/*
- * 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.
*
*/
package jalview.appletgui;
-import jalview.datamodel.SearchResults;
+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.event.KeyEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
-import java.util.Vector;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
public class Finder extends Panel implements ActionListener
{
- AlignViewport av;
+ private AlignViewportI av;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
- Frame frame;
+ private TextField textfield = new TextField();
- SearchResults searchResults;
+ private Button findAll = new Button();
- int seqIndex = 0;
+ private Button findNext = new Button();
- int resIndex = -1;
+ private Button createFeatures = new Button();
+
+ private Checkbox caseSensitive = new Checkbox();
+
+ private Checkbox searchDescription = new Checkbox();
+
+ private SearchResultsI searchResults;
+
+ /*
+ * Finder agent per viewport searched
+ */
+ Map<AlignViewportI, FinderI> finders;
public Finder(final AlignmentPanel ap)
{
+ finders = new HashMap<>();
+
try
{
jbInit();
this.av = ap.av;
this.ap = ap;
- frame = new Frame();
+ Frame frame = new Frame();
frame.add(this);
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 = -1;
- 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()
{
- SequenceI[] seqs = new SequenceI[searchResults.getSize()];
- SequenceFeature[] features = new SequenceFeature[searchResults
- .getSize()];
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+ 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,
}
}
- void doSearch(boolean findAll)
+ void doSearch(boolean doFindAll)
{
if (ap.av.applet.currentAlignFrame != null)
{
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.setIncludeDescription(searchDescription.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();
-
- finder.find(searchString);
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
- searchResults = finder.getSearchResults();
- Vector idMatch = finder.getIdMatch();
- boolean haveResults = false;
- // set or reset the GUI
- if ((idMatch.size() > 0))
+ boolean isCaseSensitive = caseSensitive.getState();
+ boolean doSearchDescription = searchDescription.getState();
+ if (doFindAll)
{
- haveResults = true;
- ap.idPanel.highlightSearchResults(idMatch);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+ false);
}
else
{
- ap.idPanel.highlightSearchResults(null);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+ false);
}
- if (searchResults.getSize() > 0)
- {
- haveResults = true;
- createNewGroup.setEnabled(true);
+ searchResults = finder.getSearchResults();
+
+ List<SequenceI> idMatches = finder.getIdMatches();
+ ap.idPanel.highlightSearchResults(idMatches);
+ if (searchResults.isEmpty())
+ {
+ searchResults = null;
}
else
{
- searchResults = null;
+ createFeatures.setEnabled(true);
}
// if allResults is null, this effectively switches displaySearch flag in
ap.highlightSearchResults(searchResults);
// TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
// 'SelectRegion' selection
- if (!haveResults)
+ if (idMatches.isEmpty() && searchResults == null)
{
- ap.alignFrame.statusBar.setText(MessageManager
- .getString("label.finished_searching"));
- resIndex = -1;
- seqIndex = 0;
+ ap.alignFrame.statusBar.setText(
+ MessageManager.getString("label.finished_searching"));
}
else
{
- if (findAll)
+ if (doFindAll)
{
- String message = (idMatch.size() > 0) ? "" + idMatch.size()
- + " IDs" : "";
- if (idMatch.size() > 0 && searchResults != null
- && searchResults.getSize() > 0)
+ String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
+ : "";
+ if (idMatches.size() > 0 && searchResults != null
+ && searchResults.getCount() > 0)
{
message += " and ";
}
if (searchResults != null)
{
- message += searchResults.getSize() + " subsequence matches.";
+ message += searchResults.getCount() + " subsequence matches.";
}
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.search_results", new String[]
+ 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[]
+ 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 actionsPanel = new Panel();
-
- GridLayout gridLayout1 = new GridLayout();
-
- protected Button createNewGroup = new Button();
-
- Checkbox caseSensitive = new Checkbox();
-
- Checkbox searchDescription = new Checkbox();
-
private void jbInit() throws Exception
{
+ Label jLabel1 = new Label(MessageManager.getString("action.find"));
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.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);
findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
findNext.setLabel(MessageManager.getString("action.find_next"));
findNext.addActionListener(this);
+
+ 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(MessageManager.getString("label.new_feature"));
- createNewGroup.addActionListener(this);
+ 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.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);
+ actionsPanel.add(createFeatures, null);
this.add(caseSensitive);
this.add(textfield, null);
this.add(jLabel1, null);
this.add(searchDescription);
}
- void textfield_keyTyped(KeyEvent e)
+ void textfield_keyTyped()
{
findNext.setEnabled(true);
}
git://source.jalview.org / jalview.git / blobdiff