From: jprocter Date: Wed, 24 Jan 2007 17:15:23 +0000 (+0000) Subject: refactored to use jalview.analysis.Finder for searching alignment. X-Git-Tag: Release_2_3~453 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=7c94a4aa0eab3272df0fdae2efcedf50f050296c;hp=3edbc91b06e90aaeb795168f7361208d639c3a27;p=jalview.git refactored to use jalview.analysis.Finder for searching alignment. --- diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index 830eeeb..25b924a 100755 --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -1,358 +1,227 @@ -/* - * 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.appletgui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import java.awt.Rectangle; - -public class Finder extends Panel implements ActionListener -{ - AlignViewport av; - AlignmentPanel ap; - Frame frame; - - SearchResults searchResults; - - int seqIndex = 0; - int resIndex = 0; - public Finder(final AlignmentPanel ap) - { - try - { - jbInit(); - } - catch (Exception e) - { - e.printStackTrace(); - } - - this.av = ap.av; - this.ap = ap; - frame = new Frame(); - frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120); - frame.repaint(); - frame.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent evt) - { - ap.highlightSearchResults(null); - } - }); - } - - public void actionPerformed(ActionEvent evt) - { - if (evt.getSource() == textfield) - doSearch(false); - - else if (evt.getSource() == findNext) - doSearch(false); - - else if (evt.getSource() == findAll) - { - resIndex = 0; - seqIndex = 0; - doSearch(true); - } - else if(evt.getSource() == createNewGroup) - createNewGroup_actionPerformed(); - } - - - public void createNewGroup_actionPerformed() - { - - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null); - cap.accept.setLabel("Accept"); - Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true); - dialog.add(cap); - - cap.setText(textfield.getText()); - - dialog.setBounds( frame.getLocation().x+frame.getSize().width+5, - frame.getLocation().y+20,300,100); - dialog.show(); - - - String featureName = cap.getText().trim(); - if(featureName.length()<1) - return; - - - for (int i = 0; i < searchResults.getSize(); i ++ ) - { - SequenceI seq = searchResults.getResultSequence(i); - - SequenceFeature sf = new SequenceFeature(featureName, - null, null, - searchResults.getResultStart(i), - searchResults.getResultEnd(i), "Search Results"); - - ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature( - featureName, new Color(60,160,115)); - seq.addSequenceFeature(sf); - } - - ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures(); - ap.alignFrame.sequenceFeatures.setState(true); - av.showSequenceFeatures(true); - ap.highlightSearchResults(null); - } - - void doSearch(boolean findAll) - { - if(jalview.bin.JalviewLite.currentAlignFrame!=null) - { - ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel; - av = ap.av; - } - createNewGroup.setEnabled(false); - - String searchString = textfield.getText(); - if(!caseSensitive.getState()) - searchString = searchString.toUpperCase(); - - 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() < 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() < 1 || - (selection.getEndRes() - selection.getStartRes() < 2)) - { - selection = null; - } - } - - while (!found && seqIndex < end) - { - - seq = (Sequence) av.alignment.getSequenceAt(seqIndex); - - if (selection != null && !selection.getSequences(null).contains(seq)) - { - seqIndex++; - resIndex = 0; - continue; - } - - item = seq.getSequenceAsString(); - if(!caseSensitive.getState()) - item = item.toUpperCase(); - - if (selection != null && selection.getEndRes() < av.alignment.getWidth()) - { - 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.addElement(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.elementAt(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.addElement(av.alignment.getSequenceAt(id)); - } - } - - if (searchResults.getSize() == 0 && idMatch.size() > 0) - { - ap.idPanel.highlightSearchResults(idMatch); - } - - if (searchResults.getSize() > 0) - { - createNewGroup.setEnabled(true); - } - else - { - searchResults = null; - resIndex = 0; - seqIndex = 0; - } - - // if allResults is null, this