Add globalcolourscheme

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 03e0c5a..905255a 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -4,6 +4,7 @@ import java.awt.*;
 import jalview.io.*;\r
 import jalview.analysis.NJTree;\r
 import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
 import java.util.*;\r
 \r
 public class AlignViewport\r
@@ -20,18 +21,18 @@ public class AlignViewport
   boolean showBoxes=true;\r
   boolean wrapAlignment=false;\r
   boolean renderGaps = false;\r
-\r
   boolean groupEdit    = false;\r
+  boolean groupDefiningMode = true;\r
+\r
+  ColourSchemeI globalColourScheme = null;\r
 \r
-  RendererI renderer = new SequenceRenderer();\r
+  RendererI renderer = new SequenceRenderer(this);\r
 \r
   int             charHeight;\r
-  double          charWidth;\r
+  int          charWidth;\r
   int             chunkWidth;\r
   int             chunkHeight;\r
 \r
-  Color           backgroundColour;\r
-\r
   Font            font = new Font("SansSerif",Font.PLAIN,10);\r
   AlignmentI      alignment;\r
 \r
@@ -87,18 +88,6 @@ public class AlignViewport
     setFont( font );\r
  }\r
 \r
-  public AlignViewport(int startRes, int endRes,\r
-                       int startSeq, int endSeq,\r
-                       boolean showScores,\r
-                       boolean showText,\r
-                       boolean showBoxes,\r
-                       boolean wrapAlignment,\r
-                       Color backgroundColour) {\r
-    this(startRes,endRes,startSeq,endSeq,showScores,showText,showBoxes,wrapAlignment);\r
-\r
-    this.backgroundColour = backgroundColour;\r
-  }\r
-\r
 \r
   public String getVisibleConsensus()\r
   {\r
@@ -138,6 +127,16 @@ public class AlignViewport
     return startSeq;\r
   }\r
 \r
+  public void setGlobalColourScheme(ColourSchemeI cs)\r
+  {\r
+     globalColourScheme = cs;\r
+  }\r
+\r
+  public ColourSchemeI getGlobalColourScheme()\r
+  {\r
+    return globalColourScheme;\r
+  }\r
+\r
 \r
   public void setStartRes(int res) {\r
     this.startRes = res;\r
@@ -180,10 +179,10 @@ public class AlignViewport
   public Font getFont() {\r
     return font;\r
   }\r
-  public void setCharWidth(double w) {\r
+  public void setCharWidth(int w) {\r
     this.charWidth = w;\r
   }\r
-  public double getCharWidth() {\r
+  public int getCharWidth() {\r
     return charWidth;\r
   }\r
   public void setCharHeight(int h) {\r

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 33b8665..605450b 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -93,6 +93,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)\r
   {\r
     seqPanel.setColourScheme(cs, conservation);\r
+\r
+    av.setGlobalColourScheme(cs);\r
+\r
     if(overviewPanel!=null)\r
       overviewPanel.updateOverviewImage();\r
   }\r
@@ -118,7 +121,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
   public void setScrollValues(int x, int y)\r
   {\r
-    hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());\r
+    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();\r
     vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();\r
 \r
     if(hextent+x  >  av.getAlignment().getWidth())\r
@@ -147,7 +150,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {\r
       int x = hscroll.getValue();\r
       av.setStartRes(x);\r
-      av.setEndRes(x + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1));\r
+      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
     }\r
 \r
     if (evt.getSource() == vscroll)\r
@@ -175,15 +178,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     int pheight = (int)pf.getImageableHeight();\r
     int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
 \r
-    //BufferedImage printImage = new BufferedImage(pwidth,pheight,BufferedImage.TYPE_INT_RGB);\r
-   // Graphics pg = printImage.getGraphics();\r
     pg.setColor(Color.white);\r
     pg.fillRect(0,0,pwidth, pheight);\r
     pg.setFont( av.getFont() );\r
 \r
     ////////////////////////////////////\r
     /// How many sequences and residues can we fit on a printable page?\r
-    int totalRes = (int)((pwidth - idWidth)/av.getCharWidth());\r
+    int totalRes = (pwidth - idWidth)/av.getCharWidth();\r
     int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;\r
     int pagesWide = av.getAlignment().getWidth() / totalRes +1;\r
     int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;\r
@@ -230,7 +231,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
       pg.setColor(currentColor);\r
       pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),\r
-                              getWidth(),\r
+                              idWidth,\r
                               av.getCharHeight());\r
 \r
       pg.setColor(currentTextColor);\r
@@ -242,9 +243,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 \r
     // draw main sequence panel\r
     pg.translate(idWidth,0);\r
+    pg.setClip(0,0,pwidth-idWidth, pheight);\r
     seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);\r
 \r
     return Printable.PAGE_EXISTS;\r
   }\r
+\r
 }\r
 \r
+\r
+\r