Cursor added

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

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index ac7bc2c..1201278 100755 (executable)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -31,7 +31,6 @@ public class Finder extends Panel implements ActionListener
   AlignViewport av;\r
   AlignmentPanel ap;\r
   Frame frame;\r
-  SuperGroup searchGroup;\r
 \r
   SearchResults searchResults;\r
 \r
@@ -84,36 +83,40 @@ public class Finder extends Panel implements ActionListener
 \r
   public void createNewGroup_actionPerformed()\r
   {\r
-    Color[] newColors = new Color[24];\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(\r
-        newColors);\r
-    String searchString = textfield.getText();\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);\r
+    Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);\r
+    dialog.add(cap);\r
+\r
+    cap.setText(textfield.getText());\r
+\r
+    dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,\r
+                      frame.getLocation().y+20,300,100);\r
+    dialog.show();\r
+\r
+\r
+    String featureName = cap.getText().trim();\r
+    if(featureName.length()<1)\r
+      return;\r
 \r
-    searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
 \r
     for (int i = 0; i < searchResults.getSize(); i ++ )\r
     {\r
-      // its possible edits may have occurred since search was performed\r
-      // account for this here\r
-\r
-      SequenceI seq = searchResults.getResultSequence(i);\r
-      int startRes = seq.findIndex(searchResults.getResultStart(i)) - 1;\r
-            int endRes = seq.findIndex(searchResults.getResultEnd(i)) - 1;\r
+        SequenceI seq = searchResults.getResultSequence(i);\r
 \r
-      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
-                                           startRes, endRes);\r
-      sg.addSequence(seq, false);\r
-      av.alignment.addGroup(sg);\r
-      searchGroup.addGroup(sg);\r
+        SequenceFeature sf = new SequenceFeature(featureName,\r
+            null, null,\r
+            searchResults.getResultStart(i),\r
+           searchResults.getResultEnd(i), "Search Results");\r
 \r
+        ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
+            featureName, new Color(60,160,115));\r
+        seq.addSequenceFeature(sf);\r
     }\r
 \r
-    ap.av.alignment.addSuperGroup(searchGroup);\r
+    ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
+    ap.alignFrame.sequenceFeatures.setState(true);\r
+    av.showSequenceFeatures(true);\r
     ap.highlightSearchResults(null);\r
   }\r
 \r
@@ -169,6 +172,7 @@ public class Finder extends Panel implements ActionListener
 \r
     while (!found && seqIndex < end)\r
     {\r
+\r
       seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
 \r
       if (selection != null && !selection.sequences.contains(seq))\r
@@ -186,7 +190,7 @@ public class Finder extends Panel implements ActionListener
       }\r
 \r
       ///Shall we ignore gaps????\r
-      StringBuffer noGaps = new StringBuffer();\r
+      StringBuffer noGapsSB = new StringBuffer();\r
       int insertCount = 0;\r
       Vector spaces = new Vector();\r
 \r
@@ -195,7 +199,7 @@ public class Finder extends Panel implements ActionListener
 \r
         if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
         {\r
-          noGaps.append(item.charAt(j));\r
+          noGapsSB.append(item.charAt(j));\r
           spaces.addElement(new Integer(insertCount));\r
         }\r
         else\r
@@ -204,10 +208,12 @@ public class Finder extends Panel implements ActionListener
         }\r
       }\r
 \r
+      String noGaps = noGapsSB.toString();\r
+\r
       for (int r = resIndex; r < noGaps.length(); r++)\r
       {\r
 \r
-        if (regex.searchFrom(noGaps.toString(), r))\r
+        if (regex.searchFrom(noGaps, r))\r
         {\r
           resIndex = regex.matchedFrom();\r
           if (selection != null &&\r
@@ -278,8 +284,8 @@ public class Finder extends Panel implements ActionListener
 \r
     if (findAll)\r
     {\r
-      String message = (searchResults.getSize()) + " matches found.";\r
-      System.out.println(message);\r
+      String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";\r
+      ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);\r
     }\r
 \r
   }\r
@@ -321,7 +327,7 @@ public class Finder extends Panel implements ActionListener
       gridLayout1.setVgap(2);\r
       createNewGroup.setEnabled(false);\r
       createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
-      createNewGroup.setLabel("Create new group");\r
+      createNewGroup.setLabel("New Feature");\r
       createNewGroup.addActionListener(this);\r
       jPanel1.add(findNext, null);\r
       jPanel1.add(findAll, null);\r