Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index f7ad818..675b862 100644 (file)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -39,17 +41,19 @@ import java.awt.event.ActionListener;
 import java.awt.event.KeyEvent;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.util.ArrayList;
+import java.util.List;
 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 +79,7 @@ public class Finder extends Panel implements ActionListener
     frame.repaint();
     frame.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent evt)
       {
         ap.highlightSearchResults(null);
@@ -83,6 +88,7 @@ public class Finder extends Panel implements ActionListener
     textfield.requestFocus();
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == textfield)
@@ -109,17 +115,15 @@ public class Finder extends Panel implements ActionListener
 
   public void createNewGroup_actionPerformed()
   {
-    SequenceI[] seqs = new SequenceI[searchResults.getSize()];
-    SequenceFeature[] features = new SequenceFeature[searchResults
-            .getSize()];
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+    String searchString = textfield.getText().trim();
 
-    for (int i = 0; i < searchResults.getSize(); i++)
+    for (SearchResultMatchI match : searchResults.getResults())
     {
-      seqs[i] = searchResults.getResultSequence(i);
-
-      features[i] = new SequenceFeature(textfield.getText().trim(),
-              "Search Results", null, searchResults.getResultStart(i),
-              searchResults.getResultEnd(i), "Search Results");
+      seqs.add(match.getSequence().getDatasetSequence());
+      features.add(new SequenceFeature(searchString, "Search Results",
+              match.getStart(), match.getEnd(), "Search Results"));
     }
 
     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
@@ -151,7 +155,7 @@ 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))
@@ -182,8 +186,8 @@ public class Finder extends Panel implements ActionListener
     // 'SelectRegion' selection
     if (!haveResults)
     {
-      ap.alignFrame.statusBar.setText(MessageManager
-              .getString("label.finished_searching"));
+      ap.alignFrame.statusBar.setText(
+              MessageManager.getString("label.finished_searching"));
       resIndex = -1;
       seqIndex = 0;
     }
@@ -191,8 +195,8 @@ public class Finder extends Panel implements ActionListener
     {
       if (findAll)
       {
-        String message = (idMatch.size() > 0) ? "" + idMatch.size()
-                + " IDs" : "";
+        String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+                : "";
         if (idMatch.size() > 0 && searchResults != null
                 && searchResults.getSize() > 0)
         {
@@ -202,16 +206,16 @@ public class Finder extends Panel implements ActionListener
         {
           message += searchResults.getSize() + " subsequence matches.";
         }
-        ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
-                "label.search_results", new String[]
+        ap.alignFrame.statusBar.setText(MessageManager
+                .formatMessage("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[]
+        ap.alignFrame.statusBar.setText(MessageManager
+                .formatMessage("label.found_match_for", new String[]
                 { searchString }));
       }
     }
@@ -246,6 +250,7 @@ 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);
@@ -271,8 +276,8 @@ public class Finder extends Panel implements ActionListener
     caseSensitive.setLabel(MessageManager.getString("label.match_case"));
     caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
 
-    searchDescription.setLabel(MessageManager
-            .getString("label.include_description"));
+    searchDescription.setLabel(
+            MessageManager.getString("label.include_description"));
     searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
     actionsPanel.add(findNext, null);
     actionsPanel.add(findAll, null);