Coverage Report
File AlignExportOptions.java
Coverage histogram
56% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignExportOptions | 45 | 60 | 15 |
Contributing tests
This file is covered by 17 tests.
.
Source view
| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.gui; | |
| 22 | ||
| 23 | import java.awt.BorderLayout; | |
| 24 | import java.awt.FlowLayout; | |
| 25 | import java.awt.event.ActionEvent; | |
| 26 | import java.awt.event.ActionListener; | |
| 27 | import java.awt.event.ItemEvent; | |
| 28 | import java.awt.event.ItemListener; | |
| 29 | ||
| 30 | import javax.swing.JCheckBox; | |
| 31 | import javax.swing.JPanel; | |
| 32 | ||
| 33 | import jalview.api.AlignExportSettingsI; | |
| 34 | import jalview.api.AlignViewportI; | |
| 35 | import jalview.bin.Jalview; | |
| 36 | import jalview.io.FileFormatI; | |
| 37 | import jalview.util.MessageManager; | |
| 38 | ||
| 39 | /** | |
| 40 | * A dialog that allows the user to specify whether to include hidden columns or | |
| 41 | * sequences in an alignment export, and possibly features, annotations and | |
| 42 | * groups, if applicable to the output file format | |
| 43 | */ | |
| 44 | @SuppressWarnings("serial") | |
| 45 | public class AlignExportOptions extends JPanel | |
| 46 | { | |
| 47 | protected JCheckBox chkHiddenSeqs = new JCheckBox(); | |
| 48 | ||
| 49 | protected JCheckBox chkHiddenCols = new JCheckBox(); | |
| 50 | ||
| 51 | protected JCheckBox chkExportAnnots = new JCheckBox(); | |
| 52 | ||
| 53 | protected JCheckBox chkExportFeats = new JCheckBox(); | |
| 54 | ||
| 55 | protected JCheckBox chkExportGrps = new JCheckBox(); | |
| 56 | ||
| 57 | protected AlignExportSettingsI settings; | |
| 58 | ||
| 59 | private boolean isComplexAlignFile; | |
| 60 | ||
| 61 | JvOptionPane dialog; | |
| 62 | ||
| 63 | /** | |
| 64 | * A convenience method that answers true if this dialog should be shown - | |
| 65 | * that is, if the alignment has any hidden rows or columns, or if the file | |
| 66 | * format is one that can (optionally) represent annotations, features or | |
| 67 | * groups data - else false | |
| 68 | * | |
| 69 | * @param viewport | |
| 70 | * @param format | |
| 71 | * @return | |
| 72 | */ | |
| 73 | 120 |  public static boolean isNeeded(AlignViewportI viewport, |
| 74 | FileFormatI format) | |
| 75 | { | |
| 76 | 120 | return !Jalview.getInstance().isHeadlessMode() |
| 77 | && (viewport.hasHiddenColumns() || viewport.hasHiddenRows() | |
| 78 | || format.isComplexAlignFile()); | |
| 79 | } | |
| 80 | ||
| 81 | /** | |
| 82 | * Constructor that passes in an initial set of export options. User choices | |
| 83 | * in the dialog should update this object, and the <em>same</em> object | |
| 84 | * should be used in any action handler set by calling | |
| 85 | * <code>setResponseAction</code>. | |
| 86 | * | |
| 87 | * @param viewport | |
| 88 | * @param format | |
| 89 | * @param defaults | |
| 90 | */ | |
| 91 | 0 | public AlignExportOptions(AlignViewportI viewport, FileFormatI format, |
| 92 | AlignExportSettingsI defaults) | |
| 93 | { | |
| 94 | 0 | this.settings = defaults; |
