added description of alignment quality scores and separated

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 9c3e908..48f075e 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -57,9 +57,11 @@ public class OverviewPanel
     sr = new SequenceRenderer(av);\r
     sr.graphics = nullFrame.getGraphics();\r
     sr.renderGaps( false );\r
+    sr.forOverview = true;\r
     fr = new FeatureRenderer(av);\r
-    fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
-    fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
+    fr.drawText = false;\r
+    fr.overview = true;\r
+\r
 \r
 \r
     // scale the initial size of overviewpanel to shape of alignment\r
@@ -183,6 +185,14 @@ public class OverviewPanel
         return;\r
     }\r
 \r
+    if (av.showSequenceFeatures)\r
+   {\r
+     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
+     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+     fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;\r
+   }\r
+\r
+\r
     resizing = true;\r
 \r
     if ( (getSize().width > 0) && (getSize().height > 0))\r
@@ -228,16 +238,18 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;\r
     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 lastcol=-1, lastrow=0;\r
+    Color color = Color.yellow;\r
+    int row, col;\r
+    jalview.datamodel.SequenceI sequence;\r
+    for (row = 0; row < sequencesHeight; row++)\r
     {\r
-      for (int row = 0; row < sequencesHeight; row++)\r
+      sequence = av.getAlignment().getSequenceAt(lastrow);\r
+      for (col = 0; col < width; col++)\r
       {\r
         if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
         {\r
-          mg.setColor(color);\r
-          mg.fillRect(col,row,1,1);\r
+          mg.drawLine(col, row, col, row);\r
           continue;\r
         }\r
 \r
@@ -246,19 +258,28 @@ public class OverviewPanel
 \r
         if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)\r
         {\r
-          color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
+\r
+          color = sr.findSequenceColour(sequence, lastcol);\r
 \r
           if (av.showSequenceFeatures)\r
             color = fr.findFeatureColour(color,\r
-                                         av.alignment.getSequenceAt(lastrow),\r
-                                         lastcol);\r
+                                        sequence,\r
+                                        lastcol);\r
         }\r
-\r
+        else\r
+          color = color.white;\r
 \r
         mg.setColor(color);\r
-        mg.fillRect(col,row,1,1);\r
+        mg.drawLine(col,row,col,row);\r
+\r
+      }\r
+    }\r
 \r
-        if (av.conservation != null)\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
@@ -266,11 +287,13 @@ public class OverviewPanel
                                        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
+\r
+\r
     System.gc();\r
 \r
     resizing = false;\r