X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=cc91ebfbecd90eeebbf3ffc6e74486c61302f5b5;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=fcac4d29b2ee26cbadc43642b295ed4f73d46647;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index fcac4d2..cc91ebf 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,70 +1,103 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.util.*; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GFinder; +import jalview.util.MessageManager; -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; +import java.awt.event.ActionEvent; +import java.util.Vector; +import java.util.regex.Pattern; +import java.util.regex.PatternSyntaxException; -import jalview.datamodel.*; -import jalview.jbgui.*; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JOptionPane; /** - * DOCUMENT ME! - * + * 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 + * option to create a new feature on the alignment for the matched positions. + * + * Searches can be for a simple base sequence, or may use a regular expression. + * Any gaps are ignored. + * * @author $author$ * @version $Revision$ */ -public class Finder - extends GFinder +public class Finder extends GFinder { + private static final int HEIGHT = 110; + + private static final int WIDTH = 340; + AlignViewport av; + AlignmentPanel ap; + JInternalFrame frame; + int seqIndex = 0; - int resIndex = 0; + + int resIndex = -1; SearchResults searchResults; /** - * Creates a new Finder object. - * - * @param av DOCUMENT ME! - * @param ap DOCUMENT ME! - * @param f DOCUMENT ME! + * Creates a new Finder object with no associated viewport or panel. */ public Finder() { + this(null, null); + focusfixed = false; + } + + /** + * Constructor given an associated viewport and alignment panel. Constructs + * and displays an internal frame where the user can enter a search string. + * + * @param viewport + * @param alignPanel + */ + public Finder(AlignViewport viewport, AlignmentPanel alignPanel) + { + av = viewport; + ap = alignPanel; + focusfixed = true; frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); - Desktop.addInternalFrame(frame, "Find", 340, 110); + Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), + WIDTH, HEIGHT); textfield.requestFocus(); } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Performs the 'Find Next' action. + * + * @param e */ public void findNext_actionPerformed(ActionEvent e) { @@ -75,62 +108,82 @@ public class Finder } /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * Performs the 'Find All' action. + * + * @param e */ public void findAll_actionPerformed(ActionEvent e) { if (getFocusedViewport()) { - resIndex = 0; + 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 + * + * @return false if no alignment window was found + */ boolean getFocusedViewport() { - JInternalFrame frame = Desktop.desktop.getAllFrames()[1]; - - if (frame != null && frame instanceof AlignFrame) + if (focusfixed || Desktop.desktop == null) { - av = ( (AlignFrame) frame).viewport; - ap = ( (AlignFrame) frame).alignPanel; - return true; + if (ap != null && av != null) + { + return true; + } + // we aren't in a desktop environment, so give up now. + return false; + } + // now checks further down the window stack to fix bug + // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008 + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + for (int f = 0; f < frames.length; f++) + { + JInternalFrame frame = frames[f]; + if (frame != null && frame instanceof AlignFrame) + { + av = ((AlignFrame) frame).viewport; + ap = ((AlignFrame) frame).alignPanel; + return true; + } } return false; } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void createNewGroup_actionPerformed(ActionEvent e) { - JLabel label = new JLabel("Enter name of new sequence feature"); - JTextField textinput = new JTextField(textfield.getText()); - JPanel panel = new JPanel(new BorderLayout()); - panel.add(label, BorderLayout.NORTH); - panel.add(textinput, BorderLayout.SOUTH); - SequenceI[] seqs = new SequenceI[searchResults.getSize()]; - SequenceFeature[] features = new SequenceFeature[searchResults.getSize()]; + SequenceFeature[] features = new SequenceFeature[searchResults + .getSize()]; for (int i = 0; i < searchResults.getSize(); i++) { seqs[i] = searchResults.getResultSequence(i).getDatasetSequence(); - features[i] = new SequenceFeature(textinput.getText(), - "Search Results", null, - searchResults.getResultStart(i), - searchResults.getResultEnd(i), - "Search Results"); + features[i] = new