X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=a342736bd6f9c7d732cc8cbc5711059c3d5e6de9;hb=954039bbfbde3648ac4c795277e788e49be5181b;hp=93ab3147dbc611abf79fa767535a177e85c7c601;hpb=21c29b20790ac555b2e2a124a034f6c6b4486270;p=jalview.git
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 93ab314..a342736 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,39 +1,57 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.Vector;
public class Finder extends Panel implements ActionListener
{
- AlignViewport av;
+ AlignmentViewport av;
AlignmentPanel ap;
Frame frame;
- SearchResults searchResults;
+ SearchResultsI searchResults;
int seqIndex = 0;
@@ -54,10 +72,12 @@ public class Finder extends Panel implements ActionListener
this.ap = ap;
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.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);
@@ -66,6 +86,7 @@ public class Finder extends Panel implements ActionListener
textfield.requestFocus();
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == textfield)
@@ -95,21 +116,24 @@ 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,
features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
- av.showSequenceFeatures(true);
+ av.setShowSequenceFeatures(true);
ap.highlightSearchResults(null);
}
}
@@ -125,6 +149,7 @@ 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();
@@ -133,7 +158,7 @@ public class Finder extends Panel implements ActionListener
seqIndex = finder.getSeqIndex();
resIndex = finder.getResIndex();
searchResults = finder.getSearchResults();
- Vector idMatch = finder.getIdMatch();
+ Vector idMatch = finder.getIdMatch();
boolean haveResults = false;
// set or reset the GUI
if ((idMatch.size() > 0))
@@ -164,7 +189,8 @@ 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;
}
@@ -183,13 +209,16 @@ 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}));
+ 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[]{searchString}));
+ ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.found_match_for", new String[] { searchString }));
}
}
}
@@ -202,7 +231,7 @@ public class Finder extends Panel implements ActionListener
protected Button findNext = new Button();
- Panel jPanel1 = new Panel();
+ Panel actionsPanel = new Panel();
GridLayout gridLayout1 = new GridLayout();
@@ -210,6 +239,8 @@ 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));
@@ -218,9 +249,10 @@ 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);
@@ -234,8 +266,8 @@ 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);
@@ -244,14 +276,19 @@ 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)