From dedbb25d7f54f28aaa36592be27c80487090e10d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:13:55 +0000
Subject: [PATCH] Add new feature from seqrch results

---
 src/jalview/appletgui/Finder.java |   36 ++++++++++++++++++++++++++++--------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index fb8c280..8905b52 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -84,20 +84,37 @@ public class Finder extends Panel implements ActionListener
   public void createNewGroup_actionPerformed()
   {
 
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
+    Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
+    dialog.add(cap);
+
+    cap.setText(textfield.getText());
+
+    dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,
+                      frame.getLocation().y+20,300,100);
+    dialog.show();
+
+
+    String featureName = cap.getText().trim();
+    if(featureName.length()<1)
+      return;
+
+
     for (int i = 0; i < searchResults.getSize(); i ++ )
     {
         SequenceI seq = searchResults.getResultSequence(i);
 
-        SequenceFeature sf = new SequenceFeature(textfield.getText(),
-            "Search Results", null,
+        SequenceFeature sf = new SequenceFeature(featureName,
+            null, null,
             searchResults.getResultStart(i),
            searchResults.getResultEnd(i));
 
         ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
-            textfield.getText(), new Color(60,160,115));
+            featureName, new Color(60,160,115));
         seq.addSequenceFeature(sf);
     }
 
+    ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
     ap.alignFrame.sequenceFeatures.setState(true);
     av.showSequenceFeatures(true);
     ap.highlightSearchResults(null);
@@ -155,6 +172,7 @@ public class Finder extends Panel implements ActionListener
 
     while (!found && seqIndex < end)
     {
+
       seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
       if (selection != null && !selection.sequences.contains(seq))
@@ -172,7 +190,7 @@ public class Finder extends Panel implements ActionListener
       }
 
       ///Shall we ignore gaps????
-      StringBuffer noGaps = new StringBuffer();
+      StringBuffer noGapsSB = new StringBuffer();
       int insertCount = 0;
       Vector spaces = new Vector();
 
@@ -181,7 +199,7 @@ public class Finder extends Panel implements ActionListener
 
         if (!jalview.util.Comparison.isGap(item.charAt(j)))
         {
-          noGaps.append(item.charAt(j));
+          noGapsSB.append(item.charAt(j));
           spaces.addElement(new Integer(insertCount));
         }
         else
@@ -190,10 +208,12 @@ public class Finder extends Panel implements ActionListener
         }
       }
 
+      String noGaps = noGapsSB.toString();
+
       for (int r = resIndex; r < noGaps.length(); r++)
       {
 
-        if (regex.searchFrom(noGaps.toString(), r))
+        if (regex.searchFrom(noGaps, r))
         {
           resIndex = regex.matchedFrom();
           if (selection != null &&
@@ -264,8 +284,8 @@ public class Finder extends Panel implements ActionListener
 
     if (findAll)
     {
-      String message = (searchResults.getSize()) + " matches found.";
-      System.out.println(message);
+      String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";
+      ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);
     }
 
   }
-- 
1.7.10.2