X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=909b55df92ad10e3d05ac0f7db7590f7d165d3c8;hb=59d682209891099d46b960509907c79e3fb276fe;hp=cad734b297d7ae1932e621f0f5251a09a9b21c31;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index cad734b..909b55d 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 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 + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; @@ -43,7 +42,7 @@ public class Finder extends GFinder int seqIndex = 0; - int resIndex = 0; + int resIndex = -1; SearchResults searchResults; @@ -51,14 +50,23 @@ public class Finder extends GFinder * Creates a new Finder object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! * @param ap - * DOCUMENT ME! + * DOCUMENT ME! * @param f - * DOCUMENT ME! + * 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); @@ -71,7 +79,7 @@ public class Finder extends GFinder * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void findNext_actionPerformed(ActionEvent e) { @@ -85,27 +93,53 @@ public class Finder extends GFinder * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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 +148,7 @@ public class Finder extends GFinder * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void createNewGroup_actionPerformed(ActionEvent e) { @@ -141,10 +175,10 @@ public class Finder extends GFinder } /** - * DOCUMENT ME! + * incrementally search the alignment * * @param findAll - * DOCUMENT ME! + * true means find all results and raise a dialog box */ void doSearch(boolean findAll) { @@ -161,7 +195,7 @@ 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.setFindAll(findAll); @@ -171,18 +205,23 @@ 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)) { + 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 @@ -195,19 +234,30 @@ 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; + resIndex = -1; seqIndex = 0; } if (findAll) { - String message = resultSize + " matches 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; } }