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

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 (file)
--- 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) {\r
     int startpos, endpos;\r
     startpos = fromStart[0]; // first position in fromStart\r
-    endpos = fromEnd[0] + fromEnd[2] * (fromRatio2 - 1); // last position in\r
-                                                         // fromEnd\r
+    endpos = fromEnd[0]; // last position in fromEnd\r
+    int endindx = (fromRatio2 - 1); // additional positions to get to last\r
+    // position from endpos\r
     int intv = 0, intvSize = fromShifts2.size();\r
-    int iv[], i = 0, fs = -1, fe = -1; // containing intervals\r
-    while (intv < intvSize && (fs == -1 || fe == -1)) {\r
+    int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals\r
+    // search intervals to locate ones containing startpos and count endindx\r
+    // positions on from endpos\r
+    while (intv < intvSize && (fs == -1 || fe == -1))\r
+    {\r
       iv = (int[]) fromShifts2.elementAt(intv++);\r
-      if (iv[0] <= iv[1]) {\r
-        if (fs == -1 && startpos >= iv[0] && startpos <= iv[1]) {\r
+      if (fe_s > -1)\r
+      {\r
+        endpos = iv[0]; // start counting from beginning of interval\r
+        endindx--; // inclusive of endpos\r
+      }\r
+      if (iv[0] <= iv[1])\r
+      {\r
+        if (fs == -1 && startpos >= iv[0] && startpos <= iv[1])\r
+        {\r
           fs = i;\r
         }\r
-        if (fe == -1 && endpos >= iv[0] && endpos <= iv[1]) {\r
+        if (endpos >= iv[0] && endpos <= iv[1])\r
+        {\r
+          if (fe_s == -1)\r
+          {\r
+            fe_s = i;\r
+          }\r
+          if (fe_s != -1)\r
+          {\r
+            if (endpos + endindx <= iv[1])\r
+            {\r
           fe = i;\r
+              endpos = endpos + endindx; // end of end token is within this\r
+                                          // interval\r
         }\r
-      } else {\r
-        if (fs == -1 && startpos <= iv[0] && startpos >= iv[1]) {\r
+            else\r
+            {\r
+              endindx -= iv[1] - endpos; // skip all this interval too\r
+            }\r
+          }\r
+        }\r
+      }\r
+      else\r
+      {\r
+        if (fs == -1 && startpos <= iv[0] && startpos >= iv[1])\r
+        {\r
           fs = i;\r
         }\r
-        if (fe == -1 && endpos <= iv[0] && endpos >= iv[1]) {\r
+        if (endpos <= iv[0] && endpos >= iv[1])\r
+        {\r
+          if (fe_s == -1)\r
+          {\r
+            fe_s = i;\r
+          }\r
+          if (fe_s != -1)\r
+          {\r
+            if (endpos - endindx >= iv[1])\r
+            {\r
           fe = i;\r
+              endpos = endpos - endindx; // end of end token is within this\r
+                                          // interval\r
+        }\r
+            else\r
+            {\r
+              endindx -= endpos - iv[1]; // skip all this interval too\r
+      }\r
+          }\r
         }\r
       }\r
       i++;\r
@@ -477,41 +525,53 @@ public class MapList {
     if (fs == fe && fe == -1)\r
       return null;\r
     Vector ranges = new Vector();\r
-    if (fs <= fe) {\r
+    if (fs <= fe)\r
+    {\r
       intv = fs;\r
       i = fs;\r
       // truncate initial interval\r
       iv = (int[]) fromShifts2.elementAt(intv++);\r
-      iv = new int[] { iv[0], iv[1] };// clone\r
+      iv = new int[]\r
+      { iv[0], iv[1] };// clone\r
       if (i == fs)\r
         iv[0] = startpos;\r
-      while (i != fe) {\r
+      while (i != fe)\r
+      {\r
