X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=2756b14fa60c4e59de6ba52305d097453d3da1e6;hb=930e48ff657a783ae52370e49ff4f5bb5a2a4016;hp=537c323fa4b259f13ba80b6211bffe64245a2b30;hpb=3d2750d886f1b6015b2fc3f8671a6cf3e32bb07a;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index 537c323..2756b14 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -20,22 +20,15 @@ */ 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 java.awt.Dimension; -import java.awt.Graphics; 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 java.util.List; +import java.util.Locale; import java.util.Map; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; @@ -48,6 +41,15 @@ import javax.swing.KeyStroke; 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 @@ -82,35 +84,64 @@ public class Finder extends GFinder private SearchResultsI searchResults; + /* + * true if Finder always acts on the same alignment, + * false if it acts on the alignment with focus + */ + private boolean focusFixed; + /** * Constructor given an associated alignment panel. Constructs and displays an - * internal frame where the user can enter a search string. + * 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 alignPanel + * @param fixedFocus + * @param scope */ - public Finder(AlignmentPanel alignPanel) + public Finder(AlignmentPanel alignPanel, boolean fixedFocus, String scope) { av = alignPanel.getAlignViewport(); ap = alignPanel; + focusFixed = fixedFocus; finders = new HashMap<>(); frame = new JInternalFrame(); + frame.setFrameIcon(null); 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(); } /** @@ -157,17 +188,18 @@ public class Finder extends GFinder /** * 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. Also sets the 'ignore hidden' checkbox disabled if the viewport - * has no hidden columns. + * 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 (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. @@ -193,15 +225,19 @@ public class Finder extends GFinder /** * 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 seqs = new ArrayList<>(); List features = new ArrayList<>(); - String searchString = searchBox.getEditor().getItem().toString().trim(); + String searchString = searchBox.getUserInput(); String desc = "Search Results"; /* @@ -211,22 +247,22 @@ public class Finder extends GFinder 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)) + new FeatureEditor(ap, seqs, features, true).showDialog(); + } + + @Override + protected void copyToClipboard_actionPerformed() + { + if (searchResults.isEmpty()) { - /* - * 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); + return; // shouldn't happen } + // assume viewport controller has same searchResults as we do... + ap.alignFrame.avc.copyHighlightedRegionsToClipboard(); } /** @@ -238,8 +274,9 @@ public class Finder extends GFinder void doSearch(boolean doFindAll) { createFeatures.setEnabled(false); + copyToClipboard.setEnabled(false); - String searchString = searchBox.getUserInput().trim(); + String searchString = searchBox.getUserInput(); if (isInvalidSearchString(searchString)) { @@ -258,19 +295,21 @@ public class Finder extends GFinder finder = new jalview.analysis.Finder(av); finders.put(av, finder); } + finder.setFeatureRenderer(ap.getFeatureRenderer()); boolean isCaseSensitive = caseSensitive.isSelected(); boolean doSearchDescription = searchDescription.isSelected(); + boolean doSearchfeatures = searchFeatures.isSelected(); boolean skipHidden = ignoreHidden.isSelected(); if (doFindAll) { finder.findAll(searchString, isCaseSensitive, doSearchDescription, - skipHidden); + doSearchfeatures, skipHidden); } else { finder.findNext(searchString, isCaseSensitive, doSearchDescription, - skipHidden); + doSearchfeatures, skipHidden); } searchResults = finder.getSearchResults(); @@ -284,8 +323,11 @@ public class Finder extends GFinder else { createFeatures.setEnabled(true); + copyToClipboard.setEnabled(true); } + searchBox.updateCache(); + ap.highlightSearchResults(searchResults); // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or // 'SelectRegion' selection @@ -293,29 +335,33 @@ public class Finder extends GFinder { 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.getCount() > 0) { - message += " and "; + message.append(" ").append(MessageManager.getString("label.and") + .toLowerCase(Locale.ROOT)).append(" "); } - message += searchResults.getCount() - + " 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(); } /** @@ -378,15 +424,4 @@ public class Finder extends GFinder ap.alignFrame.requestFocus(); } } - - @Override - protected void paintComponent(Graphics g) - { - /* - * enable 'hidden regions' option only if - * 'top' viewport has hidden columns - */ - getFocusedViewport(); - super.paintComponent(g); - } }