From: jprocter <Jim Procter>
Date: Wed, 24 Jan 2007 17:08:58 +0000 (+0000)
Subject: Map arbitrary series of non-overlapping integer intervals on one range to another... 
X-Git-Tag: Release_2_3~455
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eb57149512e6f339336a19d88a6da081c5f35843;p=jalview.git

Map arbitrary series of non-overlapping integer intervals on one range to another on another range - with an integer ratio for each range
---

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
new file mode 100644
index 0000000..d76ec33
--- /dev/null
+++ b/src/jalview/util/MapList.java
@@ -0,0 +1,278 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import java.util.*;
+
+/**
+ * MapList
+ * Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range
+ * Use at your own risk!
+ * TODO: efficient implementation of private posMap method
+ * TODO: test/ensure that sense of from and to ratio start position is conserved (codon start position recovery)
+ * TODO: optimize to use int[][] arrays rather than vectors.
+ */
+public class MapList
+{
+    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
+  public MapList(int from[], int to[], int fromRatio, int toRatio)
+  {
+    fromShifts = new Vector();
+    for (int i=0;i<from.length; i+=2)
+        fromShifts.add(new int[] { from[i], from[i+1]});
+    toShifts = new Vector();
+    for (int i=0;i<to.length; i+=2)
+        toShifts.add(new int[] { to[i], to[i+1]});
+    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}}
+   */
+  public int[][] makeFromMap() {
+      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);
+  }
+  /**
+   * 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) {
+      Iterator iv = intVals.iterator();
+      if (!iv.hasNext())
+          return null;
+      int[] intv=(int[]) iv.next();
+      int from=intv[0],to=intv[1];
+      if (from>to) {
+          from = intv[1];
+          to=intv[0];
+      }
+      while (iv.hasNext()) {
+          intv = (int[]) iv.next();
+          if (intv[0]<from)
+              from=intv[0];
+          if (intv[1]<from)
+              from=intv[1];
+          if (intv[0]>to)
+              to=intv[0];
+          if (intv[1]>to)
+              to=intv[1];
+      }
+      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);
+          if (m!=null) {
+              if (i==0) {
+                  tF=tT=m[0];
+              } else {
+                  if (m[0]<tF) {
+                      tF=m[0];
+                  }
+                  if (m[0]>tT) {
+                      tT=m[0];
+                  }
+              }
+          }
+          mp[i] = m;
+      }
+      int[][] map=new int[][] { new int[]{from, to, tF, tT}, new int[to-from+2]};
+
+      map[0][2] = tF;
+      map[0][3] = tT;
+      
+      for (int i=0;i<mp.length; i++) {
+          if (mp[i]!=null) {
+              map[1][i] = mp[i][0]-tF;
+          } else {
+              map[1][i] = -1; // indicates an out of range mapping
+          }
+      }
+      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)
+  {
+    int sidx = 0;
+    int[] rshift=null;
+    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
+   */
+  public int[] shiftFrom(int pos)
+  {
+      return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
+  }
+
+  /**
+   * inverse of shiftFrom - maps pos in To to a position in From
+   * @param pos (in To)
+   * @return shifted position in From, frameshift in To
+   */
+  public int[] shiftTo(int pos) {
+      return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
+  }
+  /**
+   * 
+   * @param fromShifts
+   * @param fromRatio
+   * @param toShifts
+   * @param toRatio
+   * @return
+   */
+  private int[] shift(int pos, Vector fromShifts, int fromRatio, Vector toShifts, int toRatio) {
+      int[] fromCount = countPos(fromShifts.iterator(), 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)
+          return null; // throw new Error("Bad Mapping!");
+      //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
+      return new int[] {toPos[0], fromRemainder};
+  }
+  /**
+   * 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) {
+      int count=0,intv[];
+      while (intVals.hasNext()) {
+          intv = (int[])intVals.next();
+          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;
+              }
+          } else {
+              if (pos>=intv[1] && pos<=intv[0]) {
+                  return new int[] { count+intv[0]-pos+1, -1 };
+              } else {
+                  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) {
+      int count=0,diff=0,intv[]={0,0};
+      while (intVals.hasNext()) {
+          intv = (int[])intVals.next();
+          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;
+              }
+          } else {
+              if (pos<=count+1-diff) {
+                  return new int[] { intv[0]-(pos-count-1),-1 };
+              } else {
+                  count+=1-diff;
+              }
+          }
+      }
+      return null;//(diff<0) ? (intv[1]-1) : (intv[0]+1);
+  }
+  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)
+              System.out.print("NaN\n");
+          else {
+              System.out.print(too[0]+" % "+too[1]);
+              System.out.print("\t+--+\t");
+              int[] toofrom=ml.shiftTo(too[0]);
+              if (toofrom!=null)
+                  System.out.println("ShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
+              else
+                  System.out.println("ShiftTo("+too[0]+")=="+"NaN! - not Bijective Mapping!");
+          }
+      }
+      int mmap[][] = ml.makeFromMap();
+      System.out.println("FromMap : ("+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");
+              
+          } else {
+              System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
+          }
+          if (i % 20==0)
+              System.out.print("\n");
+          else
+              System.out.print(",");
+      }
+      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);
+      MapList ml1=new MapList(new int[] { 1,3,17,4}, 
+              new int[] { 51,1}, 1, 3);
+      
+      // test internal consistency
+      int to[] = new int[51];
+      MapList.testMap(ml, 1, 25);
+      /*
+      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!
+  }
+}