| 95 | 0 | this.isComplexAlignFile = format.isComplexAlignFile(); |
| 96 | 0 | init(viewport.hasHiddenRows(), viewport.hasHiddenColumns()); |
| 97 | 0 | dialog = JvOptionPane.newOptionDialog(Desktop.desktop); |
| 98 | } | |
| 99 | ||
| 100 | /** | |
| 101 | * Shows the dialog, and runs any registered response actions that correspond | |
| 102 | * to user choices | |
| 103 | */ | |
| 104 | 0 | public void showDialog() |
| 105 | { | |
| 106 | 0 | Object[] options = new Object[] { MessageManager.getString("action.ok"), |
| 107 | MessageManager.getString("action.cancel") }; | |
| 108 | 0 | dialog.showInternalDialog(this, |
| 109 | MessageManager.getString("label.export_settings"), | |
| 110 | JvOptionPane.OK_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, null, | |
| 111 | options, MessageManager.getString("action.ok")); | |
| 112 | } | |
| 113 | ||
| 114 | /** | |
| 115 | * Registers a Runnable action to be performed for a particular user response | |
| 116 | * in the dialog | |
| 117 | * | |
| 118 | * @param action | |
| 119 | */ | |
| 120 | 0 | public void setResponseAction(Object response, Runnable action) |
| 121 | { | |
| 122 | 0 | dialog.setResponseHandler(response, action); |
| 123 | } | |
| 124 | ||
| 125 | /** | |
| 126 | * Selects/deselects all enabled and shown options on 'Check all' selected or | |
| 127 | * deselected | |
| 128 | * | |
| 129 | * @param isSelected | |
| 130 | */ | |
| 131 | 0 | void checkAllAction(boolean isSelected) |
| 132 | { | |
| 133 | 0 | boolean set = chkHiddenSeqs.isEnabled() && isSelected; |
| 134 | 0 | chkHiddenSeqs.setSelected(set); |
| 135 | 0 | settings.setExportHiddenSequences(set); |
| 136 | ||
| 137 | 0 | set = chkHiddenCols.isEnabled() && isSelected; |
| 138 | 0 | chkHiddenCols.setSelected(set); |
| 139 | 0 | settings.setExportHiddenColumns(set); |
| 140 | ||
| 141 | 0 | set = isComplexAlignFile && chkExportAnnots.isEnabled() && isSelected; |
| 142 | 0 | chkExportAnnots.setSelected(set); |
| 143 | 0 | settings.setExportAnnotations(set); |
| 144 | ||
| 145 | 0 | set = isComplexAlignFile && chkExportFeats.isEnabled() && isSelected; |
| 146 | 0 | chkExportFeats.setSelected(set); |
| 147 | 0 | settings.setExportFeatures(set); |
| 148 | ||
| 149 | 0 | set = isComplexAlignFile && chkExportGrps.isEnabled() && isSelected; |
| 150 | 0 | chkExportGrps.setSelected(set); |
| 151 | 0 | settings.setExportGroups(set); |
| 152 | } | |
| 153 | ||
| 154 | /** | |
| 155 | * Initialises the components of the display | |
| 156 | * | |
| 157 | * @param hasHiddenSeq | |
| 158 | * @param hasHiddenCols | |
| 159 | */ | |
| 160 | 0 | private void init(boolean hasHiddenSeq, boolean hasHiddenCols) |
| 161 | { | |
| 162 | 0 | chkHiddenSeqs.setText( |
| 163 | MessageManager.getString("action.export_hidden_sequences")); | |
| 164 | 0 | chkHiddenSeqs.addActionListener(new ActionListener() |
| 165 | { | |
| 166 | 0 | @Override |
| 167 | public void actionPerformed(ActionEvent e) | |
| 168 | { | |
| 169 | 0 | settings.setExportHiddenSequences(chkHiddenSeqs.isSelected()); |
| 170 | } | |
| 171 | }); | |
| 172 | ||
| 173 | 0 | chkHiddenCols.setText( |
| 174 | MessageManager.getString("action.export_hidden_columns")); | |
