X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7719f024b8ed750bea0db1900adc0a288e46b416;hb=00386d5511d779b555e93dbf71f33675937e1570;hp=1324c1ecc40fe43c01619e902185787a41913333;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1324c1e..7719f02 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -4,6 +4,7 @@ import java.awt.*;
 import jalview.io.*;
 import jalview.analysis.NJTree;
 import jalview.datamodel.*;
+import jalview.schemes.*;
 import java.util.*;
 
 public class AlignViewport
@@ -14,31 +15,34 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
-  boolean showScores;
-  boolean showText;
-  boolean showColourText;
-  boolean showBoxes;
-  boolean wrapAlignment;
+  boolean showScores=false;
+  boolean showText=true;
+  boolean showColourText=false;
+  boolean showBoxes=true;
+  boolean wrapAlignment=false;
+  boolean renderGaps = true;
+  boolean showSequenceFeatures = false;
 
-  boolean groupEdit    = false;
+  boolean colourAppliesToAllGroups = true;
+  ColourSchemeI globalColourScheme = null;
+  boolean conservationColourSelected = false;
+  boolean abovePIDThreshold = false;
 
-  RendererI renderer = new SequenceRenderer();
+  SequenceGroup rubberbandGroup = null;
+
+  RendererI renderer = new SequenceRenderer(this);
 
   int             charHeight;
-  double          charWidth;
+  int             charWidth;
   int             chunkWidth;
   int             chunkHeight;
 
-  Color           backgroundColour;
-
   Font            font = new Font("SansSerif",Font.PLAIN,10);
   AlignmentI      alignment;
 
-  Selection       sel    = new Selection();
+  Selection       sel    = new Selection(this);
   ColumnSelection colSel = new ColumnSelection();
 
-  OutputGenerator og;
-
   String visibleConsensus;
 
   int threshold;
@@ -46,10 +50,6 @@ public class AlignViewport
 
   NJTree currentTree = null;
 
-  int window   = 50;
-  int baseline = 30;
-
-  Vector kmers;
 
   public AlignViewport(AlignmentI da,
                        boolean showScores,
@@ -86,18 +86,10 @@ public class AlignViewport
     setFont( font );
  }
 
-  public AlignViewport(int startRes, int endRes,
-                       int startSeq, int endSeq,
-                       boolean showScores,
-                       boolean showText,
-                       boolean showBoxes,
-                       boolean wrapAlignment,
-                       Color backgroundColour) {
-    this(startRes,endRes,startSeq,endSeq,showScores,showText,showBoxes,wrapAlignment);
-
-    this.backgroundColour = backgroundColour;
-  }
-
+ public void showSequenceFeatures(boolean b)
+ {
+   showSequenceFeatures = b;
+ }
 
   public String getVisibleConsensus()
   {
@@ -105,7 +97,6 @@ public class AlignViewport
   }
 
   Vector consensus = new Vector();
-
   public Vector getConsensus(boolean recalculate)
   {
     if(recalculate || consensus.size()<1)
@@ -125,6 +116,35 @@ public class AlignViewport
     return consensus;
   }
 
+  public SequenceGroup getRubberbandGroup()
+  {
+    return rubberbandGroup;
+  }
+
+  public void setRubberbandGroup(SequenceGroup sg)
+  {
+    rubberbandGroup = sg;
+  }
+
+ public boolean getConservationSelected()
+ {
+   return conservationColourSelected;
+ }
+
+ public void setConservationSelected(boolean b)
+ {
+   conservationColourSelected = b;
+ }
+
+ public boolean getAbovePIDThreshold()
+ {
+   return abovePIDThreshold;
+ }
+
+ public void setAbovePIDThreshold(boolean b)
+ {
+   abovePIDThreshold = b;
+ }
 
   public int getStartRes() {
     return startRes;
@@ -138,6 +158,16 @@ public class AlignViewport
     return startSeq;
   }
 
+  public void setGlobalColourScheme(ColourSchemeI cs)
+  {
+     globalColourScheme = cs;
+  }
+
+  public ColourSchemeI getGlobalColourScheme()
+  {
+    return globalColourScheme;
+  }
+
 
   public void setStartRes(int res) {
     this.startRes = res;
@@ -180,10 +210,10 @@ public class AlignViewport
   public Font getFont() {
     return font;
   }
-  public void setCharWidth(double w) {
+  public void setCharWidth(int w) {
     this.charWidth = w;
   }
-  public double getCharWidth() {
+  public int getCharWidth() {
     return charWidth;
   }
   public void setCharHeight(int h) {
@@ -220,6 +250,16 @@ public class AlignViewport
     showText = state;
   }
 
+  public void setRenderGaps(boolean state){
+    renderGaps = state;
+    if(renderer instanceof SequenceRenderer)
+    {
+      SequenceRenderer sr = (SequenceRenderer)renderer;
+      sr.renderGaps(state);
+    }
+  }
+
+
   public boolean getColourText()
   {
     return showColourText;
@@ -245,19 +285,11 @@ public class AlignViewport
   public boolean getShowBoxes() {
     return showBoxes;
   }
- // public CommandParser getCommandLog() {
- ///   return log;
- // }
-  public boolean getGroupEdit() {
-    return groupEdit;
-  }
-  public void setGroupEdit(boolean state) {
-    groupEdit = state;
-  }
-  public String getGapCharacter() {
+
+  public char getGapCharacter() {
     return getAlignment().getGapCharacter();
   }
-  public void setGapCharacter(String gap) {
+  public void setGapCharacter(char gap) {
     if (getAlignment() != null) {
       getAlignment().setGapCharacter(gap);
     }
@@ -299,9 +331,7 @@ public class AlignViewport
   public ColumnSelection getColumnSelection() {
     return colSel;
   }
-  public OutputGenerator getOutputGenerator() {
-    return og;
-  }
+
   public void resetSeqLimits(int height) {
     setStartSeq(0);
     setEndSeq(height/getCharHeight());
@@ -320,27 +350,12 @@ public class AlignViewport
     public RendererI getRenderer() {
 	return renderer;
     }
-    public int getPIDWindow() {
-	return window;
-    }
-    public void setPIDWindow(int window) {
-	this.window = window;
-    }
-
-    public int getPIDBaseline() {
-	return baseline;
-    }
-    public void setPIDBaseline(int baseline) {
-	this.baseline = baseline;
-    }
 
-    public void setKmers(Vector kmers) {
-        this.kmers = kmers;
-    }
+  public void setColourAppliesToAllGroups(boolean b)
+  {   colourAppliesToAllGroups = b; }
 
-    public Vector getKmers() {
-        return this.kmers;
-    }
+  public boolean getColourAppliesToAllGroups()
+  {return colourAppliesToAllGroups; }
 
 
 }