         ranges.addElement(iv); // add initial range\r
         iv = (int[]) fromShifts2.elementAt(intv++); // get next interval\r
-        iv = new int[] { iv[0], iv[1] };// clone\r
+        iv = new int[]\r
+        { iv[0], iv[1] };// clone\r
         i++;\r
       }\r
       if (i == fe)\r
         iv[1] = endpos;\r
       ranges.addElement(iv); // add only - or final range\r
-    } else {\r
+    }\r
+    else\r
+    {\r
       // walk from end of interval.\r
       i = fromShifts2.size() - 1;\r
-      while (i > fs) {\r
+      while (i > fs)\r
+      {\r
         i--;\r
       }\r
       iv = (int[]) fromShifts2.elementAt(i);\r
-      iv = new int[] { iv[1], iv[0] };// reverse and clone\r
+      iv = new int[]\r
+      { iv[1], iv[0] };// reverse and clone\r
       // truncate initial interval\r
-      if (i == fs) {\r
+      if (i == fs)\r
+      {\r
         iv[0] = startpos;\r
       }\r
-      while (--i != fe) { // fix apparent logic bug when fe==-1\r
+      while (--i != fe)\r
+      { // fix apparent logic bug when fe==-1\r
         ranges.addElement(iv); // add (truncated) reversed interval\r
         iv = (int[]) fromShifts2.elementAt(i);\r
-        iv = new int[] { iv[1], iv[0] }; // reverse and clone\r
+        iv = new int[]\r
+        { iv[1], iv[0] }; // reverse and clone\r
       }\r
-      if (i == fe) {\r
+      if (i == fe)\r
+      {\r
         // interval is already reversed\r
         iv[1] = endpos;\r
       }\r
@@ -519,12 +579,14 @@ public class MapList {
     }\r
     // create array of start end intervals.\r
     int[] range = null;\r
-    if (ranges != null && ranges.size() > 0) {\r
+    if (ranges != null && ranges.size() > 0)\r
+    {\r
       range = new int[ranges.size() * 2];\r
       intv = 0;\r
       intvSize = ranges.size();\r
       i = 0;\r
-      while (intv < intvSize) {\r
+      while (intv < intvSize)\r
+      {\r
         iv = (int[]) ranges.elementAt(intv);\r
         range[i++] = iv[0];\r
         range[i++] = iv[1];\r
@@ -595,24 +657,33 @@ public class MapList {
    * @param fromS\r
    * @param fromE\r
    */\r
-  public static void testMap(MapList ml, int fromS, int fromE) {\r
-    for (int from = 1; from <= 25; from++) {\r
+  public static void testMap(MapList ml, int fromS, int fromE)\r
+  {\r
+    for (int from = 1; from <= 25; from++)\r
+    {\r
       int[] too = ml.shiftFrom(from);\r
       System.out.print("ShiftFrom(" + from + ")==");\r
-      if (too == null) {\r
+      if (too == null)\r
+      {\r
         System.out.print("NaN\n");\r
-      } else {\r
+      }\r
+      else\r
+      {\r
         System.out.print(too[0] + " % " + too[1] + " (" + too[2] + ")");\r
         System.out.print("\t+--+\t");\r
         int[] toofrom = ml.shiftTo(too[0]);\r
-        if (toofrom != null) {\r
-          if (toofrom[0] != from) {\r
-            System.err.println("Mapping not reflexive:" + from + " " + too[0]\r
-                + "->" + toofrom[0]);\r
+        if (toofrom != null)\r
+        {\r
+          if (toofrom[0] != from)\r
+          {\r
+            System.err.println("Mapping not reflexive:" + from + " "\r
+                    + too[0] + "->" + toofrom[0]);\r
           }\r
-          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % "\r
-              + toofrom[1] + " (" + toofrom[2] + ")");\r
-        } else {\r
+          System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0]\r
+                  + " % " + toofrom[1] + " (" + toofrom[2] + ")");\r
+        }\r
+        else\r
+        {\r
           System.out.println("ShiftTo(" + too[0] + ")=="\r
