Can set description for new features

[jalview.git] / src / jalview / gui / FeatureRenderer.java

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 7c60327..ec03b85 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -25,6 +25,8 @@ import java.awt.*;
 import java.util.*;\r
 \r
 import java.awt.image.*;\r
+import javax.swing.*;\r
+import javax.swing.JOptionPane;\r
 \r
 \r
 /**\r
@@ -54,9 +56,6 @@ public class FeatureRenderer
 \r
     String [] renderOrder;\r
 \r
-    boolean newFeatureAdded = false;\r
-\r
-\r
     /**\r
      * Creates a new FeatureRenderer object.\r
      *\r
@@ -168,7 +167,6 @@ public class FeatureRenderer
           || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
         return;\r
 \r
-\r
       if(g!=null)\r
         fm = g.getFontMetrics();\r
 \r
@@ -334,16 +332,26 @@ public class FeatureRenderer
       }\r
     }\r
 \r
-    int count = 0;\r
-    synchronized public void featuresAdded()\r
+\r
+    boolean newFeatureAdded = false;\r
+\r
+    public void featuresAdded()\r
     {\r
-      newFeatureAdded = true;\r
       findAllFeatures();\r
-      newFeatureAdded = false;\r
     }\r
 \r
+   boolean findingFeatures = false;\r
    synchronized void findAllFeatures()\r
    {\r
+      newFeatureAdded = false;\r
+\r
+      if(findingFeatures)\r
+      {\r
+        newFeatureAdded = true;\r
+        return;\r
+      }\r
+\r
+      findingFeatures = true;\r
       jalview.schemes.UserColourScheme ucs = new\r
           jalview.schemes.UserColourScheme();\r
 \r
@@ -396,6 +404,8 @@ public class FeatureRenderer
         renderOrder[i] = en.nextElement().toString();\r
         i--;\r
       }\r
+\r
+      findingFeatures = false;\r
     }\r
 \r
     public Color getColour(String featureType)\r
@@ -405,17 +415,122 @@ public class FeatureRenderer
     }\r
 \r
 \r
-    public void addNewFeature(String name, Color col, String group)\r
+    static String lastFeatureAdded;\r
+    static String lastFeatureGroupAdded;\r
+    static String lastDescriptionAdded;\r
+\r
+    public boolean createNewFeatures(SequenceI[] sequences,\r
+                                  SequenceFeature [] features)\r
     {\r
 \r
-      setColour(name, col);\r
-      if(av.featuresDisplayed==null)\r
-        av.featuresDisplayed = new Hashtable();\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
+\r
+      JPanel panel = new JPanel(new GridLayout(2, 2));\r
+      panel.add(new JLabel("New Sequence Feature Name: ",JLabel.RIGHT));\r
+      panel.add(name);\r
+      panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));\r
+      panel.add(source);\r
+      name.setEditable(true);\r
+      source.setEditable(true);\r
+\r
+      bigPanel.add(panel, BorderLayout.NORTH);\r
+      panel = new JPanel();\r
+      panel.add(new JLabel("Description: ", JLabel.RIGHT));\r
+      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
+      {\r
+        en = av.featuresDisplayed.keys();\r
+        while (en.hasMoreElements())\r
+        {\r
+          name.addItem(en.nextElement().toString());\r
+        }\r
+      }\r
 \r
-      if(group == null)\r
-        group = "NOGROUP";\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 (lastFeatureAdded == null)\r
+        if (features[0].type != null)\r
+          lastFeatureAdded = features[0].type;\r
+        else\r
+          lastFeatureAdded = "feature_1";\r
+\r
+      if (lastFeatureGroupAdded == null)\r
+        if (features[0].featureGroup != null)\r
+          lastFeatureGroupAdded = features[0].featureGroup;\r
+        else\r
+          lastFeatureAdded = "Jalview";\r
+\r
+\r
+      name.setSelectedItem(lastFeatureAdded);\r
+      source.setSelectedItem(lastFeatureGroupAdded);\r
+      description.setText(\r
+          lastDescriptionAdded == null ?\r
+          features[0].description : lastDescriptionAdded);\r
+\r
+\r
+      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+          bigPanel, "Create New Sequence Feature(s)",\r
+          JOptionPane.OK_CANCEL_OPTION);\r
+\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
+\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
+\r
+        if(featureGroups==null)\r
+          featureGroups = new Hashtable();\r
+\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
+\r
+        av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col.getRGB()));\r
+        findAllFeatures();\r
+        return true;\r
+      }\r
+      else\r
+        return false;\r
 \r
-      av.featuresDisplayed.put(name, new Integer(col.getRGB()));\r
     }\r
 \r
     public void setColour(String featureType, Color col)\r