X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGFinder.java;h=3cbef12d74a6e469f0ffda2c41dba9ffd2c676bf;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=ed03a80655342b01ff8e5cb2280ee8e83690e23b;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index ed03a80..3cbef12 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
@@ -24,6 +24,7 @@ import javax.swing.*;
 import javax.swing.event.*;
 import jalview.io.FormatAdapter;
 import jalview.datamodel.SequenceI;
+import java.awt.BorderLayout;
 
 public class GFinder
     extends JPanel
@@ -41,8 +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
@@ -70,7 +71,6 @@ public class GFinder
         findAll_actionPerformed(e);
       }
     });
-    findNext.setEnabled(false);
     findNext.setFont(new java.awt.Font("Verdana", 0, 12));
     findNext.setText("Find Next");
     findNext.addActionListener(new java.awt.event.ActionListener()
@@ -86,9 +86,8 @@ public class GFinder
     gridLayout1.setVgap(2);
     createNewGroup.setEnabled(false);
     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)
@@ -117,6 +116,8 @@ 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);
@@ -126,9 +127,9 @@ 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)
@@ -142,13 +143,11 @@ public class GFinder
 
   protected void textfield_keyPressed(KeyEvent e)
   {
-
     if(e.getKeyCode()==KeyEvent.VK_ENTER)
     {
       e.consume();
       findNext_actionPerformed(null);
     }
-    findNext.setEnabled(true);
   }
 
   public void createNewGroup_actionPerformed(ActionEvent e)
@@ -164,11 +163,14 @@ 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(
-                jalview.util.Comparison.GapChars, sequences[0].getSequence());
+                jalview.util.Comparison.GapChars,
+                sequences[0].getSequenceAsString());
 
             textfield.setText(str);
           }