X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=1aa29e0f85885efa9223338770df8ec4154ac5c1;hb=e309b8d9bd62fb304fdd612c7385e76027d2f2d7;hp=04914fc181863d11a7e7cf4e744de6c52c1464ae;hpb=be415b56e8ce1bc00f5004c64793ce5d0cb17be8;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 04914fc..1aa29e0 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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;
 
@@ -68,6 +71,8 @@ public class Conservation
 
   int[][] cons2;
 
+  private String[] consSymbs;
+
   /**
    * Creates a new Conservation object.
    * 
@@ -85,7 +90,7 @@ public class Conservation
    *          end residue position
    */
   public Conservation(String name, Hashtable propHash, int threshold,
-          Vector sequences, int start, int end)
+          List<SequenceI> sequences, int start, int end)
   {
     this.name = name;
     this.propHash = propHash;
@@ -99,20 +104,22 @@ public class Conservation
     int s, sSize = sequences.size();
     SequenceI[] sarray = new SequenceI[sSize];
     this.sequences = sarray;
-    try {
-    for (s = 0; s < sSize; s++)
+    try
     {
-      sarray[s] = (SequenceI) sequences.elementAt(s);
-      if (sarray[s].getLength() > maxLength)
+      for (s = 0; s < sSize; s++)
       {
-        maxLength = sarray[s].getLength();
+        sarray[s] = (SequenceI) sequences.get(s);
+        if (sarray[s].getLength() > maxLength)
+        {
+          maxLength = sarray[s].getLength();
+        }
       }
-    }
     } catch (ArrayIndexOutOfBoundsException ex)
     {
-      // bail - another thread has modified the sequence array, so the current calculation is probably invalid. 
-      this.sequences=new SequenceI[0];
-      maxLength=0;
+      // bail - another thread has modified the sequence array, so the current
+      // calculation is probably invalid.
+      this.sequences = new SequenceI[0];
+      maxLength = 0;
     }
   }
 
@@ -276,7 +283,8 @@ public class Conservation
         }
       }
 
-      if (total.length>0) {
+      if (total.length > 0)
+      {
         total[i - start] = resultHash;
       }
     }
@@ -360,17 +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();
@@ -379,12 +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++;
             }
           }
@@ -392,6 +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++;
             }
           }
@@ -677,7 +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)));
 
@@ -694,4 +710,61 @@ public class Conservation
       }
     }
   }
+
+  /**
+   * construct and call the calculation methods on a new Conservation object
+   * 
+   * @param name
+   *          - name of conservation
+   * @param consHash
+   *          - hash table of properties for each amino acid (normally
+   *          ResidueProperties.propHash)
+   * @param threshold
+   *          - minimum number of conserved residues needed to indicate
+   *          conservation (typically 3)
+   * @param seqs
+   * @param start
+   *          first column in calculation window
+   * @param end
+   *          last column in calculation window
+   * @param posOrNeg
+   *          positive (true) or negative (false) conservation
+   * @param consPercGaps
+   *          percentage of gaps tolerated in column
+   * @param calcQuality
+   *          flag indicating if alignment quality should be calculated
+   * @return Conservation object ready for use in visualization
+   */
+  public static Conservation calculateConservation(String name,
+          Hashtable consHash, int threshold, List<SequenceI> seqs,
+          int start, int end, boolean posOrNeg, int consPercGaps,
+          boolean calcQuality)
+  {
+    Conservation cons = new Conservation(name, consHash, threshold, seqs,
+            start, end);
+    return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
+  }
+
+  /**
+   * @param b
+   *          positive (true) or negative (false) conservation
+   * @param consPercGaps
+   *          percentage of gaps tolerated in column
+   * @param calcQuality
+   *          flag indicating if alignment quality should be calculated
+   * @return Conservation object ready for use in visualization
+   */
+  public static Conservation calculateConservation(Conservation cons,
+          boolean b, int consPercGaps, boolean calcQuality)
+  {
+    cons.calculate();
+    cons.verdict(b, consPercGaps);
+
+    if (calcQuality)
+    {
+      cons.findQuality();
+    }
+
+    return cons;
+  }
 }