package jalview.gui;
import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Vector;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
/**
private JInternalFrame frame;
/*
- * sequence and column position of the last match,
- * as currently used, and saved for each viewport
+ * Finder agent per viewport searched
*/
- private int seqIndex = 0;
-
- private int resIndex = -1;
-
- Map<AlignViewportI, Integer> seqIndices;
-
- Map<AlignViewportI, Integer> resIndices;
+ private Map<AlignViewportI, FinderI> finders;
private SearchResultsI searchResults;
+ /*
+ * true if we only search a given alignment view
+ */
+ private boolean focusfixed;
+
/**
- * Creates a new Finder object with no associated viewport or panel.
+ * Creates a new Finder object with no associated viewport or panel. Each Find
+ * or Find Next action will act on whichever viewport has focus at the time.
*/
public Finder()
{
this(null, null);
- focusfixed = false;
}
/**
{
av = viewport;
ap = alignPanel;
- seqIndices = new HashMap<>();
- resIndices = new HashMap<>();
- focusfixed = true;
+ finders = new HashMap<>();
+ focusfixed = viewport != null;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
+ new InternalFrameAdapter()
{
@Override
public void internalFrameClosing(InternalFrameEvent e)
});
addEscapeHandler();
Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
- MY_WIDTH, MY_HEIGHT);
- frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
- searchBox.requestFocus();
+ true, MY_WIDTH, MY_HEIGHT, true, true);
+ searchBox.getComponent().requestFocus();
}
/**
}
/**
- * Performs the 'Find Next' action.
- *
- * @param e
+ * Performs the 'Find Next' action on the alignment panel with focus
*/
@Override
- public void findNext_actionPerformed(ActionEvent e)
+ public void findNext_actionPerformed()
{
if (getFocusedViewport())
{
}
/**
- * Performs the 'Find All' action.
- *
- * @param e
+ * Performs the 'Find All' action on the alignment panel with focus
*/
@Override
- public void findAll_actionPerformed(ActionEvent e)
+ public void findAll_actionPerformed()
{
if (getFocusedViewport())
{
- resIndex = -1;
- seqIndex = 0;
doSearch(true);
}
}
/**
- * do we only search a given alignment view ?
- */
- private boolean focusfixed;
-
- /**
* if !focusfixed and not in a desktop environment, checks that av and ap are
* valid. Otherwise, gets the topmost alignment window and sets av and ap
* accordingly
{
av = ((AlignFrame) alignFrame).viewport;
ap = ((AlignFrame) alignFrame).alignPanel;
-
- /*
- * restore search position if switching to a
- * panel where we have previously searched
- */
- seqIndex = 0;
- resIndex = -1;
- if (seqIndices.containsKey(av))
- {
- seqIndex = seqIndices.get(av).intValue();
- }
- if (resIndices.containsKey(av))
- {
- resIndex = resIndices.get(av).intValue();
- }
return true;
}
}
/**
* Opens a dialog that allows the user to create sequence features for the
- * find match results.
+ * find match results
*/
@Override
public void createFeatures_actionPerformed()
{
+ if (searchResults.isEmpty())
+ {
+ return; // shouldn't happen
+ }
List<SequenceI> seqs = new ArrayList<>();
List<SequenceFeature> features = new ArrayList<>();
- String searchString = searchBox.getEditor().getItem().toString().trim();
+ String searchString = searchBox.getUserInput();
String desc = "Search Results";
/*
for (SearchResultMatchI match : searchResults.getResults())
{
seqs.add(match.getSequence().getDatasetSequence());
- features.add(new SequenceFeature(searchString, desc,
- match
- .getStart(), match.getEnd(), desc));
+ features.add(new SequenceFeature(searchString, desc, match.getStart(),
+ match.getEnd(), desc));
}
- if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
- {
- /*
- * ensure feature display is turned on to show the new features,
- * and remove them as highlighted regions
- */
- ap.alignFrame.showSeqFeatures.setSelected(true);
- av.setShowSequenceFeatures(true);
- ap.highlightSearchResults(null);
- }
+ new FeatureEditor(ap, seqs, features, true).showDialog();
}
/**
{
createFeatures.setEnabled(false);
- String searchString = searchBox.getUserInput().trim();
+ String searchString = searchBox.getUserInput();
if (isInvalidSearchString(searchString))
{
// other stuff
// TODO: add switches to control what is searched - sequences, IDS,
// descriptions, features
- jalview.analysis.Finder finder = new jalview.analysis.Finder(
- av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
- finder.setCaseSensitive(caseSensitive.isSelected());
- finder.setIncludeDescription(searchDescription.isSelected());
-
- finder.setFindAll(doFindAll);
-
- finder.find(searchString);
+ FinderI finder = finders.get(av);
+ if (finder == null)
+ {
+ /*
+ * first time we've searched this viewport
+ */
+ finder = new jalview.analysis.Finder(av);
+ finders.put(av, finder);
+ }
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
- seqIndices.put(av, seqIndex);
- resIndices.put(av, resIndex);
+ boolean isCaseSensitive = caseSensitive.isSelected();
+ boolean doSearchDescription = searchDescription.isSelected();
+ if (doFindAll)
+ {
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription);
+ }
+ else
+ {
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription);
+ }
searchResults = finder.getSearchResults();
- Vector<SequenceI> idMatch = finder.getIdMatch();
+ List<SequenceI> idMatch = finder.getIdMatches();
ap.getIdPanel().highlightSearchResults(idMatch);
if (searchResults.isEmpty())
createFeatures.setEnabled(true);
}
+ searchBox.updateCache();
+
ap.highlightSearchResults(searchResults);
// TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
// 'SelectRegion' selection
{
JvOptionPane.showInternalMessageDialog(this,
MessageManager.getString("label.finished_searching"), null,
- JvOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
+ JvOptionPane.PLAIN_MESSAGE);
}
else
{
+ " subsequence matches found.";
}
JvOptionPane.showInternalMessageDialog(this, message, null,
- JvOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
+ JvOptionPane.PLAIN_MESSAGE);
}
}
- searchBox.updateCache();
}
/**