X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=c40b958d44a54b761e07b974dec339f393782418;hb=refs%2Fheads%2Ffeatures%2Fr2_11_2_alphafold%2FJAL-2349_JAL-3855;hp=c5b25bf7519035d2937b1f8dd1df847f14807983;hpb=3ba65b98445f192453664357a1df25128fe07c84;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index c5b25bf..c40b958 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -20,23 +20,16 @@ */ package jalview.gui; -import jalview.api.AlignViewportI; -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.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.Vector; 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 @@ -65,7 +67,7 @@ public class Finder extends GFinder 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; @@ -76,64 +78,69 @@ public class Finder extends GFinder 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 seqIndices; - - private Map colIndices; + private Map finders; private SearchResultsI searchResults; /* - * true if we only search a given alignment view + * true if Finder always acts on the same alignment, + * false if it acts on the alignment with focus */ - private boolean focusfixed; + 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. 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; - seqIndices = new HashMap<>(); - colIndices = new HashMap<>(); - focusfixed = viewport != null; + focusFixed = fixedFocus; + 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(); - } - }); + 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(); } /** @@ -173,8 +180,6 @@ public class Finder extends GFinder { if (getFocusedViewport()) { - colIndex = -1; - seqIndex = 0; doSearch(true); } } @@ -182,16 +187,18 @@ 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 + * 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. @@ -208,21 +215,7 @@ public class Finder extends GFinder { 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; } } @@ -231,15 +224,19 @@ 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"; /* @@ -249,22 +246,22 @@ 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(); } /** @@ -276,8 +273,9 @@ 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)) { @@ -287,22 +285,34 @@ 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, 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); + } + finder.setFeatureRenderer(ap.getFeatureRenderer()); - seqIndex = finder.getSequenceIndex(); - colIndex = finder.getColumnIndex(); - seqIndices.put(av, seqIndex); - colIndices.put(av, colIndex); + boolean isCaseSensitive = caseSensitive.isSelected(); + boolean doSearchDescription = searchDescription.isSelected(); + boolean doSearchfeatures = searchFeatures.isSelected(); + boolean skipHidden = ignoreHidden.isSelected(); + if (doFindAll) + { + finder.findAll(searchString, isCaseSensitive, doSearchDescription, + doSearchfeatures, skipHidden); + } + else + { + finder.findNext(searchString, isCaseSensitive, doSearchDescription, + doSearchfeatures, skipHidden); + } searchResults = finder.getSearchResults(); - Vector idMatch = finder.getIdMatch(); + List idMatch = finder.getIdMatches(); ap.getIdPanel().highlightSearchResults(idMatch); if (searchResults.isEmpty()) @@ -312,8 +322,11 @@ 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 @@ -321,33 +334,33 @@ public class Finder extends GFinder { JvOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"), null, - JvOptionPane.INFORMATION_MESSAGE); - colIndex = -1; - seqIndex = 0; + 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); - colIndex = -1; - seqIndex = 0; + JvOptionPane.showInternalMessageDialog(this, message.toString(), + null, JvOptionPane.INFORMATION_MESSAGE); } } - searchBox.updateCache(); } /**