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 e9f9d55..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
@@ -423,13 +423,14 @@ public class FeatureRenderer
     public boolean createNewFeatures(SequenceI[] sequences,\r
                                   SequenceFeature [] features)\r
     {\r
-      return amendFeatures(sequences, features, true);\r
+      return amendFeatures(sequences, features, true, null);\r
     }\r
 \r
     int featureIndex = 0;\r
-    boolean amendFeatures(SequenceI[] sequences,\r
-                           final SequenceFeature [] features,\r
-                           boolean newFeatures)\r
+    boolean amendFeatures(final SequenceI[] sequences,\r
+                          final SequenceFeature[] features,\r
+                          boolean newFeatures,\r
+                          final AlignmentPanel ap)\r
     {\r
       JPanel bigPanel = new JPanel(new BorderLayout());\r
       final JComboBox name = new JComboBox();\r
@@ -437,14 +438,14 @@ public class FeatureRenderer
       final JTextArea description = new JTextArea(3,25);\r
       final JSpinner start = new JSpinner();\r
       final JSpinner end = new JSpinner();\r
-\r
-     // final JTextField start = new JTextField(6);\r
-    //  final JTextField end = new JTextField(6);\r
-      final JButton colour = new JButton("     ");\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
-      colour.addActionListener(new ActionListener()\r
+      colour.addMouseListener(new MouseAdapter()\r
           {\r
-            public void actionPerformed(ActionEvent evt)\r
+            public void mousePressed(MouseEvent evt)\r
             {\r
               colour.setBackground(\r
                   JColorChooser.showDialog(Desktop.desktop,\r
@@ -478,9 +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
@@ -530,12 +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
@@ -567,9 +566,22 @@ 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
+                                  features[index].getBegin(),\r
+                                  features[index].getEnd());\r
+\r
+              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
@@ -582,11 +594,13 @@ public class FeatureRenderer
       else\r
         options = new Object[]{"OK", "Cancel"};\r
 \r
+      String title = newFeatures ?  "Create New Sequence Feature(s)" :\r
+                                    "Amend/Delete Features for "\r
+                                    +sequences[0].getName();\r
+\r
       int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
                                                    bigPanel,\r
-                                                   newFeatures ?\r
-                                                   "Create New Sequence Feature(s)" :\r
-                                                   "Amend/Delete Features",\r
+                                                   title,\r
                                                    JOptionPane.YES_NO_CANCEL_OPTION,\r
                                                    JOptionPane.QUESTION_MESSAGE,\r
                                                    null,\r