/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 jalview.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+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.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class Finder extends Panel implements ActionListener
+{
+ private AlignViewportI av;
-import java.awt.*;
-import java.awt.event.*;
+ private AlignmentPanel ap;
-import jalview.datamodel.*;
+ private TextField textfield = new TextField();
-public class Finder
- extends Panel implements ActionListener
-{
- AlignViewport av;
- AlignmentPanel ap;
- Frame frame;
+ private Button findAll = new Button();
+
+ private Button findNext = new Button();
+
+ private Button createFeatures = new Button();
- SearchResults searchResults;
+ private Checkbox caseSensitive = new Checkbox();
+
+ private Checkbox searchDescription = new Checkbox();
+
+ private SearchResultsI searchResults;
+
+ /*
+ * Finder agent per viewport searched
+ */
+ Map<AlignViewportI, FinderI> finders;
- int seqIndex = 0;
- int resIndex = 0;
public Finder(final AlignmentPanel ap)
{
+ finders = new HashMap<>();
+
try
{
jbInit();
- }
- catch (Exception e)
+
+ } catch (Exception e)
{
e.printStackTrace();
}
this.av = ap.av;
this.ap = ap;
- frame = new Frame();
+ Frame 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);
}
});
+ textfield.requestFocus();
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == textfield)
else if (evt.getSource() == findAll)
{
- resIndex = 0;
- seqIndex = 0;
doSearch(true);
}
- else if (evt.getSource() == createNewGroup)
+ else if (evt.getSource() == createFeatures)
{
- createNewGroup_actionPerformed();
+ createFeatures_actionPerformed();
}
}
- public void createNewGroup_actionPerformed()
+ public void createFeatures_actionPerformed()
{
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+ String searchString = textfield.getText().trim();
- 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)
+ for (SearchResultMatchI match : searchResults.getResults())
{
- return;
+ seqs.add(match.getSequence().getDatasetSequence());
+ features.add(new SequenceFeature(searchString, "Search Results",
+ match.getStart(), match.getEnd(), "Search Results"));
}
- for (int i = 0; i < searchResults.getSize(); i++)
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
{
- SequenceI seq = searchResults.getResultSequence(i);
-
- SequenceFeature sf = new SequenceFeature(featureName,
- null, null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i),
- "Search Results");
-
- ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
- featureName, new Color(60, 160, 115));
- seq.addSequenceFeature(sf);
+ ap.alignFrame.sequenceFeatures.setState(true);
+ av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
}
-
- ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
- ap.alignFrame.sequenceFeatures.setState(true);
- av.showSequenceFeatures(true);
- ap.highlightSearchResults(null);
}
- void doSearch(boolean findAll)
+ void doSearch(boolean doFindAll)
{
- 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);
- finder.setCaseSensitive(caseSensitive.getState());
- finder.setFindAll(findAll);
+ createFeatures.setEnabled(false);
+ FinderI finder = finders.get(av);
+ if (finder == null)
+ {
+ /*
+ * first time we searched this viewport
+ */
+ finder = new jalview.analysis.Finder(av);
+ finders.put(av, finder);
+ }
String searchString = textfield.getText();
+ boolean isCaseSensitive = caseSensitive.getState();
+ boolean doSearchDescription = searchDescription.getState();
+ if (doFindAll)
+ {
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+ false);
+ }
+ else
+ {
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+ false);
+ }
- finder.find(searchString);
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
searchResults = finder.getSearchResults();
- Vector idMatch = finder.getIdMatch();
- if (searchResults.getSize() == 0 && idMatch.size() > 0)
- {
- ap.idPanel.highlightSearchResults(idMatch);
- }
+ List<SequenceI> idMatches = finder.getIdMatches();
+ ap.idPanel.highlightSearchResults(idMatches);
- if (searchResults.getSize() > 0)
+ if (searchResults.isEmpty())
{
- createNewGroup.setEnabled(true);
-
+ searchResults = null;
}
else
{
- searchResults = null;
- resIndex = 0;
- seqIndex = 0;
+ createFeatures.setEnabled(true);
}
- // 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 (idMatches.isEmpty() && searchResults == null)
{
- 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"));
}
+ else
+ {
+ if (doFindAll)
+ {
+ String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
+ : "";
+ if (idMatches.size() > 0 && searchResults != null
+ && searchResults.getCount() > 0)
+ {
+ message += " and ";
+ }
+ if (searchResults != null)
+ {
+ message += searchResults.getCount() + " 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
+ private void jbInit() throws Exception
{
+ Label jLabel1 = new Label(MessageManager.getString("action.find"));
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.setBounds(new Rectangle(40, 17, 133, 21));
textfield.addKeyListener(new java.awt.event.KeyAdapter()
{
+ @Override
public void keyTyped(KeyEvent e)
{
- textfield_keyTyped(e);
+ textfield_keyTyped();
}
});
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);
+
+ Panel actionsPanel = new Panel();
+ actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
+ GridLayout gridLayout1 = new GridLayout();
+ 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.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);
+ createFeatures.setEnabled(false);
+ createFeatures.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ createFeatures.setLabel(MessageManager.getString("label.new_feature"));
+ createFeatures.addActionListener(this);
+ 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(createFeatures, 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)
+ void textfield_keyTyped()
{
findNext.setEnabled(true);
}
git://source.jalview.org / jalview.git / blobdiff