From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 19 Feb 2010 09:22:11 +0000 (+0000)
Subject: bugfix and new containment test method from jalview.utils.MapList in jalview 2.4... 
X-Git-Tag: Release_0.2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e87af6aca43fc949d3e29f47a09fd74f916ca7e9;p=vamsas.git

bugfix and new containment test method from jalview.utils.MapList in jalview 2.4 branch

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@515 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/uk/ac/vamsas/objects/utils/MapList.java b/src/uk/ac/vamsas/objects/utils/MapList.java
index 3c3526c..ab4e866 100644
--- a/src/uk/ac/vamsas/objects/utils/MapList.java
+++ b/src/uk/ac/vamsas/objects/utils/MapList.java
@@ -451,25 +451,73 @@ public class MapList {
       int[] fromEnd, int fromRatio2) {
     int startpos, endpos;
     startpos = fromStart[0]; // first position in fromStart
-    endpos = fromEnd[0] + fromEnd[2] * (fromRatio2 - 1); // last position in
-                                                         // fromEnd
+    endpos = fromEnd[0]; // last position in fromEnd
+    int endindx = (fromRatio2 - 1); // additional positions to get to last
+    // position from endpos
     int intv = 0, intvSize = fromShifts2.size();
-    int iv[], i = 0, fs = -1, fe = -1; // containing intervals
-    while (intv < intvSize && (fs == -1 || fe == -1)) {
+    int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
+    // search intervals to locate ones containing startpos and count endindx
+    // positions on from endpos
+    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]) {
+      if (fe_s > -1)
+      {
+        endpos = iv[0]; // start counting from beginning of interval
+        endindx--; // inclusive of endpos
+      }
+      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]) {
+        if (endpos >= iv[0] && endpos <= iv[1])
+        {
+          if (fe_s == -1)
+          {
+            fe_s = i;
+          }
+          if (fe_s != -1)
+          {
+            if (endpos + endindx <= iv[1])
+            {
           fe = i;
+              endpos = endpos + endindx; // end of end token is within this
+                                          // interval
         }
-      } else {
-        if (fs == -1 && startpos <= iv[0] && startpos >= iv[1]) {
+            else
+            {
+              endindx -= iv[1] - endpos; // skip all this interval too
+            }
+          }
+        }
+      }
+      else
+      {
+        if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])
+        {
           fs = i;
         }
-        if (fe == -1 && endpos <= iv[0] && endpos >= iv[1]) {
+        if (endpos <= iv[0] && endpos >= iv[1])
+        {
+          if (fe_s == -1)
+          {
+            fe_s = i;
+          }
+          if (fe_s != -1)
+          {
+            if (endpos - endindx >= iv[1])
+            {
           fe = i;
+              endpos = endpos - endindx; // end of end token is within this
+                                          // interval
+        }
+            else
+            {
+              endindx -= endpos - iv[1]; // skip all this interval too
+      }
+          }
         }
       }
       i++;
@@ -477,41 +525,53 @@ public class MapList {
     if (fs == fe && fe == -1)
       return null;
     Vector ranges = new Vector();
-    if (fs <= fe) {
+    if (fs <= fe)
+    {
       intv = fs;
       i = fs;
       // truncate initial interval
       iv = (int[]) fromShifts2.elementAt(intv++);
-      iv = new int[] { iv[0], iv[1] };// clone
+      iv = new int[]
+      { iv[0], iv[1] };// clone
       if (i == fs)
         iv[0] = startpos;
-      while (i != fe) {
+      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
+        iv = new int[]
+        { iv[0], iv[1] };// clone
         i++;
       }
       if (i == fe)
         iv[1] = endpos;
       ranges.addElement(iv); // add only - or final range
-    } else {
+    }
+    else
+    {
       // walk from end of interval.
       i = fromShifts2.size() - 1;
-      while (i > fs) {
+      while (i > fs)
+      {
         i--;
       }
       iv = (int[]) fromShifts2.elementAt(i);
-      iv = new int[] { iv[1], iv[0] };// reverse and clone
+      iv = new int[]
+      { iv[1], iv[0] };// reverse and clone
       // truncate initial interval
-      if (i == fs) {
+      if (i == fs)
+      {
         iv[0] = startpos;
       }
-      while (--i != fe) { // fix apparent logic bug when fe==-1
+      while (--i != fe)
+      { // fix apparent logic bug when fe==-1
         ranges.addElement(iv); // add (truncated) reversed interval
         iv = (int[]) fromShifts2.elementAt(i);
-        iv = new int[] { iv[1], iv[0] }; // reverse and clone
+        iv = new int[]
+        { iv[1], iv[0] }; // reverse and clone
       }
-      if (i == fe) {
+      if (i == fe)
+      {
         // interval is already reversed
         iv[1] = endpos;
       }
@@ -519,12 +579,14 @@ public class MapList {
     }
     // create array of start end intervals.
     int[] range = null;
-    if (ranges != null && ranges.size() > 0) {
+    if (ranges != null && ranges.size() > 0)
+    {
       range = new int[ranges.size() * 2];
       intv = 0;
       intvSize = ranges.size();
       i = 0;
-      while (intv < intvSize) {
+      while (intv < intvSize)
+      {
         iv = (int[]) ranges.elementAt(intv);
         range[i++] = iv[0];
         range[i++] = iv[1];
@@ -595,24 +657,33 @@ public class MapList {
    * @param fromS
    * @param fromE
    */
-  public static void testMap(MapList ml, int fromS, int fromE) {
-    for (int from = 1; from <= 25; from++) {
+  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) {
+      if (too == null)
+      {
         System.out.print("NaN\n");
-      } else {
+      }
+      else
+      {
         System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");
         System.out.print("\t+--+\t");
         int[] toofrom = ml.shiftTo(too[0]);
-        if (toofrom != null) {
-          if (toofrom[0] != from) {
-            System.err.println("Mapping not reflexive:" + from + " " + too[0]
-                + "->" + toofrom[0]);
+        if (toofrom != null)
+        {
+          if (toofrom[0] != from)
+          {
+            System.err.println("Mapping not reflexive:" + from + " "
+                    + too[0] + "->" + toofrom[0]);
           }
-          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % "
-              + toofrom[1] + " (" + toofrom[2] + ")");
-        } else {
+          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]
+                  + " % " + toofrom[1] + " (" + toofrom[2] + ")");
+        }
+        else
+        {
           System.out.println("ShiftTo(" + too[0] + ")=="
               + "NaN! - not Bijective Mapping!");
         }
@@ -621,16 +692,23 @@ public class MapList {
     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) {
+    for (int i = 1; i <= mmap[1].length; i++)
+    {
+      if (mmap[1][i - 1] == -1)
+      {
         System.out.print(i + "=XXX");
 
