X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=cad734b297d7ae1932e621f0f5251a09a9b21c31;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=0811f826d67b697a3b817e2a67a4dd7bccf2bc58;hpb=7c94a4aa0eab3272df0fdae2efcedf50f050296c;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index 0811f82..cad734b 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,205 +1,214 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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.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 = 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); + + 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 findAll_actionPerformed(ActionEvent e) + { + if (getFocusedViewport()) + { + resIndex = 0; + seqIndex = 0; + doSearch(true); } + } + boolean getFocusedViewport() + { + JInternalFrame frame = Desktop.desktop.getAllFrames()[1]; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findNext_actionPerformed(ActionEvent e) + if (frame != null && frame instanceof AlignFrame) { - if (getFocusedViewport()) - doSearch(false); + 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"); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findAll_actionPerformed(ActionEvent e) + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) { - if(getFocusedViewport()) - { - resIndex = 0; - seqIndex = 0; - doSearch(true); - } + ap.alignFrame.showSeqFeatures.setSelected(true); + av.setShowSequenceFeatures(true); + ap.highlightSearchResults(null); } + } - boolean getFocusedViewport() + /** + * DOCUMENT ME! + * + * @param findAll + * DOCUMENT ME! + */ + void doSearch(boolean findAll) + { + 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)) { - JInternalFrame frame = Desktop.desktop.getAllFrames()[1]; - - if(frame!=null && frame instanceof AlignFrame) - { - av = ((AlignFrame)frame).viewport; - ap = ((AlignFrame)frame).alignPanel; - return true; - } - return false; + ap.idPanel.highlightSearchResults(idMatch); } + int resultSize = searchResults.getSize(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void createNewGroup_actionPerformed(ActionEvent e) + if (searchResults.getSize() > 0) + { + createNewGroup.setEnabled(true); + } + else { - 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); - } + searchResults = null; } - /** - * DOCUMENT ME! - * - * @param findAll DOCUMENT ME! - */ - void doSearch(boolean findAll) + // 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) { - 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(); - - if (searchResults.getSize() > 0) - 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 (findAll) - { - String message = resultSize + " matches found."; - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); - } + 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); } + + } }