| 175 | 0 | chkHiddenCols.addActionListener(new ActionListener() |
| 176 | { | |
| 177 | 0 | @Override |
| 178 | public void actionPerformed(ActionEvent e) | |
| 179 | { | |
| 180 | 0 | settings.setExportHiddenColumns(chkHiddenCols.isSelected()); |
| 181 | } | |
| 182 | }); | |
| 183 | ||
| 184 | 0 | chkExportAnnots |
| 185 | .setText(MessageManager.getString("action.export_annotations")); | |
| 186 | 0 | chkExportAnnots.addActionListener(new ActionListener() |
| 187 | { | |
| 188 | 0 | @Override |
| 189 | public void actionPerformed(ActionEvent e) | |
| 190 | { | |
| 191 | 0 | settings.setExportAnnotations(chkExportAnnots.isSelected()); |
| 192 | } | |
| 193 | }); | |
| 194 | ||
| 195 | 0 | chkExportFeats |
| 196 | .setText(MessageManager.getString("action.export_features")); | |
| 197 | 0 | chkExportFeats.addActionListener(new ActionListener() |
| 198 | { | |
| 199 | 0 | @Override |
| 200 | public void actionPerformed(ActionEvent e) | |
| 201 | { | |
| 202 | 0 | settings.setExportFeatures(chkExportFeats.isSelected()); |
| 203 | } | |
| 204 | }); | |
| 205 | ||
| 206 | 0 | chkExportGrps.setText(MessageManager.getString("action.export_groups")); |
| 207 | 0 | chkExportGrps.addActionListener(new ActionListener() |
| 208 | { | |
| 209 | 0 | @Override |
| 210 | public void actionPerformed(ActionEvent e) | |
| 211 | { | |
| 212 | 0 | settings.setExportGroups(chkExportGrps.isSelected()); |
| 213 | } | |
| 214 | }); | |
| 215 | ||
| 216 | 0 | JCheckBox chkAll = new JCheckBox( |
| 217 | MessageManager.getString("action.select_all")); | |
| 218 | ||
| 219 | 0 | JPanel hiddenRegionConfPanel = new JPanel(new BorderLayout()); |
| 220 | 0 | JPanel complexExportPanel = new JPanel(new BorderLayout()); |
| 221 | 0 | this.setLayout(new BorderLayout()); |
| 222 | ||
| 223 | 0 | chkAll.addItemListener(new ItemListener() |
| 224 | { | |
| 225 | 0 | @Override |
| 226 | public void itemStateChanged(ItemEvent e) | |
| 227 | { | |
| 228 | 0 | checkAllAction(chkAll.isSelected()); |
| 229 | } | |
| 230 | }); | |
| 231 | ||
| 232 | 0 | hiddenRegionConfPanel.add(chkHiddenSeqs, BorderLayout.CENTER); |
| 233 | 0 | hiddenRegionConfPanel.add(chkHiddenCols, BorderLayout.SOUTH); |
| 234 | 0 | chkHiddenSeqs.setEnabled(hasHiddenSeq); |
| 235 | 0 | chkHiddenCols.setEnabled(hasHiddenCols); |
| 236 | ||
| 237 | 0 | complexExportPanel.add(chkExportAnnots, BorderLayout.NORTH); |
| 238 | 0 | complexExportPanel.add(chkExportFeats, BorderLayout.CENTER); |
| 239 | 0 | complexExportPanel.add(chkExportGrps, BorderLayout.SOUTH); |
| 240 | ||
| 241 | 0 | JPanel actionPanel = new JPanel(new FlowLayout(FlowLayout.CENTER)); |
| 242 | 0 | actionPanel.add(chkAll); |
| 243 | ||
| 244 | 0 | JPanel optionsPanel = new JPanel(); |
| 245 | 0 | if (this.isComplexAlignFile) |
| 246 | { | |
| 247 | 0 | optionsPanel.add(complexExportPanel); |
| 248 | } | |
| 249 | ||
| 250 | 0 | if (hasHiddenSeq || hasHiddenCols) |
| 251 | { | |
| 252 | 0 | optionsPanel.add(hiddenRegionConfPanel); |
| 253 | } | |
| 254 | ||
| 255 | 0 | add(optionsPanel, BorderLayout.NORTH); |
| 256 | 0 | add(actionPanel, BorderLayout.SOUTH); |
| 257 | } | |
| 258 | } |