From ecb5ab32cb7599f6665117ad4e25c61f0a650720 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 30 Oct 2006 16:31:38 +0000
Subject: [PATCH] Update features

---
 src/jalview/gui/FeatureRenderer.java |  228 +++++++++++++++++++++++++---------
 src/jalview/gui/SeqPanel.java        |   36 ++++--
 2 files changed, 194 insertions(+), 70 deletions(-)

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index ec03b85..14dd1a0 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -27,6 +27,7 @@ import java.util.*;
 import java.awt.image.*;
 import javax.swing.*;
 import javax.swing.JOptionPane;
+import java.awt.event.*;
 
 
 /**
@@ -422,17 +423,43 @@ public class FeatureRenderer
     public boolean createNewFeatures(SequenceI[] sequences,
                                   SequenceFeature [] features)
     {
+      return amendFeatures(sequences, features, true);
+    }
 
+    boolean amendFeatures(SequenceI[] sequences,
+                           final SequenceFeature [] features,
+                           boolean newFeatures)
+    {
       JPanel bigPanel = new JPanel(new BorderLayout());
-      JComboBox name = new JComboBox();
-      JComboBox source = new JComboBox();
-      JTextArea description = new JTextArea(3,25);
+      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("     ");
+      colour.setMaximumSize(new Dimension(40,10));
+      colour.setBackground(new Color(60, 160, 115));
+      colour.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent evt)
+            {
+              colour.setBackground(
+                  JColorChooser.showDialog(Desktop.desktop,
+                                           "Select Feature Colour",
+                                           colour.getBackground()));
+            }
+          });
 
-      JPanel panel = new JPanel(new GridLayout(2, 2));
-      panel.add(new JLabel("New Sequence Feature Name: ",JLabel.RIGHT));
+      JPanel panel = new JPanel(new GridLayout(3, 2));
+      panel.add(new JLabel("Sequence Feature Name: ",JLabel.RIGHT));
       panel.add(name);
       panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
       panel.add(source);
+      panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
+      JPanel tmp = new JPanel();
+      tmp.add(colour);
+      colour.setPreferredSize(new Dimension(150,15));
+      panel.add(tmp);
       name.setEditable(true);
       source.setEditable(true);
 
@@ -442,27 +469,20 @@ public class FeatureRenderer
       description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
       description.setLineWrap(true);
       panel.add(new JScrollPane(description));
-      bigPanel.add(panel, BorderLayout.CENTER);
-
 
-      Enumeration en;
-      if (av.featuresDisplayed != null)
+      if(!newFeatures)
       {
-        en = av.featuresDisplayed.keys();
-        while (en.hasMoreElements())
-        {
-          name.addItem(en.nextElement().toString());
-        }
-      }
-
-      if (featureGroups != null)
-      {
-        en = featureGroups.keys();
-        while (en.hasMoreElements())
-        {
-          source.addItem(en.nextElement().toString());
-        }
+        bigPanel.add(panel, BorderLayout.SOUTH);
+
+        panel = new JPanel();
+        panel.add(new JLabel("Start: ", JLabel.RIGHT));
+        panel.add(start);
+        panel.add(new JLabel("End: ", JLabel.RIGHT));
+        panel.add(end);
+        bigPanel.add(panel, BorderLayout.CENTER);
       }
+      else
+        bigPanel.add(panel, BorderLayout.CENTER);
 
       if (lastFeatureAdded == null)
         if (features[0].type != null)
@@ -477,60 +497,148 @@ public class FeatureRenderer
           lastFeatureAdded = "Jalview";
 
