X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=11bf1ac22b43bb8d649d4879382b8a0834f6fc3e;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=2b742b21ba8418995add99fb07f998821a313d7d;hpb=0eca27bca577e774acd5aefb165e7c6396a1995e;p=jalview.git diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index 2b742b2..11bf1ac 100755 --- 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) 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 2.8.0b1) + * 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.*; @@ -26,25 +25,27 @@ 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(); } @@ -79,7 +80,7 @@ public class Finder else if (evt.getSource() == findAll) { - resIndex = 0; + resIndex = -1; seqIndex = 0; doSearch(true); } @@ -92,21 +93,20 @@ public class Finder public void createNewGroup_actionPerformed() { SequenceI[] seqs = new SequenceI[searchResults.getSize()]; - SequenceFeature[] features = new SequenceFeature[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"); + "Search Results", null, searchResults.getResultStart(i), + searchResults.getResultEnd(i), "Search Results"); } - if (ap.seqPanel.seqCanvas.getFeatureRenderer() - .createNewFeatures(seqs, features, ap)) + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) { ap.alignFrame.sequenceFeatures.setState(true); av.showSequenceFeatures(true); @@ -116,14 +116,14 @@ public class Finder 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); @@ -134,48 +134,84 @@ 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");