X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=3cce82c1b046b8f37c8aaf71dc91acb2794d59cf;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=c2c02d1cb5427b14aa42e84f9b07c1e8117c5f0c;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index c2c02d1..3cce82c 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,41 +1,59 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 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. + * + * 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 jalview.viewmodel.AlignmentViewport; -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 { - AlignViewport av; + private static final int HEIGHT = 110; + + private static final int WIDTH = 340; + + AlignmentViewport av; AlignmentPanel ap; @@ -43,35 +61,44 @@ public class Finder extends GFinder 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(AlignmentViewport 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! + * Performs the 'Find Next' action. * * @param e - * DOCUMENT ME! */ public void findNext_actionPerformed(ActionEvent e) { @@ -82,30 +109,55 @@ public class Finder extends GFinder } /** - * DOCUMENT ME! + * Performs the 'Find All' action. * * @param e - * DOCUMENT ME! */ 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) + { + 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++) { - av = ((AlignFrame) frame).viewport; - ap = ((AlignFrame) frame).alignPanel; - return true; + JInternalFrame frame = frames[f]; + if (frame != null && frame instanceof AlignFrame) + { + av = ((AlignFrame) frame).viewport; + ap = ((AlignFrame) frame).alignPanel; + return true; + } } return false; } @@ -114,7 +166,7 @@ public class Finder extends GFinder * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void createNewGroup_actionPerformed(ActionEvent e) { @@ -131,7 +183,7 @@ public class Finder extends GFinder searchResults.getResultEnd(i), "Search Results"); } - if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { ap.alignFrame.showSeqFeatures.setSelected(true); @@ -141,10 +193,10 @@ public class Finder extends GFinder } /** - * 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 - * DOCUMENT ME! */ void doSearch(boolean findAll) { @@ -152,7 +204,7 @@ public class Finder extends GFinder String searchString = textfield.getText().trim(); - if (searchString.length() < 1) + if (isInvalidSearchString(searchString)) { return; } @@ -161,8 +213,10 @@ public class Finder extends GFinder // 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); + 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 @@ -171,18 +225,23 @@ public class Finder extends GFinder resIndex = finder.getResIndex(); searchResults = finder.getSearchResults(); // find(regex, - // caseSensitive.isSelected(), ) + // 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)) { - ap.idPanel.highlightSearchResults(idMatch); + haveResults = true; + ap.getIdPanel().highlightSearchResults(idMatch); + } + else + { + ap.getIdPanel().highlightSearchResults(null); } - - int resultSize = searchResults.getSize(); if (searchResults.getSize() > 0) { + haveResults = true; createNewGroup.setEnabled(true); } else @@ -195,20 +254,86 @@ public class Finder extends GFinder ap.highlightSearchResults(searchResults); // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or // 'SelectRegion' selection - if (!findAll && resultSize == 0) + 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; } }