From 157004a864888ed2e690b907a28f715d3d42b666 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Dec 2004 16:26:08 +0000
Subject: [PATCH] Add globalcolourscheme

---
 src/jalview/gui/AlignViewport.java  |   37 +++++++++++++++++------------------
 src/jalview/gui/AlignmentPanel.java |   17 ++++++++++------
 2 files changed, 29 insertions(+), 25 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 03e0c5a..905255a 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
@@ -20,18 +21,18 @@ public class AlignViewport
   boolean showBoxes=true;
   boolean wrapAlignment=false;
   boolean renderGaps = false;
-
   boolean groupEdit    = false;
+  boolean groupDefiningMode = true;
+
+  ColourSchemeI globalColourScheme = null;
 
-  RendererI renderer = new SequenceRenderer();
+  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;
 
@@ -87,18 +88,6 @@ 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 String getVisibleConsensus()
   {
@@ -138,6 +127,16 @@ 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 +179,10 @@ 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) {
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 33b8665..605450b 100755
--- 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)
   {
     seqPanel.setColourScheme(cs, conservation);
+
+    av.setGlobalColourScheme(cs);
+
     if(overviewPanel!=null)
       overviewPanel.updateOverviewImage();
   }
@@ -118,7 +121,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setScrollValues(int x, int y)
   {
-    hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());
+    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
     vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
 
     if(hextent+x  >  av.getAlignment().getWidth())
@@ -147,7 +150,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1));
+      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
     }
 
     if (evt.getSource() == vscroll)
@@ -175,15 +178,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     int pheight = (int)pf.getImageableHeight();
     int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
 
-    //BufferedImage printImage = new BufferedImage(pwidth,pheight,BufferedImage.TYPE_INT_RGB);
-   // Graphics pg = printImage.getGraphics();
     pg.setColor(Color.white);
     pg.fillRect(0,0,pwidth, pheight);
     pg.setFont( av.getFont() );
 
     ////////////////////////////////////
     /// How many sequences and residues can we fit on a printable page?
-    int totalRes = (int)((pwidth - idWidth)/av.getCharWidth());
+    int totalRes = (pwidth - idWidth)/av.getCharWidth();
     int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
     int pagesWide = av.getAlignment().getWidth() / totalRes +1;
     int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
@@ -230,7 +231,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
       pg.setColor(currentColor);
       pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
-                              getWidth(),
+                              idWidth,
                               av.getCharHeight());
 
       pg.setColor(currentTextColor);
@@ -242,9 +243,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     // draw main sequence panel
     pg.translate(idWidth,0);
+    pg.setClip(0,0,pwidth-idWidth, pheight);
     seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
 
     return Printable.PAGE_EXISTS;
   }
+
 }
 
+
+
-- 
1.7.10.2