From 95032c2e3e635e40bd92f3c6e218dde19a7db068 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 18 Oct 2006 13:03:22 +0000
Subject: [PATCH] Can set description for new features

---
 src/jalview/gui/FeatureRenderer.java |   61 ++++++++++++++++++++++++++--------
 1 file changed, 47 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index d20fa63..ec03b85 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -25,9 +25,7 @@ import java.awt.*;
 import java.util.*;
 
 import java.awt.image.*;
-import javax.swing.JComboBox;
-import javax.swing.JPanel;
-import javax.swing.JLabel;
+import javax.swing.*;
 import javax.swing.JOptionPane;
 
 
@@ -417,25 +415,36 @@ public class FeatureRenderer
     }
 
 
-    static String lastFeatureAdded = "feature_1";
-    static String lastSourceAdded = "Jalview";
+    static String lastFeatureAdded;
+    static String lastFeatureGroupAdded;
+    static String lastDescriptionAdded;
 
     public boolean createNewFeatures(SequenceI[] sequences,
                                   SequenceFeature [] features)
     {
 
+      JPanel bigPanel = new JPanel(new BorderLayout());
       JComboBox name = new JComboBox();
       JComboBox source = new JComboBox();
+      JTextArea description = new JTextArea(3,25);
 
       JPanel panel = new JPanel(new GridLayout(2, 2));
-      panel.add(new JLabel("New Sequence Feature Name"));
+      panel.add(new JLabel("New Sequence Feature Name: ",JLabel.RIGHT));
       panel.add(name);
-      panel.add(new JLabel("Source:"));
+      panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
       panel.add(source);
-     // name.setPreferredSize(new Dimension(300, 20));
       name.setEditable(true);
       source.setEditable(true);
 
+      bigPanel.add(panel, BorderLayout.NORTH);
+      panel = new JPanel();
+      panel.add(new JLabel("Description: ", JLabel.RIGHT));
+      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)
       {
@@ -455,11 +464,28 @@ public class FeatureRenderer
         }
       }
 
+      if (lastFeatureAdded == null)
+        if (features[0].type != null)
+          lastFeatureAdded = features[0].type;
+        else
+          lastFeatureAdded = "feature_1";
+
+      if (lastFeatureGroupAdded == null)
+        if (features[0].featureGroup != null)
+          lastFeatureGroupAdded = features[0].featureGroup;
+        else
+          lastFeatureAdded = "Jalview";
+
+
       name.setSelectedItem(lastFeatureAdded);
-      source.setSelectedItem(lastSourceAdded);
+      source.setSelectedItem(lastFeatureGroupAdded);
+      description.setText(
+          lastDescriptionAdded == null ?
+          features[0].description : lastDescriptionAdded);
+
 
       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-          panel, "Create New Sequence Feature(s)",
+          bigPanel, "Create New Sequence Feature(s)",
           JOptionPane.OK_CANCEL_OPTION);
 
 
@@ -468,12 +494,19 @@ public class FeatureRenderer
          && source.getSelectedItem()!=null)
       {
         lastFeatureAdded = name.getSelectedItem().toString();
-        lastSourceAdded = source.getSelectedItem().toString();
+        lastFeatureGroupAdded = source.getSelectedItem().toString();
+        lastDescriptionAdded = description.getText().replaceAll("\n"," ");
+
+        jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+
         for(int i=0; i<sequences.length; i++)
         {
           features[i].type = lastFeatureAdded;
-          features[i].featureGroup = lastSourceAdded;
+          features[i].featureGroup = lastFeatureGroupAdded;
+          features[i].description = lastDescriptionAdded;
           sequences[i].addSequenceFeature(features[i]);
+          ffile.parseDescriptionHTML(features[i], false);
         }
 
         if (av.featuresDisplayed == null)
@@ -482,7 +515,7 @@ public class FeatureRenderer
         if(featureGroups==null)
           featureGroups = new Hashtable();
 
-        featureGroups.put(lastSourceAdded, new Boolean(true));
+        featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 
         Color col = getColour(lastFeatureAdded);
         if(col==null)
@@ -491,7 +524,7 @@ public class FeatureRenderer
           setColour(lastFeatureAdded, col);
         }
 
-        av.featuresDisplayed.put(lastSourceAdded, new Integer(col.getRGB()));
+        av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col.getRGB()));
         findAllFeatures();
         return true;
       }
-- 
1.7.10.2