*/
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.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GFinder;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
+import java.util.Locale;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.HashMap;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+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;
+
/**
* Performs the menu option for searching the alignment, for the next or all
* matches. If matches are found, they are highlighted, and the user has the
private static final int MIN_HEIGHT = 120;
- private static final int MY_HEIGHT = 120;
+ private static final int MY_HEIGHT = 150;
private static final int MY_WIDTH = 400;
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. Each Find
- * or Find Next action will act on whichever viewport has focus at the time.
+ * true if Finder always acts on the same alignment,
+ * false if it acts on the alignment with focus
*/
- public Finder()
- {
- this(null, null);
- }
+ private boolean focusFixed;
/**
- * 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. The Finder may
+ * have 'fixed focus' (always act the panel for which it is constructed), or
+ * not (acts on the alignment that has focus). An optional 'scope' may be
+ * added to be shown in the title of the Finder frame.
*
- * @param viewport
* @param alignPanel
+ * @param fixedFocus
+ * @param scope
*/
- public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel)
+ public Finder(AlignmentPanel alignPanel, boolean fixedFocus, String scope)
{
- av = viewport;
+ av = alignPanel.getAlignViewport();
ap = alignPanel;
+ focusFixed = fixedFocus;
finders = new HashMap<>();
- focusfixed = viewport != null;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.addInternalFrameListener(
- new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosing(InternalFrameEvent e)
- {
- closeAction();
- }
- });
+ frame.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent e)
+ {
+ closeAction();
+ }
+ });
+ frame.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ /*
+ * ensure 'ignore hidden columns' is only enabled
+ * if the alignment with focus has hidden columns
+ */
+ getFocusedViewport();
+ }
+ });
+
addEscapeHandler();
- Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
- MY_WIDTH, MY_HEIGHT);
+
+ String title = MessageManager.getString("label.find");
+ if (scope != null)
+ {
+ title += " " + scope;
+ }
+ Desktop.addInternalFrame(frame, title, MY_WIDTH, MY_HEIGHT);
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
- searchBox.requestFocus();
+ searchBox.getComponent().requestFocus();
}
/**
/**
* 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 (focusFixed || Desktop.desktop == null)
{
if (ap != null && av != null)
{
+ ignoreHidden.setEnabled(av.hasHiddenColumns());
return true;
}
// we aren't in a desktop environment, so give up now.
{
av = ((AlignFrame) alignFrame).viewport;
ap = ((AlignFrame) alignFrame).alignPanel;
+ ignoreHidden.setEnabled(av.hasHiddenColumns());
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))
{
/*
* first time we've searched this viewport
*/
- finder = new jalview.analysis.Finder(av.getAlignment());
+ finder = new jalview.analysis.Finder(av);
finders.put(av, finder);
}
- SequenceGroup selectionGroup = av.getSelectionGroup();
boolean isCaseSensitive = caseSensitive.isSelected();
boolean doSearchDescription = searchDescription.isSelected();
+ boolean doSearchfeatures = searchFeatures.isSelected();
+ boolean skipHidden = ignoreHidden.isSelected();
if (doFindAll)
{
- finder.findAll(searchString, selectionGroup, isCaseSensitive,
- doSearchDescription);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+ doSearchfeatures, skipHidden);
}
else
{
- finder.findNext(searchString, selectionGroup, isCaseSensitive,
- doSearchDescription);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+ doSearchfeatures, skipHidden);
}
searchResults = finder.getSearchResults();
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);
+ JvOptionPane.PLAIN_MESSAGE);
}
else
{
if (doFindAll)
{
// then we report the matches that were found
- String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
- : "";
+ StringBuilder message = new StringBuilder();
+ if (idMatch.size() > 0)
+ {
+ message.append(idMatch.size()).append(" IDs");
+ }
if (searchResults != null)
{
- if (idMatch.size() > 0 && searchResults.getSize() > 0)
+ if (idMatch.size() > 0 && searchResults.getCount() > 0)
{
- message += " and ";
+ message.append(" ").append(MessageManager.getString("label.and")
+ .toLowerCase(Locale.ROOT)).append(" ");
}
- message += searchResults.getSize()
- + " subsequence matches found.";
+ message.append(MessageManager.formatMessage(
+ "label.subsequence_matches_found",
+ searchResults.getCount()));
}
- JvOptionPane.showInternalMessageDialog(this, message, null,
- JvOptionPane.INFORMATION_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(this, message.toString(),
+ null, JvOptionPane.INFORMATION_MESSAGE);
}
}
- searchBox.updateCache();
}
/**
git://source.jalview.org / jalview.git / blobdiff