X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=12876edb05e464d704cf1a736cad7ae595332d27;hb=3f9c1d052c8fe2e92ae0d7a1c3088ccb82c58ba5;hp=ec03b859b49a66f09151777f4b5422246403778e;hpb=95032c2e3e635e40bd92f3c6e218dde19a7db068;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index ec03b85..12876ed 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.*;
 
 
 /**
@@ -211,7 +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
@@ -308,7 +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))
             {
@@ -422,17 +423,47 @@ public class FeatureRenderer
     public boolean createNewFeatures(SequenceI[] sequences,
                                   SequenceFeature [] features)
     {
+      return amendFeatures(sequences, features, true, null);
+    }
 
+    int featureIndex = 0;
+    boolean amendFeatures(final SequenceI[] sequences,
+                          final SequenceFeature[] features,
+                          boolean newFeatures,
+                          final AlignmentPanel ap)
+    {
       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 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.addMouseListener(new MouseAdapter()
+          {
+            public void mousePressed(MouseEvent 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 +473,20 @@ 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)
-      {
-        en = av.featuresDisplayed.keys();
-        while (en.hasMoreElements())
-        {
-          name.addItem(en.nextElement().toString());
-        }
-      }
 
-      if (featureGroups != null)
+      if(!newFeatures)
       {
-        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 +501,188 @@ 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);
+
+        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());
+        }
+
+        description.setText(features[0].getDescription());
+        source.setSelectedItem(features[0].getFeatureGroup());
+        start.setValue(new Integer(features[0].getBegin()));
+        end.setValue(new Integer(features[0].getEnd()));
+        colour.setBackground(
+                getColour(name.getSelectedItem().toString()));
+        name.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            int index = name.getSelectedIndex();
+            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);
+          }
+        });
+
+      }
+
+
+      Object [] options;
+      if(!newFeatures)
+        options = new Object[]{"Amend", "Delete", "Cancel"};
+      else
+        options = new Object[]{"OK", "Cancel"};
 
+      String title = newFeatures ?  "Create New Sequence Feature(s)" :
+                                    "Amend/Delete Features for "
+                                    +sequences[0].getName();
 
-      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-          bigPanel, "Create New Sequence Feature(s)",
-          JOptionPane.OK_CANCEL_OPTION);
+      int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+                                                   bigPanel,
+                                                   title,
+                                                   JOptionPane.YES_NO_CANCEL_OPTION,
+                                                   JOptionPane.QUESTION_MESSAGE,
+                                                   null,
+                                                   options, "OK");
 
+      jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 
-      if(reply==JOptionPane.OK_OPTION
-         && name.getSelectedItem()!=null
-         && source.getSelectedItem()!=null)
+      if (reply == JOptionPane.OK_OPTION
+          && 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"," ");
-
-        jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+        lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+      }
 
+      if(!newFeatures)
+      {
+        SequenceFeature sf = features[featureIndex];
 
-        for(int i=0; i<sequences.length; i++)
+        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)start.getValue()).intValue();
+            sf.end = ((Integer)end.getValue()).intValue();
+          }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();
+
+          return true;
         }
+        else
+          return false;
+      }
 
-        av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col.getRGB()));
+      if(name.getSelectedIndex()==-1)
         findAllFeatures();
-        return true;
-      }
-      else
-        return false;
 
+
+      return true;
     }
 
     public void setColour(String featureType, Color col)