 
-      name.setSelectedItem(lastFeatureAdded);
-      source.setSelectedItem(lastFeatureGroupAdded);
-      description.setText(
-          lastDescriptionAdded == null ?
-          features[0].description : lastDescriptionAdded);
+      Enumeration en;
+      if (featureGroups != null)
+      {
+        en = featureGroups.keys();
+        while (en.hasMoreElements())
+        {
+          source.addItem(en.nextElement().toString());
+        }
+      }
+
+      if (newFeatures)
+      {
+        if(av.featuresDisplayed != null)
+        {
+          en = av.featuresDisplayed.keys();
+          while (en.hasMoreElements())
+          {
+            name.addItem(en.nextElement().toString());
+          }
+        }
+
+        name.setSelectedItem(lastFeatureAdded);
+        source.setSelectedItem(lastFeatureGroupAdded);
+        description.setText(
+            lastDescriptionAdded == null ?
+            features[0].description : lastDescriptionAdded);
+      }
+      else if (!newFeatures)
+      {
+        for(int f=0; f<features.length; f++)
+        {
+          name.addItem(features[f].getType().toString());
+        }
 
+        description.setText(features[0].getDescription());
+        source.setSelectedItem(features[0].getFeatureGroup());
+        start.setText(features[0].getBegin()+"");
+        end.setText(features[0].getEnd()+"");
+        colour.setBackground(
+                getColour(name.getSelectedItem().toString()));
+        name.addItemListener(new ItemListener()
+        {
+          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()));
+          }
+        });
 
-      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-          bigPanel, "Create New Sequence Feature(s)",
-          JOptionPane.OK_CANCEL_OPTION);
+      }
 
 
-      if(reply==JOptionPane.OK_OPTION
-         && name.getSelectedItem()!=null
-         && source.getSelectedItem()!=null)
+      Object [] options;
+      if(!newFeatures)
+        options = new Object[]{"Amend", "Delete", "Cancel"};
+      else
+        options = new Object[]{"OK", "Cancel"};
+
+      int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+                                                   bigPanel,
+                                                   newFeatures ?
+                                                   "Create New Sequence Feature(s)" :
+                                                   "Amend/Delete Features",
+                                                   JOptionPane.YES_NO_CANCEL_OPTION,
+                                                   JOptionPane.QUESTION_MESSAGE,
+                                                   null,
+                                                   options, null);
+
+      jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+      if (reply == JOptionPane.OK_OPTION
+          && name.getSelectedItem() != null
+          && source.getSelectedItem() != null)
       {
         lastFeatureAdded = name.getSelectedItem().toString();
         lastFeatureGroupAdded = source.getSelectedItem().toString();
-        lastDescriptionAdded = description.getText().replaceAll("\n"," ");
-
-        jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
-
+        lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+      }
 
-        for(int i=0; i<sequences.length; i++)
+      if(!newFeatures)
+      {
+        SequenceFeature sf = features[name.getSelectedIndex()];
+        if(reply==JOptionPane.NO_OPTION)
+          sequences[0].getDatasetSequence().deleteFeature(sf);
+        else if(reply==JOptionPane.YES_OPTION)
         {
-          features[i].type = lastFeatureAdded;
-          features[i].featureGroup = lastFeatureGroupAdded;
-          features[i].description = lastDescriptionAdded;
-          sequences[i].addSequenceFeature(features[i]);
-          ffile.parseDescriptionHTML(features[i], false);
+          sf.type = lastFeatureAdded;
+          sf.featureGroup = lastFeatureGroupAdded;
+          sf.description = lastDescriptionAdded;
+          setColour(sf.type, colour.getBackground());
+          try{
+            sf.begin = Integer.parseInt( start.getText() );
+            sf.end = Integer.parseInt( end.getText() );
+          }catch(NumberFormatException ex)
+          {}
+
+          ffile.parseDescriptionHTML(sf, false);
         }
+      }
+      else
+      {
+        if (reply == JOptionPane.OK_OPTION
+            && name.getSelectedItem() != null
+            && source.getSelectedItem() != null)
+        {
+          for (int i = 0; i < sequences.length; i++)
+          {
+            features[i].type = lastFeatureAdded;
+            features[i].featureGroup = lastFeatureGroupAdded;
+            features[i].description = lastDescriptionAdded;
+            sequences[i].addSequenceFeature(features[i]);
+            ffile.parseDescriptionHTML(features[i], false);
+          }
 
