From 3edbc91b06e90aaeb795168f7361208d639c3a27 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 24 Jan 2007 17:09:40 +0000
Subject: [PATCH] kkv change

---
 src/jalview/util/MapList.java |  556 ++++++++++++++++++++---------------------
 1 file changed, 278 insertions(+), 278 deletions(-)

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index d76ec33..87199bb 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,278 +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!
-  }
-}
+/*
+ * 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!
+  }
+}
-- 
1.7.10.2