X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=4a59f88aa50066da55870f06ec3651a68fb968db;hb=539bd323123b239afdac5ef7b7706d6ccfc6a41d;hp=215ece943af8f0e10fa792732c5233c30e5fa88b;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 215ece9..4a59f88 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -30,28 +30,107 @@ import java.util.*;
  */
 public class MapList
 {
+  /* (non-Javadoc)
+   * @see java.lang.Object#clone()
+   */
+  protected Object clone() throws CloneNotSupportedException {
+    // TODO Auto-generated method stub
+    return super.clone();
+  }
+  /* (non-Javadoc)
+   * @see java.lang.Object#equals(java.lang.Object)
+   */
+  public boolean equals(MapList obj) {
+    if (obj==this)
+      return true;
+    if (obj!=null && obj.fromRatio==fromRatio && obj.toRatio==toRatio
+        && obj.fromShifts!=null && obj.toShifts!=null) {
+      int i,iSize=fromShifts.size(),j,jSize=obj.fromShifts.size();
+      if (iSize!=jSize)
+        return false;
+      for (i=0,iSize=fromShifts.size(),j=0, jSize=obj.fromShifts.size(); i<iSize;) {
+        int[] mi=(int[]) fromShifts.elementAt(i++);
+        int[] mj=(int[]) obj.fromShifts.elementAt(j++);
+        if (mi[0]!=mj[0] || mi[1]!=mj[1])
+          return false;
+      }
+      iSize=toShifts.size();
+      jSize=obj.toShifts.size();
+      if (iSize!=jSize)
+        return false;
+      for (i=0,j=0; i<iSize;) {
+        int[] mi=(int[]) toShifts.elementAt(i++);
+        int[] mj=(int[]) obj.toShifts.elementAt(j++);
+        if (mi[0]!=mj[0] || mi[1]!=mj[1])
+          return false;
+      }
+      return true;
+    }
+    return false;
+  }
   public Vector fromShifts;
   public Vector toShifts;
   int fromRatio; // number of steps in fromShifts to one toRatio unit
   int toRatio; // number of steps in toShifts to one fromRatio
+  /**
+   * lowest and highest value in the from Map
+   */
+  int[] fromRange=null;
+  /**
+   * lowest and highest value in the to Map
+   */
+  int[] toRange=null;
+  public int getFromRatio()
+  {
+    return fromRatio;
+  }
+  public int getToRatio()
+  {
+    return toRatio;
+  }
+  public int getFromLowest() {
+    return fromRange[0];
+  }
+  public int getFromHighest() {
+    return fromRange[1];
+  }
+  public int getToLowest() {
+    return toRange[0];
+  }
+  public int getToHighest() {
+    return toRange[1];
+  }
+  private void ensureRange(int[] limits, int pos) {
+    if (limits[0]>pos)
+      limits[0]=pos;
+    if (limits[1]<pos)
+      limits[1]=pos;
+  }
   public MapList(int from[], int to[], int fromRatio, int toRatio)
   {
+    fromRange=new int[] { from[0],from[1] };
+    toRange=new int[] { to[0],to[1] };
+
     fromShifts = new Vector();
-    for (int i = 0; i < from.length; i += 2)
+    for (int i=0;i<from.length; i+=2)
     {
-      fromShifts.add(new int[]
-                     {from[i], from[i + 1]});
+      ensureRange(fromRange, from[i]);
+      ensureRange(fromRange, from[i+1]);
+
+      fromShifts.addElement(new int[]
+                             {from[i], from[i + 1]});
     }
     toShifts = new Vector();
-    for (int i = 0; i < to.length; i += 2)
+    for (int i=0;i<to.length; i+=2)
     {
-      toShifts.add(new int[]
-                   {to[i], to[i + 1]});
+      ensureRange(toRange, to[i]);
+      ensureRange(toRange, to[i+1]);
+      toShifts.addElement(new int[]
+                           {to[i], to[i + 1]});
     }
-    this.fromRatio = fromRatio;
-    this.toRatio = toRatio;
+    this.fromRatio=fromRatio;
+    this.toRatio=toRatio;
   }
-
   /**
    * get all mapped positions from 'from' to 'to'
    * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
@@ -60,86 +139,84 @@ public class MapList
   {
     return posMap(fromShifts, fromRatio, toShifts, toRatio);
   }
-
   /**
    * get all mapped positions from 'to' to 'from'
    * @return int[to position]=position mapped in from
    */
   public int[][] makeToMap()
   {
-    return posMap(toShifts, toRatio, fromShifts, fromRatio);
+    return posMap(toShifts,toRatio, fromShifts, fromRatio);
   }
-
   /**
    * construct an int map for intervals in intVals
    * @param intVals
    * @return int[] { from, to pos in range }, int[range.to-range.from+1] returning mapped position
    */
   private int[][] posMap(Vector intVals, int ratio, Vector toIntVals,
-                         int toRatio)
+      int toRatio)
   {
-    Iterator iv = intVals.iterator();
-    if (!iv.hasNext())
+    int iv=0,ivSize = intVals.size();
+    if (iv>=ivSize)
     {
       return null;
     }
