JAL-885 more efficient calculation and robust for mismatch between WUSS and alignment...

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 9e9471f..6957b5c 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -85,9 +85,8 @@ 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;
     this.threshold = threshold;
@@ -100,15 +99,21 @@ public class Conservation
     int s, sSize = sequences.size();
     SequenceI[] sarray = new SequenceI[sSize];
     this.sequences = sarray;
-
+    try {
     for (s = 0; s < sSize; s++)
     {
-      sarray[s] = (SequenceI) sequences.elementAt(s);
+      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;
+    }
   }
 
   /**
@@ -271,7 +276,9 @@ public class Conservation
         }
       }
 
-      total[i - start] = resultHash;
+      if (total.length>0) {
+        total[i - start] = resultHash;
+      }
     }
   }
 
@@ -687,4 +694,42 @@ 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;
+  }
 }