JAL-2310 don't double-count sequence matches; code tidying

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

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 4796bca..d18295c 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 2.8.2)
- * 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.
  * 
@@ -20,23 +20,37 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+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.Vector;
 
 public class Finder extends Panel implements ActionListener
 {
-  AlignViewport av;
+  AlignmentViewport av;
 
   AlignmentPanel ap;
 
   Frame frame;
 
-  SearchResults searchResults;
+  SearchResultsI searchResults;
 
   int seqIndex = 0;
 
@@ -62,6 +76,7 @@ public class Finder extends Panel implements ActionListener
     frame.repaint();
     frame.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent evt)
       {
         ap.highlightSearchResults(null);
@@ -70,6 +85,7 @@ public class Finder extends Panel implements ActionListener
     textfield.requestFocus();
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == textfield)
@@ -129,6 +145,7 @@ 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();
@@ -137,7 +154,7 @@ 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))
@@ -189,16 +206,15 @@ 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 }));
       }
     }
   }
@@ -211,7 +227,7 @@ public class Finder extends Panel implements ActionListener
 
   protected Button findNext = new Button();
 
-  Panel jPanel1 = new Panel();
+  Panel actionsPanel = new Panel();
 
   GridLayout gridLayout1 = new GridLayout();
 
@@ -219,6 +235,8 @@ 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));
@@ -227,9 +245,10 @@ public class Finder extends Panel implements ActionListener
     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);
@@ -243,8 +262,8 @@ public class Finder extends Panel implements ActionListener
     findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
     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);
@@ -253,14 +272,19 @@ public class Finder extends Panel implements ActionListener
     createNewGroup.setLabel(MessageManager.getString("label.new_feature"));
     createNewGroup.addActionListener(this);
     caseSensitive.setLabel(MessageManager.getString("label.match_case"));
-    caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
-    jPanel1.add(findNext, null);
-    jPanel1.add(findAll, null);
-    jPanel1.add(createNewGroup, null);
+    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)