From 3a2924d94334b170106141ec4e4773034c5995ce Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 25 Apr 2007 16:46:11 +0000
Subject: [PATCH] moving word methods to MapList and begin bug-fix for
 single-residue codon span feature location (see TODOs)

---
 src/jalview/datamodel/Mapping.java |   40 ++++++++++------------
 src/jalview/util/MapList.java      |   64 ++++++++++++++++++++++++++++++++----
 2 files changed, 76 insertions(+), 28 deletions(-)

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 2594c31..b9874a4 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -5,9 +5,9 @@ import jalview.util.MapList;
 public class Mapping {
   /**
    * Contains the
-   * start-end pairs mapping from 
-   * the associated sequence to the 
-   * sequence in the database 
+   * start-end pairs mapping from
+   * the associated sequence to the
+   * sequence in the database
    * coordinate system
    * it also takes care of step difference between coordinate systems
    */
@@ -37,14 +37,14 @@ public class Mapping {
     this(to, new MapList(exon, is, i, j));
   }
   /**
-   * create a duplicate (and independent) mapping object with 
+   * create a duplicate (and independent) mapping object with
    * the same reference to any SequenceI being mapped to.
    * @param map2
    */
   public Mapping(Mapping map2)
   {
     if (map2!=this && map2!=null) {
-      if (map2.map!=null) 
+      if (map2.map!=null)
       {
         map=new MapList(map2.map);
       }
@@ -67,7 +67,7 @@ public class Mapping {
   /**
    * Equals that compares both the to references and MapList mappings.
    * @param other
-   * @return 
+   * @return
    */
   public boolean equals(Mapping other) {
     if (other==null)
@@ -88,7 +88,7 @@ public class Mapping {
    * @param mpos
    * @return
    */
-  public int getPosition(int mpos) 
+  public int getPosition(int mpos)
   {
     if (map!=null) {
       int[] mp = map.shiftTo(mpos);
@@ -103,14 +103,14 @@ public class Mapping {
     if (map!=null) {
       int[] mp=map.shiftTo(mpos);
       if (mp!=null) {
-        return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)}; 
+        return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)};
       }
     }
     return null;
   }
   /**
-   * width of mapped unit in associated sequence 
-   * 
+   * width of mapped unit in associated sequence
+   *
    */
   public int getWidth() {
     if (map!=null) {
@@ -157,18 +157,13 @@ public class Mapping {
     return null;
   }
   /**
-   * locates the region of feature f in the associated sequence's reference frame 
+   * locates the region of feature f in the associated sequence's reference frame
    * @param f
    * @return one or more features corresponding to f
    */
   public SequenceFeature[] locateFeature(SequenceFeature f)
   {
-    // this is a stopgap - features broken over exon boundaries will not be
-    // broken into a collection of feature fragments.
-    // TODO: implement creation of several features from a single feature on a discontinuously mapped seuqence
-    // need a function like int [] fromrange = map.getRange(from,to)
-    // need to make subgrouped sequence features.
-    if (true) {
+    if (true) { // f.getBegin()!=f.getEnd()) {
       if (map!=null) {
         int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
         SequenceFeature[] vf = new SequenceFeature[frange.length/2];
@@ -182,16 +177,17 @@ public class Mapping {
         return vf;
       }
     }
-    if (false){
+    if (false) //else
+    {
       int[] word = getWord(f.getBegin());
-      if (word[0]<word[1]) 
+      if (word[0]<word[1])
       {
         f.setBegin(word[0]);
       } else {
         f.setBegin(word[1]);
       }
       word = getWord(f.getEnd());
-      if (word[0]>word[1]) 
+      if (word[0]>word[1])
       {
         f.setEnd(word[0]);
       } else {
@@ -201,7 +197,7 @@ public class Mapping {
     // give up and just return the feature.
     return new SequenceFeature[] { f };
   }
-      
+
     /**
    * return a series of contigs on the associated sequence corresponding to
    * the from,to interval on the mapped reference frame
@@ -221,7 +217,7 @@ public class Mapping {
    * @return
    */
   public int[] locateMappedRange(int from, int to) {
-    //TODO 
+    //TODO
     return null;
   }
 }
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 4922267..826ead7 100644
--- 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) {
-- 
1.7.10.2