-      } else {
+      }
+      else
+      {
         System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
       }
-      if (i % 20 == 0) {
+      if (i % 20 == 0)
+      {
         System.out.print("\n");
-      } else {
+      }
+      else
+      {
         System.out.print(",");
       }
     }
@@ -638,23 +716,32 @@ 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) {
-          for (int i = 0; i < rng.length; i++) {
+        if (rng != null)
+        {
+          for (int i = 0; i < rng.length; i++)
+          {
             System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
           }
-        } else {
+        }
+        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++) {
+        if (rng != null)
+        {
+          for (int i = 0; i < rng.length; i++)
+          {
             System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
           }
-        } else {
+        }
+        else
+        {
           System.out.println("No range!");
         }
         System.out.print("\n");
@@ -666,16 +753,23 @@ public class MapList {
     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) {
+    for (int i = 1; i <= mmap[1].length; i++)
+    {
+      if (mmap[1][i - 1] == -1)
+      {
         System.out.print(i + "=XXX");
 
-      } else {
+      }
+      else
+      {
         System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));
       }
-      if (i % 20 == 0) {
+      if (i % 20 == 0)
+      {
         System.out.print("\n");
-      } else {
+      }
+      else
+      {
         System.out.print(",");
       }
     }
@@ -684,23 +778,32 @@ 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) {
-          for (int i = 0; i < rng.length; i++) {
+        if (rng != null)
+        {
+          for (int i = 0; i < rng.length; i++)
+          {
             System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
           }
-        } else {
+        }
+        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++) {
+        if (rng != null)
+        {
+          for (int i = 0; i < rng.length; i++)
+          {
             System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));
           }
-        } else {
+        }
+        else
+        {
           System.out.println("No range!");
         }
         f++;
@@ -711,15 +814,27 @@ public class MapList {
 
   }
 
-  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);
-    MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3, 1);
+  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);
+    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, 60);
+    MapList mldna = new MapList(new int[]
+    { 2, 2, 6, 8, 12, 16 }, new int[]
+    { 1, 3 }, 3, 1);
+    int[] frm = mldna.locateInFrom(1, 1);
+    testLocateFrom(mldna, 1, 1, new int[]
+    { 2, 2, 6, 7 });
+    MapList.testMap(mldna, 1, 3);
     /*
      * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
      * toofrom=ml.shiftFrom(too[0]);
@@ -731,13 +846,53 @@ public class MapList {
                                     // working!
   }
 
+  private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
+  {
+    int[] frm = mldna.locateInFrom(i, j);
+    if (frm == ks || java.util.Arrays.equals(frm, ks))
+    {
+      System.out.println("Success test locate from " + i + " to " + j);
+    }
+    else
+    {
+      System.err.println("Failed test locate from " + i + " to " + j);
+      for (int c = 0; c < frm.length; c++)
+      {
+        System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));
+      }
+      System.err.println("Expected");
+      for (int c = 0; c < ks.length; c++)
+      {
+        System.err.print(ks[c] + ((c % 2 == 0) ? "," : ";"));
+      }
+    }
+  }
+
   /**
    * 
    * @return a MapList whose From range is this maplist's To Range, and vice
    *         versa
    */
-  public MapList getInverse() {
+  public MapList getInverse()
+  {
     return new MapList(getToRanges(), getFromRanges(), getToRatio(),
         getFromRatio());
   }
+
+  /**
+   * test for containment rather than equivalence to another mapping
+   * @param map to be tested for containment
+   * @return true if local or mapped range map contains or is contained by this mapping 
+   */
+  public boolean containsEither(boolean local, MapList map)
+  {
+    if (local)
+    {
+      return ((getFromLowest()>=map.getFromLowest() && getFromHighest()<=map.getFromHighest())
+        || (getFromLowest()<=map.getFromLowest() && getFromHighest()>=map.getFromHighest()));
+    } else {
+      return ((getToLowest()>=map.getToLowest() && getToHighest()<=map.getToHighest())
+              || (getToLowest()<=map.getToLowest() && getToHighest()>=map.getToHighest()));
+    }
+  }
 }