X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGFinder.java;h=c3ed1686be5bac42c8f4d3f6499e2edc8a9e764b;hb=7bc213bae5828287329a3490faba291706599b03;hp=32d2f24683c90ca83b6c1cba11133c1e54c3805e;hpb=f18cbb26b5cd3d800b4d0317e544ae4e4075a4c3;p=jalview.git

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 32d2f24..c3ed168 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -22,6 +22,9 @@ import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
+import jalview.io.FormatAdapter;
+import jalview.datamodel.SequenceI;
+import java.awt.BorderLayout;
 
 public class GFinder
     extends JPanel
@@ -39,8 +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
@@ -86,7 +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)
@@ -115,6 +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);
@@ -124,9 +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)
@@ -155,17 +160,23 @@ public class GFinder
 
   public void textfield_caretUpdate(CaretEvent e)
   {
-    if (textfield.getText().indexOf("\t") > -1)
+    if (textfield.getText().indexOf(">") > -1)
     {
       SwingUtilities.invokeLater(new Runnable()
       {
         public void run()
         {
-          String text = textfield.getText();
-          text = text.substring(text.lastIndexOf("\t") + 1).trim();
-          text = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, text);
-          textfield.setText(text);
+          String str = textfield.getText();
+          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());
+
+            textfield.setText(str);
+          }
         }
       });
     }