added description of alignment quality scores and separated

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

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index bcc2866..4bc8ed5 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -579,14 +579,11 @@ public class AnnotationPanel
     g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 \r
 \r
-    if(aa.graphLines!=null)\r
+    if(aa.threshold!=null)\r
     {\r
-      for(int l=0; l<aa.graphLines.size(); l++)\r
-      {\r
-        g.setColor(aa.getGraphLine(l).colour);\r
-        y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*graphHeight);\r
+        g.setColor(aa.threshold.colour);\r
+        y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
         g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
-      }\r
     }\r
 \r
     eRes = Math.min(eRes, aa.annotations.length);\r
@@ -617,14 +614,11 @@ public class AnnotationPanel
 \r
     float range = max - min;\r
 \r
-    if(aa.graphLines!=null)\r
+    if(aa.threshold!=null)\r
     {\r
-      for(int l=0; l<aa.graphLines.size(); l++)\r
-      {\r
-        g.setColor(aa.getGraphLine(l).colour);\r
-        y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*aa.graphHeight);\r
+        g.setColor(aa.threshold.colour);\r
+        y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
         g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
-       }\r
     }\r
 \r
     y1 = y2 = y;\r
@@ -672,7 +666,7 @@ public class AnnotationPanel
 \r
       for (int j = sRes; j < eRes; j++)\r
       {\r
-          g.setColor(new Color(0, 0, 180));\r
+          g.setColor(aa.annotations[j].colour);\r
 \r
           height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
           if(height>y)\r