X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=8fe4d5d21fefcba6d8584132d30fdb5d2e672b6d;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=25b924a7704e753f24cc0474152644db497af61e;hpb=7c94a4aa0eab3272df0fdae2efcedf50f050296c;p=jalview.git diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java old mode 100755 new mode 100644 index 25b924a..8fe4d5d --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -1,22 +1,21 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * 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.*; @@ -25,25 +24,29 @@ import java.awt.*; import java.awt.event.*; import jalview.datamodel.*; -import java.awt.Rectangle; +import jalview.util.MessageManager; public class Finder extends Panel implements ActionListener { AlignViewport av; + AlignmentPanel ap; + Frame frame; SearchResults searchResults; int seqIndex = 0; - int resIndex = 0; + + int resIndex = -1; + public Finder(final AlignmentPanel ap) { try { jbInit(); - } - catch (Exception e) + + } catch (Exception e) { e.printStackTrace(); } @@ -52,7 +55,7 @@ public class Finder extends Panel implements ActionListener this.ap = ap; frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.find"), 340, 120); frame.repaint(); frame.addWindowListener(new WindowAdapter() { @@ -61,167 +64,200 @@ public class Finder extends Panel implements ActionListener 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 = 0; + resIndex = -1; seqIndex = 0; doSearch(true); } - else if(evt.getSource() == createNewGroup) + else if (evt.getSource() == createNewGroup) + { createNewGroup_actionPerformed(); + } } - public void createNewGroup_actionPerformed() { + SequenceI[] seqs = new SequenceI[searchResults.getSize()]; + SequenceFeature[] features = new SequenceFeature[searchResults + .getSize()]; - 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 ++ ) + 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"); + seqs[i] = searchResults.getResultSequence(i); - ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature( - featureName, new Color(60,160,115)); - seq.addSequenceFeature(sf); + features[i] = new SequenceFeature(textfield.getText().trim(), + "Search Results", null, searchResults.getResultStart(i), + searchResults.getResultEnd(i), "Search Results"); } - ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures(); - ap.alignFrame.sequenceFeatures.setState(true); - av.showSequenceFeatures(true); - ap.highlightSearchResults(null); + 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(jalview.bin.JalviewLite.currentAlignFrame!=null) + if (ap.av.applet.currentAlignFrame != null) { - ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel; + 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); + 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(); + seqIndex = finder.getSeqIndex(); + resIndex = finder.getResIndex(); searchResults = finder.getSearchResults(); Vector idMatch = finder.getIdMatch(); - - if (searchResults.getSize() == 0 && idMatch.size() > 0) + 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; - resIndex = 0; - seqIndex = 0; } - // if allResults is null, this effectively switches displaySearch flag in seqCanvas + // if allResults is null, this effectively switches displaySearch flag in + // seqCanvas ap.highlightSearchResults(searchResults); - - if (findAll) + // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or + // 'SelectRegion' selection + if (!haveResults) { - String message = (searchResults==null?0 : searchResults.getSize()) + " matches found."; - ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message); + ap.alignFrame.statusBar.setText(MessageManager.getString("label.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(MessageManager.formatMessage("label.search_results", new String[] {searchString, message})); + } + else + { + // TODO: indicate sequence and matching position in status bar + ap.alignFrame.statusBar.setText(MessageManager.formatMessage("label.found_match_for", new String[]{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"); + private void jbInit() throws Exception + { + jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); + jLabel1.setText(MessageManager.getString("action.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(MessageManager.getString("action.find_all")); + findAll.addActionListener(this); + findNext.setEnabled(false); + findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); + findNext.setLabel(MessageManager.getString("action.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(MessageManager.getString("label.new_feature")); + createNewGroup.addActionListener(this); + caseSensitive.setLabel(MessageManager.getString("label.match_case")); caseSensitive.setBounds(new Rectangle(40, 49, 126, 23)); jPanel1.add(findNext, null); - jPanel1.add(findAll, null); - jPanel1.add(createNewGroup, null); + jPanel1.add(findAll, null); + jPanel1.add(createNewGroup, null); this.add(caseSensitive); this.add(textfield, null); - this.add(jLabel1, null); - this.add(jPanel1, null); + this.add(jLabel1, null); + this.add(jPanel1, null); } - void textfield_keyTyped(KeyEvent e) { - findNext.setEnabled(true); + void textfield_keyTyped(KeyEvent e) + { + findNext.setEnabled(true); } }