X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=ee0d4a074478478911c1622b5220021e6c1588be;hb=dfc18d64376ae95cfdbf3c112825587a8891179c;hp=529b0b388b12967a58ee4311ba4acfc5a9e93bde;hpb=50bc9bfda9c71e968f53e6a77ba3ea9cdfd6d3ee;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 529b0b3..ee0d4a0 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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)
@@ -109,24 +115,22 @@ 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<>();
+    List<SequenceFeature> features = new ArrayList<>();
+    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,
             features, true, ap))
     {
       ap.alignFrame.sequenceFeatures.setState(true);
-      av.showSequenceFeatures(true);
+      av.setShowSequenceFeatures(true);
       ap.highlightSearchResults(null);
     }
   }
@@ -151,28 +155,16 @@ public class Finder extends Panel implements ActionListener
     seqIndex = finder.getSeqIndex();
     resIndex = finder.getResIndex();
     searchResults = finder.getSearchResults();
-    Vector idMatch = finder.getIdMatch();
-    boolean haveResults = false;
-    // set or reset the GUI
-    if ((idMatch.size() > 0))
-    {
-      haveResults = true;
-      ap.idPanel.highlightSearchResults(idMatch);
-    }
-    else
-    {
-      ap.idPanel.highlightSearchResults(null);
-    }
+    Vector<SequenceI> idMatch = finder.getIdMatch();
+    ap.idPanel.highlightSearchResults(idMatch);
 
-    if (searchResults.getSize() > 0)
+    if (searchResults.isEmpty())
     {
-      haveResults = true;
-      createNewGroup.setEnabled(true);
-
+      searchResults = null;
     }
     else
     {
-      searchResults = null;
+      createNewGroup.setEnabled(true);
     }
 
     // if allResults is null, this effectively switches displaySearch flag in
@@ -180,10 +172,10 @@ public class Finder extends Panel implements ActionListener
     ap.highlightSearchResults(searchResults);
     // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
     // 'SelectRegion' selection
-    if (!haveResults)
+    if (idMatch.isEmpty() && searchResults == null)
     {
-      ap.alignFrame.statusBar.setText(MessageManager
-              .getString("label.finished_searching"));
+      ap.alignFrame.statusBar.setText(
+              MessageManager.getString("label.finished_searching"));
       resIndex = -1;
       seqIndex = 0;
     }
@@ -191,8 +183,8 @@ 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 +194,16 @@ 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 +238,7 @@ 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 +264,8 @@ 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);