X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=db46177cedc6ff7b694ffcf3674655db184f855b;hb=27e04880edb301447f2e57b5156b8c685b853b68;hp=8905b5256026cb3cb9830312ada0e9bb9fac5003;hpb=dedbb25d7f54f28aaa36592be27c80487090e10d;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 8905b52..db46177 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.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
@@ -25,6 +25,7 @@ import java.awt.*;
 import java.awt.event.*;
 
 import jalview.datamodel.*;
+import java.awt.Rectangle;
 
 public class Finder extends Panel implements ActionListener
 {
@@ -107,7 +108,7 @@ public class Finder extends Panel implements ActionListener
         SequenceFeature sf = new SequenceFeature(featureName,
             null, null,
             searchResults.getResultStart(i),
-           searchResults.getResultEnd(i));
+           searchResults.getResultEnd(i), "Search Results");
 
         ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
             featureName, new Color(60,160,115));
@@ -122,9 +123,16 @@ public class Finder extends Panel implements ActionListener
 
   void doSearch(boolean findAll)
   {
+    if(jalview.bin.JalviewLite.currentAlignFrame!=null)
+    {
+      ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
+      av = ap.av;
+    }
     createNewGroup.setEnabled(false);
 
-    String searchString = textfield.getText().toUpperCase();
+    String searchString = textfield.getText();
+    if(!caseSensitive.getState())
+      searchString = searchString.toUpperCase();
 
     com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
@@ -140,7 +148,7 @@ public class Finder extends Panel implements ActionListener
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
+      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
       {
         seq = (Sequence) av.getAlignment().getSequenceAt(0);
       }
@@ -163,7 +171,7 @@ public class Finder extends Panel implements ActionListener
     SequenceGroup selection = av.getSelectionGroup();
     if (selection != null)
     {
-      if (selection.getSize() < 1 ||
+      if (selection.getSize(false) < 1 ||
           (selection.getEndRes() - selection.getStartRes() < 2))
       {
         selection = null;
@@ -175,14 +183,16 @@ public class Finder extends Panel implements ActionListener
 
       seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
-      if (selection != null && !selection.sequences.contains(seq))
+      if (selection != null && !selection.getSequences(false).contains(seq))
       {
         seqIndex++;
         resIndex = 0;
         continue;
       }
 
-      item = seq.getSequence().toUpperCase();
+      item = seq.getSequence();
+      if(!caseSensitive.getState())
+        item = item.toUpperCase();
 
       if (selection != null && selection.getEndRes() < av.alignment.getWidth())
       {
@@ -297,7 +307,7 @@ public class Finder extends Panel implements ActionListener
   Panel jPanel1 = new Panel();
   GridLayout gridLayout1 = new GridLayout();
   protected Button createNewGroup = new Button();
-
+  Checkbox caseSensitive = new Checkbox();
 
   private void jbInit() throws Exception {
       jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
@@ -329,10 +339,13 @@ public class Finder extends Panel implements ActionListener
       createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
       createNewGroup.setLabel("New Feature");
       createNewGroup.addActionListener(this);
-      jPanel1.add(findNext, null);
+    caseSensitive.setLabel("Match Case");
+    caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
+    jPanel1.add(findNext, null);
       jPanel1.add(findAll, null);
       jPanel1.add(createNewGroup, null);
-      this.add(textfield, null);
+    this.add(caseSensitive);
+    this.add(textfield, null);
       this.add(jLabel1, null);
       this.add(jPanel1, null);
   }