JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index e6f035f..1aa29e0 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
@@ -69,6 +71,8 @@ public class Conservation
 
   int[][] cons2;
 
+  private String[] consSymbs;
+
   /**
    * Creates a new Conservation object.
    * 
@@ -364,17 +368,17 @@ public class Conservation
     {
       consString.append('-');
     }
-
+    consSymbs = new String[end-start+1];
     for (int i = start; i <= end; i++)
     {
       gapcons = countConsNGaps(i);
       totGaps = gapcons[1];
       pgaps = ((float) totGaps * 100) / (float) sequences.length;
-
+      consSymbs[i-start]=new String();
+      
       if (percentageGaps > pgaps)
       {
         resultHash = total[i - start];
-
         // Now find the verdict
         count = 0;
         enumeration = resultHash.keys();
@@ -383,12 +387,12 @@ public class Conservation
         {
           type = (String) enumeration.nextElement();
           result = (Integer) resultHash.get(type);
-
           // Do we want to count +ve conservation or +ve and -ve cons.?
           if (consflag)
           {
             if (result.intValue() == 1)
             {
+              consSymbs[i-start] = type+" "+consSymbs[i-start];
               count++;
             }
           }
@@ -396,6 +400,14 @@ public class Conservation
           {
             if (result.intValue() != -1)
             {
+              { 
+                 if (result.intValue()==0) {
+                   consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
+                 } else {
+                   consSymbs[i-start] = type+" "+consSymbs[i-start];
+                 }
+              }
+              
               count++;
             }
           }
@@ -681,7 +693,7 @@ public class Conservation
       float vprop = value - min;
       vprop /= max;
       conservation.annotations[i] = new Annotation(String.valueOf(c),
-              String.valueOf(value), ' ', value, new Color(minR
+              consSymbs[i-start], ' ', value, new Color(minR
                       + (maxR * vprop), minG + (maxG * vprop), minB
                       + (maxB * vprop)));