               + "NaN! - not Bijective Mapping!");\r
         }\r
@@ -621,16 +692,23 @@ public class MapList {
     int mmap[][] = ml.makeFromMap();\r
     System.out.println("FromMap : (" + mmap[0][0] + " " + mmap[0][1] + " "\r
         + mmap[0][2] + " " + mmap[0][3] + " ");\r
-    for (int i = 1; i <= mmap[1].length; i++) {\r
-      if (mmap[1][i - 1] == -1) {\r
+    for (int i = 1; i <= mmap[1].length; i++)\r
+    {\r
+      if (mmap[1][i - 1] == -1)\r
+      {\r
         System.out.print(i + "=XXX");\r
 \r
-      } else {\r
+      }\r
+      else\r
+      {\r
         System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));\r
       }\r
-      if (i % 20 == 0) {\r
+      if (i % 20 == 0)\r
+      {\r
         System.out.print("\n");\r
-      } else {\r
+      }\r
+      else\r
+      {\r
         System.out.print(",");\r
       }\r
     }\r
@@ -638,23 +716,32 @@ public class MapList {
     System.out.print("\nTest locateInFrom\n");\r
     {\r
       int f = mmap[0][2], t = mmap[0][3];\r
-      while (f <= t) {\r
+      while (f <= t)\r
+      {\r
         System.out.println("Range " + f + " to " + t);\r
         int rng[] = ml.locateInFrom(f, t);\r
-        if (rng != null) {\r
-          for (int i = 0; i < rng.length; i++) {\r
+        if (rng != null)\r
+        {\r
+          for (int i = 0; i < rng.length; i++)\r
+          {\r
             System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));\r
           }\r
-        } else {\r
+        }\r
+        else\r
+        {\r
           System.out.println("No range!");\r
         }\r
         System.out.print("\nReversed\n");\r
         rng = ml.locateInFrom(t, f);\r
-        if (rng != null) {\r
-          for (int i = 0; i < rng.length; i++) {\r
+        if (rng != null)\r
+        {\r
+          for (int i = 0; i < rng.length; i++)\r
+          {\r
             System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));\r
           }\r
-        } else {\r
+        }\r
+        else\r
+        {\r
           System.out.println("No range!");\r
         }\r
         System.out.print("\n");\r
@@ -666,16 +753,23 @@ public class MapList {
     mmap = ml.makeToMap();\r
     System.out.println("ToMap : (" + mmap[0][0] + " " + mmap[0][1] + " "\r
         + mmap[0][2] + " " + mmap[0][3] + " ");\r
-    for (int i = 1; i <= mmap[1].length; i++) {\r
-      if (mmap[1][i - 1] == -1) {\r
+    for (int i = 1; i <= mmap[1].length; i++)\r
+    {\r
+      if (mmap[1][i - 1] == -1)\r
+      {\r
         System.out.print(i + "=XXX");\r
 \r
-      } else {\r
+      }\r
+      else\r
+      {\r
         System.out.print(i + "=" + (mmap[0][2] + mmap[1][i - 1]));\r
       }\r
-      if (i % 20 == 0) {\r
+      if (i % 20 == 0)\r
+      {\r
         System.out.print("\n");\r
-      } else {\r
+      }\r
+      else\r
+      {\r
         System.out.print(",");\r
       }\r
     }\r
@@ -684,23 +778,32 @@ public class MapList {
     System.out.print("\nTest locateInTo\n");\r
     {\r
       int f = mmap[0][2], t = mmap[0][3];\r
-      while (f <= t) {\r
+      while (f <= t)\r
+      {\r
         System.out.println("Range " + f + " to " + t);\r
         int rng[] = ml.locateInTo(f, t);\r
-        if (rng != null) {\r
-          for (int i = 0; i < rng.length; i++) {\r
+        if (rng != null)\r
+        {\r
+          for (int i = 0; i < rng.length; i++)\r
+          {\r
             System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));\r
           }\r
-        } else {\r
+        }\r
+        else\r
+        {\r
           System.out.println("No range!");\r
