X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FFinder.java;h=d328452950575333ad76b13f7a7b6a276b490061;hb=bed0c230be450b16213e30ee1dcaf3e76ddfc669;hp=c5b25bf7519035d2937b1f8dd1df847f14807983;hpb=3ba65b98445f192453664357a1df25128fe07c84;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index c5b25bf..d328452 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -21,22 +21,22 @@ 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; @@ -65,7 +65,7 @@ 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; @@ -76,47 +76,23 @@ 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 - */ - 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); @@ -130,10 +106,10 @@ public class Finder extends GFinder } }); addEscapeHandler(); + Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), - MY_WIDTH, MY_HEIGHT); - frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); - searchBox.requestFocus(); + true, MY_WIDTH, MY_HEIGHT, true, true); + searchBox.getComponent().requestFocus(); } /** @@ -173,8 +149,6 @@ public class Finder extends GFinder { if (getFocusedViewport()) { - colIndex = -1; - seqIndex = 0; doSearch(true); } } @@ -182,13 +156,14 @@ 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 (Desktop.desktop == null) { if (ap != null && av != null) { @@ -208,21 +183,7 @@ 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 +192,19 @@ 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 +214,11 @@ 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)) - { - /* - * 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(); } /** @@ -277,7 +231,7 @@ public class Finder extends GFinder { createFeatures.setEnabled(false); - String searchString = searchBox.getUserInput().trim(); + String searchString = searchBox.getUserInput(); if (isInvalidSearchString(searchString)) { @@ -287,22 +241,32 @@ 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); + } - 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 idMatch = finder.getIdMatch(); + List idMatch = finder.getIdMatches(); ap.getIdPanel().highlightSearchResults(idMatch); if (searchResults.isEmpty()) @@ -314,6 +278,8 @@ public class Finder extends GFinder createFeatures.setEnabled(true); } + searchBox.updateCache(); + ap.highlightSearchResults(searchResults); // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or // 'SelectRegion' selection @@ -321,9 +287,7 @@ 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 { @@ -334,20 +298,17 @@ public class Finder extends GFinder : ""; 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; + JvOptionPane.PLAIN_MESSAGE); } } - searchBox.updateCache(); } /** @@ -410,4 +371,15 @@ 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); + } }