*/
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.datamodel.SequenceI;
import jalview.jbgui.GFinder;
import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
import java.awt.Dimension;
+import java.awt.Graphics;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
-import java.util.Vector;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
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;
/**
* 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 WIDTH = 400;
-
- AlignmentViewport av;
-
- AlignmentPanel ap;
-
private static final int MIN_WIDTH = 350;
private static final int MIN_HEIGHT = 120;
- JInternalFrame frame;
+ private static final int MY_HEIGHT = 150;
- int seqIndex = 0;
+ private static final int MY_WIDTH = 400;
- int resIndex = -1;
+ private AlignViewportI av;
- SearchResultsI searchResults;
+ private AlignmentPanel ap;
- /**
- * Creates a new Finder object with no associated viewport or panel.
+ private JInternalFrame frame;
+
+ /*
+ * Finder agent per viewport searched
*/
- public Finder()
- {
- this(null, null);
- focusfixed = false;
- }
+ private Map<AlignViewportI, FinderI> finders;
+
+ private SearchResultsI searchResults;
/**
- * Constructor given an associated viewport and alignment panel. Constructs
- * and displays an internal frame where the user can enter a search string.
+ * Constructor given an associated alignment panel. Constructs and displays an
+ * internal frame where the user can enter a search string.
*
- * @param viewport
* @param alignPanel
*/
- public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
+ public Finder(AlignmentPanel alignPanel)
{
- av = viewport;
+ av = alignPanel.getAlignViewport();
ap = alignPanel;
- focusfixed = true;
+ finders = new HashMap<>();
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.addInternalFrameListener(
+ new 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
+ * 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
+ * accordingly. Also sets the 'ignore hidden' checkbox disabled if the viewport
+ * has no hidden columns.
*
* @return false if no alignment window was found
*/
boolean getFocusedViewport()
{
- if (focusfixed || Desktop.desktop == null)
+ if (Desktop.desktop == null)
{
if (ap != null && av != null)
{
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;
+ ignoreHidden.setEnabled(av.hasHiddenColumns());
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<>();
- int i = 0;
+ String searchString = searchBox.getEditor().getItem().toString().trim();
+ String desc = "Search Results";
+
+ /*
+ * 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))
{
// 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(findAll);
-
- finder.find(searchString); // returns true if anything was actually found
-
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
+ 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);
+ }
- searchResults = finder.getSearchResults(); // find(regex,
- // caseSensitive.isSelected(), )
- Vector<SequenceI> idMatch = finder.getIdMatch();
- boolean haveResults = false;
- // set or reset the GUI
- if ((idMatch.size() > 0))
+ boolean isCaseSensitive = caseSensitive.isSelected();
+ boolean doSearchDescription = searchDescription.isSelected();
+ boolean skipHidden = ignoreHidden.isSelected();
+ if (doFindAll)
{
- haveResults = true;
- ap.getIdPanel().highlightSearchResults(idMatch);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+ skipHidden);
}
else
{
- ap.getIdPanel().highlightSearchResults(null);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+ skipHidden);
}
- if (searchResults.getSize() > 0)
+ searchResults = finder.getSearchResults();
+ List<SequenceI> idMatch = finder.getIdMatches();
+ ap.getIdPanel().highlightSearchResults(idMatch);
+
+ 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,
JvOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
}
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)
+ if (idMatch.size() > 0 && searchResults.getCount() > 0)
{
message += " and ";
}
- message += searchResults.getSize()
+ message += searchResults.getCount()
+ " subsequence matches found.";
}
JvOptionPane.showInternalMessageDialog(this, message, null,
JvOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
}
}
-
+ searchBox.updateCache();
}
/**
}
return error;
}
+
+ protected void closeAction()
+ {
+ frame.setVisible(false);
+ frame.dispose();
+ searchBox.persistCache();
+ if (getFocusedViewport())
+ {
+ ap.alignFrame.requestFocus();
+ }
+ }
+
+ @Override
+ protected void paintComponent(Graphics g)
+ {
+ /*
+ * enable 'hidden regions' option only if
+ * 'top' viewport has hidden columns
+ */
+ getFocusedViewport();
+ super.paintComponent(g);
+ }
}
git://source.jalview.org / jalview.git / blobdiff