merge from 2_4_Release branch

[jalview.git] / src / jalview / analysis / Conservation.java

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index c216471..31a4b66 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.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
@@ -45,9 +45,10 @@ public class Conservation
   Hashtable[] total;
 
   boolean canonicaliseAa = true; // if true then conservation calculation will
-                                  // map all symbols to canonical aa numbering
-                                  // rather than consider conservation of that
-                                  // symbol
+
+  // map all symbols to canonical aa numbering
+  // rather than consider conservation of that
+  // symbol
 
   /** Stores calculated quality values */
   public Vector quality;
@@ -95,7 +96,7 @@ public class Conservation
     this.end = end;
 
     maxLength = end - start + 1; // default width includes bounds of
-                                  // calculation
+    // calculation
 
     int s, sSize = sequences.size();
     SequenceI[] sarray = new SequenceI[sSize];
@@ -112,8 +113,8 @@ public class Conservation
   }
 
   /**
-   * Translate sequence i into a numerical 
-   * representation and store it in the i'th position of the seqNums array.
+   * Translate sequence i into a numerical representation and store it in the
+   * i'th position of the seqNums array.
    * 
    * @param i
    */
@@ -146,7 +147,7 @@ public class Conservation
         }
 
         sqnum = new int[len + 1]; // better to always make a new array -
-                                  // sequence can change its length
+        // sequence can change its length
         sqnum[0] = sq.hashCode();
 
         for (j = 1; j <= len; j++)
@@ -276,7 +277,8 @@ public class Conservation
   }
 
   /*****************************************************************************
-   * count conservation  for the j'th column of the alignment
+   * count conservation for the j'th column of the alignment
+   * 
    * @return { gap count, conserved residue count}
    */
   public int[] countConsNGaps(int j)
@@ -477,8 +479,7 @@ public class Conservation
        * maxj = -1;
        * 
        * for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j];
-       * maxi = i; maxj = j; }
-       *  } }
+       * maxi = i; maxj = j; } } }
        */
     }
   }