X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=1e944759321e08171fe32c196b4f92b80e877e4e;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=e5c94bd5b90e0e41d4ff3443695ad443706eb67f;hpb=8a474786319224db5ad12dfefe91ed663140a859;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index e5c94bd..1e94475 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,369 +1,338 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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; - SuperGroup searchGroup; - Vector searchResults; - int seqIndex = 0; - int resIndex = 0; - - /** - * Creates a new Finder object. - * - * @param av DOCUMENT ME! - * @param ap DOCUMENT ME! - * @param f DOCUMENT ME! - */ - public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f) - { - this.av = av; - this.ap = ap; - frame = f; - - // 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 evt DOCUMENT ME! - */ - public void internalFrameClosing(InternalFrameEvent evt) - { - cancel_actionPerformed(null); - } - }); - } - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findNext_actionPerformed(ActionEvent e) - { - doSearch(false); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findAll_actionPerformed(ActionEvent e) - { - resIndex = 0; - seqIndex = 0; - doSearch(true); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void cancel_actionPerformed(ActionEvent e) - { - try - { - // if allResults is null, this effectively switches displaySearch flag in seqCanvas - ap.highlightSearchResults(null); - ap.idPanel.highlightSearchResults(null); - - // frame.setClosed(true); - } - catch (Exception ex) - { - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void createNewGroup_actionPerformed(ActionEvent e) - { - Color[] newColors = new Color[24]; - - for (int i = 0; i < 24; i++) - { - newColors[i] = new Color(60, 160, 115); - } - - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors); - String searchString = textfield.getText(); - - searchGroup = new SuperGroup(searchString, ucs, true, true, false); - - for (int i = 0; i < searchResults.size(); i += 3) - { - // its possible edits may have occurred since search was performed - // account for this here - SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt( - searchResults.elementAt(i).toString())); - int startRes = seq.findIndex(Integer.parseInt( - searchResults.elementAt(i + 1).toString())) - 1; - int endRes = seq.findIndex(Integer.parseInt( - searchResults.elementAt(i + 2).toString())) - 1; - - SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, - false, startRes, endRes); - sg.addSequence(seq, false); - av.alignment.addGroup(sg); - searchGroup.addGroup(sg); - } - - ap.av.alignment.addSuperGroup(searchGroup); - ap.highlightSearchResults(null); - } - - /** - * DOCUMENT ME! - * - * @param findAll DOCUMENT ME! - */ - void doSearch(boolean findAll) - { - createNewGroup.setEnabled(false); - - String searchString = textfield.getText().toUpperCase().trim(); - - com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString); - - searchResults = new Vector(); - - int[] allResults = null; - - 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() < 1) - { - seq = (Sequence) av.getAlignment().getSequenceAt(0); - } - else - { - seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0)); - } - - searchResults.add(Integer.toString(av.getAlignment().findIndex(seq))); - searchResults.add(res+""); - searchResults.add(res+""); - } - catch (NumberFormatException ex) - { - } - - /////////////////////////////////////////////// - Color[] newColors = new Color[24]; - - for (int i = 0; i < 24; i++) - { - newColors[i] = new Color(60, 160, 115); - } - - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors); - - searchGroup = new SuperGroup(searchString, ucs, true, true, false); - - int end = av.alignment.getHeight(); - - SequenceGroup selection = av.getSelectionGroup(); - - if (selection != null) - { - if ((selection.getSize() < 1) || - ((selection.getEndRes() - selection.getStartRes()) < 2)) - { - selection = null; - } - } - - while (!found && (seqIndex < end)) - { - seq = (Sequence) av.alignment.getSequenceAt(seqIndex); - - if ((selection != null) && !selection.sequences.contains(seq)) - { - seqIndex++; - resIndex = 0; - - continue; - } - - item = seq.getSequence().toUpperCase(); - - if ((selection != null) && - (selection.getEndRes() < av.alignment.getWidth())) - { - item = item.substring(0, selection.getEndRes() + 1); - } - - ///Shall we ignore gaps???? - StringBuffer noGaps = 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))) - { - noGaps.append(item.charAt(j)); - spaces.add(new Integer(insertCount)); - } - else - { - insertCount++; - } - } - - for (int r = resIndex; r < noGaps.length(); r++) - { - if (regex.searchFrom(noGaps.toString(), r)) - { - resIndex = regex.matchedFrom(); - - if ((selection != null) && - ((resIndex + - Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes())) - { - continue; - } - - searchResults.add(Integer.toString(seqIndex)); - - 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.addElement(sres + ""); - searchResults.addElement(eres + ""); - - if (!findAll) - { - // thats enough, break and display the result - found = true; - resIndex++; - - break; - } - - r = resIndex; - } - } - - 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.size() == 0) && (idMatch.size() > 0)) - { - ap.idPanel.highlightSearchResults(idMatch); - } - - if (searchResults.size() > 0) - { - allResults = new int[searchResults.size()]; - - for (int i = 0; i < searchResults.size(); i++) - { - allResults[i] = Integer.parseInt(searchResults.get(i).toString()); - } - - createNewGroup.setEnabled(true); - } - else - { - 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(allResults); - - if (findAll) - { - String message = (searchResults.size() / 3) + " matches found."; - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); - } - } -} +/* + * 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(AlignViewport av, AlignmentPanel ap, JInternalFrame f) + { + this.av = av; + this.ap = ap; + frame = f; + + // 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) + { + doSearch(false); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void findAll_actionPerformed(ActionEvent e) + { + resIndex = 0; + seqIndex = 0; + doSearch(true); + } + + + /** + * 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); + + int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + panel, "New Sequence Feature Name", + JOptionPane.OK_CANCEL_OPTION ); + + if(reply != JOptionPane.OK_OPTION) + return; + + for (int i = 0; i < searchResults.getSize(); i ++ ) + { + SequenceI seq = searchResults.getResultSequence(i); + + SequenceFeature sf = new SequenceFeature(textinput.getText(), + "Search Results", null, + searchResults.getResultStart(i), + searchResults.getResultEnd(i), + "Search Results"); + + ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature( + textinput.getText(), new Color(60,160,115), + "Search Results"); + + seq.getDatasetSequence().addSequenceFeature(sf); + } + + ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures(); + 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); + } + + } +}