X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=42424d9dc8a4a30b95cd7f93905ec5d9e0385ec5;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=42c52d3c4e7404977607db821d3539b677b95214;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 42c52d3..42424d9 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -24,6 +24,7 @@ import java.awt.*;
 import java.awt.image.*;
 
 import javax.swing.*;
+import jalview.schemes.*;
 
 
 /**
@@ -47,8 +48,6 @@ public class SeqCanvas extends JComponent
     int LABEL_WEST;
     int LABEL_EAST;
 
-    boolean isOverview = false;
-
     /**
      * Creates a new SeqCanvas object.
      *
@@ -64,6 +63,28 @@ public class SeqCanvas extends JComponent
         setBackground(Color.white);
     }
 
+    MCview.PDBCanvas pdbCanvas;
+    public SequenceRenderer getSequenceRenderer()
+    {
+      return sr;
+    }
+
+    public FeatureRenderer getFeatureRenderer()
+    {
+      return fr;
+    }
+
+    public void setPDBCanvas(MCview.PDBCanvas pc)
+    {
+      pdbCanvas = pc;
+    }
+
+    public AlignViewport getViewport()
+    {
+      return av;
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -258,18 +279,20 @@ public class SeqCanvas extends JComponent
     // Set this to false to force a full panel paint
     public void paintComponent(Graphics g)
     {
+        super.paintComponent(g);
+
         sr.renderGaps(av.renderGaps);
 
-        if ((img != null) &&
-                (fastPaint || (getWidth() != g.getClipBounds().width) ||
-                (getHeight() != g.getClipBounds().height)))
+        if ( img != null && (fastPaint
+             || (getVisibleRect().width != g.getClipBounds().width)
+             || (getVisibleRect().height != g.getClipBounds().height)))
         {
             g.drawImage(img, 0, 0, this);
             fastPaint = false;
-
             return;
         }
 
+
         // this draws the whole of the alignment
         imgWidth = getWidth();
         imgHeight = getHeight();
@@ -282,7 +305,6 @@ public class SeqCanvas extends JComponent
             return;
         }
 
-
         img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
@@ -304,6 +326,12 @@ public class SeqCanvas extends JComponent
         }
 
         g.drawImage(img, 0, 0, this);
+
+        if (pdbCanvas != null)
+        {
+         pdbCanvas.updateSeqColours();
+        }
+
     }
 
     /**
@@ -510,32 +538,36 @@ public class SeqCanvas extends JComponent
       repaint();
     }
 
+
     synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
         int y2, int startx, int starty, int offset)
     {
-        Graphics2D g = (Graphics2D) g1;
-        g.setFont(av.getFont());
-
-
-  SequenceI nextSeq;
-
-  SequenceI dna = null;
+      Graphics2D g = (Graphics2D) g1;
+      g.setFont(av.getFont());
 
-  int aaHeight = (int)(av.getCharHeight()*aaRatio);
-  int dnaHeight =(int)(av.getCharHeight() * (1-aaRatio));
+      SequenceI nextSeq, dna = null;
+      int aaHeight = av.charHeight, dnaHeight = av.charHeight;
+      Font dnafont = null, aafont = av.getFont();
 
+ /*     if (av.getShowTranslation())
+      {
+        aaHeight = (int) (av.getCharHeight() * aaRatio);
+        dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));
+        java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();
+        transform.scale(1f / 3f, 1);
+        dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
+                                dnaHeight);
+        dnafont = dnafont.deriveFont(transform);
+
+        aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
+                               aaHeight);
+        transform = new java.awt.geom.AffineTransform();
+        transform.scale(1 / aaRatio, 1);
+        aafont = aafont.deriveFont(transform);
+      }
+*/
 
-  java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();
-  transform.scale(1f/3f , 1);
-  Font dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
-                              dnaHeight);
-  dnafont = dnafont.deriveFont(transform);
-
-  Font aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),
-                              aaHeight);
-  transform = new java.awt.geom.AffineTransform();
-  transform.scale(1/aaRatio, 1);
-  aafont = aafont.deriveFont(transform);
+      ColourSchemeI cs = av.getGlobalColourScheme();
 
