vamsasDemo new branch

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

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 7f9ee97..fd19721 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -24,6 +24,7 @@ import java.awt.*;
 import java.awt.image.*;\r
 \r
 import javax.swing.*;\r
+import jalview.schemes.*;\r
 \r
 \r
 /**\r
@@ -64,6 +65,11 @@ public class SeqCanvas extends JComponent
         setBackground(Color.white);\r
     }\r
 \r
+    public FeatureRenderer getFeatureRenderer()\r
+    {\r
+      return fr;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -513,28 +519,76 @@ public class SeqCanvas extends JComponent
     synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
         int y2, int startx, int starty, int offset)\r
     {\r
-        Graphics2D g = (Graphics2D) g1;\r
-        g.setFont(av.getFont());\r
+      Graphics2D g = (Graphics2D) g1;\r
+      g.setFont(av.getFont());\r
 \r
+      SequenceI nextSeq, dna = null;\r
+      int aaHeight = av.charHeight, dnaHeight = av.charHeight;\r
+      Font dnafont = null, aafont = av.getFont();\r
 \r
-  SequenceI nextSeq;\r
+ /*     if (av.getShowTranslation())\r
+      {\r
+        aaHeight = (int) (av.getCharHeight() * aaRatio);\r
+        dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));\r
+        java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();\r
+        transform.scale(1f / 3f, 1);\r
+        dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+                                dnaHeight);\r
+        dnafont = dnafont.deriveFont(transform);\r
+\r
+        aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+                               aaHeight);\r
+        transform = new java.awt.geom.AffineTransform();\r
+        transform.scale(1 / aaRatio, 1);\r
+        aafont = aafont.deriveFont(transform);\r
+      }\r
+*/\r
 \r
+      ColourSchemeI cs = av.getGlobalColourScheme();\r
 \r
         /// First draw the sequences\r
         /////////////////////////////\r
         for (int i = y1; i < y2; i++)\r
         {\r
             nextSeq = av.alignment.getSequenceAt(i);\r
-            g.setFont(av.getFont());\r
-\r
+            g.setFont(aafont);\r
+         /*   if(av.getShowTranslation())\r
+            {\r
+              dna = nextSeq;\r
+              StringBuffer sb = new StringBuffer();\r
+              for(int r = 0; r<nextSeq.getLength(); r+=3)\r
+              {\r
+                String codon = nextSeq.getSequence(r, r+3);\r
+                codon = codon.replace('U', 'T');\r
+                String res = ResidueProperties.codonTranslate(codon);\r
+                if(res !=null )\r
+                {\r
+                  if (res.equals("STOP"))\r
+                    sb.append("X");\r
+                  else\r
+                    sb.append(res);\r
+                }\r
+              }\r
+              nextSeq = new Sequence("d", sb.toString());\r
+            }*/\r
 \r
             sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
                             x1, x2, (x1 - startx) * av.charWidth,\r
                             offset + ( (i - starty) * av.charHeight), av.charWidth,\r
-                            av.charHeight);\r
-\r
+                            aaHeight);\r
 \r
 \r
+         /*   if(av.getShowTranslation())\r
+            {\r
+              av.setGlobalColourScheme(new NucleotideColourScheme());\r
+              g.setFont(dnafont);\r
+              sr.drawSequence(g, dna, null,\r
+                              x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,\r
+                              offset + ( (i - starty) * av.charHeight) + aaHeight,\r
+                              av.charWidth / 3,\r
+                              dnaHeight);\r
+              av.setGlobalColourScheme(cs);\r
+            }*/\r
 \r
             if (av.showSequenceFeatures)\r
             {\r
@@ -551,20 +605,18 @@ public class SeqCanvas extends JComponent
         // Now outline any areas if necessary\r
         /////////////////////////////////////\r
         SequenceGroup group = av.getSelectionGroup();\r
-        java.util.Vector groups = av.alignment.getGroups();\r
 \r
         int sx = -1;\r
         int sy = -1;\r
         int ex = -1;\r
         int groupIndex = -1;\r
 \r
-        if ((group == null) && (groups.size() > 0))\r
+        if ((group == null) && (av.alignment.getGroups().size() > 0))\r
         {\r
-            group = (SequenceGroup) groups.elementAt(0);\r
+            group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
             groupIndex = 0;\r
         }\r
 \r
-\r
         if (group != null && !isOverview)\r
         {\r
             do\r
@@ -701,14 +753,14 @@ public class SeqCanvas extends JComponent
 \r
                 groupIndex++;\r
 \r
-                if (groupIndex >= groups.size())\r
+                if (groupIndex >= av.alignment.getGroups().size())\r
                 {\r
                     break;\r
                 }\r
 \r
-                group = (SequenceGroup) groups.elementAt(groupIndex);\r
+                group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
             }\r
-            while (groupIndex < groups.size());\r
+            while (groupIndex < av.alignment.getGroups().size());\r
         }\r
 \r
         /// Highlight search Results once all sequences have been drawn\r