X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=6b8df4b33d1d298e08fc24e8ecc72cd5095c0ae1;hb=94bc21544b9573fdf177c500bdb981e8076a7e7d;hp=ff4fe603a736233f03ed9eb2714879e56455f64c;hpb=00cdd6a38c70ad1d2b8aff08b2b5be973c28e7f9;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index ff4fe60..6b8df4b 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -42,11 +42,11 @@ public class Finder extends GFinder
     AlignViewport av;
     AlignmentPanel ap;
     JInternalFrame frame;
-    SuperGroup searchGroup;
-    Vector searchResults;
     int seqIndex = 0;
     int resIndex = 0;
 
+    SearchResults searchResults;
+
     /**
      * Creates a new Finder object.
      *
@@ -74,16 +74,6 @@ public class Finder extends GFinder
                             }
                         });
                 }
-
-                /**
-                 * DOCUMENT ME!
-                 *
-                 * @param evt DOCUMENT ME!
-                 */
-                public void internalFrameClosing(InternalFrameEvent evt)
-                {
-                    cancel_actionPerformed(null);
-                }
             });
     }
 
@@ -110,25 +100,6 @@ public class Finder extends GFinder
         doSearch(true);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void cancel_actionPerformed(ActionEvent e)
-    {
-        try
-        {
-            // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-            ap.highlightSearchResults(null);
-            ap.idPanel.highlightSearchResults(null);
-
-            // frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
-    }
 
     /**
      * DOCUMENT ME!
@@ -137,37 +108,39 @@ public class Finder extends GFinder
      */
     public void createNewGroup_actionPerformed(ActionEvent e)
     {
-        Color[] newColors = new Color[24];
+        JLabel label = new JLabel("Enter name of new sequence feature");
+        JTextField textinput = new JTextField(textfield.getText());
+        JPanel panel = new JPanel(new BorderLayout());
+        panel.add(label, BorderLayout.NORTH);
+        panel.add(textinput, BorderLayout.SOUTH);
+
+         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            panel, "New Sequence Feature Name",
+          JOptionPane.OK_CANCEL_OPTION );
+
+         if(reply != JOptionPane.OK_OPTION)
+           return;
 
-        for (int i = 0; i < 24; i++)
+        for (int i = 0; i < searchResults.getSize(); i ++ )
         {
-            newColors[i] = new Color(60, 160, 115);
-        }
+            SequenceI seq = searchResults.getResultSequence(i);
 
-        jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
-        String searchString = textfield.getText();
+            SequenceFeature sf = new SequenceFeature(textinput.getText(),
+                "Search Results", null,
+                searchResults.getResultStart(i),
+               searchResults.getResultEnd(i),
+               "Search Results");
 
-        searchGroup = new SuperGroup(searchString, ucs, true, true, false);
+            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+                textinput.getText(), new Color(60,160,115),
+                    "Search Results");
 
-        for (int i = 0; i < searchResults.size(); i += 3)
-        {
-            // its possible edits may have occurred since search was performed
-            // account for this here
-            SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(
-                        searchResults.elementAt(i).toString()));
-            int startRes = seq.findIndex(Integer.parseInt(
-                        searchResults.elementAt(i + 1).toString())) - 1;
-            int endRes = seq.findIndex(Integer.parseInt(
-                        searchResults.elementAt(i + 2).toString())) - 1;
-
-            SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,
-                    false, startRes, endRes);
-            sg.addSequence(seq, false);
-            av.alignment.addGroup(sg);
-            searchGroup.addGroup(sg);
+            seq.getDatasetSequence().addSequenceFeature(sf);
         }
 
-        ap.av.alignment.addSuperGroup(searchGroup);
+        ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
+        ap.alignFrame.showSeqFeatures.setSelected(true);
+        av.setShowSequenceFeatures(true);
         ap.highlightSearchResults(null);
     }
 
@@ -186,9 +159,7 @@ public class Finder extends GFinder
 
         com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
-        searchResults = new Vector();
-
-        int[] allResults = null;
+        searchResults = new SearchResults();
 
         Sequence seq;
         String item = null;
@@ -208,25 +179,13 @@ public class Finder extends GFinder
               seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
             }
 
-            searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
-            searchResults.add(res+"");
-            searchResults.add(res+"");
+            searchResults.addResult(seq, res, res);
         }
         catch (NumberFormatException ex)
         {
         }
 
         ///////////////////////////////////////////////
-        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);
-
-        searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
         int end = av.alignment.getHeight();
 
@@ -256,7 +215,7 @@ public class Finder extends GFinder
             item = seq.getSequence().toUpperCase();
 
             if ((selection != null) &&
-                    (selection.getEndRes() < av.alignment.getWidth()))
+                    (selection.getEndRes() < av.alignment.getWidth()-1))
             {
                 item = item.substring(0, selection.getEndRes() + 1);
             }
@@ -295,7 +254,6 @@ public class Finder extends GFinder
                         continue;
                     }
 
-                    searchResults.add(Integer.toString(seqIndex));
 
                     int sres = seq.findPosition(resIndex +
                             Integer.parseInt(spaces.elementAt(resIndex)
@@ -304,8 +262,7 @@ public class Finder extends GFinder
                             Integer.parseInt(spaces.elementAt(regex.matchedTo() -
                                     1).toString()));
 
-                    searchResults.addElement(sres + "");
-                    searchResults.addElement(eres + "");
+                    searchResults.addResult(seq, sres, eres);
 
                     if (!findAll)
                     {
@@ -341,23 +298,23 @@ public class Finder extends GFinder
             }
         }
 
-        if ((searchResults.size() == 0) && (idMatch.size() > 0))
+        if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
         {
             ap.idPanel.highlightSearchResults(idMatch);
         }
 
-        if (searchResults.size() > 0)
-        {
-            allResults = new int[searchResults.size()];
 
-            for (int i = 0; i < searchResults.size(); i++)
-            {
-                allResults[i] = Integer.parseInt(searchResults.get(i).toString());
-            }
+        int resultSize = searchResults.getSize();
 
-            createNewGroup.setEnabled(true);
-        }
+        if (searchResults.getSize() > 0)
+          createNewGroup.setEnabled(true);
         else
+          searchResults = null;
+
+        // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+        ap.highlightSearchResults(searchResults);
+
+        if(!findAll && resultSize==0)
         {
             JOptionPane.showInternalMessageDialog(this, "Finished searching",
                 null, JOptionPane.INFORMATION_MESSAGE);
@@ -365,14 +322,12 @@ public class Finder extends GFinder
             seqIndex = 0;
         }
 
-        // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-        ap.highlightSearchResults(allResults);
-
         if (findAll)
         {
-            String message = (searchResults.size() / 3) + " matches found.";
-            JOptionPane.showInternalMessageDialog(this, message, null,
-                JOptionPane.INFORMATION_MESSAGE);
+          String message = resultSize + " matches found.";
+          JOptionPane.showInternalMessageDialog(this, message, null,
+                                                JOptionPane.INFORMATION_MESSAGE);
         }
+
     }
 }