 * hashCode + shift[0];
+      hashCode = 31 * hashCode + shift[1];
+    }
+
     return hashCode;
   }
 
@@ -347,7 +356,7 @@ public class MapList
     }
 
     boolean changed = false;
-    List<int[]> merged = new ArrayList<int[]>();
+    List<int[]> merged = new ArrayList<>();
     int[] lastRange = ranges.get(0);
     int lastDirection = lastRange[1] >= lastRange[0] ? 1 : -1;
     lastRange = new int[] { lastRange[0], lastRange[1] };
@@ -803,7 +812,7 @@ public class MapList
     {
       return null;
     }
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     if (fs <= fe)
     {
       intv = fs;
@@ -1021,81 +1030,51 @@ public class MapList
 
     for (int[] range : map.getFromRanges())
     {
-      addRange(range, fromShifts);
+      MappingUtils.addRange(range, fromShifts);
     }
     for (int[] range : map.getToRanges())
     {
-      addRange(range, toShifts);
+      MappingUtils.addRange(range, toShifts);
     }
   }
 
   /**
-   * Adds the given range to a list of ranges. If the new range just extends
-   * existing ranges, the current endpoint is updated instead.
+   * Returns true if mapping is from forward strand, false if from reverse
+   * strand. Result is just based on the first 'from' range that is not a single
+   * position. Default is true unless proven to be false. Behaviour is not well
+   * defined if the mapping has a mixture of forward and reverse ranges.
    * 
-   * @param range
-   * @param addTo
+   * @return
    */
-  static void addRange(int[] range, List<int[]> addTo)
+  public boolean isFromForwardStrand()
   {
-    /*
-     * 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;
-    }
+    return isForwardStrand(getFromRanges());
+  }
 
-    /*
-     * just add the new range
-     */
-    addTo.add(range);
+  /**
+   * Returns true if mapping is to forward strand, false if to reverse strand.
+   * Result is just based on the first 'to' range that is not a single position.
+   * Default is true unless proven to be false. Behaviour is not well defined if
+   * the mapping has a mixture of forward and reverse ranges.
+   * 
+   * @return
+   */
+  public boolean isToForwardStrand()
+  {
+    return isForwardStrand(getToRanges());
   }
 
   /**
-   * Returns true if mapping is from forward strand, false if from reverse
-   * strand. Result is just based on the first 'from' range that is not a single
-   * position. Default is true unless proven to be false. Behaviour is not well
-   * defined if the mapping has a mixture of forward and reverse ranges.
+   * A helper method that returns true unless at least one range has start > end.
+   * Behaviour is undefined for a mixture of forward and reverse ranges.
    * 
+   * @param ranges
    * @return
    */
-  public boolean isFromForwardStrand()
+  private boolean isForwardStrand(List<int[]> ranges)
   {
     boolean forwardStrand = true;
-    for (int[] range : getFromRanges())
+    for (int[] range : ranges)
     {
       if (range[1] > range[0])
       {