ensure lastSeq is refreshed if new feature added

[jalview.git] / src / jalview / appletgui / Finder.java

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 1201278..4c195e8 100755 (executable)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.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
@@ -25,6 +25,7 @@ import java.awt.*;
 import java.awt.event.*;\r
 \r
 import jalview.datamodel.*;\r
+import java.awt.Rectangle;\r
 \r
 public class Finder extends Panel implements ActionListener\r
 {\r
@@ -85,6 +86,7 @@ public class Finder extends Panel implements ActionListener
   {\r
 \r
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);\r
+    cap.ok.setLabel("Accept");\r
     Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);\r
     dialog.add(cap);\r
 \r
@@ -122,9 +124,16 @@ public class Finder extends Panel implements ActionListener
 \r
   void doSearch(boolean findAll)\r
   {\r
+    if(jalview.bin.JalviewLite.currentAlignFrame!=null)\r
+    {\r
+      ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;\r
+      av = ap.av;\r
+    }\r
     createNewGroup.setEnabled(false);\r
 \r
-    String searchString = textfield.getText().toUpperCase();\r
+    String searchString = textfield.getText();\r
+    if(!caseSensitive.getState())\r
+      searchString = searchString.toUpperCase();\r
 \r
     com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
 \r
@@ -140,7 +149,7 @@ public class Finder extends Panel implements ActionListener
       int res = Integer.parseInt(searchString);\r
       found = true;\r
 \r
-      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
+      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
       {\r
         seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
       }\r
@@ -163,7 +172,7 @@ public class Finder extends Panel implements ActionListener
     SequenceGroup selection = av.getSelectionGroup();\r
     if (selection != null)\r
     {\r
-      if (selection.getSize() < 1 ||\r
+      if (selection.getSize(false) < 1 ||\r
           (selection.getEndRes() - selection.getStartRes() < 2))\r
       {\r
         selection = null;\r
@@ -175,14 +184,16 @@ public class Finder extends Panel implements ActionListener
 \r
       seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
 \r
-      if (selection != null && !selection.sequences.contains(seq))\r
+      if (selection != null && !selection.getSequences(false).contains(seq))\r
       {\r
         seqIndex++;\r
         resIndex = 0;\r
         continue;\r
       }\r
 \r
-      item = seq.getSequence().toUpperCase();\r
+      item = seq.getSequenceAsString();\r
+      if(!caseSensitive.getState())\r
+        item = item.toUpperCase();\r
 \r
       if (selection != null && selection.getEndRes() < av.alignment.getWidth())\r
       {\r
@@ -297,7 +308,7 @@ public class Finder extends Panel implements ActionListener
   Panel jPanel1 = new Panel();\r
   GridLayout gridLayout1 = new GridLayout();\r
   protected Button createNewGroup = new Button();\r
-\r
+  Checkbox caseSensitive = new Checkbox();\r
 \r
   private void jbInit() throws Exception {\r
       jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
@@ -329,10 +340,13 @@ public class Finder extends Panel implements ActionListener
       createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
       createNewGroup.setLabel("New Feature");\r
       createNewGroup.addActionListener(this);\r
-      jPanel1.add(findNext, null);\r
+    caseSensitive.setLabel("Match Case");\r
+    caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));\r
+    jPanel1.add(findNext, null);\r
       jPanel1.add(findAll, null);\r
       jPanel1.add(createNewGroup, null);\r
-      this.add(textfield, null);\r
+    this.add(caseSensitive);\r
+    this.add(textfield, null);\r
       this.add(jLabel1, null);\r
       this.add(jPanel1, null);\r
   }\r