X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=6bff69a5905dad0a97c3f232a3a13945cedcec54;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=e1431a99cc4ac073569830cbb3b7403293a2be5b;hpb=fe17c9998066fe039ba952c266c2445db5adfe82;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index e1431a9..6bff69a 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,352 +1,369 @@ -/* - * 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 - */ -package jalview.gui; - -import jalview.datamodel.*; - -import jalview.jbgui.*; - -import java.awt.*; -import java.awt.event.*; - -import java.util.*; - -import javax.swing.*; -import javax.swing.event.*; - - -/** - * 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() - { - frame = new JInternalFrame(); - frame.setContentPane(this); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - Desktop.addInternalFrame(frame, "Find", 340, 110); - - - // all a big pain, but we need to wait until the frame is visible before the textfield can - // obtain the focus///////////////////////// - frame.addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameOpened(InternalFrameEvent evt) - { - SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - textfield.requestFocus(); - } - }); - } - }); - } - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findNext_actionPerformed(ActionEvent e) - { - if (getFocusedViewport()) - doSearch(false); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findAll_actionPerformed(ActionEvent e) - { - if(getFocusedViewport()) - { - resIndex = 0; - seqIndex = 0; - doSearch(true); - } - } - - boolean getFocusedViewport() - { - JInternalFrame frame = Desktop.desktop.getAllFrames()[1]; - - if(frame!=null && frame instanceof AlignFrame) - { - av = ((AlignFrame)frame).viewport; - ap = ((AlignFrame)frame).alignPanel; - return true; - } - return false; - } - - - /** - * 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()]; - - - 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"); - } - - if( ap.seqPanel.seqCanvas.getFeatureRenderer() - .createNewFeatures(seqs, features)) - { - ap.alignFrame.showSeqFeatures.setSelected(true); - av.setShowSequenceFeatures(true); - ap.highlightSearchResults(null); - } - } - - /** - * DOCUMENT ME! - * - * @param findAll DOCUMENT ME! - */ - void doSearch(boolean findAll) - { - createNewGroup.setEnabled(false); - - String searchString = textfield.getText().trim(); - if(!caseSensitive.isSelected()) - searchString = searchString.toUpperCase(); - - if(searchString.length()<1) - return; - - com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString); - - searchResults = new SearchResults(); - - Sequence seq; - String item = null; - boolean found = false; - - ////// is the searchString a residue number? - try - { - int res = Integer.parseInt(searchString); - found = true; - if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1) - { - seq = (Sequence) av.getAlignment().getSequenceAt(0); - } - else - { - seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0)); - } - - searchResults.addResult(seq, res, res); - } - catch (NumberFormatException ex) - { - } - - /////////////////////////////////////////////// - - int end = av.alignment.getHeight(); - - SequenceGroup selection = av.getSelectionGroup(); - - if (selection != null) - { - if ((selection.getSize(false) < 1) || - ((selection.getEndRes() - selection.getStartRes()) < 2)) - { - selection = null; - } - } - - while (!found && (seqIndex < end)) - { - seq = (Sequence) av.alignment.getSequenceAt(seqIndex); - - if ((selection != null) && !selection.getSequences(false).contains(seq)) - { - seqIndex++; - resIndex = 0; - - continue; - } - - item = seq.getSequence(); - if(!caseSensitive.isSelected()) - item = item.toUpperCase(); - - if ((selection != null) && - (selection.getEndRes() < av.alignment.getWidth()-1)) - { - item = item.substring(0, selection.getEndRes() + 1); - } - - ///Shall we ignore gaps???? - StringBuffer noGapsSB = new StringBuffer(); - int insertCount = 0; - Vector spaces = new Vector(); - - for (int j = 0; j < item.length(); j++) - { - if (!jalview.util.Comparison.isGap(item.charAt(j))) - { - noGapsSB.append(item.charAt(j)); - spaces.add(new Integer(insertCount)); - } - else - { - insertCount++; - } - } - - String noGaps = noGapsSB.toString(); - - for (int r = resIndex; r < noGaps.length(); r++) - { - - if (regex.searchFrom(noGaps, r)) - { - resIndex = regex.matchedFrom(); - - if ((selection != null) && - ((resIndex + - Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes())) - { - continue; - } - - - int sres = seq.findPosition(resIndex + - Integer.parseInt(spaces.elementAt(resIndex) - .toString())); - int