X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGFinder.java;h=b4596da197e8d8755bac35abf02ad4c2cc6b9280;hb=7f7fc2e5533f7b00c86465f964e37c55bcf12fd7;hp=872d49019e27507e3483cb1c6e893f4484b386ed;hpb=008ad05ffd2964c864cdab0f18dff2fb36c82242;p=jalview.git

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 872d490..b4596da 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -24,8 +24,7 @@ import javax.swing.*;
 import javax.swing.event.*;
 import jalview.io.FormatAdapter;
 import jalview.datamodel.SequenceI;
-import java.awt.datatransfer.DataFlavor;
-import jalview.io.IdentifyFile;
+import java.awt.BorderLayout;
 
 public class GFinder
     extends JPanel
@@ -43,8 +42,8 @@ public class GFinder
   JPanel jPanel3 = new JPanel();
   JPanel jPanel4 = new JPanel();
   BorderLayout borderLayout2 = new BorderLayout();
-  JPanel jPanel5 = new JPanel();
   JPanel jPanel6 = new JPanel();
+  protected JCheckBox caseSensitive = new JCheckBox();
   public GFinder()
   {
     try
@@ -90,7 +89,7 @@ public class GFinder
     createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));
     createNewGroup.setToolTipText("");
     createNewGroup.setMargin(new Insets(0, 0, 0, 0));
-    createNewGroup.setText("Create new group");
+    createNewGroup.setText("New Feature");
     createNewGroup.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -119,6 +118,8 @@ public class GFinder
     jPanel4.setLayout(borderLayout2);
     jPanel2.setPreferredSize(new Dimension(10, 1));
     jPanel3.setPreferredSize(new Dimension(10, 1));
+    caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
+    caseSensitive.setText("Match Case");
     jPanel1.add(findNext, null);
     jPanel1.add(findAll, null);
     jPanel1.add(createNewGroup, null);
@@ -128,9 +129,9 @@ public class GFinder
     this.add(jPanel3, java.awt.BorderLayout.NORTH);
     this.add(jPanel4, java.awt.BorderLayout.CENTER);
     jPanel4.add(jScrollPane1, java.awt.BorderLayout.CENTER);
-    jPanel4.add(jPanel5, java.awt.BorderLayout.SOUTH);
-    jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);
     jScrollPane1.getViewport().add(textfield);
+    jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);
+    jPanel4.add(caseSensitive, java.awt.BorderLayout.SOUTH);
   }
 
   protected void findNext_actionPerformed(ActionEvent e)
@@ -166,7 +167,9 @@ public class GFinder
         public void run()
         {
           String str = textfield.getText();
-          SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");
+          SequenceI[] sequences = null;
+          try{sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");}
+          catch(Exception ex){}
           if(sequences!=null && sequences.length>0)
           {
             str = jalview.analysis.AlignSeq.extractGaps(