From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 17 Nov 2005 15:16:48 +0000 (+0000)
Subject: Optimized Overview
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=63e023b9b4aedc87fe7f69e2b3887d70aa6a02c1;p=jalview.git

Optimized Overview
---

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 7910f2d..6164468 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -39,7 +39,8 @@ public class OverviewPanel
 
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
-  SeqCanvas overviewSeq;
+  SequenceRenderer sr;
+  //FeatureRenderer fr;
 
 
   Frame nullFrame;
@@ -52,9 +53,13 @@ public class OverviewPanel
     nullFrame = new Frame();
     nullFrame.addNotify();
 
-    overviewSeq = new SeqCanvas(av);
-    overviewSeq.isOverview = true;
-    overviewSeq.sr.renderGaps = false;
+
+    sr = new SequenceRenderer(av);
+    sr.renderGaps( false );
+    //fr = new FeatureRenderer(av);
+    //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
+    //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
+
 
 
     // scale the initial size of overviewpanel to shape of alignment
@@ -231,31 +236,40 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
+    int lastcol=-1, lastrow=-1;
+    Color color = Color.white;
     for (int col = 0; col < width; col++)
     {
       for (int row = 0; row < sequencesHeight; row++)
       {
-        overviewSeq.drawPanel(mg,
-                                        (int) (col * sampleCol),
-                                        (int) (col * sampleCol),
-                                        (int) (row * sampleRow),
-                                        (int) (row * sampleRow) + 1,
-                                        (int) (col * sampleCol),
-                                        (int) (row * sampleRow), 0);
-        mg.translate(0, 1);
+        if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
+        {
+          mg.setColor(color);
+          mg.fillRect(col,row,1,1);
+          continue;
+        }
+
+        lastrow = (int)(row*sampleRow);
+        lastcol = (int)(col*sampleCol);
+
+        color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);
+
+        mg.setColor(color);
+        mg.fillRect(col,row,1,1);
 
         if (av.conservation != null)
+        {
+          mg.translate(col, sequencesHeight);
           ap.annotationPanel.drawGraph(mg, av.conservation,
                                        (int) (sampleCol) + 1,
                                        graphHeight,
                                        (int) (col * sampleCol),
                                        (int) (col * sampleCol) + 1);
-
+          mg.translate(-col, -sequencesHeight);
+        }
       }
-      mg.translate(0, -sequencesHeight);
-      mg.translate(1, 0);
+    }
 
-        }
     System.gc();
 
     resizing = false;
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index fc8bb5c..5d02825 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -43,7 +43,6 @@ public class SeqCanvas
 
   boolean fastPaint = false;
 
-  boolean isOverview = false;
 
   public SeqCanvas(AlignViewport av)
   {
@@ -472,7 +471,7 @@ public class SeqCanvas
       group = (SequenceGroup) groups.elementAt(0);
       groupIndex = 0;
     }
-    if (group != null && !isOverview)
+    if (group != null)
     {
         do
         {
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 534f68f..5391e78 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -49,7 +49,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     // Can set different properties in this seqCanvas than
     // main visible SeqCanvas
-    SeqCanvas overviewSeq;
+    SequenceRenderer sr;
+    FeatureRenderer fr;
 
     /**
      * Creates a new OverviewPanel object.
@@ -62,9 +63,11 @@ public class OverviewPanel extends JPanel implements Runnable
         this.ap = ap;
         setLayout(null);
 
-        overviewSeq = new SeqCanvas(av);
-        overviewSeq.isOverview = true;
-        overviewSeq.sr.renderGaps = false;
+        sr = new SequenceRenderer(av);
+        sr.renderGaps( false );
+        fr = new FeatureRenderer(av);
+        fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
+        fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
 
         // scale the initial size of overviewpanel to shape of alignment
         float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();
@@ -257,34 +260,50 @@ public class OverviewPanel extends JPanel implements Runnable
 
 
         Graphics mg = miniMe.getGraphics();
+        mg.setColor(Color.orange);
+        mg.fillRect(0,0,width, miniMe.getHeight());
 
         float sampleCol = (float) alwidth / (float) width;
         float sampleRow = (float) alheight / (float) sequencesHeight;
 
+        int lastcol=-1, lastrow=-1;
+        Color color = Color.white;
         for (int col = 0; col < width; col++)
         {
           for (int row = 0; row < sequencesHeight; row++)
           {
-            overviewSeq.drawPanel(mg,
-                                            (int) (col * sampleCol),
-                                            (int) (col * sampleCol),
-                                            (int) (row * sampleRow),
-                                            (int) (row * sampleRow) + 1,
-                                            (int) (col * sampleCol),
-                                            (int) (row * sampleRow), 0);
-            mg.translate(0, 1);
+            if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
+            {
+              miniMe.setRGB(col,row,color.getRGB());
+              continue;
+            }
+
+            lastrow = (int)(row*sampleRow);
+            lastcol = (int)(col*sampleCol);
+
+            color = sr.findSequenceColour(Color.white,
+                av.alignment.getSequenceAt(lastrow), lastcol);
+
+            if(av.showSequenceFeatures)
+            {
+              color = fr.findFeatureColour(color,
+                                                       av.alignment.getSequenceAt(lastrow),
+                                                       lastcol);
+            }
+
+            miniMe.setRGB(col,row,color.getRGB());
 
             if (av.conservation != null)
+            {
+              mg.translate(col, sequencesHeight);
               ap.annotationPanel.drawGraph(mg, av.conservation,
                                            (int) (sampleCol) + 1,
                                            graphHeight,
                                            (int) (col * sampleCol),
                                            (int) (col * sampleCol) + 1);
-
+              mg.translate(-col, -sequencesHeight);
+            }
           }
-          mg.translate(0, -sequencesHeight);
-          mg.translate(1, 0);
-
         }
 
         System.gc();