Sequence is char []

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

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index b584d89..003200d 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -212,7 +212,7 @@ public class FeatureRenderer
        {\r
         type =  renderOrder[renderIndex];\r
 \r
-        if(!av.featuresDisplayed.containsKey(type))\r
+        if(type==null || !av.featuresDisplayed.containsKey(type))\r
           continue;\r
 \r
         // loop through all features in sequence to find\r
@@ -309,7 +309,7 @@ public class FeatureRenderer
           int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
           for (i = fstart; i <= fend; i++)\r
           {\r
-            s = seq.getSequence().charAt(i);\r
+            s = seq.getCharAt(i);\r
 \r
             if (jalview.util.Comparison.isGap(s))\r
             {\r
@@ -438,6 +438,8 @@ public class FeatureRenderer
       final JTextArea description = new JTextArea(3,25);\r
       final JSpinner start = new JSpinner();\r
       final JSpinner end = new JSpinner();\r
+      start.setPreferredSize(new Dimension(80,20));\r
+      end.setPreferredSize(new Dimension(80,20));\r
       final JPanel colour = new JPanel();\r
       colour.setBorder(BorderFactory.createEtchedBorder());\r
       colour.setMaximumSize(new Dimension(40,10));\r
@@ -477,9 +479,9 @@ public class FeatureRenderer
         bigPanel.add(panel, BorderLayout.SOUTH);\r
 \r
         panel = new JPanel();\r
-        panel.add(new JLabel(" Start: ", JLabel.RIGHT));\r
+        panel.add(new JLabel(" Start:", JLabel.RIGHT));\r
         panel.add(start);\r
-        panel.add(new JLabel("  End: ", JLabel.RIGHT));\r
+        panel.add(new JLabel("  End:", JLabel.RIGHT));\r
         panel.add(end);\r
         bigPanel.add(panel, BorderLayout.CENTER);\r
       }\r
@@ -529,12 +531,10 @@ public class FeatureRenderer
         if (getColour(lastFeatureAdded) != null)\r
         {\r
           colour.setBackground(getColour(lastFeatureAdded));\r
-          colour.setForeground(getColour(lastFeatureAdded));\r
         }\r
         else\r
         {\r
           colour.setBackground(new Color(60, 160, 115));\r
-          colour.setForeground(new Color(60, 160, 115));\r
         }\r
 \r
       }\r
@@ -566,8 +566,6 @@ public class FeatureRenderer
               end.setValue(new Integer(features[index].getEnd()));\r
               colour.setBackground(\r
                   getColour(name.getSelectedItem().toString()));\r
-              colour.setForeground(\r
-                  getColour(name.getSelectedItem().toString()));\r
 \r
               SearchResults highlight = new SearchResults();\r
               highlight.addResult(sequences[0],\r
@@ -577,6 +575,13 @@ public class FeatureRenderer
               ap.seqPanel.seqCanvas.highlightSearchResults(highlight);\r
 \r
             }\r
+            Color col = getColour(name.getSelectedItem().toString());\r
+            if (col == null)\r
+              col = new\r
+                  jalview.schemes.UserColourScheme()\r
+                  .createColourFromName(name.getSelectedItem().toString());\r
+\r
+            colour.setBackground(col);\r
           }\r
         });\r
 \r