uses jalviewfilechooser

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1c6c453..2f40de4 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -21,11 +21,14 @@ public class AlignViewport
   boolean showBoxes=true;\r
   boolean wrapAlignment=false;\r
   boolean renderGaps = 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
+  SequenceGroup selectionGroup = new SequenceGroup();\r
 \r
   RendererI renderer = new SequenceRenderer(this);\r
 \r
@@ -37,11 +40,8 @@ public class AlignViewport
   Font            font = new Font("SansSerif",Font.PLAIN,10);\r
   AlignmentI      alignment;\r
 \r
-  Selection       sel    = new Selection(this);\r
   ColumnSelection colSel = new ColumnSelection();\r
 \r
-  OutputGenerator og;\r
-\r
   String visibleConsensus;\r
 \r
   int threshold;\r
@@ -49,10 +49,6 @@ 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
@@ -89,6 +85,10 @@ public class AlignViewport
     setFont( font );\r
  }\r
 \r
+ public void showSequenceFeatures(boolean b)\r
+ {\r
+   showSequenceFeatures = b;\r
+ }\r
 \r
   public String getVisibleConsensus()\r
   {\r
@@ -115,16 +115,17 @@ public class AlignViewport
     return consensus;\r
   }\r
 \r
-  public SequenceGroup getRubberbandGroup()\r
+  public SequenceGroup getSelectionGroup()\r
   {\r
-    return rubberbandGroup;\r
+    return selectionGroup;\r
   }\r
 \r
-  public void setRubberbandGroup(SequenceGroup sg)\r
+  public void setSelectionGroup(SequenceGroup sg)\r
   {\r
-    rubberbandGroup = sg;\r
+    selectionGroup = sg;\r
   }\r
 \r
+\r
  public boolean getConservationSelected()\r
  {\r
    return conservationColourSelected;\r
@@ -135,6 +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
@@ -314,15 +325,11 @@ public class AlignViewport
     }\r
     return -1;\r
   }\r
-  public Selection getSelection() {\r
-    return sel;\r
-  }\r
+\r
   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
@@ -341,27 +348,12 @@ 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
+  public void setColourAppliesToAllGroups(boolean b)\r
+  {   colourAppliesToAllGroups = b; }\r
 \r
-    public void setKmers(Vector kmers) {\r
-        this.kmers = kmers;\r
-    }\r
-\r
-    public Vector getKmers() {\r
-        return this.kmers;\r
-    }\r
+  public boolean getColourAppliesToAllGroups()\r
+  {return colourAppliesToAllGroups; }\r
 \r
 \r
 }\r