From ac07859006686a2c62bcf57b24742eb610bc46f0 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 14 Apr 2005 14:43:25 +0000
Subject: [PATCH] consistent percentage gaps filter for conservation
 calculation.

---
 src/jalview/gui/AlignFrame.java     |    4 ++--
 src/jalview/gui/AlignViewport.java  |   11 ++++++-----
 src/jalview/gui/AlignmentPanel.java |    2 +-
 src/jalview/gui/PopupMenu.java      |    2 +-
 src/jalview/gui/TreeCanvas.java     |    2 +-
 5 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3048b2c..c1a7105 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -783,7 +783,7 @@ public class AlignFrame extends GAlignFrame
                                             sg.sequences, sg.getStartRes(),
                                             sg.getEndRes());
           c.calculate();
-          c.verdict(false, 100);
+          c.verdict(false, viewport.ConsPercGaps);
           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
           sg.cs = ccs;
@@ -827,7 +827,7 @@ if ( viewport.getConservationSelected() )
                                      al.getWidth());
 
    c.calculate();
-   c.verdict(false, 100);
+   c.verdict(false, viewport.ConsPercGaps);
 
    ccs = new ConservationColourScheme(c, cs);
 
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5535dbb..89aac5c 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -79,15 +79,16 @@ public class AlignViewport
   AlignmentAnnotation conservation;
   AlignmentAnnotation quality;
 
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
   public void updateConservation()
   {
-    int percGaps = 100; // JBPNote : This should be a scalable property!
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 1,
         alignment.getSequences(), 0,
         alignment.getWidth());
     cons.calculate();
-    cons.verdict(false, percGaps);
+    cons.verdict(false, ConsPercGaps);
     cons.findQuality();
     int alWidth = alignment.getWidth();
     Annotation [] annotations = new Annotation[alWidth];
@@ -123,14 +124,14 @@ public class AlignViewport
       value = ((Double) cons.quality.get(i)).floatValue();
       vprop = value - qmin;
       vprop/=qmax;
-      qannotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      new String().valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+      qannotations[i] = new Annotation(" ",
+                                      String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
     }
 
     if(conservation==null)
     {
       conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than "+percGaps+"% gaps",
+                                             "Conservation of total alignment less than "+ConsPercGaps+"% gaps",
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e0a1cac..0cbdfbe 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -248,7 +248,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
                             al.getWidth() );
 
        c.calculate();
-       c.verdict(false, 100);
+       c.verdict(false, av.ConsPercGaps);
        ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
        av.setGlobalColourScheme( ccs );
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8d747c2..8d505ea 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -458,7 +458,7 @@ else // remove PIDColouring
                                           ap.av.alignment.getWidth());
 
         c.calculate();
-        c.verdict(false, 100);
+        c.verdict(false, ap.av.ConsPercGaps);
         ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
 
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index e4d695d..600683f 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -447,7 +447,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
                                                       sg.getEndRes());
 
                     c.calculate();
-                    c.verdict(false, 100);
+                    c.verdict(false, av.ConsPercGaps);
                     ccs = new ConservationColourScheme(c, ccs.cs);
 
                     sg.cs = ccs;
-- 
1.7.10.2