         /// First draw the sequences
         /////////////////////////////
@@ -543,36 +575,46 @@ public class SeqCanvas extends JComponent
         {
             nextSeq = av.alignment.getSequenceAt(i);
             g.setFont(aafont);
-/*
-            StringBuffer dnasb = new StringBuffer();
-            for (int j = 0; j < nextSeq.getLength(); j++)
+         /*   if(av.getShowTranslation())
             {
-              java.util.Vector codons = jalview.schemes.ResidueProperties.getCodons(nextSeq.getSequence(j,
-                  j + 1));
-              if (codons != null && codons.size() > 0)
-                dnasb.append(codons.elementAt(0).toString());
-            }
-
-            dna = new Sequence("dna", dnasb.toString());*/
-
+              dna = nextSeq;
+              StringBuffer sb = new StringBuffer();
+              for(int r = 0; r<nextSeq.getLength(); r+=3)
+              {
+                String codon = nextSeq.getSequence(r, r+3);
+                codon = codon.replace('U', 'T');
+                String res = ResidueProperties.codonTranslate(codon);
+                if(res !=null )
+                {
+                  if (res.equals("STOP"))
+                    sb.append("X");
+                  else
+                    sb.append(res);
+                }
+              }
+              nextSeq = new Sequence("d", sb.toString());
+            }*/
 
             sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),
                             x1, x2, (x1 - startx) * av.charWidth,
                             offset + ( (i - starty) * av.charHeight), av.charWidth,
                             aaHeight);
 
-
-         /*   g.setFont(dnafont);
-
-            sr.drawSequence(g, dna, null,
-                            x1, x2 * 3 +2, ( (x1 - startx) * av.charWidth) / 3,
-                            offset + ( (i - starty) * av.charHeight) + aaHeight, av.charWidth / 3,
-                            dnaHeight);*/
+         /*   if(av.getShowTranslation())
+            {
+              av.setGlobalColourScheme(new NucleotideColourScheme());
+              g.setFont(dnafont);
+              sr.drawSequence(g, dna, null,
+                              x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,
+                              offset + ( (i - starty) * av.charHeight) + aaHeight,
+                              av.charWidth / 3,
+                              dnaHeight);
+              av.setGlobalColourScheme(cs);
+            }*/
 
             if (av.showSequenceFeatures)
             {
-                fr.drawSequence(g, nextSeq,
-                    av.alignment.findAllGroups(nextSeq), x1, x2,
+                fr.drawSequence(g, nextSeq, x1, x2,
                     (x1 - startx) * av.charWidth,
                     offset + ((i - starty) * av.charHeight), av.charWidth,
                     av.charHeight);
@@ -584,21 +626,19 @@ public class SeqCanvas extends JComponent
         // Now outline any areas if necessary
         /////////////////////////////////////
         SequenceGroup group = av.getSelectionGroup();
-        java.util.Vector groups = av.alignment.getGroups();
 
         int sx = -1;
         int sy = -1;
         int ex = -1;
         int groupIndex = -1;
 
-        if ((group == null) && (groups.size() > 0))
+        if ((group == null) && (av.alignment.getGroups().size() > 0))
         {
-            group = (SequenceGroup) groups.elementAt(0);
+            group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
             groupIndex = 0;
         }
 
-
-        if (group != null && !isOverview)
+        if (group != null)
         {
             do
             {
@@ -734,14 +774,14 @@ public class SeqCanvas extends JComponent
 
                 groupIndex++;
 
-                if (groupIndex >= groups.size())
+                if (groupIndex >= av.alignment.getGroups().size())
                 {
                     break;
                 }
 
-                group = (SequenceGroup) groups.elementAt(groupIndex);
+                group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
             }
-            while (groupIndex < groups.size());
+            while (groupIndex < av.alignment.getGroups().size());
         }
 
         /// Highlight search Results once all sequences have been drawn