X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=537c323fa4b259f13ba80b6211bffe64245a2b30;hb=3d2750d886f1b6015b2fc3f8671a6cf3e32bb07a;hp=a314cefff6b5a28a12983eec824415b589404fb1;hpb=d12575dda59477de09c74c4666e2f1d1fac63524;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index a314cef..537c323 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -20,17 +20,23 @@ */ 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; @@ -39,6 +45,7 @@ import javax.swing.JComponent; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.KeyStroke; +import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; /** @@ -54,58 +61,55 @@ import javax.swing.event.InternalFrameEvent; */ public class Finder extends GFinder { - private static final int HEIGHT = 110; + private static final int MIN_WIDTH = 350; - private static final int WIDTH = 340; + private static final int MIN_HEIGHT = 120; - AlignmentViewport av; + private static final int MY_HEIGHT = 150; - AlignmentPanel ap; + private static final int MY_WIDTH = 400; - JInternalFrame frame; + private AlignViewportI av; - int seqIndex = 0; + private AlignmentPanel ap; - int resIndex = -1; + private JInternalFrame frame; - SearchResultsI searchResults; - - /** - * Creates a new Finder object with no associated viewport or panel. + /* + * Finder agent per viewport searched */ - public Finder() - { - this(null, null); - focusfixed = false; - } + private Map 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 javax.swing.event.InternalFrameAdapter() - { - @Override - public void internalFrameClosing(InternalFrameEvent e) - { - closeAction(); - } - }); + frame.addInternalFrameListener( + new InternalFrameAdapter() + { + @Override + public void internalFrameClosing(InternalFrameEvent e) + { + closeAction(); + } + }); addEscapeHandler(); - Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), - WIDTH, HEIGHT); + Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), + MY_WIDTH, MY_HEIGHT); + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); searchBox.requestFocus(); } @@ -114,34 +118,23 @@ public class Finder extends GFinder */ 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()) { @@ -150,36 +143,28 @@ public class Finder extends GFinder } /** - * 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) { @@ -193,11 +178,13 @@ public class Finder extends GFinder 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; } } @@ -205,33 +192,37 @@ public class Finder extends GFinder } /** - * 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 seqs = new ArrayList<>(); + List 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(searchBox.getEditor().getItem() - .toString().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); @@ -242,11 +233,11 @@ public class Finder extends GFinder * 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 = searchBox.getUserInput().trim(); @@ -258,76 +249,70 @@ public class Finder extends GFinder // 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 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 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(); @@ -385,7 +370,23 @@ public class Finder extends GFinder 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); } }