X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=727e103eb24eeee57fa9816ab5dfea4f14e80548;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=5668b42312a9e64c0b75ec0ffbc0fe9afed0c93f;hpb=cbfa4d2bc1282662ad88756f1b0b2d8b3b82bd11;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index 5668b42..727e103 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,58 +1,73 @@ /* - * 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 - * 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. - * - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * 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. + * + * 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.util.*; - -import java.awt.*; import java.awt.event.*; + import javax.swing.*; import jalview.datamodel.*; import jalview.jbgui.*; +import jalview.util.MessageManager; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class Finder - extends GFinder +public class Finder extends GFinder { 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! + * + * @param av + * DOCUMENT ME! + * @param ap + * DOCUMENT ME! + * @param f + * DOCUMENT ME! */ public Finder() { + this(null, null); + focusfixed = false; + } + + public Finder(AlignViewport viewport, AlignmentPanel alignPanel) + { + av = viewport; + ap = alignPanel; + focusfixed = true; frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); @@ -63,8 +78,9 @@ public class Finder /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void findNext_actionPerformed(ActionEvent e) { @@ -76,55 +92,82 @@ public class Finder /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @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; } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void createNewGroup_actionPerformed(ActionEvent e) { 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(textfield.getText().trim(), - "Search Results", null, - searchResults.getResultStart(i), - searchResults.getResultEnd(i), - "Search Results"); + "Search Results", null, searchResults.getResultStart(i), + searchResults.getResultEnd(i), "Search Results"); } - if (ap.seqPanel.seqCanvas.getFeatureRenderer() - .amendFeatures(seqs, features, true, ap)) + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) { ap.alignFrame.showSeqFeatures.setSelected(true); av.setShowSequenceFeatures(true); @@ -133,9 +176,10 @@ public class Finder } /** - * DOCUMENT ME! - * - * @param findAll DOCUMENT ME! + * incrementally search the alignment + * + * @param findAll + * true means find all results and raise a dialog box */ void doSearch(boolean findAll) { @@ -147,10 +191,12 @@ public class Finder { 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); @@ -159,18 +205,24 @@ 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 @@ -178,23 +230,37 @@ 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; - } - - if (findAll) - { - String message = resultSize + " matches found."; - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); + } 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; + } } }