X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=beef70c25c67a68e50f9df5b5a550ea84b355f4e;hb=bc77e2f0f477053147a4e56b681131c710eb3ec8;hp=14dd1a05f6f29363e10f21fe6f78d8d1d5076036;hpb=ecb5ab32cb7599f6665117ad4e25c61f0a650720;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 14dd1a0..beef70c 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
@@ -423,25 +423,29 @@ public class FeatureRenderer
     public boolean createNewFeatures(SequenceI[] sequences,
                                   SequenceFeature [] features)
     {
-      return amendFeatures(sequences, features, true);
+      return amendFeatures(sequences, features, true, null);
     }
 
-    boolean amendFeatures(SequenceI[] sequences,
-                           final SequenceFeature [] features,
-                           boolean newFeatures)
+    int featureIndex = 0;
+    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,
@@ -475,9 +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);
       }
@@ -523,9 +527,20 @@ 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)
       {
+        featureIndex = 0;
         for(int f=0; f<features.length; f++)
         {
           name.addItem(features[f].getType().toString());
@@ -533,8 +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()
@@ -542,12 +557,31 @@ public class FeatureRenderer
           public void itemStateChanged(ItemEvent e)
           {
             int index = name.getSelectedIndex();
-            description.setText(features[index].getDescription());
-            source.setSelectedItem(features[index].getFeatureGroup());
-            start.setText(features[index].getBegin() + "");
-            end.setText(features[index].getEnd() + "");
-            colour.setBackground(
-                getColour(name.getSelectedItem().toString()));
+            if(index!=-1)
+            {
+              featureIndex = index;
+              description.setText(features[index].getDescription());
+              source.setSelectedItem(features[index].getFeatureGroup());
+              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);
           }
         });
 
@@ -560,15 +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();
 
@@ -583,7 +619,8 @@ public class FeatureRenderer
 
       if(!newFeatures)
       {
-        SequenceFeature sf = features[name.getSelectedIndex()];
+        SequenceFeature sf = features[featureIndex];
+
         if(reply==JOptionPane.NO_OPTION)
           sequences[0].getDatasetSequence().deleteFeature(sf);
         else if(reply==JOptionPane.YES_OPTION)
@@ -593,8 +630,8 @@ 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)
           {}
 
@@ -638,6 +675,10 @@ public class FeatureRenderer
           return false;
       }
 
+      if(name.getSelectedIndex()==-1)
+        findAllFeatures();
+
+
       return true;
     }