effectively switches displaySearch flag in seqCanvas - ap.highlightSearchResults(searchResults); - - if (findAll) - { - String message = (searchResults==null?0 : searchResults.getSize()) + " matches found."; - ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message); - } - - } - - Label jLabel1 = new Label(); - protected TextField textfield = new TextField(); - protected Button findAll = new Button(); - protected Button findNext = new Button(); - Panel jPanel1 = new Panel(); - GridLayout gridLayout1 = new GridLayout(); - protected Button createNewGroup = new Button(); - Checkbox caseSensitive = new Checkbox(); - - private void jbInit() throws Exception { - jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); - jLabel1.setText("Find"); - jLabel1.setBounds(new Rectangle(3, 30, 34, 15)); - this.setLayout(null); - textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - textfield.setText(""); - textfield.setBounds(new Rectangle(40, 27, 133, 21)); - textfield.addKeyListener(new java.awt.event.KeyAdapter() { - public void keyTyped(KeyEvent e) { - textfield_keyTyped(e); - } - }); - textfield.addActionListener(this); - findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - findAll.setLabel("Find all"); - findAll.addActionListener(this); - findNext.setEnabled(false); - findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - findNext.setLabel("Find Next"); - findNext.addActionListener(this); - jPanel1.setBounds(new Rectangle(180, 5, 141, 64)); - jPanel1.setLayout(gridLayout1); - gridLayout1.setHgap(0); - gridLayout1.setRows(3); - gridLayout1.setVgap(2); - createNewGroup.setEnabled(false); - createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - createNewGroup.setLabel("New Feature"); - createNewGroup.addActionListener(this); - caseSensitive.setLabel("Match Case"); - caseSensitive.setBounds(new Rectangle(40, 49, 126, 23)); - jPanel1.add(findNext, null); - jPanel1.add(findAll, null); - jPanel1.add(createNewGroup, null); - this.add(caseSensitive); - this.add(textfield, null); - this.add(jLabel1, null); - this.add(jPanel1, null); - } - - void textfield_keyTyped(KeyEvent e) { - findNext.setEnabled(true); - } - -} +/* + * 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.appletgui; + +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.datamodel.*; +import java.awt.Rectangle; + +public class Finder extends Panel implements ActionListener +{ + AlignViewport av; + AlignmentPanel ap; + Frame frame; + + SearchResults searchResults; + + int seqIndex = 0; + int resIndex = 0; + public Finder(final AlignmentPanel ap) + { + try + { + jbInit(); + } + catch (Exception e) + { + e.printStackTrace(); + } + + this.av = ap.av; + this.ap = ap; + frame = new Frame(); + frame.add(this); + jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120); + frame.repaint(); + frame.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent evt) + { + ap.highlightSearchResults(null); + } + }); + } + + public void actionPerformed(ActionEvent evt) + { + if (evt.getSource() == textfield) + doSearch(false); + + else if (evt.getSource() == findNext) + doSearch(false); + + else if (evt.getSource() == findAll) + { + resIndex = 0; + seqIndex = 0; + doSearch(true); + } + else if(evt.getSource() == createNewGroup) + createNewGroup_actionPerformed(); + } + + + public void createNewGroup_actionPerformed() + { + + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null); + cap.accept.setLabel("Accept"); + Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true); + dialog.add(cap); + + cap.setText(textfield.getText()); + + dialog.setBounds( frame.getLocation().x+frame.getSize().width+5, + frame.getLocation().y+20,300,100); + dialog.show(); + + + String featureName = cap.getText().trim(); + if(featureName.length()<1) + return; + + + for (int i = 0; i < searchResults.getSize(); i ++ ) + { + SequenceI seq = searchResults.getResultSequence(i); + + SequenceFeature sf = new SequenceFeature(featureName, + null, null, + searchResults.getResultStart(i), + searchResults.getResultEnd(i), "Search Results"); + + ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature( + featureName, new Color(60,160,115)); + seq.addSequenceFeature(sf); + } + + ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures(); + ap.alignFrame.sequenceFeatures.setState(true); + av.showSequenceFeatures(true); + ap.highlightSearchResults(null); + } + + void doSearch(boolean findAll) + { + if(jalview.bin.JalviewLite.currentAlignFrame!