Update features

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index ec03b85..14dd1a0 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -27,6 +27,7 @@ import java.util.*;
 import java.awt.image.*;\r
 import javax.swing.*;\r
 import javax.swing.JOptionPane;\r
+import java.awt.event.*;\r
 \r
 \r
 /**\r
@@ -422,17 +423,43 @@ public class FeatureRenderer
     public boolean createNewFeatures(SequenceI[] sequences,\r
                                   SequenceFeature [] features)\r
     {\r
+      return amendFeatures(sequences, features, true);\r
+    }\r
 \r
+    boolean amendFeatures(SequenceI[] sequences,\r
+                           final SequenceFeature [] features,\r
+                           boolean newFeatures)\r
+    {\r
       JPanel bigPanel = new JPanel(new BorderLayout());\r
-      JComboBox name = new JComboBox();\r
-      JComboBox source = new JComboBox();\r
-      JTextArea description = new JTextArea(3,25);\r
+      final JComboBox name = new JComboBox();\r
+      final JComboBox source = new JComboBox();\r
+      final JTextArea description = new JTextArea(3,25);\r
+      final JTextField start = new JTextField(6);\r
+      final JTextField end = new JTextField(6);\r
+      final JButton colour = new JButton("     ");\r
+      colour.setMaximumSize(new Dimension(40,10));\r
+      colour.setBackground(new Color(60, 160, 115));\r
+      colour.addActionListener(new ActionListener()\r
+          {\r
+            public void actionPerformed(ActionEvent evt)\r
+            {\r
+              colour.setBackground(\r
+                  JColorChooser.showDialog(Desktop.desktop,\r
+                                           "Select Feature Colour",\r
+                                           colour.getBackground()));\r
+            }\r
+          });\r
 \r
-      JPanel panel = new JPanel(new GridLayout(2, 2));\r
-      panel.add(new JLabel("New Sequence Feature Name: ",JLabel.RIGHT));\r
+      JPanel panel = new JPanel(new GridLayout(3, 2));\r
+      panel.add(new JLabel("Sequence Feature Name: ",JLabel.RIGHT));\r
       panel.add(name);\r
       panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));\r
       panel.add(source);\r
+      panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));\r
+      JPanel tmp = new JPanel();\r
+      tmp.add(colour);\r
+      colour.setPreferredSize(new Dimension(150,15));\r
+      panel.add(tmp);\r
       name.setEditable(true);\r
       source.setEditable(true);\r
 \r
@@ -442,27 +469,20 @@ public class FeatureRenderer
       description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
       description.setLineWrap(true);\r
       panel.add(new JScrollPane(description));\r
-      bigPanel.add(panel, BorderLayout.CENTER);\r
-\r
 \r
-      Enumeration en;\r
-      if (av.featuresDisplayed != null)\r
+      if(!newFeatures)\r
       {\r
-        en = av.featuresDisplayed.keys();\r
-        while (en.hasMoreElements())\r
-        {\r
-          name.addItem(en.nextElement().toString());\r
-        }\r
-      }\r
-\r
-      if (featureGroups != null)\r
-      {\r
-        en = featureGroups.keys();\r
-        while (en.hasMoreElements())\r
-        {\r
-          source.addItem(en.nextElement().toString());\r
-        }\r
+        bigPanel.add(panel, BorderLayout.SOUTH);\r
+\r
+        panel = new JPanel();\r
+        panel.add(new JLabel("Start: ", JLabel.RIGHT));\r
+        panel.add(start);\r
+        panel.add(new JLabel("End: ", JLabel.RIGHT));\r
+        panel.add(end);\r
+        bigPanel.add(panel, BorderLayout.CENTER);\r
       }\r
+      else\r
+        bigPanel.add(panel, BorderLayout.CENTER);\r
 \r
       if (lastFeatureAdded == null)\r
         if (features[0].type != null)\r
@@ -477,60 +497,148 @@ public class FeatureRenderer
           lastFeatureAdded = "Jalview";\r
 \r
 \r
-      name.setSelectedItem(lastFeatureAdded);\r
-      source.setSelectedItem(lastFeatureGroupAdded);\r
-      description.setText(\r
-          lastDescriptionAdded == null ?\r
-          features[0].description : lastDescriptionAdded);\r
+      Enumeration en;\r
+      if (featureGroups != null)\r
+      {\r
+        en = featureGroups.keys();\r
+        while (en.hasMoreElements())\r
+        {\r
+          source.addItem(en.nextElement().toString());\r
+        }\r
+      }\r
+\r
+      if (newFeatures)\r
+      {\r
+        if(av.featuresDisplayed != null)\r
+        {\r
+          en = av.featuresDisplayed.keys();\r
+          while (en.hasMoreElements())\r
+          {\r
+            name.addItem(en.nextElement().toString());\r
+          }\r
+        }\r
+\r