         }\r
         System.out.print("\nReversed\n");\r
         rng = ml.locateInTo(t, f);\r
-        if (rng != null) {\r
-          for (int i = 0; i < rng.length; i++) {\r
+        if (rng != null)\r
+        {\r
+          for (int i = 0; i < rng.length; i++)\r
+          {\r
             System.out.print(rng[i] + ((i % 2 == 0) ? "," : ";"));\r
           }\r
-        } else {\r
+        }\r
+        else\r
+        {\r
           System.out.println("No range!");\r
         }\r
         f++;\r
@@ -711,15 +814,27 @@ public class MapList {
 \r
   }\r
 \r
-  public static void main(String argv[]) {\r
-    MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {\r
-        51, 1 }, 1, 3);\r
-    MapList ml1 = new MapList(new int[] { 1, 3, 17, 4 }, new int[] { 51, 1 },\r
-        1, 3);\r
-    MapList ml2 = new MapList(new int[] { 1, 60 }, new int[] { 1, 20 }, 3, 1);\r
+  public static void main(String argv[])\r
+  {\r
+    MapList ml = new MapList(new int[]\r
+    { 1, 5, 10, 15, 25, 20 }, new int[]\r
+    { 51, 1 }, 1, 3);\r
+    MapList ml1 = new MapList(new int[]\r
+    { 1, 3, 17, 4 }, new int[]\r
+    { 51, 1 }, 1, 3);\r
+    MapList ml2 = new MapList(new int[]\r
+    { 1, 60 }, new int[]\r
+    { 1, 20 }, 3, 1);\r
     // test internal consistency\r
     int to[] = new int[51];\r
     MapList.testMap(ml, 1, 60);\r
+    MapList mldna = new MapList(new int[]\r
+    { 2, 2, 6, 8, 12, 16 }, new int[]\r
+    { 1, 3 }, 3, 1);\r
+    int[] frm = mldna.locateInFrom(1, 1);\r
+    testLocateFrom(mldna, 1, 1, new int[]\r
+    { 2, 2, 6, 7 });\r
+    MapList.testMap(mldna, 1, 3);\r
     /*\r
      * for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]\r
      * toofrom=ml.shiftFrom(too[0]);\r
@@ -731,13 +846,53 @@ public class MapList {
                                     // working!\r
   }\r
 \r
+  private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)\r
+  {\r
+    int[] frm = mldna.locateInFrom(i, j);\r
+    if (frm == ks || java.util.Arrays.equals(frm, ks))\r
+    {\r
+      System.out.println("Success test locate from " + i + " to " + j);\r
+    }\r
+    else\r
+    {\r
+      System.err.println("Failed test locate from " + i + " to " + j);\r
+      for (int c = 0; c < frm.length; c++)\r
+      {\r
+        System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));\r
+      }\r
+      System.err.println("Expected");\r
+      for (int c = 0; c < ks.length; c++)\r
+      {\r
+        System.err.print(ks[c] + ((c % 2 == 0) ? "," : ";"));\r
+      }\r
+    }\r
+  }\r
+\r
   /**\r
    * \r
    * @return a MapList whose From range is this maplist's To Range, and vice\r
    *         versa\r
    */\r
-  public MapList getInverse() {\r
+  public MapList getInverse()\r
+  {\r
     return new MapList(getToRanges(), getFromRanges(), getToRatio(),\r
         getFromRatio());\r
   }\r
+\r
+  /**\r
+   * test for containment rather than equivalence to another mapping\r
+   * @param map to be tested for containment\r
+   * @return true if local or mapped range map contains or is contained by this mapping \r
+   */\r
+  public boolean containsEither(boolean local, MapList map)\r
+  {\r
+    if (local)\r
+    {\r
+      return ((getFromLowest()>=map.getFromLowest() && getFromHighest()<=map.getFromHighest())\r
+        || (getFromLowest()<=map.getFromLowest() && getFromHighest()>=map.getFromHighest()));\r
+    } else {\r
+      return ((getToLowest()>=map.getToLowest() && getToHighest()<=map.getToHighest())\r
+              || (getToLowest()<=map.getToLowest() && getToHighest()>=map.getToHighest()));\r
+    }\r
+  }\r
 }\r