X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=f12d8016905fbc9dd990d62f340624d2d2c91593;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=8641629d0337c35ee03f607ba2721ce833face87;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 8641629..f12d801 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,27 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
 
-import java.awt.Color;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * Calculates conservation values for a given set of sequences
@@ -69,6 +77,8 @@ public class Conservation
 
   int[][] cons2;
 
+  private String[] consSymbs;
+
   /**
    * Creates a new Conservation object.
    * 
@@ -104,7 +114,7 @@ public class Conservation
     {
       for (s = 0; s < sSize; s++)
       {
-        sarray[s] = (SequenceI) sequences.get(s);
+        sarray[s] = sequences.get(s);
         if (sarray[s].getLength() > maxLength)
         {
           maxLength = sarray[s].getLength();
@@ -270,8 +280,7 @@ public class Conservation
                 resultHash.put(type, ht.get("-"));
               }
             }
-            else if (((Integer) resultHash.get(type)).equals((Integer) ht
-                    .get(res)) == false)
+            else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
             {
               resultHash.put(type, new Integer(-1));
             }
@@ -364,17 +373,17 @@ 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;
+      pgaps = ((float) totGaps * 100) / 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 +392,12 @@ 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 +405,17 @@ 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++;
             }
           }
@@ -667,7 +687,7 @@ public class Conservation
 
       if (Character.isDigit(c))
       {
-        value = (int) (c - '0');
+        value = c - '0';
       }
       else if (c == '*')
       {
@@ -680,10 +700,12 @@ public class Conservation
 
       float vprop = value - min;
       vprop /= max;
+      int consp = i - start;
+      String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+              : "";
       conservation.annotations[i] = new Annotation(String.valueOf(c),
-              String.valueOf(value), ' ', value, new Color(minR
-                      + (maxR * vprop), minG + (maxG * vprop), minB
-                      + (maxB * vprop)));
+              conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+                      + (maxG * vprop), minB + (maxB * vprop)));
 
       // Quality calc
       if (quality2 != null)