+        name.setSelectedItem(lastFeatureAdded);\r
+        source.setSelectedItem(lastFeatureGroupAdded);\r
+        description.setText(\r
+            lastDescriptionAdded == null ?\r
+            features[0].description : lastDescriptionAdded);\r
+      }\r
+      else if (!newFeatures)\r
+      {\r
+        for(int f=0; f<features.length; f++)\r
+        {\r
+          name.addItem(features[f].getType().toString());\r
+        }\r
 \r
+        description.setText(features[0].getDescription());\r
+        source.setSelectedItem(features[0].getFeatureGroup());\r
+        start.setText(features[0].getBegin()+"");\r
+        end.setText(features[0].getEnd()+"");\r
+        colour.setBackground(\r
+                getColour(name.getSelectedItem().toString()));\r
+        name.addItemListener(new ItemListener()\r
+        {\r
+          public void itemStateChanged(ItemEvent e)\r
+          {\r
+            int index = name.getSelectedIndex();\r
+            description.setText(features[index].getDescription());\r
+            source.setSelectedItem(features[index].getFeatureGroup());\r
+            start.setText(features[index].getBegin() + "");\r
+            end.setText(features[index].getEnd() + "");\r
+            colour.setBackground(\r
+                getColour(name.getSelectedItem().toString()));\r
+          }\r
+        });\r
 \r
-      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
-          bigPanel, "Create New Sequence Feature(s)",\r
-          JOptionPane.OK_CANCEL_OPTION);\r
+      }\r
 \r
 \r
-      if(reply==JOptionPane.OK_OPTION\r
-         && name.getSelectedItem()!=null\r
-         && source.getSelectedItem()!=null)\r
+      Object [] options;\r
+      if(!newFeatures)\r
+        options = new Object[]{"Amend", "Delete", "Cancel"};\r
+      else\r
+        options = new Object[]{"OK", "Cancel"};\r
+\r
+      int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
+                                                   bigPanel,\r
+                                                   newFeatures ?\r
+                                                   "Create New Sequence Feature(s)" :\r
+                                                   "Amend/Delete Features",\r
+                                                   JOptionPane.YES_NO_CANCEL_OPTION,\r
+                                                   JOptionPane.QUESTION_MESSAGE,\r
+                                                   null,\r
+                                                   options, null);\r
+\r
+      jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
+\r
+      if (reply == JOptionPane.OK_OPTION\r
+          && name.getSelectedItem() != null\r
+          && source.getSelectedItem() != null)\r
       {\r
         lastFeatureAdded = name.getSelectedItem().toString();\r
         lastFeatureGroupAdded = source.getSelectedItem().toString();\r
-        lastDescriptionAdded = description.getText().replaceAll("\n"," ");\r
-\r
-        jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();\r
-\r
+        lastDescriptionAdded = description.getText().replaceAll("\n", " ");\r
+      }\r
 \r
-        for(int i=0; i<sequences.length; i++)\r
+      if(!newFeatures)\r
+      {\r
+        SequenceFeature sf = features[name.getSelectedIndex()];\r
+        if(reply==JOptionPane.NO_OPTION)\r
+          sequences[0].getDatasetSequence().deleteFeature(sf);\r
+        else if(reply==JOptionPane.YES_OPTION)\r
         {\r
-          features[i].type = lastFeatureAdded;\r
-          features[i].featureGroup = lastFeatureGroupAdded;\r
-          features[i].description = lastDescriptionAdded;\r
-          sequences[i].addSequenceFeature(features[i]);\r
-          ffile.parseDescriptionHTML(features[i], false);\r
+          sf.type = lastFeatureAdded;\r
+          sf.featureGroup = lastFeatureGroupAdded;\r
+          sf.description = lastDescriptionAdded;\r
+          setColour(sf.type, colour.getBackground());\r
+          try{\r
+            sf.begin = Integer.parseInt( start.getText() );\r
+            sf.end = Integer.parseInt( end.getText() );\r
+          }catch(NumberFormatException ex)\r
+          {}\r
+\r
+          ffile.parseDescriptionHTML(sf, false);\r
         }\r
+      }\r
+      else\r
+      {\r
+        if (reply == JOptionPane.OK_OPTION\r
+            && name.getSelectedItem() != null\r
+            && source.getSelectedItem() != null)\r
+        {\r
+          for (int i = 0; i < sequences.length; i++)\r
+          {\r
+            features[i].type = lastFeatureAdded;\r
+            features[i].featureGroup = lastFeatureGroupAdded;\r
+            features[i].description = lastDescriptionAdded;\r
