only set graphics black once at beginning of text

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7352495..7719f02 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -21,10 +21,12 @@ public class AlignViewport
   boolean showBoxes=true;\r
   boolean wrapAlignment=false;\r
   boolean renderGaps = true;\r
-  boolean showSequenceFeatures = true;\r
+  boolean showSequenceFeatures = false;\r
 \r
+  boolean colourAppliesToAllGroups = true;\r
   ColourSchemeI globalColourScheme = null;\r
   boolean conservationColourSelected = false;\r
+  boolean abovePIDThreshold = false;\r
 \r
   SequenceGroup rubberbandGroup = null;\r
 \r
@@ -41,8 +43,6 @@ public class AlignViewport
   Selection       sel    = new Selection(this);\r
   ColumnSelection colSel = new ColumnSelection();\r
 \r
-  OutputGenerator og;\r
-\r
   String visibleConsensus;\r
 \r
   int threshold;\r
@@ -50,10 +50,6 @@ public class AlignViewport
 \r
   NJTree currentTree = null;\r
 \r
-  int window   = 50;\r
-  int baseline = 30;\r
-\r
-  Vector kmers;\r
 \r
   public AlignViewport(AlignmentI da,\r
                        boolean showScores,\r
@@ -140,6 +136,16 @@ public class AlignViewport
    conservationColourSelected = b;\r
  }\r
 \r
+ public boolean getAbovePIDThreshold()\r
+ {\r
+   return abovePIDThreshold;\r
+ }\r
+\r
+ public void setAbovePIDThreshold(boolean b)\r
+ {\r
+   abovePIDThreshold = b;\r
+ }\r
+\r
   public int getStartRes() {\r
     return startRes;\r
   }\r
@@ -325,9 +331,7 @@ public class AlignViewport
   public ColumnSelection getColumnSelection() {\r
     return colSel;\r
   }\r
-  public OutputGenerator getOutputGenerator() {\r
-    return og;\r
-  }\r
+\r
   public void resetSeqLimits(int height) {\r
     setStartSeq(0);\r
     setEndSeq(height/getCharHeight());\r
@@ -346,27 +350,12 @@ public class AlignViewport
     public RendererI getRenderer() {\r
        return renderer;\r
     }\r
-    public int getPIDWindow() {\r
-       return window;\r
-    }\r
-    public void setPIDWindow(int window) {\r
-       this.window = window;\r
-    }\r
-\r
-    public int getPIDBaseline() {\r
-       return baseline;\r
-    }\r
-    public void setPIDBaseline(int baseline) {\r
-       this.baseline = baseline;\r
-    }\r
 \r
-    public void setKmers(Vector kmers) {\r
-        this.kmers = kmers;\r
-    }\r
+  public void setColourAppliesToAllGroups(boolean b)\r
+  {   colourAppliesToAllGroups = b; }\r
 \r
-    public Vector getKmers() {\r
-        return this.kmers;\r
-    }\r
+  public boolean getColourAppliesToAllGroups()\r
+  {return colourAppliesToAllGroups; }\r
 \r
 \r
 }\r