X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=675b862e58100c222300b023c8b09a970fa2391a;hb=75aceeffea6e41f77a85ce6732780e760db739e5;hp=583a5ade62fb1236c5a2c738424c54b05c7f7f23;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
old mode 100755
new mode 100644
index 583a5ad..675b862
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,38 +1,59 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+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;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+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;
 
@@ -53,10 +74,12 @@ public class Finder extends Panel implements ActionListener
     this.ap = ap;
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
+    jalview.bin.JalviewLite.addFrame(frame,
+            MessageManager.getString("action.find"), 340, 120);
     frame.repaint();
     frame.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent evt)
       {
         ap.highlightSearchResults(null);
@@ -65,6 +88,7 @@ public class Finder extends Panel implements ActionListener
     textfield.requestFocus();
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == textfield)
@@ -91,24 +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<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,
             features, true, ap))
     {
       ap.alignFrame.sequenceFeatures.setState(true);
-      av.showSequenceFeatures(true);
+      av.setShowSequenceFeatures(true);
       ap.highlightSearchResults(null);
     }
   }
@@ -124,6 +146,7 @@ public class Finder extends Panel implements ActionListener
     jalview.analysis.Finder finder = new jalview.analysis.Finder(
             av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
     finder.setCaseSensitive(caseSensitive.getState());
+    finder.setIncludeDescription(searchDescription.getState());
     finder.setFindAll(findAll);
 
     String searchString = textfield.getText();
@@ -132,7 +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))
@@ -163,14 +186,17 @@ public class Finder extends Panel implements ActionListener
     // 'SelectRegion' selection
     if (!haveResults)
     {
-      ap.alignFrame.statusBar.setText("Finished searching.");
+      ap.alignFrame.statusBar.setText(
+              MessageManager.getString("label.finished_searching"));
       resIndex = -1;
       seqIndex = 0;
-    } else { 
+    }
+    else
+    {
       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)
         {
@@ -180,14 +206,17 @@ public class Finder extends Panel implements ActionListener
         {
           message += searchResults.getSize() + " subsequence matches.";
         }
-        ap.alignFrame.statusBar.setText("Search results: " + searchString
-                + " : " + message);
+        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("Found match for " + searchString);
+        ap.alignFrame.statusBar.setText(MessageManager
+                .formatMessage("label.found_match_for", new String[]
+                { searchString }));
       }
     }
   }
@@ -200,7 +229,7 @@ public class Finder extends Panel implements ActionListener
 
   protected Button findNext = new Button();
 
-  Panel jPanel1 = new Panel();
+  Panel actionsPanel = new Panel();
 
   GridLayout gridLayout1 = new GridLayout();
 
@@ -208,17 +237,20 @@ public class Finder extends Panel implements ActionListener
 
   Checkbox caseSensitive = new Checkbox();
 
+  Checkbox searchDescription = new Checkbox();
+
   private void jbInit() throws Exception
   {
     jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
-    jLabel1.setText("Find");
+    jLabel1.setText(MessageManager.getString("action.find"));
     jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
     this.setLayout(null);
     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
     textfield.setText("");
-    textfield.setBounds(new Rectangle(40, 27, 133, 21));
+    textfield.setBounds(new Rectangle(40, 17, 133, 21));
     textfield.addKeyListener(new java.awt.event.KeyAdapter()
     {
+      @Override
       public void keyTyped(KeyEvent e)
       {
         textfield_keyTyped(e);
@@ -226,30 +258,35 @@ public class Finder extends Panel implements ActionListener
     });
     textfield.addActionListener(this);
     findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    findAll.setLabel("Find all");
+    findAll.setLabel(MessageManager.getString("action.find_all"));
     findAll.addActionListener(this);
     findNext.setEnabled(false);
     findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    findNext.setLabel("Find Next");
+    findNext.setLabel(MessageManager.getString("action.find_next"));
     findNext.addActionListener(this);
-    jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
-    jPanel1.setLayout(gridLayout1);
+    actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
+    actionsPanel.setLayout(gridLayout1);
     gridLayout1.setHgap(0);
     gridLayout1.setRows(3);
     gridLayout1.setVgap(2);
     createNewGroup.setEnabled(false);
     createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-    createNewGroup.setLabel("New Feature");
+    createNewGroup.setLabel(MessageManager.getString("label.new_feature"));
     createNewGroup.addActionListener(this);
-    caseSensitive.setLabel("Match Case");
-    caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
-    jPanel1.add(findNext, null);
-    jPanel1.add(findAll, null);
-    jPanel1.add(createNewGroup, null);
+    caseSensitive.setLabel(MessageManager.getString("label.match_case"));
+    caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
+
+    searchDescription.setLabel(
+            MessageManager.getString("label.include_description"));
+    searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
+    actionsPanel.add(findNext, null);
+    actionsPanel.add(findAll, null);
+    actionsPanel.add(createNewGroup, null);
     this.add(caseSensitive);
     this.add(textfield, null);
     this.add(jLabel1, null);
-    this.add(jPanel1, null);
+    this.add(actionsPanel, null);
+    this.add(searchDescription);
   }
 
   void textfield_keyTyped(KeyEvent e)