X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=a1693f713aca74250886bfe13b5a233d9dbc6827;hb=4f77328104498504339216829abf5ea87e2791ec;hp=04c512a2918d1695b41c26589403581f0cdeecda;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index 04c512a..a1693f7 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,20 +20,32 @@ */ package jalview.gui; -import jalview.datamodel.SearchResults; +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.event.ActionEvent; -import java.util.Vector; +import java.awt.event.KeyEvent; +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; +import javax.swing.AbstractAction; +import javax.swing.JComponent; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; -import javax.swing.JOptionPane; +import javax.swing.KeyStroke; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; /** * Performs the menu option for searching the alignment, for the next or all @@ -48,29 +60,39 @@ import javax.swing.JOptionPane; */ 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; - AlignViewport av; + private static final int MY_HEIGHT = 120; - 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; - SearchResults searchResults; + /* + * Finder agent per viewport searched + */ + 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. + * 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); - focusfixed = false; } /** @@ -80,26 +102,52 @@ public class Finder extends GFinder * @param viewport * @param alignPanel */ - public Finder(AlignViewport viewport, AlignmentPanel alignPanel) + public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel) { av = viewport; ap = alignPanel; - focusfixed = true; + finders = new HashMap<>(); + focusfixed = viewport != null; frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); + frame.addInternalFrameListener( + new InternalFrameAdapter() + { + @Override + public void internalFrameClosing(InternalFrameEvent e) + { + closeAction(); + } + }); + addEscapeHandler(); Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), - WIDTH, HEIGHT); + true, MY_WIDTH, MY_HEIGHT, true, true); + searchBox.getComponent().requestFocus(); + } - textfield.requestFocus(); + /** + * Add a handler for the Escape key when the window has focus + */ + private void addEscapeHandler() + { + 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) + { + closeAction(); + } + }); } /** - * Performs the 'Find Next' action. - * - * @param e + * Performs the 'Find Next' action on the alignment panel with focus */ - public void findNext_actionPerformed(ActionEvent e) + @Override + public void findNext_actionPerformed() { if (getFocusedViewport()) { @@ -108,26 +156,18 @@ public class Finder extends GFinder } /** - * Performs the 'Find All' action. - * - * @param e + * Performs the 'Find All' action on the alignment panel with focus */ - public void findAll_actionPerformed(ActionEvent e) + @Override + 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 @@ -150,11 +190,12 @@ 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; return true; } } @@ -162,46 +203,47 @@ 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 */ - public void createNewGroup_actionPerformed(ActionEvent e) + @Override + public void createFeatures_actionPerformed() { - SequenceI[] seqs = new SequenceI[searchResults.getSize()]; - SequenceFeature[] features = new SequenceFeature[searchResults - .getSize()]; - - for (int i = 0; i < searchResults.getSize(); i++) + if (searchResults.isEmpty()) { - seqs[i] = searchResults.getResultSequence(i).getDatasetSequence(); - - features[i] = new SequenceFeature(textfield.getText().trim(), - "Search Results", null, searchResults.getResultStart(i), - searchResults.getResultEnd(i), "Search Results"); + return; // shouldn't happen } + List seqs = new ArrayList<>(); + List features = new ArrayList<>(); + + String searchString = searchBox.getUserInput(); + String desc = "Search Results"; - if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + for (SearchResultMatchI match : searchResults.getResults()) { - ap.alignFrame.showSeqFeatures.setSelected(true); - av.setShowSequenceFeatures(true); - ap.highlightSearchResults(null); + seqs.add(match.getSequence().getDatasetSequence()); + features.add(new SequenceFeature(searchString, desc, match.getStart(), + match.getEnd(), desc)); } + + new FeatureEditor(ap, seqs, features, true).showDialog(); } /** * 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 = textfield.getText().trim(); + String searchString = searchBox.getUserInput(); if (isInvalidSearchString(searchString)) { @@ -211,63 +253,58 @@ 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(); + if (doFindAll) { - haveResults = true; - ap.getIdPanel().highlightSearchResults(idMatch); + finder.findAll(searchString, isCaseSensitive, doSearchDescription); } else { - ap.getIdPanel().highlightSearchResults(null); + finder.findNext(searchString, isCaseSensitive, doSearchDescription); } - 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 + searchBox.updateCache(); + ap.highlightSearchResults(searchResults); // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or // 'SelectRegion' selection - if (!haveResults) + if (idMatch.isEmpty() && searchResults == null) { - JOptionPane.showInternalMessageDialog(this, + JvOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"), null, - JOptionPane.INFORMATION_MESSAGE); - resIndex = -1; - seqIndex = 0; + JvOptionPane.PLAIN_MESSAGE); } 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) @@ -277,13 +314,10 @@ public class Finder extends GFinder message += searchResults.getSize() + " subsequence matches found."; } - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); - resIndex = -1; - seqIndex = 0; + JvOptionPane.showInternalMessageDialog(this, message, null, + JvOptionPane.PLAIN_MESSAGE); } } - } /** @@ -300,9 +334,9 @@ public class Finder extends GFinder { return false; } - JOptionPane.showInternalMessageDialog(this, error, + JvOptionPane.showInternalMessageDialog(this, error, MessageManager.getString("label.invalid_search"), // $NON-NLS-1$ - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); return true; } @@ -335,4 +369,15 @@ public class Finder extends GFinder } return error; } + + protected void closeAction() + { + frame.setVisible(false); + frame.dispose(); + searchBox.persistCache(); + if (getFocusedViewport()) + { + ap.alignFrame.requestFocus(); + } + } }