/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
import java.util.*;
import java.awt.event.*;
import jalview.datamodel.*;
-import java.awt.Rectangle;
+import jalview.util.MessageManager;
public class Finder extends Panel implements ActionListener
{
AlignViewport av;
+
AlignmentPanel ap;
+
Frame frame;
SearchResults searchResults;
int seqIndex = 0;
- int resIndex = 0;
+
+ int resIndex = -1;
+
public Finder(final AlignmentPanel ap)
{
try
{
jbInit();
- }
- catch (Exception e)
+
+ } catch (Exception e)
{
e.printStackTrace();
}
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()
{
ap.highlightSearchResults(null);
}
});
+ textfield.requestFocus();
}
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == textfield)
+ {
doSearch(false);
+ }
else if (evt.getSource() == findNext)
+ {
doSearch(false);
+ }
else if (evt.getSource() == findAll)
{
- resIndex = 0;
+ resIndex = -1;
seqIndex = 0;
doSearch(true);
}
- else if(evt.getSource() == createNewGroup)
+ else if (evt.getSource() == createNewGroup)
+ {
createNewGroup_actionPerformed();
+ }
}
-
public void createNewGroup_actionPerformed()
{
+ SequenceI[] seqs = new SequenceI[searchResults.getSize()];
+ SequenceFeature[] features = new SequenceFeature[searchResults
+ .getSize()];
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
- cap.accept.setLabel("Accept");
- Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
- dialog.add(cap);
-
- cap.setText(textfield.getText());
-
- dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,
- frame.getLocation().y+20,300,100);
- dialog.show();
-
-
- String featureName = cap.getText().trim();
- if(featureName.length()<1)
- return;
-
-
- for (int i = 0; i < searchResults.getSize(); i ++ )
+ for (int i = 0; i < searchResults.getSize(); i++)
{
- SequenceI seq = searchResults.getResultSequence(i);
-
- SequenceFeature sf = new SequenceFeature(featureName,
- null, null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i), "Search Results");
+ seqs[i] = searchResults.getResultSequence(i);
- ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
- featureName, new Color(60,160,115));
- seq.addSequenceFeature(sf);
+ features[i] = new SequenceFeature(textfield.getText().trim(),
+ "Search Results", null, searchResults.getResultStart(i),
+ searchResults.getResultEnd(i), "Search Results");
}
- ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
- ap.alignFrame.sequenceFeatures.setState(true);
- av.showSequenceFeatures(true);
- ap.highlightSearchResults(null);
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.sequenceFeatures.setState(true);
+ av.showSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
}
void doSearch(boolean findAll)
{
- if(jalview.bin.JalviewLite.currentAlignFrame!=null)
+ if (ap.av.applet.currentAlignFrame != null)
{
- ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
+ ap = ap.av.applet.currentAlignFrame.alignPanel;
av = ap.av;
}
createNewGroup.setEnabled(false);
- jalview.analysis.Finder finder=new jalview.analysis.Finder(av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+ jalview.analysis.Finder finder = new jalview.analysis.Finder(
+ av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
finder.setCaseSensitive(caseSensitive.getState());
finder.setFindAll(findAll);
-
+
String searchString = textfield.getText();
-
+
finder.find(searchString);
- seqIndex=finder.getSeqIndex();
- resIndex=finder.getResIndex();
+ seqIndex = finder.getSeqIndex();
+ resIndex = finder.getResIndex();
searchResults = finder.getSearchResults();
Vector idMatch = finder.getIdMatch();
-
- if (searchResults.getSize() == 0 && idMatch.size() > 0)
+ boolean haveResults = false;
+ // set or reset the GUI
+ if ((idMatch.size() > 0))
{
+ haveResults = true;
ap.idPanel.highlightSearchResults(idMatch);
}
+ else
+ {
+ ap.idPanel.highlightSearchResults(null);
+ }
if (searchResults.getSize() > 0)
{
+ haveResults = true;
createNewGroup.setEnabled(true);
-
+
}
else
{
searchResults = null;
- resIndex = 0;
- seqIndex = 0;
}
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+ // if allResults is null, this effectively switches displaySearch flag in
+ // seqCanvas
ap.highlightSearchResults(searchResults);
-
- if (findAll)
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+ // 'SelectRegion' selection
+ if (!haveResults)
{
- String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";
- ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);
+ ap.alignFrame.statusBar.setText(MessageManager.getString("label.finished_searching"));
+ resIndex = -1;
+ seqIndex = 0;
}
+ else
+ {
+ if (findAll)
+ {
+ String message = (idMatch.size() > 0) ? "" + idMatch.size()
+ + " IDs" : "";
+ if (idMatch.size() > 0 && searchResults != null
+ && searchResults.getSize() > 0)
+ {
+ message += " and ";
+ }
+ if (searchResults != null)
+ {
+ message += searchResults.getSize() + " subsequence matches.";
+ }
+ 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}));
+ }
+ }
}
Label jLabel1 = new Label();
+
protected TextField textfield = new TextField();
+
protected Button findAll = new Button();
+
protected Button findNext = new Button();
+
Panel jPanel1 = new Panel();
+
GridLayout gridLayout1 = new GridLayout();
+
protected Button createNewGroup = new Button();
+
Checkbox caseSensitive = new Checkbox();
- private void jbInit() throws Exception {
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel1.setText("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.addKeyListener(new java.awt.event.KeyAdapter() {
- public void keyTyped(KeyEvent e) {
- textfield_keyTyped(e);
- }
- });
- textfield.addActionListener(this);
- findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- findAll.setLabel("Find all");
- findAll.addActionListener(this);
- findNext.setEnabled(false);
- findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- findNext.setLabel("Find Next");
- findNext.addActionListener(this);
- jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
- jPanel1.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.addActionListener(this);
- caseSensitive.setLabel("Match Case");
+ private void jbInit() throws Exception
+ {
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+ 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.addKeyListener(new java.awt.event.KeyAdapter()
+ {
+ public void keyTyped(KeyEvent e)
+ {
+ textfield_keyTyped(e);
+ }
+ });
+ textfield.addActionListener(this);
+ findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ 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(MessageManager.getString("action.find_next"));
+ findNext.addActionListener(this);
+ jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
+ jPanel1.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(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);
+ jPanel1.add(findAll, null);
+ jPanel1.add(createNewGroup, null);
this.add(caseSensitive);
this.add(textfield, null);
- this.add(jLabel1, null);
- this.add(jPanel1, null);
+ this.add(jLabel1, null);
+ this.add(jPanel1, null);
}
- void textfield_keyTyped(KeyEvent e) {
- findNext.setEnabled(true);
+ void textfield_keyTyped(KeyEvent e)
+ {
+ findNext.setEnabled(true);
}
}
git://source.jalview.org / jalview.git / blobdiff