-    int[] intv = (int[]) iv.next();
-    int from = intv[0], to = intv[1];
+    int[] intv=(int[]) intVals.elementAt(iv++);
+    int from=intv[0],to=intv[1];
     if (from > to)
     {
       from = intv[1];
-      to = intv[0];
+      to=intv[0];
     }
-    while (iv.hasNext())
+    while (iv<ivSize)
     {
-      intv = (int[]) iv.next();
-      if (intv[0] < from)
+      intv = (int[]) intVals.elementAt(iv++);
+      if (intv[0]<from)
       {
-        from = intv[0];
+        from=intv[0];
       }
-      if (intv[1] < from)
+      if (intv[1]<from)
       {
-        from = intv[1];
+        from=intv[1];
       }
-      if (intv[0] > to)
+      if (intv[0]>to)
       {
-        to = intv[0];
+        to=intv[0];
       }
-      if (intv[1] > to)
+      if (intv[1]>to)
       {
-        to = intv[1];
+        to=intv[1];
       }
     }
-    int tF = 0, tT = 0;
-    int mp[][] = new int[to - from + 2][];
+    int tF=0,tT=0;
+    int mp[][] = new int[to-from+2][];
     for (int i = 0; i < mp.length; i++)
     {
-      int[] m = shift(i + from, intVals, ratio, toIntVals, toRatio);
+      int[] m = shift(i+from,intVals,ratio,toIntVals, toRatio);
       if (m != null)
       {
         if (i == 0)
         {
-          tF = tT = m[0];
+          tF=tT=m[0];
         }
         else
         {
           if (m[0] < tF)
           {
-            tF = m[0];
+            tF=m[0];
           }
           if (m[0] > tT)
           {
-            tT = m[0];
+            tT=m[0];
           }
         }
       }
       mp[i] = m;
     }
     int[][] map = new int[][]
-        {
+                            {
         new int[]
-        {
-        from, to, tF, tT}, new int[to - from + 2]};
+                {
+            from, to, tF, tT}, new int[to - from + 2]};
 
     map[0][2] = tF;
     map[0][3] = tT;
@@ -148,7 +225,7 @@ public class MapList
     {
       if (mp[i] != null)
       {
-        map[1][i] = mp[i][0] - tF;
+        map[1][i] = mp[i][0]-tF;
       }
       else
       {
@@ -157,29 +234,28 @@ public class MapList
     }
     return map;
   }
-
   /**
    * addShift
    * @param pos start position for shift (in original reference frame)
    * @param shift length of shift
    *
-     public void addShift(int pos, int shift)
-     {
+  public void addShift(int pos, int shift)
+  {
     int sidx = 0;
     int[] rshift=null;
-   while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
+    while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
       sidx++;
     if (sidx==shifts.size())
       shifts.insertElementAt(new int[] { pos, shift}, sidx);
     else
       rshift[1]+=shift;
-     }
+  }
    */
   /**
    * shift from pos to To(pos)
    *
    * @param pos int
-   * @return int shifted position in To, frameshift in From
+   * @return int shifted position in To, frameshift in From, direction of mapped symbol in To
    */
   public int[] shiftFrom(int pos)
   {
@@ -189,13 +265,12 @@ public class MapList
   /**
    * inverse of shiftFrom - maps pos in To to a position in From
    * @param pos (in To)
-   * @return shifted position in From, frameshift in To
+   * @return shifted position in From, frameshift in To, direction of mapped symbol in From
    */
   public int[] shiftTo(int pos)
   {
     return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
   }
-
   /**
    *
    * @param fromShifts
@@ -205,49 +280,48 @@ public class MapList
    * @return
    */
   private int[] shift(int pos, Vector fromShifts, int fromRatio,
-                      Vector toShifts, int toRatio)
+      Vector toShifts, int toRatio)
   {
-    int[] fromCount = countPos(fromShifts.iterator(), pos);
-    if (fromCount == null)
+    int[] fromCount = countPos(fromShifts, pos);
+    if (fromCount==null)
     {
       return null;
     }
-    int fromRemainder = (fromCount[0] - 1) % fromRatio;
-    int toCount = 1 + ( ( (fromCount[0] - 1) / fromRatio) * toRatio);
-    int[] toPos = countToPos(toShifts.iterator(), toCount);
-    if (toPos == null)
+    int fromRemainder=(fromCount[0]-1) % fromRatio;
+    int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
+    int[] toPos = countToPos(toShifts, toCount);
+    if (toPos==null)
     {
       return null; // throw new Error("Bad Mapping!");
     }
     //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
     return new int[]
-        {
-        toPos[0], fromRemainder};
+                   {
+        toPos[0], fromRemainder, toPos[1]};
   }
-
   /**
    * count how many positions pos is along the series of intervals.
