JAL-1620 version bump and release notes

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index b557c5a..0625a9a 100755 (executable)
--- 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 2.8.2b1)
+ * Copyright (C) 2014 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;
 
@@ -85,9 +88,8 @@ 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;
@@ -100,14 +102,22 @@ public class Conservation
     int s, sSize = sequences.size();
     SequenceI[] sarray = new SequenceI[sSize];
     this.sequences = sarray;
-
-    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;
     }
   }
 
@@ -271,7 +281,10 @@ public class Conservation
         }
       }
 
-      total[i - start] = resultHash;
+      if (total.length > 0)
+      {
+        total[i - start] = resultHash;
+      }
     }
   }
 
@@ -687,4 +700,61 @@ 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;
+  }
 }