=null) + { + ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel; + av = ap.av; + } + createNewGroup.setEnabled(false); + jalview.analysis.Finder finder=new jalview.analysis.Finder(av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex); + finder.setCaseSensitive(caseSensitive.getState()); + finder.setFindAll(findAll); + + String searchString = textfield.getText(); + + finder.find(searchString); + seqIndex=finder.getSeqIndex(); + resIndex=finder.getResIndex(); + searchResults = finder.getSearchResults(); + Vector idMatch = finder.getIdMatch(); + + if (searchResults.getSize() == 0 && idMatch.size() > 0) + { + ap.idPanel.highlightSearchResults(idMatch); + } + + if (searchResults.getSize() > 0) + { + createNewGroup.setEnabled(true); + + } + else + { + searchResults = null; + resIndex = 0; + seqIndex = 0; + } + + // if allResults is null, this effectively switches displaySearch flag in seqCanvas + ap.highlightSearchResults(searchResults); + + if (findAll) + { + String message = (searchResults==null?0 : searchResults.getSize()) + " matches found."; + ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message); + } + + } + + Label jLabel1 = new Label(); + protected TextField textfield = new TextField(); + protected Button findAll = new Button(); + protected Button findNext = new Button(); + Panel jPanel1 = new Panel(); + GridLayout gridLayout1 = new GridLayout(); + protected Button createNewGroup = new Button(); + Checkbox caseSensitive = new Checkbox(); + + private void jbInit() throws Exception { + jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); + jLabel1.setText("Find"); + jLabel1.setBounds(new Rectangle(3, 30, 34, 15)); + this.setLayout(null); + textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); + textfield.setText(""); + textfield.setBounds(new Rectangle(40, 27, 133, 21)); + textfield.addKeyListener(new java.awt.event.KeyAdapter() { + public void keyTyped(KeyEvent e) { + textfield_keyTyped(e); + } + }); + textfield.addActionListener(this); + findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); + findAll.setLabel("Find all"); + findAll.addActionListener(this); + findNext.setEnabled(false); + findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); + findNext.setLabel("Find Next"); + findNext.addActionListener(this); + jPanel1.setBounds(new Rectangle(180, 5, 141, 64)); + jPanel1.setLayout(gridLayout1); + gridLayout1.setHgap(0); + gridLayout1.setRows(3); + gridLayout1.setVgap(2); + createNewGroup.setEnabled(false); + createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); + createNewGroup.setLabel("New Feature"); + createNewGroup.addActionListener(this); + caseSensitive.setLabel("Match Case"); + caseSensitive.setBounds(new Rectangle(40, 49, 126, 23)); + jPanel1.add(findNext, null); + jPanel1.add(findAll, null); + jPanel1.add(createNewGroup, null); + this.add(caseSensitive); + this.add(textfield, null); + this.add(jLabel1, null); + this.add(jPanel1, null); + } + + void textfield_keyTyped(KeyEvent e) { + findNext.setEnabled(true); + } + +} diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index 0e340dc..0811f82 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,337 +1,205 @@ -/* - * 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); - - 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() < 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() < 1) || - ((selection.getEndRes() - selection.getStartRes()) < 2)) - { - selection = null; - } - } - - while (!found && (seqIndex < end)) - { - seq = (Sequence) av.alignment.getSequenceAt(seqIndex); - - if ((selection != null) && !selection.getSequences(null).contains(seq)) - { - seqIndex++; - resIndex = 0; - - continue; - } - - item = seq.getSequenceAsString(); - 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 + * 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); + + 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(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); + } + + } +}