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 e20084c..7ffac1e 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -65,8 +65,10 @@ public class OverviewPanel extends JPanel implements Runnable
 \r
         sr = new SequenceRenderer(av);\r
         sr.renderGaps( false );\r
+        sr.forOverview = true;\r
         fr = new FeatureRenderer(av);\r
-        fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\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
@@ -243,6 +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
@@ -266,14 +276,15 @@ public class OverviewPanel extends JPanel implements Runnable
         float sampleRow = (float) alheight / (float) sequencesHeight;\r
 \r
         int lastcol=-1, lastrow=-1;\r
-        Color color = Color.white;\r
-        for (int col = 0; col < width; col++)\r
+        int color = Color.white.getRGB();\r
+        int row, col;\r
+        for (row = 0; row < sequencesHeight; row++)\r
         {\r
-          for (int 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.getRGB());\r
+              miniMe.setRGB(col,row,color);\r
               continue;\r
             }\r
 \r
@@ -283,17 +294,28 @@ public class OverviewPanel extends JPanel implements Runnable
             if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
             {\r
              color = sr.getResidueBoxColour(\r
-                av.alignment.getSequenceAt(lastrow), lastcol);\r
+                av.alignment.getSequenceAt(lastrow), lastcol).getRGB();\r
 \r
              if(av.showSequenceFeatures)\r
-                 color = fr.findFeatureColour(color,  av.alignment.getSequenceAt(lastrow),\r
-                                             lastcol);\r
+                 color = fr.findFeatureColour(color,  lastrow, lastcol);\r
 \r
-            }\r
+             }\r
+             else\r
+             {\r
+               color = -1; //White\r
+             }\r
+\r
+            miniMe.setRGB(col,row,color);\r
 \r
-            miniMe.setRGB(col,row,color.getRGB());\r
 \r
-            if (av.conservation != null)\r
+          }\r
+        }\r
+\r
+        if (av.conservation != null)\r
+        {\r
+          for (col = 0; col < width; col++)\r
+          {\r
+            lastcol = (int) (col * sampleCol);\r
             {\r
               mg.translate(col, sequencesHeight);\r
               ap.annotationPanel.drawGraph(mg, av.conservation,\r
@@ -301,11 +323,10 @@ public class OverviewPanel extends JPanel implements Runnable
                                            graphHeight,\r
                                            (int) (col * sampleCol),\r
                                            (int) (col * sampleCol) + 1);\r
-              mg.translate(-col, -sequencesHeight);\r
+              mg.translate( -col, -sequencesHeight);\r
             }\r
           }\r
         }\r
-\r
         System.gc();\r
 \r
         resizing = false;\r