X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=ee0d4a074478478911c1622b5220021e6c1588be;hb=dfc18d64376ae95cfdbf3c112825587a8891179c;hp=8fe4d5d21fefcba6d8584132d30fdb5d2e672b6d;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java index 8fe4d5d..ee0d4a0 100644 --- a/src/jalview/appletgui/Finder.java +++ b/src/jalview/appletgui/Finder.java @@ -1,40 +1,59 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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. + * 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 . + * 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.*; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.Button; +import java.awt.Checkbox; +import java.awt.Font; +import java.awt.Frame; +import java.awt.GridLayout; +import java.awt.Label; +import java.awt.Panel; +import java.awt.Rectangle; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.KeyEvent; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.util.ArrayList; +import java.util.List; +import java.util.Vector; public class Finder extends Panel implements ActionListener { - AlignViewport av; + AlignmentViewport av; AlignmentPanel ap; Frame frame; - SearchResults searchResults; + SearchResultsI searchResults; int seqIndex = 0; @@ -55,10 +74,12 @@ public class Finder extends Panel implements ActionListener this.ap = ap; frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.find"), 340, 120); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("action.find"), 340, 120); frame.repaint(); frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent evt) { ap.highlightSearchResults(null); @@ -67,6 +88,7 @@ public class Finder extends Panel implements ActionListener textfield.requestFocus(); } + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == textfield) @@ -93,24 +115,22 @@ public class Finder extends Panel implements ActionListener public void createNewGroup_actionPerformed() { - SequenceI[] seqs = new SequenceI[searchResults.getSize()]; - SequenceFeature[] features = new SequenceFeature[searchResults - .getSize()]; + List seqs = new ArrayList<>(); + List features = new ArrayList<>(); + String searchString = textfield.getText().trim(); - for (int i = 0; i < searchResults.getSize(); i++) + for (SearchResultMatchI match : searchResults.getResults()) { - seqs[i] = searchResults.getResultSequence(i); - - features[i] = new SequenceFeature(textfield.getText().trim(), - "Search Results", null, searchResults.getResultStart(i), - searchResults.getResultEnd(i), "Search Results"); + seqs.add(match.getSequence().getDatasetSequence()); + features.add(new SequenceFeature(searchString, "Search Results", + match.getStart(), match.getEnd(), "Search Results")); } if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { ap.alignFrame.sequenceFeatures.setState(true); - av.showSequenceFeatures(true); + av.setShowSequenceFeatures(true); ap.highlightSearchResults(null); } } @@ -126,6 +146,7 @@ public class Finder extends Panel implements ActionListener jalview.analysis.Finder finder = new jalview.analysis.Finder( av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex); finder.setCaseSensitive(caseSensitive.getState()); + finder.setIncludeDescription(searchDescription.getState()); finder.setFindAll(findAll); String searchString = textfield.getText(); @@ -134,28 +155,16 @@ public class Finder extends Panel implements ActionListener 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); - } + Vector idMatch = finder.getIdMatch(); + ap.idPanel.highlightSearchResults(idMatch); - if (searchResults.getSize() > 0) + if (searchResults.isEmpty()) { - haveResults = true; - createNewGroup.setEnabled(true); - + searchResults = null; } else { - searchResults = null; + createNewGroup.setEnabled(true); } // if allResults is null, this effectively switches displaySearch flag in @@ -163,9 +172,10 @@ public class Finder extends Panel implements ActionListener ap.highlightSearchResults(searchResults); // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or // 'SelectRegion' selection - if (!haveResults) + if (idMatch.isEmpty() && searchResults == null) { - ap.alignFrame.statusBar.setText(MessageManager.getString("label.finished_searching")); + ap.alignFrame.statusBar.setText( + MessageManager.getString("label.finished_searching")); resIndex = -1; seqIndex = 0; } @@ -173,8 +183,8 @@ public class Finder extends Panel implements ActionListener { if (findAll) { - String message = (idMatch.size() > 0) ? "" + idMatch.size() - + " IDs" : ""; + String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs" + : ""; if (idMatch.size() > 0 && searchResults != null && searchResults.getSize() > 0) { @@ -184,13 +194,17 @@ public class Finder extends Panel implements ActionListener { message += searchResults.getSize() + " subsequence matches."; } - ap.alignFrame.statusBar.setText(MessageManager.formatMessage("label.search_results", new String[] {searchString, message})); + 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})); + ap.alignFrame.statusBar.setText(MessageManager + .formatMessage("label.found_match_for", new String[] + { searchString })); } } } @@ -203,7 +217,7 @@ public class Finder extends Panel implements ActionListener protected Button findNext = new Button(); - Panel jPanel1 = new Panel(); + Panel actionsPanel = new Panel(); GridLayout gridLayout1 = new GridLayout(); @@ -211,6 +225,8 @@ public class Finder extends Panel implements ActionListener Checkbox caseSensitive = new Checkbox(); + Checkbox searchDescription = new Checkbox(); + private void jbInit() throws Exception { jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); @@ -219,9 +235,10 @@ public class Finder extends Panel implements ActionListener this.setLayout(null); textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); textfield.setText(""); - textfield.setBounds(new Rectangle(40, 27, 133, 21)); + textfield.setBounds(new Rectangle(40, 17, 133, 21)); textfield.addKeyListener(new java.awt.event.KeyAdapter() { + @Override public void keyTyped(KeyEvent e) { textfield_keyTyped(e); @@ -235,8 +252,8 @@ public class Finder extends Panel implements ActionListener 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); + actionsPanel.setBounds(new Rectangle(195, 5, 141, 64)); + actionsPanel.setLayout(gridLayout1); gridLayout1.setHgap(0); gridLayout1.setRows(3); gridLayout1.setVgap(2); @@ -245,14 +262,19 @@ public class Finder extends Panel implements ActionListener 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); + caseSensitive.setBounds(new Rectangle(30, 39, 126, 23)); + + searchDescription.setLabel( + MessageManager.getString("label.include_description")); + searchDescription.setBounds(new Rectangle(30, 59, 170, 23)); + actionsPanel.add(findNext, null); + actionsPanel.add(findAll, null); + actionsPanel.add(createNewGroup, null); this.add(caseSensitive); this.add(textfield, null); this.add(jLabel1, null); - this.add(jPanel1, null); + this.add(actionsPanel, null); + this.add(searchDescription); } void textfield_keyTyped(KeyEvent e)