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

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);
 

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index c30fdad..7b0d4fb 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1206,11 +1206,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     if (conservationMenuItem.getState())
     {
-
-      sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
-              sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
-                      .getAlignment().getWidth(), false, ap.av
-                      .getConsPercGaps(), false));
+      sg.cs.setConservation(Conservation.calculateConservation("Group", sg
+              .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+              .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
+              false));
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 3b509e5..8292a5a 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -676,8 +676,8 @@ public class TreeCanvas extends Panel implements MouseListener,
       if (av.getGlobalColourScheme() != null
               && av.getGlobalColourScheme().conservationApplied())
       {
-        Conservation c = new Conservation("Group", 3,
-                sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
+        Conservation c = new Conservation("Group", sg.getSequences(null),
+                sg.getStartRes(), sg.getEndRes());
 
         c.calculate();
         c.verdict(false, av.getConsPercGaps());

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 2870a2c..ca90003 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -543,8 +543,8 @@ public class SequenceGroup implements AnnotatedCollectionI
       if ((conservation != null)
               || (cs != null && cs.conservationApplied()))
       {
-        Conservation c = new Conservation(groupName, 3, sequences,
-                startRes, endRes + 1);
+        Conservation c = new Conservation(groupName, sequences, startRes,
+                endRes + 1);
         c.calculate();
         c.verdict(false, consPercGaps);
         if (conservation != null)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1c90889..bc5e1d8 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -3401,8 +3401,8 @@ public class Jalview2XML
         }
         if (jGroup.getConsThreshold() != 0)
         {
-          Conservation c = new Conservation("All", 3,
-                  sg.getSequences(null), 0, sg.getWidth() - 1);
+          Conservation c = new Conservation("All", sg.getSequences(null),
+                  0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index f8a296f..3b39be7 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -359,8 +359,8 @@ public class Jalview2XML_V1
 
         if (groups[i].getConsThreshold() != 0)
         {
-          Conservation c = new Conservation("All", 3,
-                  sg.getSequences(null), 0, sg.getWidth() - 1);
+          Conservation c = new Conservation("All", sg.getSequences(null),
+                  0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index e2d397f..7b70ff0 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -2048,7 +2048,7 @@ public class PopupMenu extends JPopupMenu
     if (conservationMenuItem.isSelected())
     {
       // JBPNote: Conservation name shouldn't be i18n translated
-      Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
+      Conservation c = new Conservation("Group", sg.getSequences(ap.av
               .getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1);
 

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 0e513f7..84fd82f 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1017,8 +1017,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         if (aps[a].av.getGlobalColourScheme() != null
                 && aps[a].av.getGlobalColourScheme().conservationApplied())
         {
-          Conservation c = new Conservation("Group", 3,
-                  sg.getSequences(null), sg.getStartRes(), sg.getEndRes());
+          Conservation c = new Conservation("Group", sg.getSequences(null),
+                  sg.getStartRes(), sg.getEndRes());
           c.calculate();
           c.verdict(false, aps[a].av.getConsPercGaps());
           sg.cs.setConservation(c);

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 34fdabe..61a30f8 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1637,9 +1637,8 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("consThreshold"))
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
-          Conservation c = new Conservation("Group", 3,
-                  sg.getSequences(null), sg.getStartRes(),
-                  sg.getEndRes() + 1);
+          Conservation c = new Conservation("Group", sg.getSequences(null),
+                  sg.getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25); // TODO: refer to conservation percent threshold

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 254a201..57258ef 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1867,7 +1867,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       cs.setConsensus(hconsensus);
       if (cs.conservationApplied())
       {
-        cs.setConservation(Conservation.calculateConservation("All", 3,
+        cs.setConservation(Conservation.calculateConservation("All",
                 alignment.getSequences(), 0, alignment.getWidth(), false,
                 getConsPercGaps(), false));
       }

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 11ec521..e71c4f5 100644 (file)
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -94,7 +94,7 @@ public class ConservationThread extends AlignCalcWorker
       }
       try
       {
-        cons = Conservation.calculateConservation("All", 3,
+        cons = Conservation.calculateConservation("All",
                 alignment.getSequences(), 0, alWidth - 1, false,
                 ConsPercGaps, quality != null);
       } catch (IndexOutOfBoundsException x)

diff --git a/test/jalview/analysis/ConservationTest.java b/test/jalview/analysis/ConservationTest.java
index c419687..123fcd6 100644 (file)
--- a/test/jalview/analysis/ConservationTest.java
+++ b/test/jalview/analysis/ConservationTest.java
@@ -48,7 +48,7 @@ public class ConservationTest
     seqs.add(new Sequence("seq3", "VG-Y"));
     seqs.add(new Sequence("seq4", "VGNW"));
 
-    Conservation cons = new Conservation("", 3, seqs, 0, 50);
+    Conservation cons = new Conservation("", seqs, 0, 50);
     int[] counts = cons.countConservationAndGaps(0);
     assertEquals(counts[0], 1); // conserved
     assertEquals(counts[1], 1); // gap count