eres = seq.findPosition(regex.matchedTo() - 1 + - Integer.parseInt(spaces.elementAt(regex.matchedTo() - - 1).toString())); - - searchResults.addResult(seq, sres, eres); - - if (!findAll) - { - // thats enough, break and display the result - found = true; - resIndex++; - - break; - } - - r = resIndex; - } - else - { - break; - } - } - - if (!found) - { - seqIndex++; - resIndex = 0; - } - } - - Vector idMatch = new Vector(); - - for (int id = 0; id < av.alignment.getHeight(); id++) - { - if (regex.search(av.alignment.getSequenceAt(id).getName())) - { - idMatch.add(av.alignment.getSequenceAt(id)); - } - } - - if ((searchResults.getSize() == 0) && (idMatch.size() > 0)) - { - ap.idPanel.highlightSearchResults(idMatch); - } - - - int resultSize = searchResults.getSize(); - - if (searchResults.getSize() > 0) - createNewGroup.setEnabled(true); - else - searchResults = null; - - // if allResults is null, this effectively switches displaySearch flag in seqCanvas - ap.highlightSearchResults(searchResults); - - if(!findAll && resultSize==0) - { - JOptionPane.showInternalMessageDialog(this, "Finished searching", - null, JOptionPane.INFORMATION_MESSAGE); - resIndex = 0; - seqIndex = 0; - } - - if (findAll) - { - String message = resultSize + " matches found."; - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); - } - - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 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.event.ActionEvent; +import java.awt.event.KeyEvent; +import java.util.Vector; +import java.util.regex.Pattern; +import java.util.regex.PatternSyntaxException; + +import javax.swing.AbstractAction; +import javax.swing.JComponent; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JOptionPane; +import javax.swing.KeyStroke; + +/** + * 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 +{ + private static final int HEIGHT = 110; + + private static final int WIDTH = 340; + + AlignmentViewport av; + + AlignmentPanel ap; + + JInternalFrame frame; + + int seqIndex = 0; + + int resIndex = -1; + + SearchResults searchResults; + + /** + * 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); + addEscapeHandler(); + Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), + WIDTH, HEIGHT); + + textfield.requestFocus(); + } + + /** + * Add a handler for the Escape key when the window has focus + */ + private void addEscapeHandler() + { + getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( + KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel"); + getRootPane().getActionMap().put("Cancel", new AbstractAction() + { + public void actionPerformed(ActionEvent e) + { + escapeActionPerformed(); + } + }); + } + + /** + * Close the panel on Escape key press + */ + protected void escapeActionPerformed() + { + setVisible(false); + frame.dispose(); + } + + /** + * Performs the 'Find Next' action. + * + * @param e + */ + public void findNext_actionPerformed(ActionEvent e) + { + if (getFocusedViewport()) + { + doSearch(false); + } + } + + /** + * Performs the 'Find All' action. + * + * @param e + */ + public void findAll_actionPerformed(ActionEvent e) + { + if (getFocusedViewport()) + { + 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() + { + 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++) + { + 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! + */ + 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++) + { + seqs[i] = searchResults.getResultSequence(i).getDatasetSequence(); + + features[i] = new SequenceFeature(textfield.getText().trim(), + "Search Results", null, searchResults.getResultStart(i), + searchResults.getResultEnd(i), "Search Results"); + } + + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) + { + ap.alignFrame.showSeqFeatures.setSelected(true); + av.setShowSequenceFeatures(true); + ap.highlightSearchResults(null); + } + } + + /** + * 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) + { + createNewGroup.setEnabled(false); + + String searchString = textfield.getText().trim(); + + 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.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 + + 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)) + { + haveResults = true; + ap.getIdPanel().highlightSearchResults(idMatch); + } + else + { + ap.getIdPanel().highlightSearchResults(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 (!haveResults) + { + 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; + } + } + + } + + /** + * 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) + { + 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; + } +}