showqual, showcons never used

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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 58e2993..8697552 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
@@ -114,31 +114,29 @@ public class Finder extends GFinder
         panel.add(label, BorderLayout.NORTH);\r
         panel.add(textinput, BorderLayout.SOUTH);\r
 \r
-         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
-            panel, "New Sequence Feature Name",\r
-          JOptionPane.OK_CANCEL_OPTION );\r
 \r
-         if(reply != JOptionPane.OK_OPTION)\r
-           return;\r
+        SequenceI [] seqs = new SequenceI[searchResults.getSize()];\r
+        SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];\r
+\r
 \r
         for (int i = 0; i < searchResults.getSize(); i ++ )\r
         {\r
-            SequenceI seq = searchResults.getResultSequence(i);\r
+            seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();\r
 \r
-            SequenceFeature sf = new SequenceFeature(textinput.getText(),\r
+            features[i] = new SequenceFeature(textinput.getText(),\r
                 "Search Results", null,\r
                 searchResults.getResultStart(i),\r
-               searchResults.getResultEnd(i));\r
-\r
-            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
-                textinput.getText(), new Color(60,160,115));\r
-\r
-            seq.getDatasetSequence().addSequenceFeature(sf);\r
+                searchResults.getResultEnd(i),\r
+               "Search Results");\r
         }\r
 \r
-        ap.alignFrame.showSeqFeatures.setSelected(true);\r
-        av.setShowSequenceFeatures(true);\r
-        ap.highlightSearchResults(null);\r
+        if( ap.seqPanel.seqCanvas.getFeatureRenderer()\r
+            .createNewFeatures(seqs, features))\r
+        {\r
+          ap.alignFrame.showSeqFeatures.setSelected(true);\r
+          av.setShowSequenceFeatures(true);\r
+          ap.highlightSearchResults(null);\r
+        }\r
     }\r
 \r
     /**\r
@@ -150,7 +148,10 @@ 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 +168,7 @@ 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 +191,7 @@ 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 +202,7 @@ 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 +210,9 @@ 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