*/
package jalview.gui;
+import jalview.api.AlignViewportI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
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.InternalFrameEvent;
/**
* Performs the menu option for searching the alignment, for the next or all
*/
public class Finder extends GFinder
{
- private static final int HEIGHT = 120;
+ private static final int MIN_WIDTH = 350;
- private static final int WIDTH = 400;
+ private static final int MIN_HEIGHT = 120;
- AlignmentViewport av;
+ private static final int MY_HEIGHT = 120;
- AlignmentPanel ap;
+ private static final int MY_WIDTH = 400;
- private static final int MIN_WIDTH = 350;
+ private AlignViewportI av;
- private static final int MIN_HEIGHT = 120;
+ private AlignmentPanel ap;
+
+ private JInternalFrame frame;
- JInternalFrame frame;
+ /*
+ * sequence and column position of the last match,
+ * as currently used, and saved for each viewport
+ */
+ private int seqIndex = 0;
+
+ private int resIndex = -1;
- int seqIndex = 0;
+ Map<AlignViewportI, Integer> seqIndices;
- int resIndex = -1;
+ Map<AlignViewportI, Integer> resIndices;
- SearchResultsI searchResults;
+ private SearchResultsI searchResults;
/**
* Creates a new Finder object with no associated viewport or panel.
{
av = viewport;
ap = alignPanel;
+ seqIndices = new HashMap<>();
+ resIndices = new HashMap<>();
focusfixed = true;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent e)
+ {
+ closeAction();
+ }
+ });
addEscapeHandler();
Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
- WIDTH, HEIGHT);
+ MY_WIDTH, MY_HEIGHT);
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
- textfield.requestFocus();
+ searchBox.requestFocus();
}
/**
*/
private void addEscapeHandler()
{
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
- KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
+ .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
getRootPane().getActionMap().put("Cancel", new AbstractAction()
{
@Override
public void actionPerformed(ActionEvent e)
{
- escapeActionPerformed();
+ closeAction();
}
});
}
/**
- * Close the panel on Escape key press
- */
- protected void escapeActionPerformed()
- {
- setVisible(false);
- frame.dispose();
- }
-
- /**
* Performs the 'Find Next' action.
*
* @param e
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int f = 0; f < frames.length; f++)
{
- JInternalFrame frame = frames[f];
- if (frame != null && frame instanceof AlignFrame)
+ JInternalFrame alignFrame = frames[f];
+ if (alignFrame != null && alignFrame instanceof AlignFrame
+ && !alignFrame.isIcon())
{
- av = ((AlignFrame) frame).viewport;
- ap = ((AlignFrame) frame).alignPanel;
+ 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;
}
}
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Opens a dialog that allows the user to create sequence features for the
+ * find match results.
*/
@Override
- public void createNewGroup_actionPerformed(ActionEvent e)
+ 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 = searchBox.getEditor().getItem().toString().trim();
+ String desc = "Search Results";
- int i = 0;
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
for (SearchResultMatchI match : searchResults.getResults())
{
- seqs[i] = match.getSequence().getDatasetSequence();
-
- features[i] = new SequenceFeature(textfield.getText().trim(),
- "Search Results", null, match.getStart(), match.getEnd(),
- "Search Results");
- i++;
+ seqs.add(match.getSequence().getDatasetSequence());
+ 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);
* Search the alignment for the next or all matches. If 'all matches', a
* dialog is shown with the number of sequence ids and subsequences matched.
*
- * @param findAll
+ * @param doFindAll
*/
- void doSearch(boolean findAll)
+ void doSearch(boolean doFindAll)
{
- createNewGroup.setEnabled(false);
+ createFeatures.setEnabled(false);
- String searchString = textfield.getText().trim();
+ String searchString = searchBox.getUserInput().trim();
if (isInvalidSearchString(searchString))
{
finder.setCaseSensitive(caseSensitive.isSelected());
finder.setIncludeDescription(searchDescription.isSelected());
- finder.setFindAll(findAll);
+ finder.setFindAll(doFindAll);
- finder.find(searchString); // returns true if anything was actually found
+ finder.find(searchString);
seqIndex = finder.getSeqIndex();
resIndex = finder.getResIndex();
+ seqIndices.put(av, seqIndex);
+ resIndices.put(av, resIndex);
- searchResults = finder.getSearchResults(); // find(regex,
- // caseSensitive.isSelected(), )
+ searchResults = finder.getSearchResults();
Vector<SequenceI> idMatch = finder.getIdMatch();
- boolean haveResults = false;
- // set or reset the GUI
- if ((idMatch.size() > 0))
- {
- haveResults = true;
- ap.getIdPanel().highlightSearchResults(idMatch);
- }
- else
- {
- ap.getIdPanel().highlightSearchResults(null);
- }
+ ap.getIdPanel().highlightSearchResults(idMatch);
- if (searchResults.getSize() > 0)
+ if (searchResults.isEmpty())
{
- haveResults = true;
- createNewGroup.setEnabled(true);
+ searchResults = null;
}
else
{
- searchResults = null;
+ createFeatures.setEnabled(true);
}
- // if allResults is null, this effectively switches displaySearch flag in
- // seqCanvas
ap.highlightSearchResults(searchResults);
// TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
// 'SelectRegion' selection
- if (!haveResults)
+ if (idMatch.isEmpty() && searchResults == null)
{
JvOptionPane.showInternalMessageDialog(this,
MessageManager.getString("label.finished_searching"), null,
}
else
{
- if (findAll)
+ if (doFindAll)
{
// then we report the matches that were found
- String message = (idMatch.size() > 0) ? "" + idMatch.size()
- + " IDs" : "";
+ String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ : "";
if (searchResults != null)
{
if (idMatch.size() > 0 && searchResults.getSize() > 0)
seqIndex = 0;
}
}
-
+ searchBox.updateCache();
}
/**
}
return error;
}
+
+ protected void closeAction()
+ {
+ frame.setVisible(false);
+ frame.dispose();
+ searchBox.persistCache();
+ if (getFocusedViewport())
+ {
+ ap.alignFrame.requestFocus();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff