header updated

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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 58e2993..e8c16d2 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/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
@@ -128,14 +128,17 @@ public class Finder extends GFinder
             SequenceFeature sf = new SequenceFeature(textinput.getText(),\r
                 "Search Results", null,\r
                 searchResults.getResultStart(i),\r
-               searchResults.getResultEnd(i));\r
+               searchResults.getResultEnd(i),\r
+               "Search Results");\r
 \r
             ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
-                textinput.getText(), new Color(60,160,115));\r
+                textinput.getText(), new Color(60,160,115),\r
+                    "Search Results");\r
 \r
             seq.getDatasetSequence().addSequenceFeature(sf);\r
         }\r
 \r
+        ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
         ap.alignFrame.showSeqFeatures.setSelected(true);\r
         av.setShowSequenceFeatures(true);\r
         ap.highlightSearchResults(null);\r
@@ -150,7 +153,10 @@ public class Finder extends GFinder
     {\r
         createNewGroup.setEnabled(false);\r
 \r
-        String searchString = textfield.getText().toUpperCase().trim();\r
+        String searchString = textfield.getText().trim();\r
+        if(!caseSensitive.isSelected())\r
+          searchString = searchString.toUpperCase();\r
+\r
         if(searchString.length()<1)\r
           return;\r
 \r
@@ -167,7 +173,7 @@ public class Finder extends GFinder
         {\r
             int res = Integer.parseInt(searchString);\r
             found = true;\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
@@ -190,7 +196,7 @@ public class Finder extends GFinder
 \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
@@ -201,7 +207,7 @@ public class Finder extends GFinder
         {\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
@@ -209,7 +215,9 @@ public class Finder extends GFinder
                 continue;\r
             }\r
 \r
-            item = seq.getSequence().toUpperCase();\r
+            item = seq.getSequence();\r
+            if(!caseSensitive.isSelected())\r
+              item = item.toUpperCase();\r
 \r
             if ((selection != null) &&\r
                     (selection.getEndRes() < av.alignment.getWidth()-1))\r