Sequence numbering maintained

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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 6a73bd1..49a9656 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -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
@@ -183,16 +189,6 @@ public class Finder extends GFinder
         }\r
 \r
         ///////////////////////////////////////////////\r
-        Color[] newColors = new Color[24];\r
-\r
-        for (int i = 0; i < 24; i++)\r
-        {\r
-            newColors[i] = new Color(60, 160, 115);\r
-        }\r
-\r
-        jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
-\r
-      //SG  searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
 \r
         int end = av.alignment.getHeight();\r
 \r
@@ -219,7 +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