+            sequences[i].addSequenceFeature(features[i]);\r
+            ffile.parseDescriptionHTML(features[i], false);\r
+          }\r
 \r
-        if (av.featuresDisplayed == null)\r
-          av.featuresDisplayed = new Hashtable();\r
+          if (av.featuresDisplayed == null)\r
+            av.featuresDisplayed = new Hashtable();\r
 \r
-        if(featureGroups==null)\r
-          featureGroups = new Hashtable();\r
+          if (featureGroups == null)\r
+            featureGroups = new Hashtable();\r
 \r
-        featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
+          featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
 \r
-        Color col = getColour(lastFeatureAdded);\r
-        if(col==null)\r
-        {\r
-          col = new Color(60, 160, 115);\r
-          setColour(lastFeatureAdded, col);\r
-        }\r
+          Color col = colour.getBackground();\r
+          setColour(lastFeatureAdded, colour.getBackground());\r
+\r
+          av.featuresDisplayed.put(lastFeatureGroupAdded,\r
+                                   new Integer(col.getRGB()));\r
+\r
+          findAllFeatures();\r
 \r
-        av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col.getRGB()));\r
-        findAllFeatures();\r
-        return true;\r
+          return true;\r
+        }\r
+        else\r
+          return false;\r
       }\r
-      else\r
-        return false;\r
 \r
+      return true;\r
     }\r
 \r
     public void setColour(String featureType, Color col)\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e51b13c..a4c2279 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -179,7 +179,6 @@ public class SeqPanel extends JPanel implements MouseListener,
   {\r
     Vector tmp = new Vector();\r
     SequenceFeature[] features = sequence.getSequenceFeatures();\r
-\r
     if (features != null)\r
     {\r
       for (int i = 0; i < features.length; i++)\r
@@ -188,8 +187,8 @@ public class SeqPanel extends JPanel implements MouseListener,
             || !av.featuresDisplayed.containsKey(features[i].getType()))\r
           continue;\r
 \r
-        if ( (features[i].getBegin() <= sequence.findPosition(res)) &&\r
-            (features[i].getEnd() >= sequence.findPosition(res)))\r
+        if ( (features[i].getBegin() <= res) &&\r
+            (features[i].getEnd() >= res))\r
         {\r
           tmp.addElement(features[i]);\r
         }\r
@@ -558,7 +557,7 @@ public class SeqPanel extends JPanel implements MouseListener,
             tooltipText.setLength(6); // Cuts the buffer back to <html>\r
 \r
             SequenceFeature[] features = findFeaturesAtRes(\r
-                sequence.getDatasetSequence(), res);\r
+                sequence.getDatasetSequence(), sequence.findPosition(res));\r
 \r
             if(features!=null)\r
             {\r
@@ -649,7 +648,6 @@ public class SeqPanel extends JPanel implements MouseListener,
                 }\r
               }\r
 \r
-\r
               if(tooltipText.length()==6) // <html></html>\r
               {\r
 \r
@@ -1202,17 +1200,35 @@ public class SeqPanel extends JPanel implements MouseListener,
 \r
     public void mouseClicked(MouseEvent evt)\r
     {\r
+      SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) );\r
       if(evt.getClickCount()>1)\r
       {\r
+        if (av.getSelectionGroup().getSize(false) == 1\r
+            && av.getSelectionGroup().getEndRes()\r
+            - av.getSelectionGroup().getStartRes() < 2)\r
+          av.setSelectionGroup(null);\r
 \r
         SequenceFeature[] features = findFeaturesAtRes(\r
-            av.alignment.getSequenceAt( findSeq(evt) ).getDatasetSequence(),\r
-            findRes(evt)\r
+            sequence.getDatasetSequence(),\r
+            sequence.findPosition( findRes(evt) )\r
             );\r
-        for(int f=0; f<features.length; f++)\r
-          System.out.println("SELECT: "+features[f].getType()+" "\r
-      +features[f].getBegin()+" "+features[f].getEnd());\r
 \r
+        if(features!=null && features.length==1)\r
+        {\r
+          SearchResults highlight = new SearchResults();\r
+          highlight.addResult(sequence,\r
+                              features[0].getBegin(),\r
+                              features[0].getEnd());\r
+          seqCanvas.highlightSearchResults(highlight);\r
+        }\r
+        if(features!=null)\r
+        {\r
+          seqCanvas.getFeatureRenderer().amendFeatures(\r
+              new SequenceI[]\r
+              {sequence}, features, false);\r
+\r
+          seqCanvas.highlightSearchResults(null);\r
+        }\r
       }\r
     }\r
 \r