X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=a342736bd6f9c7d732cc8cbc5711059c3d5e6de9;hb=cce9a433443d6407b561679c4c489cdbfca2d12e;hp=3f8a54d27183dfc2afaa0ffede8c5460dbf681c4;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 3f8a54d..a342736 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -20,10 +20,12 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Button;
 import java.awt.Checkbox;
@@ -43,13 +45,13 @@ import java.util.Vector;
 
 public class Finder extends Panel implements ActionListener
 {
-  AlignViewport av;
+  AlignmentViewport av;
 
   AlignmentPanel ap;
 
   Frame frame;
 
-  SearchResults searchResults;
+  SearchResultsI searchResults;
 
   int seqIndex = 0;
 
@@ -75,6 +77,7 @@ public class Finder extends Panel implements ActionListener
     frame.repaint();
     frame.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent evt)
       {
         ap.highlightSearchResults(null);
@@ -83,6 +86,7 @@ public class Finder extends Panel implements ActionListener
     textfield.requestFocus();
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == textfield)
@@ -112,14 +116,17 @@ public class Finder extends Panel implements ActionListener
     SequenceI[] seqs = new SequenceI[searchResults.getSize()];
     SequenceFeature[] features = new SequenceFeature[searchResults
             .getSize()];
+    String searchString = textfield.getText().trim();
 
-    for (int i = 0; i < searchResults.getSize(); i++)
+    int i = 0;
+    for (SearchResultMatchI match : searchResults.getResults())
     {
-      seqs[i] = searchResults.getResultSequence(i);
+      seqs[i] = match.getSequence().getDatasetSequence();
 
-      features[i] = new SequenceFeature(textfield.getText().trim(),
-              "Search Results", null, searchResults.getResultStart(i),
-              searchResults.getResultEnd(i), "Search Results");
+      features[i] = new SequenceFeature(searchString,
+              "Search Results", null, match.getStart(), match.getEnd(),
+              "Search Results");
+      i++;
     }
 
     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
@@ -151,7 +158,7 @@ public class Finder extends Panel implements ActionListener
     seqIndex = finder.getSeqIndex();
     resIndex = finder.getResIndex();
     searchResults = finder.getSearchResults();
-    Vector idMatch = finder.getIdMatch();
+    Vector<SequenceI> idMatch = finder.getIdMatch();
     boolean haveResults = false;
     // set or reset the GUI
     if ((idMatch.size() > 0))
@@ -203,16 +210,15 @@ public class Finder extends Panel implements ActionListener
           message += searchResults.getSize() + " subsequence matches.";
         }
         ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
-                "label.search_results", new String[]
-                { searchString, message }));
+                "label.search_results", new String[] { searchString,
+                    message }));
 
       }
       else
       {
         // TODO: indicate sequence and matching position in status bar
         ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
-                "label.found_match_for", new String[]
-                { searchString }));
+                "label.found_match_for", new String[] { searchString }));
       }
     }
   }
@@ -246,6 +252,7 @@ public class Finder extends Panel implements ActionListener
     textfield.setBounds(new Rectangle(40, 17, 133, 21));
     textfield.addKeyListener(new java.awt.event.KeyAdapter()
     {
+      @Override
       public void keyTyped(KeyEvent e)
       {
         textfield_keyTyped(e);