X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=5f697ea32e93296d012de68eb2b8c7064413cb5d;hb=fd026dead85b733e64fdc7c2e6c88d1adc10626a;hp=e1236c9c65918f914c3e364e611da8f9d292668c;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index e1236c9..5f697ea 100755 --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -1,22 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . */ - package jalview.appletgui; import java.util.*; @@ -26,24 +24,27 @@ import java.awt.event.*; import jalview.datamodel.*; -public class Finder - extends Panel implements ActionListener +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(); } @@ -61,6 +62,7 @@ public class Finder ap.highlightSearchResults(null); } }); + textfield.requestFocus(); } public void actionPerformed(ActionEvent evt) @@ -77,7 +79,7 @@ public class Finder else if (evt.getSource() == findAll) { - resIndex = 0; + resIndex = -1; seqIndex = 0; doSearch(true); } @@ -89,55 +91,38 @@ public class Finder 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; - } + SequenceI[] seqs = new SequenceI[searchResults.getSize()]; + SequenceFeature[] features = new SequenceFeature[searchResults + .getSize()]; 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); @@ -148,48 +133,82 @@ public class Finder 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("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 + private void jbInit() throws Exception { jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); jLabel1.setText("Find");