From 81c319be6445aadda7c29045b37d6ee2ad26aa3e Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 13 Jul 2007 14:54:55 +0000
Subject: [PATCH] bugfix and comments

---
 src/jalview/util/MapList.java |   47 +++++++++++++++++++++++++++++++++++++++--
 1 file changed, 45 insertions(+), 2 deletions(-)

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 2464264..f67b47f 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -65,6 +65,33 @@ public class MapList
   public Vector toShifts;
   int fromRatio; // number of steps in fromShifts to one toRatio unit
   int toRatio; // number of steps in toShifts to one fromRatio
+  
+  /**
+   * 
+   * @return series of intervals mapped in from
+   */
+  public int[] getFromRanges()
+  {
+    return getRanges(fromShifts);
+  }
+  public int[] getToRanges()
+  {
+    return getRanges(toShifts);
+  }
+  
+  private int[] getRanges(Vector shifts)
+  {
+    int[] rnges = new int[2*shifts.size()];
+    Enumeration e = shifts.elements();
+    int i=0;
+    while (e.hasMoreElements())
+    {
+      int r[] = (int[]) e.nextElement();
+      rnges[i++] = r[0];
+      rnges[i++] = r[1];
+    }
+    return rnges;
+  }
   /**
    * lowest and highest value in the from Map
    */
@@ -73,10 +100,18 @@ public class MapList
    * lowest and highest value in the to Map
    */
   int[] toRange=null;
+  /**
+   * 
+   * @return length of mapped phrase in from
+   */
   public int getFromRatio()
   {
     return fromRatio;
   }
+  /**
+   * 
+   * @return length of mapped phrase in to
+   */
   public int getToRatio()
   {
     return toRatio;
@@ -507,9 +542,9 @@ public class MapList
       {
         iv[0] = startpos;
       }
-      while (i!=fe) {
+      while (--i!=fe) { // fix apparent logic bug when fe==-1
         ranges.addElement(iv); // add (truncated) reversed interval
-        iv = (int[]) fromShifts2.elementAt(--i);
+        iv = (int[]) fromShifts2.elementAt(i);
         iv = new int[] { iv[1], iv[0] }; // reverse and clone
       }
       if (i==fe) {
@@ -763,4 +798,12 @@ public int[] getMappedWord(int pos) {
       }*/
     System.out.print("Success?\n"); // if we get here - something must be working!
   }
+  /**
+   * 
+   * @return a MapList whose From range is this maplist's To Range, and vice versa
+   */
+  public MapList getInverse()
+  {
+    return new MapList(getToRanges(), getFromRanges(), getToRatio(), getFromRatio());
+  }
 }
-- 
1.7.10.2