SequenceFeature(textfield.getText().trim(), + "Search Results", null, searchResults.getResultStart(i), + searchResults.getResultEnd(i), "Search Results"); } - if (ap.seqPanel.seqCanvas.getFeatureRenderer() - .createNewFeatures(seqs, features)) + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) { ap.alignFrame.showSeqFeatures.setSelected(true); av.setShowSequenceFeatures(true); @@ -139,9 +192,10 @@ public class Finder } /** - * DOCUMENT ME! - * - * @param findAll DOCUMENT ME! + * 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 */ void doSearch(boolean findAll) { @@ -149,14 +203,16 @@ public class Finder String searchString = textfield.getText().trim(); - if (searchString.length() < 1) + if (isInvalidSearchString(searchString)) { return; } - // TODO: extend finder to match descriptions, features and annotation, and other stuff - // TODO: add switches to control what is searched - sequences, IDS, descriptions, features - jalview.analysis.Finder finder = new jalview.analysis.Finder(av.alignment, - av.getSelectionGroup(), seqIndex, resIndex); + // TODO: extend finder to match descriptions, features and annotation, and + // 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.setFindAll(findAll); @@ -165,18 +221,24 @@ public class Finder seqIndex = finder.getSeqIndex(); resIndex = finder.getResIndex(); - searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), ) + searchResults = finder.getSearchResults(); // find(regex, + // caseSensitive.isSelected(), ) Vector idMatch = finder.getIdMatch(); + boolean haveResults = false; // set or reset the GUI - if ( (searchResults.getSize() == 0) && (idMatch.size() > 0)) + if ((idMatch.size() > 0)) { + haveResults = true; ap.idPanel.highlightSearchResults(idMatch); } - - int resultSize = searchResults.getSize(); + else + { + ap.idPanel.highlightSearchResults(null); + } if (searchResults.getSize() > 0) { + haveResults = true; createNewGroup.setEnabled(true); } else @@ -184,24 +246,91 @@ public class Finder searchResults = null; } - // if allResults is null, this effectively switches displaySearch flag in seqCanvas + // 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 (!findAll && resultSize == 0) + // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or + // 'SelectRegion' selection + if (!haveResults) { - JOptionPane.showInternalMessageDialog(this, "Finished searching", - null, - JOptionPane.INFORMATION_MESSAGE); - resIndex = 0; + JOptionPane.showInternalMessageDialog(this, + MessageManager.getString("label.finished_searching"), null, + JOptionPane.INFORMATION_MESSAGE); + resIndex = -1; seqIndex = 0; } + else + { + if (findAll) + { + // then we report the matches that were found + String message = (idMatch.size() > 0) ? "" + idMatch.size() + + " IDs" : ""; + if (searchResults != null) + { + if (idMatch.size() > 0 && searchResults.getSize() > 0) + { + message += " and "; + } + message += searchResults.getSize() + + " subsequence matches found."; + } + JOptionPane.showInternalMessageDialog(this, message, null, + JOptionPane.INFORMATION_MESSAGE); + resIndex = -1; + seqIndex = 0; + } + } - if (findAll) + } + + /** + * Displays an error dialog, and answers false, if the search string is + * invalid, else answers true. + * + * @param searchString + * @return + */ + protected boolean isInvalidSearchString(String searchString) + { + String error = getSearchValidationError(searchString); + if (error == null) { - String message = resultSize + " matches found."; - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); + return false; } + JOptionPane.showInternalMessageDialog(this, error, + MessageManager.getString("label.invalid_search"), // $NON-NLS-1$ + JOptionPane.ERROR_MESSAGE); + return true; + } + /** + * Returns an error message string if the search string is invalid, else + * returns null. + * + * Currently validation is limited to checking the string is not empty, and is + * a valid regular expression (simple searches for base sub-sequences will + * pass this test). Additional validations may be added in future if the + * search syntax is expanded. + * + * @param searchString + * @return + */ + protected String getSearchValidationError(String searchString) + { + String error = null; + if (searchString == null || searchString.length() == 0) + { + error = MessageManager.getString("label.invalid_search"); + } + try + { + Pattern.compile(searchString); + } catch (PatternSyntaxException e) + { + error = MessageManager.getString("error.invalid_regex") + ": " + + e.getDescription(); + } + return error; } }