    * @param intVals
    * @param pos
    * @return number of positions or null if pos is not within intervals
    */
-  private int[] countPos(Iterator intVals, int pos)
+  private int[] countPos(Vector intVals, int pos)
   {
-    int count = 0, intv[];
-    while (intVals.hasNext())
+    int count=0,intv[],iv=0,ivSize=intVals.size();
+    while (iv<ivSize)
     {
-      intv = (int[]) intVals.next();
+      intv = (int[])intVals.elementAt(iv++);
       if (intv[0] <= intv[1])
       {
         if (pos >= intv[0] && pos <= intv[1])
         {
           return new int[]
-              {
+                         {
               count + pos - intv[0] + 1, +1};
         }
         else
         {
-          count += intv[1] - intv[0] + 1;
+          count+=intv[1]-intv[0]+1;
         }
       }
       else
@@ -255,44 +329,43 @@ public class MapList
         if (pos >= intv[1] && pos <= intv[0])
         {
           return new int[]
-              {
+                         {
               count + intv[0] - pos + 1, -1};
         }
         else
         {
-          count += intv[0] - intv[1] + 1;
+          count+=intv[0]-intv[1]+1;
         }
       }
     }
     return null;
   }
-
   /**
    * count out pos positions into a series of intervals and return the position
    * @param intVals
    * @param pos
    * @return position pos in interval set
    */
-  private int[] countToPos(Iterator intVals, int pos)
+  private int[] countToPos(Vector intVals, int pos)
   {
-    int count = 0, diff = 0, intv[] =
-        {
+    int count = 0, diff = 0, iv=0,ivSize=intVals.size(), intv[] =
+    {
         0, 0};
-    while (intVals.hasNext())
+    while (iv<ivSize)
     {
-      intv = (int[]) intVals.next();
-      diff = intv[1] - intv[0];
+      intv = (int[])intVals.elementAt(iv++);
+      diff = intv[1]-intv[0];
       if (diff >= 0)
       {
         if (pos <= count + 1 + diff)
         {
           return new int[]
-              {
+                         {
               pos - count - 1 + intv[0], +1};
         }
         else
         {
-          count += 1 + diff;
+          count+=1+diff;
         }
       }
       else
@@ -300,65 +373,255 @@ public class MapList
         if (pos <= count + 1 - diff)
         {
           return new int[]
-              {
+                         {
               intv[0] - (pos - count - 1), -1};
         }
         else
         {
-          count += 1 - diff;
+          count+=1-diff;
         }
       }
     }
-    return null; //(diff<0) ? (intv[1]-1) : (intv[0]+1);
+    return null;//(diff<0) ? (intv[1]-1) : (intv[0]+1);
+  }
+  /**
+   * find series of intervals mapping from start-end in the From map.
+   * @param start position in to map
+   * @param end position in to map
+   * @return series of ranges in from map
+   */
+  public int[] locateInFrom(int start, int end) {
+    // inefficient implementation
+    int fromStart[] = shiftTo(start);
+    int fromEnd[] = shiftTo(end);
+    if (fromStart==null || fromEnd==null)
+      return null;
+    int iv[] = getIntervals(fromShifts, fromStart, fromEnd,fromRatio);
+    return iv;
   }
 
+  /**
+   * find series of intervals mapping from start-end in the to map.
