Sequence is char []

[jalview.git] / src / jalview / jbgui / GFinder.java

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index ed03a80..b9bccc0 100755 (executable)
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.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
@@ -24,6 +24,7 @@ import javax.swing.*;
 import javax.swing.event.*;\r
 import jalview.io.FormatAdapter;\r
 import jalview.datamodel.SequenceI;\r
+import java.awt.BorderLayout;\r
 \r
 public class GFinder\r
     extends JPanel\r
@@ -41,8 +42,8 @@ public class GFinder
   JPanel jPanel3 = new JPanel();\r
   JPanel jPanel4 = new JPanel();\r
   BorderLayout borderLayout2 = new BorderLayout();\r
-  JPanel jPanel5 = new JPanel();\r
   JPanel jPanel6 = new JPanel();\r
+  protected JCheckBox caseSensitive = new JCheckBox();\r
   public GFinder()\r
   {\r
     try\r
@@ -86,9 +87,8 @@ public class GFinder
     gridLayout1.setVgap(2);\r
     createNewGroup.setEnabled(false);\r
     createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));\r
-    createNewGroup.setToolTipText("");\r
     createNewGroup.setMargin(new Insets(0, 0, 0, 0));\r
-    createNewGroup.setText("Create new group");\r
+    createNewGroup.setText("New Feature");\r
     createNewGroup.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -117,6 +117,8 @@ public class GFinder
     jPanel4.setLayout(borderLayout2);\r
     jPanel2.setPreferredSize(new Dimension(10, 1));\r
     jPanel3.setPreferredSize(new Dimension(10, 1));\r
+    caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);\r
+    caseSensitive.setText("Match Case");\r
     jPanel1.add(findNext, null);\r
     jPanel1.add(findAll, null);\r
     jPanel1.add(createNewGroup, null);\r
@@ -126,9 +128,9 @@ public class GFinder
     this.add(jPanel3, java.awt.BorderLayout.NORTH);\r
     this.add(jPanel4, java.awt.BorderLayout.CENTER);\r
     jPanel4.add(jScrollPane1, java.awt.BorderLayout.CENTER);\r
-    jPanel4.add(jPanel5, java.awt.BorderLayout.SOUTH);\r
-    jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);\r
     jScrollPane1.getViewport().add(textfield);\r
+    jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);\r
+    jPanel4.add(caseSensitive, java.awt.BorderLayout.SOUTH);\r
   }\r
 \r
   protected void findNext_actionPerformed(ActionEvent e)\r
@@ -164,11 +166,14 @@ public class GFinder
         public void run()\r
         {\r
           String str = textfield.getText();\r
-          SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");\r
+          SequenceI[] sequences = null;\r
+          try{sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");}\r
+          catch(Exception ex){}\r
           if(sequences!=null && sequences.length>0)\r
           {\r
             str = jalview.analysis.AlignSeq.extractGaps(\r
-                jalview.util.Comparison.GapChars, sequences[0].getSequence());\r
+                jalview.util.Comparison.GapChars,\r
+                sequences[0].getSequenceAsString());\r
 \r
             textfield.setText(str);\r
           }\r