X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=e0ceeef67f4039a5644cf334096025ac37f00343;hb=c1e82b5f51e05f64318bfc8eae4e85b58d1922b5;hp=5d800ce70b0b4a13599658e39a5ebc24237f9cab;hpb=8302463adc038c6385cde595bcb3a7ef5b2fd07c;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5d800ce..e0ceeef 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -128,16 +128,19 @@ public class Finder extends GFinder
             SequenceFeature sf = new SequenceFeature(textinput.getText(),
                 "Search Results", null,
                 searchResults.getResultStart(i),
-               searchResults.getResultEnd(i));
+               searchResults.getResultEnd(i),
+               "Search Results");
 
             ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
-                textinput.getText(), new Color(60,160,115));
+                textinput.getText(), new Color(60,160,115),
+                    "Search Results");
 
             seq.getDatasetSequence().addSequenceFeature(sf);
         }
 
-        ap.alignFrame.sequenceFeatures.setSelected(true);
-        ap.alignFrame.sequenceFeatures_actionPerformed(null);
+        ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
+        ap.alignFrame.showSeqFeatures.setSelected(true);
+        av.setShowSequenceFeatures(true);
         ap.highlightSearchResults(null);
     }
 
@@ -150,7 +153,10 @@ public class Finder extends GFinder
     {
         createNewGroup.setEnabled(false);
 
-        String searchString = textfield.getText().toUpperCase().trim();
+        String searchString = textfield.getText().trim();
+        if(!caseSensitive.isSelected())
+          searchString = searchString.toUpperCase();
+
         if(searchString.length()<1)
           return;
 
@@ -167,7 +173,7 @@ public class Finder extends GFinder
         {
             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);
             }
@@ -183,16 +189,6 @@ public class Finder extends GFinder
         }
 
         ///////////////////////////////////////////////
-        Color[] newColors = new Color[24];
-
-        for (int i = 0; i < 24; i++)
-        {
-            newColors[i] = new Color(60, 160, 115);
-        }
-
-        jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
-
-      //SG  searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
         int end = av.alignment.getHeight();
 
@@ -200,7 +196,7 @@ public class Finder extends GFinder
 
         if (selection != null)
         {
-            if ((selection.getSize() < 1) ||
+            if ((selection.getSize(false) < 1) ||
                     ((selection.getEndRes() - selection.getStartRes()) < 2))
             {
                 selection = null;
@@ -211,7 +207,7 @@ public class Finder extends GFinder
         {
             seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
-            if ((selection != null) && !selection.sequences.contains(seq))
+            if ((selection != null) && !selection.getSequences(false).contains(seq))
             {
                 seqIndex++;
                 resIndex = 0;
@@ -219,7 +215,9 @@ public class Finder extends GFinder
                 continue;
             }
 
-            item = seq.getSequence().toUpperCase();
+            item = seq.getSequence();
+            if(!caseSensitive.isSelected())
+              item = item.toUpperCase();
 
             if ((selection != null) &&
                     (selection.getEndRes() < av.alignment.getWidth()-1))