moving word methods to MapList and begin bug-fix for single-residue codon span featur...

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

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 4922267..826ead7 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -417,7 +417,7 @@ public class MapList
   public int[] locateInFrom(int start, int end) {
     // inefficient implementation
     int fromStart[] = shiftTo(start);
-    int fromEnd[] = shiftTo(end);
+    int fromEnd[] = shiftTo(end); // needs to be inclusive of end of symbol position
     if (fromStart==null || fromEnd==null)
       return null;
     int iv[] = getIntervals(fromShifts, fromStart, fromEnd,fromRatio);
@@ -450,9 +450,11 @@ public class MapList
    */
   private int[] getIntervals(Vector fromShifts2, int[] fromStart, int[] fromEnd, int fromRatio2)
   {
-    // correct for word direction for start and end
-    int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1);
-    int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1);
+    // TODO: correct for word boundary w.r.t. fromStart->fromEnd direction for startpos and endpos.
+    // test is (1,8,12,17) to (1,5) and features on to : 2,2; 3,3; 4,3; 3,4; 4,4; 5,3; 3,5; 2,4; 4,2;
+    // correct for word direction for start and end :
+    int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1); // Math.min(fromStart[0], .. );
+    int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1); // Math.max(fromEnd[0],);
     int intv=0,intvSize= fromShifts2.size();
     int iv[],i=0,fs=-1,fe=-1; // containing intervals
     while (intv<intvSize && (fs==-1 || fe==-1)) {
@@ -537,6 +539,56 @@ public class MapList
     return range;
   }
   /**
+ * get the 'initial' position of mpos in To
+ * @param mpos position in from
+ * @return position of first word in to reference frame
+ */
+public int getToPosition(int mpos)
+{
+  int[] mp = shiftTo(mpos);
+  if (mp!=null)
+  {
+    return mp[0];
+  }
+  return mpos;
+}
+/**
+ * get range of positions in To frame for the mpos word in From
+ * @param mpos position in From
+ * @return null or int[] first position in To for mpos, last position in to for Mpos
+ */
+public int[] getToWord(int mpos) {
+  int[] mp=shiftTo(mpos);
+  if (mp!=null) {
+      return new int[] {mp[0], mp[0]+mp[2]*(getFromRatio()-1)};
+  }
+  return null;
+}
+/**
+ * get From position in the associated
+ * reference frame for position pos in the
+ * associated sequence.
+ * @param pos
+ * @return
+ */
+public int getMappedPosition(int pos) {
+  int[] mp = shiftFrom(pos);
+  if (mp!=null)
+  {
+    return mp[0];
+  }
+  return pos;
+}
+public int[] getMappedWord(int pos) {
+  int[] mp = shiftFrom(pos);
+  if (mp!=null)
+  {
+    return new int[] { mp[0], mp[0]+mp[2]*(getToRatio()-1)};
+  }
+  return null;
+}
+
+  /**
    * test routine. not incremental.
    * @param ml
    * @param fromS
@@ -601,7 +653,7 @@ public class MapList
     System.out.print("\nTest locateInFrom\n");
     {
       int f=mmap[0][2],t=mmap[0][3];
-      while (f<t) {
+      while (f<=t) {
         System.out.println("Range "+f+" to "+t);
         int rng[] = ml.locateInFrom(f,t);
         if (rng!=null)
@@ -659,7 +711,7 @@ public class MapList
     System.out.print("\nTest locateInTo\n");
     {
       int f=mmap[0][2],t=mmap[0][3];
-      while (f<t) {
+      while (f<=t) {
         System.out.println("Range "+f+" to "+t);
         int rng[] = ml.locateInTo(f,t);
         if (rng!=null) {