X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=909b55df92ad10e3d05ac0f7db7590f7d165d3c8;hb=59d682209891099d46b960509907c79e3fb276fe;hp=0811f826d67b697a3b817e2a67a4dd7bccf2bc58;hpb=7c94a4aa0eab3272df0fdae2efcedf50f050296c;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index 0811f82..909b55d 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,205 +1,264 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 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) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * + * 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 . */ package jalview.gui; -import jalview.datamodel.*; - -import jalview.jbgui.*; +import java.util.*; import java.awt.*; import java.awt.event.*; - -import java.util.*; - import javax.swing.*; -import javax.swing.event.*; +import jalview.datamodel.*; +import jalview.jbgui.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ public class Finder extends GFinder { - AlignViewport av; - AlignmentPanel ap; - JInternalFrame frame; - int seqIndex = 0; - int resIndex = 0; - - SearchResults searchResults; - - /** - * Creates a new Finder object. - * - * @param av DOCUMENT ME! - * @param ap DOCUMENT ME! - * @param f DOCUMENT ME! - */ - public Finder() + AlignViewport av; + + AlignmentPanel ap; + + JInternalFrame frame; + + int seqIndex = 0; + + int resIndex = -1; + + SearchResults searchResults; + + /** + * Creates a new Finder object. + * + * @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); + Desktop.addInternalFrame(frame, "Find", 340, 110); + + textfield.requestFocus(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void findNext_actionPerformed(ActionEvent e) + { + if (getFocusedViewport()) { - frame = new JInternalFrame(); - frame.setContentPane(this); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - Desktop.addInternalFrame(frame, "Find", 340, 110); - - textfield.requestFocus(); + doSearch(false); } - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findNext_actionPerformed(ActionEvent e) + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void findAll_actionPerformed(ActionEvent e) + { + if (getFocusedViewport()) { - if (getFocusedViewport()) - doSearch(false); + resIndex = -1; + seqIndex = 0; + doSearch(true); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findAll_actionPerformed(ActionEvent e) + } + + /** + * 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() + { + if (focusfixed || Desktop.desktop == null) { - if(getFocusedViewport()) + if (ap != null && av != null) { - resIndex = 0; - seqIndex = 0; - doSearch(true); + return true; } + // we aren't in a desktop environment, so give up now. + return false; } - - boolean getFocusedViewport() + // 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 = Desktop.desktop.getAllFrames()[1]; - - if(frame!=null && frame instanceof AlignFrame) + JInternalFrame frame = frames[f]; + if (frame != null && frame instanceof AlignFrame) { - av = ((AlignFrame)frame).viewport; - ap = ((AlignFrame)frame).alignPanel; + av = ((AlignFrame) frame).viewport; + ap = ((AlignFrame) frame).alignPanel; return true; } - return false; } - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void createNewGroup_actionPerformed(ActionEvent e) + return false; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void createNewGroup_actionPerformed(ActionEvent e) + { + SequenceI[] seqs = new SequenceI[searchResults.getSize()]; + SequenceFeature[] features = new SequenceFeature[searchResults + .getSize()]; + + for (int i = 0; i < searchResults.getSize(); i++) { - 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); - + seqs[i] = searchResults.getResultSequence(i).getDatasetSequence(); - SequenceI [] seqs = new SequenceI[searchResults.getSize()]; - SequenceFeature [] features = new SequenceFeature[searchResults.getSize()]; + features[i] = new SequenceFeature(textfield.getText().trim(), + "Search Results", null, searchResults.getResultStart(i), + searchResults.getResultEnd(i), "Search Results"); + } + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) + { + ap.alignFrame.showSeqFeatures.setSelected(true); + av.setShowSequenceFeatures(true); + ap.highlightSearchResults(null); + } + } - for (int i = 0; i < searchResults.getSize(); i ++ ) - { - seqs[i] = searchResults.getResultSequence(i).getDatasetSequence(); + /** + * incrementally search the alignment + * + * @param findAll + * true means find all results and raise a dialog box + */ + void doSearch(boolean findAll) + { + createNewGroup.setEnabled(false); - features[i] = new SequenceFeature(textinput.getText(), - "Search Results", null, - searchResults.getResultStart(i), - searchResults.getResultEnd(i), - "Search Results"); - } + String searchString = textfield.getText().trim(); - if( ap.seqPanel.seqCanvas.getFeatureRenderer() - .createNewFeatures(seqs, features)) - { - ap.alignFrame.showSeqFeatures.setSelected(true); - av.setShowSequenceFeatures(true); - ap.highlightSearchResults(null); - } + if (searchString.length() < 1) + { + return; } - - /** - * DOCUMENT ME! - * - * @param findAll DOCUMENT ME! - */ - void doSearch(boolean findAll) + // 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); + + finder.find(searchString); // returns true if anything was actually found + + seqIndex = finder.getSeqIndex(); + resIndex = finder.getResIndex(); + + searchResults = finder.getSearchResults(); // find(regex, + // caseSensitive.isSelected(), ) + Vector idMatch = finder.getIdMatch(); + boolean haveResults = false; + // set or reset the GUI + if ((idMatch.size() > 0)) { - createNewGroup.setEnabled(false); - - String searchString = textfield.getText().trim(); - - if(searchString.length()<1) - 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); - finder.setCaseSensitive(caseSensitive.isSelected()); - finder.setFindAll(findAll); - - finder.find(searchString); // returns true if anything was actually found - - seqIndex=finder.getSeqIndex(); - resIndex=finder.getResIndex(); - - searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), ) - Vector idMatch = finder.getIdMatch(); - // set or reset the GUI - if ((searchResults.getSize() == 0) && (idMatch.size() > 0)) - { - ap.idPanel.highlightSearchResults(idMatch); - } - - - int resultSize = searchResults.getSize(); + haveResults = true; + ap.idPanel.highlightSearchResults(idMatch); + } + else + { + ap.idPanel.highlightSearchResults(null); + } - if (searchResults.getSize() > 0) - createNewGroup.setEnabled(true); - else - searchResults = null; + if (searchResults.getSize() > 0) + { + haveResults = true; + createNewGroup.setEnabled(true); + } + else + { + searchResults = null; + } - // 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) - { - JOptionPane.showInternalMessageDialog(this, "Finished searching", - null, JOptionPane.INFORMATION_MESSAGE); - resIndex = 0; - seqIndex = 0; - } + // 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 (!haveResults) + { + JOptionPane.showInternalMessageDialog(this, "Finished searching", + null, JOptionPane.INFORMATION_MESSAGE); + resIndex = -1; + seqIndex = 0; + } - if (findAll) + if (findAll) + { + String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs" + : ""; + if (searchResults != null) + { + if (idMatch.size() > 0 && searchResults.getSize() > 0) { - String message = resultSize + " matches found."; - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); + message += " and "; } - + message += searchResults.getSize() + " subsequence matches found."; + } + JOptionPane.showInternalMessageDialog(this, message, null, + JOptionPane.INFORMATION_MESSAGE); + resIndex = -1; + seqIndex = 0; } + + } }