+   * @param start position in from map
+   * @param end position in from map
+   * @return series of ranges in to map
+   */
+  public int[] locateInTo(int start, int end) {
+    // inefficient implementation
+    int toStart[] = shiftFrom(start);
+    int toEnd[] = shiftFrom(end);
+    if (toStart==null || toEnd==null)
+      return null;
+    int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
+    return iv;
+  }
+  /**
+   * like shift - except returns the intervals in the given vector of shifts which were spanned
+   * in traversing fromStart to fromEnd
+   * @param fromShifts2
+   * @param fromStart
+   * @param fromEnd
+   * @param fromRatio2
+   * @return
+   */
+  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);
+    int intv=0,intvSize= fromShifts2.size();
+    int iv[],i=0,fs=-1,fe=-1; // containing intervals
+    while (intv<intvSize && (fs==-1 || fe==-1)) {
+      iv = (int[]) fromShifts2.elementAt(intv++);
+      if (iv[0]<=iv[1]) {
+        if (fs==-1 && startpos>=iv[0] && startpos<=iv[1]) {
+          fs = i;
+        }
+        if (fe==-1 && endpos>=iv[0] && endpos<=iv[1]) {
+          fe = i;
+        }
+      } else {
+        if (fs==-1 && startpos<=iv[0] && startpos>=iv[1]) {
+          fs = i;
+        }
+        if (fe==-1 && endpos<=iv[0] && endpos>=iv[1]) {
+          fe = i;
+        }
+      }
+      i++;
+    }
+    if (fs==fe && fe==-1)
+      return null;
+    Vector ranges=new Vector();
+    if (fs<=fe) {
+      intv = fs;
+      i=fs;
+      // truncate initial interval
+      iv = (int[]) fromShifts2.elementAt(intv++);
+      iv = new int[] { iv[0], iv[1]};// clone
+      if (i==fs)
+        iv[0] = startpos;
+      while (i!=fe) {
+        ranges.addElement(iv); // add initial range
+        iv = (int[]) fromShifts2.elementAt(intv++); // get next interval
+        iv = new int[] { iv[0], iv[1]};// clone
+        i++;
+      }
+      if (i==fe)
+        iv[1] = endpos;
+      ranges.addElement(iv); // add only - or final range
+    } else {
+      // walk from end of interval.
+      i=fromShifts2.size()-1;
+      while (i>fs) {
+        i--;
+      }
+      iv = (int[]) fromShifts2.elementAt(i);
+      iv = new int[] { iv[1], iv[0]};//  reverse and clone
+      // truncate initial interval
+      if (i==fs)
+      {
+        iv[0] = startpos;
+      }
+      while (i!=fe) {
+        ranges.addElement(iv); // add (truncated) reversed interval
+        iv = (int[]) fromShifts2.elementAt(--i);
+        iv = new int[] { iv[1], iv[0] }; // reverse and clone
+      }
+      if (i==fe) {
+        // interval is already reversed
+        iv[1] = endpos;
+      }
+      ranges.addElement(iv); // add only - or final range
+    }
+    // create array of start end intervals.
+    int[] range = null;
+    if (ranges!=null && ranges.size()>0)
+    {
+      range = new int[ranges.size()*2];
+      intv = 0;
+      intvSize=ranges.size();
+      i=0;
+      while (intv<intvSize)
+      {
+        iv = (int[]) ranges.elementAt(intv);
+        range[i++] = iv[0];
+        range[i++] = iv[1];
+        ranges.setElementAt(null, intv++); // remove
+      }
+    }
+    return range;
+  }
+  /**
+   * test routine. not incremental.
