X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=11bf1ac22b43bb8d649d4879382b8a0834f6fc3e;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=fcca0c123d4fd9fd812d3cf0e0cdd41647500c82;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index fcca0c1..11bf1ac 100755 --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -1,374 +1,263 @@ -/* - * 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.appletgui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; - -public class Finder extends Panel -{ - AlignViewport av; - AlignmentPanel ap; - Frame frame; - SuperGroup searchGroup; - Vector 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 textfield_actionPerformed(ActionEvent e) - { - doSearch(false); - } - - public void findNext_actionPerformed(ActionEvent e) - { - doSearch(false); - } - - public void findAll_actionPerformed(ActionEvent e) - { - resIndex = 0; - seqIndex = 0; - doSearch(true); - } - - 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) - {} - } - - 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); - } - - void doSearch(boolean findAll) - { - createNewGroup.setEnabled(false); - - String searchString = textfield.getText().toUpperCase(); - - 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.addElement(Integer.toString(av.getAlignment().findIndex(seq))); - searchResults.addElement(String.valueOf(res)); - searchResults.addElement(String.valueOf(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.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.addElement(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.elementAt(resIndex).toString())) < - selection.getStartRes()) - { - continue; - } - - searchResults.addElement(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; - } - 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.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.elementAt(i).toString()); - } - - createNewGroup.setEnabled(true); - } - else - { - 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."; - System.out.println(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(); - - - 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(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - textfield_actionPerformed(e); - } - }); - findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - findAll.setLabel("Find all"); - findAll.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - findAll_actionPerformed(e); - } - }); - findNext.setEnabled(false); - findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - findNext.setLabel("Find Next"); - findNext.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - findNext_actionPerformed(e); - } - }); - 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("Create new group"); - createNewGroup.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - createNewGroup_actionPerformed(e); - } - }); - jPanel1.add(findNext, null); - jPanel1.add(findAll, null); - jPanel1.add(createNewGroup, null); - 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 (Version 2.8.0b1) + * Copyright (C) 2014 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.appletgui; + +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.datamodel.*; + +public class Finder extends Panel implements ActionListener +{ + AlignViewport av; + + AlignmentPanel ap; + + Frame frame; + + SearchResults searchResults; + + int seqIndex = 0; + + int resIndex = -1; + + 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); + } + }); + textfield.requestFocus(); + } + + public void actionPerformed(ActionEvent evt) + { + if (evt.getSource() == textfield) + { + doSearch(false); + } + + else if (evt.getSource() == findNext) + { + doSearch(false); + } + + else if (evt.getSource() == findAll) + { + resIndex = -1; + seqIndex = 0; + doSearch(true); + } + else if (evt.getSource() == createNewGroup) + { + createNewGroup_actionPerformed(); + } + } + + public void createNewGroup_actionPerformed() + { + 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); + + 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.sequenceFeatures.setState(true); + av.showSequenceFeatures(true); + ap.highlightSearchResults(null); + } + } + + void doSearch(boolean findAll) + { + if (ap.av.applet.currentAlignFrame != null) + { + ap = ap.av.applet.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(); + boolean haveResults = false; + // set or reset the GUI + if ((idMatch.size() > 0)) + { + haveResults = true; + ap.idPanel.highlightSearchResults(idMatch); + } + else + { + ap.idPanel.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) + { + ap.alignFrame.statusBar.setText("Finished searching."); + resIndex = -1; + seqIndex = 0; + } + else + { + if (findAll) + { + String message = (idMatch.size() > 0) ? "" + idMatch.size() + + " IDs" : ""; + if (idMatch.size() > 0 && searchResults != null + && searchResults.getSize() > 0) + { + message += " and "; + } + if (searchResults != null) + { + message += searchResults.getSize() + " subsequence matches."; + } + ap.alignFrame.statusBar.setText("Search results: " + searchString + + " : " + message); + + } + else + { + // TODO: indicate sequence and matching position in status bar + ap.alignFrame.statusBar.setText("Found match for " + searchString); + } + } + } + + 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); + } + +}