merge from 2_4_Release branch

[jalview.git] / src / jalview / util / MapList.java

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 90dfc8c..6405f98 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -494,7 +494,7 @@ public class MapList
     // inefficient implementation
     int fromStart[] = shiftTo(start);
     int fromEnd[] = shiftTo(end); // needs to be inclusive of end of symbol
-                                  // position
+    // position
     if (fromStart == null || fromEnd == null)
       return null;
     int iv[] = getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
@@ -539,15 +539,15 @@ public class MapList
     startpos = fromStart[0]; // first position in fromStart
     endpos = fromEnd[0]; // last position in fromEnd
     int endindx = (fromRatio2 - 1); // additional positions to get to last
-                                    // position from endpos
+    // position from endpos
     int intv = 0, intvSize = fromShifts2.size();
     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))
+    while (intv < intvSize && (fs == -1 || fe == -1))
     {
       iv = (int[]) fromShifts2.elementAt(intv++);
-      if (fe_s>-1)
+      if (fe_s > -1)
       {
         endpos = iv[0]; // start counting from beginning of interval
         endindx--; // inclusive of endpos
@@ -569,11 +569,12 @@ public class MapList
             if (endpos + endindx <= iv[1])
             {
               fe = i;
-              endpos = endpos + endindx; // end of end token is within this interval
+              endpos = endpos + endindx; // end of end token is within this
+                                          // interval
             }
             else
             {
-              endindx -= iv[1] - endpos;  // skip all this interval too
+              endindx -= iv[1] - endpos; // skip all this interval too
             }
           }
         }
@@ -595,11 +596,12 @@ public class MapList
             if (endpos - endindx >= iv[1])
             {
               fe = i;
-              endpos = endpos - endindx; // end of end token is within this interval
+              endpos = endpos - endindx; // end of end token is within this
+                                          // interval
             }
             else
             {
-              endindx -= endpos-iv[1]; // skip all this interval too
+              endindx -= endpos - iv[1]; // skip all this interval too
             }
           }
         }
@@ -922,10 +924,13 @@ public class MapList
     // 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);
+    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]);
@@ -933,17 +938,19 @@ public class MapList
      * "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]); }
      */
     System.out.print("Success?\n"); // if we get here - something must be
-                                    // working!
+    // 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))
+    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);
+      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) ? "," : ";"));