added description of alignment quality scores and separated

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 635e455..7ffac1e 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -49,7 +49,8 @@ public class OverviewPanel extends JPanel implements Runnable
 \r
     // Can set different properties in this seqCanvas than\r
     // main visible SeqCanvas\r
-    SeqCanvas overviewSeq;\r
+    SequenceRenderer sr;\r
+    FeatureRenderer fr;\r
 \r
     /**\r
      * Creates a new OverviewPanel object.\r
@@ -62,14 +63,17 @@ public class OverviewPanel extends JPanel implements Runnable
         this.ap = ap;\r
         setLayout(null);\r
 \r
-        overviewSeq = new SeqCanvas(av);\r
-        overviewSeq.isOverview = true;\r
-        overviewSeq.sr.renderGaps = false;\r
+        sr = new SequenceRenderer(av);\r
+        sr.renderGaps( false );\r
+        sr.forOverview = true;\r
+        fr = new FeatureRenderer(av);\r
+        fr.overview = true;\r
+\r
 \r
         // scale the initial size of overviewpanel to shape of alignment\r
         float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();\r
 \r
-        if(av.vconsensus==null)\r
+        if(av.conservation==null)\r
           graphHeight = 0;\r
 \r
 \r
@@ -241,6 +245,14 @@ public class OverviewPanel extends JPanel implements Runnable
     {\r
         miniMe = null;\r
 \r
+       if (av.showSequenceFeatures)\r
+       {\r
+         fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
+         fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+         fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
+         fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;\r
+       }\r
+\r
         int alwidth = av.alignment.getWidth();\r
         int alheight = av.alignment.getHeight();\r
 \r
@@ -257,36 +269,64 @@ public class OverviewPanel extends JPanel implements Runnable
 \r
 \r
         Graphics mg = miniMe.getGraphics();\r
+        mg.setColor(Color.orange);\r
+        mg.fillRect(0,0,width, miniMe.getHeight());\r
 \r
         float sampleCol = (float) alwidth / (float) width;\r
         float sampleRow = (float) alheight / (float) sequencesHeight;\r
 \r
-        for (int col = 0; col < width; col++)\r
+        int lastcol=-1, lastrow=-1;\r
+        int color = Color.white.getRGB();\r
+        int row, col;\r
+        for (row = 0; row < sequencesHeight; row++)\r
+        {\r
+            for (col = 0; col < width; col++)\r
+            {\r
+            if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
+            {\r
+              miniMe.setRGB(col,row,color);\r
+              continue;\r
+            }\r
+\r
+            lastrow = (int)(row*sampleRow);\r
+            lastcol = (int)(col*sampleCol);\r
+\r
+            if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
+            {\r
+             color = sr.getResidueBoxColour(\r
+                av.alignment.getSequenceAt(lastrow), lastcol).getRGB();\r
+\r
+             if(av.showSequenceFeatures)\r
+                 color = fr.findFeatureColour(color,  lastrow, lastcol);\r
+\r
+             }\r
+             else\r
+             {\r
+               color = -1; //White\r
+             }\r
+\r
+            miniMe.setRGB(col,row,color);\r
+\r
+\r
+          }\r
+        }\r
+\r
+        if (av.conservation != null)\r
         {\r
-          for (int row = 0; row < sequencesHeight; row++)\r
+          for (col = 0; col < width; col++)\r
           {\r
-            overviewSeq.drawPanel(mg,\r
-                                            (int) (col * sampleCol),\r
-                                            (int) (col * sampleCol),\r
-                                            (int) (row * sampleRow),\r
-                                            (int) (row * sampleRow) + 1,\r
-                                            (int) (col * sampleCol),\r
-                                            (int) (row * sampleRow), 0);\r
-            mg.translate(0, 1);\r
-\r
-            if (av.conservation != null)\r
+            lastcol = (int) (col * sampleCol);\r
+            {\r
+              mg.translate(col, sequencesHeight);\r
               ap.annotationPanel.drawGraph(mg, av.conservation,\r
                                            (int) (sampleCol) + 1,\r
                                            graphHeight,\r
                                            (int) (col * sampleCol),\r
                                            (int) (col * sampleCol) + 1);\r
-\r
+              mg.translate( -col, -sequencesHeight);\r
+            }\r
           }\r
-          mg.translate(0, -sequencesHeight);\r
-          mg.translate(1, 0);\r
-\r
         }\r
-\r
         System.gc();\r
 \r
         resizing = false;\r