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.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;
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 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 colIndex = -1;
-
- private Map<AlignViewportI, Integer> seqIndices;
-
- private Map<AlignViewportI, Integer> colIndices;
+ 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. Each Find
- * or Find Next action will act on whichever viewport has focus at the time.
- */
- public Finder()
- {
- this(null, null);
- }
-
- /**
- * 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;
- seqIndices = new HashMap<>();
- colIndices = new HashMap<>();
- focusfixed = viewport != null;
+ finders = new HashMap<>();
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
});
addEscapeHandler();
+
Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
MY_WIDTH, MY_HEIGHT);
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
{
if (getFocusedViewport())
{
- colIndex = -1;
- seqIndex = 0;
doSearch(true);
}
}
/**
* 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)
{
{
av = ((AlignFrame) alignFrame).viewport;
ap = ((AlignFrame) alignFrame).alignPanel;
-
- /*
- * restore search position if switching to a
- * panel where we have previously searched
- */
- seqIndex = 0;
- colIndex = -1;
- if (seqIndices.containsKey(av))
- {
- seqIndex = seqIndices.get(av).intValue();
- }
- if (colIndices.containsKey(av))
- {
- colIndex = colIndices.get(av).intValue();
- }
+ ignoreHidden.setEnabled(av.hasHiddenColumns());
return true;
}
}
// 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, colIndex);
- 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.getSequenceIndex();
- colIndex = finder.getColumnIndex();
- seqIndices.put(av, seqIndex);
- colIndices.put(av, colIndex);
+ boolean isCaseSensitive = caseSensitive.isSelected();
+ boolean doSearchDescription = searchDescription.isSelected();
+ boolean skipHidden = ignoreHidden.isSelected();
+ if (doFindAll)
+ {
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+ skipHidden);
+ }
+ else
+ {
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+ skipHidden);
+ }
searchResults = finder.getSearchResults();
- Vector<SequenceI> idMatch = finder.getIdMatch();
+ List<SequenceI> idMatch = finder.getIdMatches();
ap.getIdPanel().highlightSearchResults(idMatch);
if (searchResults.isEmpty())
JvOptionPane.showInternalMessageDialog(this,
MessageManager.getString("label.finished_searching"), null,
JvOptionPane.INFORMATION_MESSAGE);
- colIndex = -1;
- seqIndex = 0;
}
else
{
: "";
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);
- colIndex = -1;
- seqIndex = 0;
}
}
searchBox.updateCache();
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