-        if (av.featuresDisplayed == null)
-          av.featuresDisplayed = new Hashtable();
+          if (av.featuresDisplayed == null)
+            av.featuresDisplayed = new Hashtable();
 
-        if(featureGroups==null)
-          featureGroups = new Hashtable();
+          if (featureGroups == null)
+            featureGroups = new Hashtable();
 
-        featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 
-        Color col = getColour(lastFeatureAdded);
-        if(col==null)
-        {
-          col = new Color(60, 160, 115);
-          setColour(lastFeatureAdded, col);
-        }
+          Color col = colour.getBackground();
+          setColour(lastFeatureAdded, colour.getBackground());
+
+          av.featuresDisplayed.put(lastFeatureGroupAdded,
+                                   new Integer(col.getRGB()));
+
+          findAllFeatures();
 
-        av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col.getRGB()));
-        findAllFeatures();
-        return true;
+          return true;
+        }
+        else
+          return false;
       }
-      else
-        return false;
 
+      return true;
     }
 
     public void setColour(String featureType, Color col)
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e51b13c..a4c2279 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -179,7 +179,6 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     Vector tmp = new Vector();
     SequenceFeature[] features = sequence.getSequenceFeatures();
-
     if (features != null)
     {
       for (int i = 0; i < features.length; i++)
@@ -188,8 +187,8 @@ public class SeqPanel extends JPanel implements MouseListener,
             || !av.featuresDisplayed.containsKey(features[i].getType()))
           continue;
 
-        if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
-            (features[i].getEnd() >= sequence.findPosition(res)))
+        if ( (features[i].getBegin() <= res) &&
+            (features[i].getEnd() >= res))
         {
           tmp.addElement(features[i]);
         }
@@ -558,7 +557,7 @@ public class SeqPanel extends JPanel implements MouseListener,
             tooltipText.setLength(6); // Cuts the buffer back to <html>
 
             SequenceFeature[] features = findFeaturesAtRes(
-                sequence.getDatasetSequence(), res);
+                sequence.getDatasetSequence(), sequence.findPosition(res));
 
             if(features!=null)
             {
@@ -649,7 +648,6 @@ public class SeqPanel extends JPanel implements MouseListener,
                 }
               }
 
-
               if(tooltipText.length()==6) // <html></html>
               {
 
@@ -1202,17 +1200,35 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     public void mouseClicked(MouseEvent evt)
     {
+      SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );
       if(evt.getClickCount()>1)
       {
+        if (av.getSelectionGroup().getSize(false) == 1
+            && av.getSelectionGroup().getEndRes()
+            - av.getSelectionGroup().getStartRes() < 2)
+          av.setSelectionGroup(null);
 
         SequenceFeature[] features = findFeaturesAtRes(
-            av.alignment.getSequenceAt( findSeq(evt) ).getDatasetSequence(),
-            findRes(evt)
+            sequence.getDatasetSequence(),
+            sequence.findPosition( findRes(evt) )
             );
-        for(int f=0; f<features.length; f++)
-          System.out.println("SELECT: "+features[f].getType()+" "
-      +features[f].getBegin()+" "+features[f].getEnd());
 
+        if(features!=null && features.length==1)
+        {
+          SearchResults highlight = new SearchResults();
+          highlight.addResult(sequence,
+                              features[0].getBegin(),
+                              features[0].getEnd());
+          seqCanvas.highlightSearchResults(highlight);
+        }
+        if(features!=null)
+        {
+          seqCanvas.getFeatureRenderer().amendFeatures(
+              new SequenceI[]
+              {sequence}, features, false);
+
+          seqCanvas.highlightSearchResults(null);
+        }
       }
     }
 
-- 
1.7.10.2