X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=12876edb05e464d704cf1a736cad7ae595332d27;hb=3f9c1d052c8fe2e92ae0d7a1c3088ccb82c58ba5;hp=2ca3ca37ee205282dbce0bf1c06f998fd58cf8a8;hpb=b0530d7ac372a4b770d381f263970de9ecdb4212;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 2ca3ca3..12876ed 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -212,7 +212,7 @@ public class FeatureRenderer
        {
         type =  renderOrder[renderIndex];
 
-        if(!av.featuresDisplayed.containsKey(type))
+        if(type==null || !av.featuresDisplayed.containsKey(type))
           continue;
 
         // loop through all features in sequence to find
@@ -309,7 +309,7 @@ public class FeatureRenderer
           int pady = (y1 + av.charHeight) - av.charHeight / 5;
           for (i = fstart; i <= fend; i++)
           {
-            s = seq.getSequence().charAt(i);
+            s = seq.getCharAt(i);
 
             if (jalview.util.Comparison.isGap(s))
             {
@@ -423,26 +423,29 @@ public class FeatureRenderer
     public boolean createNewFeatures(SequenceI[] sequences,
                                   SequenceFeature [] features)
     {
-      return amendFeatures(sequences, features, true);
+      return amendFeatures(sequences, features, true, null);
     }
 
     int featureIndex = 0;
-    boolean amendFeatures(SequenceI[] sequences,
-                           final SequenceFeature [] features,
-                           boolean newFeatures)
+    boolean amendFeatures(final SequenceI[] sequences,
+                          final SequenceFeature[] features,
+                          boolean newFeatures,
+                          final AlignmentPanel ap)
     {
       JPanel bigPanel = new JPanel(new BorderLayout());
       final JComboBox name = new JComboBox();
       final JComboBox source = new JComboBox();
       final JTextArea description = new JTextArea(3,25);
-      final JTextField start = new JTextField(6);
-      final JTextField end = new JTextField(6);
-      final JButton colour = new JButton("     ");
+      final JSpinner start = new JSpinner();
+      final JSpinner end = new JSpinner();
+      start.setPreferredSize(new Dimension(80,20));
+      end.setPreferredSize(new Dimension(80,20));
+      final JPanel colour = new JPanel();
+      colour.setBorder(BorderFactory.createEtchedBorder());
       colour.setMaximumSize(new Dimension(40,10));
-      colour.setBackground(new Color(60, 160, 115));
-      colour.addActionListener(new ActionListener()
+      colour.addMouseListener(new MouseAdapter()
           {
-            public void actionPerformed(ActionEvent evt)
+            public void mousePressed(MouseEvent evt)
             {
               colour.setBackground(
                   JColorChooser.showDialog(Desktop.desktop,
@@ -476,9 +479,9 @@ public class FeatureRenderer
         bigPanel.add(panel, BorderLayout.SOUTH);
 
         panel = new JPanel();
-        panel.add(new JLabel("Start: ", JLabel.RIGHT));
+        panel.add(new JLabel(" Start:", JLabel.RIGHT));
         panel.add(start);
-        panel.add(new JLabel("End: ", JLabel.RIGHT));
+        panel.add(new JLabel("  End:", JLabel.RIGHT));
         panel.add(end);
         bigPanel.add(panel, BorderLayout.CENTER);
       }
@@ -524,6 +527,16 @@ public class FeatureRenderer
         description.setText(
             lastDescriptionAdded == null ?
             features[0].description : lastDescriptionAdded);
+
+        if (getColour(lastFeatureAdded) != null)
+        {
+          colour.setBackground(getColour(lastFeatureAdded));
+        }
+        else
+        {
+          colour.setBackground(new Color(60, 160, 115));
+        }
+
       }
       else if (!newFeatures)
       {
@@ -535,8 +548,8 @@ public class FeatureRenderer
 
         description.setText(features[0].getDescription());
         source.setSelectedItem(features[0].getFeatureGroup());
-        start.setText(features[0].getBegin()+"");
-        end.setText(features[0].getEnd()+"");
+        start.setValue(new Integer(features[0].getBegin()));
+        end.setValue(new Integer(features[0].getEnd()));
         colour.setBackground(
                 getColour(name.getSelectedItem().toString()));
         name.addItemListener(new ItemListener()
@@ -549,11 +562,26 @@ public class FeatureRenderer
               featureIndex = index;
               description.setText(features[index].getDescription());
               source.setSelectedItem(features[index].getFeatureGroup());
-              start.setText(features[index].getBegin() + "");
-              end.setText(features[index].getEnd() + "");
+              start.setValue(new Integer(features[index].getBegin()));
+              end.setValue(new Integer(features[index].getEnd()));
               colour.setBackground(
                   getColour(name.getSelectedItem().toString()));
+
+              SearchResults highlight = new SearchResults();
+              highlight.addResult(sequences[0],
+                                  features[index].getBegin(),
+                                  features[index].getEnd());
+
+              ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
             }
+            Color col = getColour(name.getSelectedItem().toString());
+            if (col == null)
+              col = new
+                  jalview.schemes.UserColourScheme()
+                  .createColourFromName(name.getSelectedItem().toString());
+
+            colour.setBackground(col);
           }
         });
 
@@ -566,15 +594,17 @@ public class FeatureRenderer
       else
         options = new Object[]{"OK", "Cancel"};
 
+      String title = newFeatures ?  "Create New Sequence Feature(s)" :
+                                    "Amend/Delete Features for "
+                                    +sequences[0].getName();
+
       int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
                                                    bigPanel,
-                                                   newFeatures ?
-                                                   "Create New Sequence Feature(s)" :
-                                                   "Amend/Delete Features",
+                                                   title,
                                                    JOptionPane.YES_NO_CANCEL_OPTION,
                                                    JOptionPane.QUESTION_MESSAGE,
                                                    null,
-                                                   options, null);
+                                                   options, "OK");
 
       jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 
@@ -582,6 +612,9 @@ public class FeatureRenderer
           && name.getSelectedItem() != null
           && source.getSelectedItem() != null)
       {
+        //This ensures that the last sequence
+        //is refreshed and new features are rendered
+        lastSeq=null;
         lastFeatureAdded = name.getSelectedItem().toString();
         lastFeatureGroupAdded = source.getSelectedItem().toString();
         lastDescriptionAdded = description.getText().replaceAll("\n", " ");
@@ -600,8 +633,8 @@ public class FeatureRenderer
           sf.description = lastDescriptionAdded;
           setColour(sf.type, colour.getBackground());
           try{
-            sf.begin = Integer.parseInt( start.getText() );
-            sf.end = Integer.parseInt( end.getText() );
+            sf.begin = ((Integer)start.getValue()).intValue();
+            sf.end = ((Integer)end.getValue()).intValue();
           }catch(NumberFormatException ex)
           {}