+   * @param ml
+   * @param fromS
+   * @param fromE
+   */
   public static void testMap(MapList ml, int fromS, int fromE)
   {
     for (int from = 1; from <= 25; from++)
     {
-      int[] too = ml.shiftFrom(from);
-      System.out.print("ShiftFrom(" + from + ")==");
-      if (too == null)
+      int[] too=ml.shiftFrom(from);
+      System.out.print("ShiftFrom("+from+")==");
+      if (too==null)
       {
         System.out.print("NaN\n");
       }
       else
       {
-        System.out.print(too[0] + " % " + too[1]);
+        System.out.print(too[0]+" % "+too[1]+" ("+too[2]+")");
         System.out.print("\t+--+\t");
-        int[] toofrom = ml.shiftTo(too[0]);
+        int[] toofrom=ml.shiftTo(too[0]);
         if (toofrom != null)
         {
-          if (toofrom[0] != from)
+          if (toofrom[0]!=from)
           {
             System.err.println("Mapping not reflexive:" + from + " " + too[0] +
-                               "->" + toofrom[0]);
+                "->" + toofrom[0]);
           }
           System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
-                             toofrom[1]);
+              toofrom[1]+" ("+toofrom[2]+")");
         }
         else
         {
           System.out.println("ShiftTo(" + too[0] + ")==" +
-                             "NaN! - not Bijective Mapping!");
+          "NaN! - not Bijective Mapping!");
         }
       }
     }
     int mmap[][] = ml.makeFromMap();
     System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
-                       mmap[0][2] + " " + mmap[0][3] + " ");
+        mmap[0][2] + " " + mmap[0][3] + " ");
+    for (int i = 1; i <= mmap[1].length; i++)
+    {
+      if (mmap[1][i - 1] == -1)
+      {
+        System.out.print(i+"=XXX");
+
+      }
+      else
+      {
+        System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
+      }
+      if (i % 20==0)
+      {
+        System.out.print("\n");
+      }
+      else
+      {
+        System.out.print(",");
+      }
+    }
+    //test range function
+    System.out.print("\nTest locateInFrom\n");
+    {
+      int f=mmap[0][2],t=mmap[0][3];
+      while (f<t) {
+        System.out.println("Range "+f+" to "+t);
+        int rng[] = ml.locateInFrom(f,t);
+        if (rng!=null)
+        {
+          for (int i=0; i<rng.length; i++) {
+            System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+          }
+        }
+        else
+        {
+          System.out.println("No range!");
+        }
+        System.out.print("\nReversed\n");
+        rng = ml.locateInFrom(t,f);
+        if (rng!=null)
+        {
+          for (int i=0; i<rng.length; i++) {
+            System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+          }
+        }
+        else
+        {
+          System.out.println("No range!");
+        }
+        System.out.print("\n");
+        f++;t--;
+      }
+    }
+    System.out.print("\n");
+    mmap = ml.makeToMap();
+    System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " " +
+        mmap[0][2] + " " + mmap[0][3] + " ");
     for (int i = 1; i <= mmap[1].length; i++)
     {
       if (mmap[1][i - 1] == -1)
       {
-        System.out.print(i + "=XXX");
+        System.out.print(i+"=XXX");
 
       }
       else
       {
-        System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
+        System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
       }
-      if (i % 20 == 0)
+      if (i % 20==0)
       {
         System.out.print("\n");
       }
@@ -368,28 +631,62 @@ public class MapList
       }
     }
     System.out.print("\n");
+    //test range function
+    System.out.print("\nTest locateInTo\n");
+    {
+      int f=mmap[0][2],t=mmap[0][3];
+      while (f<t) {
+        System.out.println("Range "+f+" to "+t);
+        int rng[] = ml.locateInTo(f,t);
+        if (rng!=null) {
+          for (int i=0; i<rng.length; i++) {
+            System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+          }
+        }
+        else
+        {
+          System.out.println("No range!");
+        }
+        System.out.print("\nReversed\n");
+        rng = ml.locateInTo(t,f);
+        if (rng!=null)
+        {
+          for (int i=0; i<rng.length; i++) {
+            System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+          }
+        }
+        else
+        {
+          System.out.println("No range!");
+        }
+        f++; t--;
+        System.out.print("\n");
+      }
+    }
+
   }
 
   public static void main(String argv[])
   {
     MapList ml = new MapList(new int[]
-                             {1, 5, 10, 15, 25, 20},
-                             new int[]
-                             {51, 1}, 1, 3);
+                                     {1, 5, 10, 15, 25, 20},
+                                     new int[]
+                                             {51, 1}, 1, 3);
     MapList ml1 = new MapList(new int[]
-                              {1, 3, 17, 4},
-                              new int[]
-                              {51, 1}, 1, 3);
-
+                                      {1, 3, 17, 4},
+                                      new int[]
+                                              {51, 1}, 1, 3);
+    MapList ml2 = new MapList(new int[] { 1, 60 },
+        new int[] { 1, 20 }, 3, 1);
     // test internal consistency
     int to[] = new int[51];
-    MapList.testMap(ml, 1, 25);
+    MapList.testMap(ml, 1, 60);
     /*
-           for (int from=1; from<=51; from++) {
-        int[] too=ml.shiftTo(from);
-        int[] toofrom=ml.shiftFrom(too[0]);
-        System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
-           }*/
+      for (int from=1; from<=51; from++) {
+          int[] too=ml.shiftTo(from);
+          int[] toofrom=ml.shiftFrom(too[0]);
+          System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
+      }*/
     System.out.print("Success?\n"); // if we get here - something must be working!
   }
 }