JAL-98 JAL-1854 encapsulate 'magic number' threshold 3 in Conservation

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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 7e72dcd..7b9da46 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -23,9 +23,9 @@ package jalview.analysis;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ResidueCount;
+import jalview.datamodel.ResidueCount.SymbolCounts;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.ResidueCount.SymbolCounts;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 
@@ -38,12 +38,15 @@ import java.util.Vector;
 
 /**
  * Calculates conservation values for a given set of sequences
- * 
- * @author $author$
- * @version $Revision$
  */
 public class Conservation
 {
+  /*
+   * need to have a minimum of 3% of sequences with a residue
+   * for it to be included in the conservation calculation
+   */
+  private static final int THRESHOLD_PERCENT = 3;
+
   private static final int TOUPPERCASE = 'a' - 'A';
 
   SequenceI[] sequences;
@@ -92,12 +95,10 @@ public class Conservation
   private String[] consSymbs;
 
   /**
-   * Creates a new Conservation object.
+   * Constructor using default threshold of 3%
    * 
    * @param name
    *          Name of conservation
-   * @param threshold
-   *          to count the residues in residueHash(). commonly used value is 3
    * @param sequences
    *          sequences to be used in calculation
    * @param start
@@ -105,6 +106,27 @@ public class Conservation
    * @param end
    *          end residue position
    */
+  public Conservation(String name, List<SequenceI> sequences, int start,
+          int end)
+  {
+    this(name, THRESHOLD_PERCENT, sequences, start, end);
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param name
+   *          Name of conservation
+   * @param threshold
+   *          percentage of sequences at or below which property conservation is
+   *          ignored
+   * @param sequences
+   *          sequences to be used in calculation
+   * @param start
+   *          start column position
+   * @param end
+   *          end column position
+   */
   public Conservation(String name, int threshold,
           List<SequenceI> sequences, int start, int end)
   {
@@ -210,7 +232,9 @@ public class Conservation
     {
       ResidueCount values = countResidues(column);
 
-      // TODO is threshold a percentage or count value?
+      /*
+       * percentage count at or below which we ignore residues
+       */
       int thresh = (threshold * height) / 100;
 
       /*
@@ -781,9 +805,6 @@ public class Conservation
    * 
    * @param name
    *          - name of conservation
-   * @param threshold
-   *          - minimum number of conserved residues needed to indicate
-   *          conservation (typically 3)
    * @param seqs
    * @param start
    *          first column in calculation window
@@ -799,10 +820,10 @@ public class Conservation
    * @return Conservation object ready for use in visualization
    */
   public static Conservation calculateConservation(String name,
-          int threshold, List<SequenceI> seqs, int start, int end,
-          boolean positiveOnly, int maxPercentGaps, boolean calcQuality)
+          List<SequenceI> seqs, int start, int end, boolean positiveOnly,
+          int maxPercentGaps, boolean calcQuality)
   {
-    Conservation cons = new Conservation(name, threshold, seqs, start, end);
+    Conservation cons = new Conservation(name, seqs, start, end);
     cons.calculate();
     cons.verdict(positiveOnly, maxPercentGaps);