Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignExportOptions	44	62	18	0.055%	Show methods

Class AlignExportOptions

Class AlignExportOptions	Line # 44	Total Statements 62	Complexity 18	TOTAL Coverage 0.055%
isNeeded(AlignViewportI,FileFormatI) : boolean   isNeeded(AlignViewportI,FileFormatI) : boolean	7272	3.03	4.04	0.6 0.660%
AlignExportOptions(AlignViewportI,FileFormatI,AlignExportSettingsI)   AlignExportOptions(AlignViewportI,FileFormatI,AlignExportSettingsI)	9393	4.04	1.01	0.0 0.00%
showDialog() : void   showDialog() : void	106106	2.02	1.01	0.0 0.00%
setResponseAction(Object,Runnable) : void   setResponseAction(Object,Runnable) : void	122122	1.01	1.01	0.0 0.00%
checkAllAction(boolean) : void   checkAllAction(boolean) : void	133133	15.015	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	168168	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	179179	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	190190	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	201201	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	211211	1.01	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	227227	1.01	1.01	0.0 0.00%
init(boolean,boolean) : void   init(boolean,boolean) : void	162162	31.031	4.04	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.05	jalview.io.BackupFilesTest.backupsEnabledNoRollMaxTestjalview.io.BackupFilesTest.backupsEnabledNoRollMaxTest	1PASS
	0.05	jalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTestjalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTest	1PASS
	0.05	jalview.io.BackupFilesTest.noBackupsEnabledTestjalview.io.BackupFilesTest.noBackupsEnabledTest	1PASS
	0.05	jalview.io.BackupFilesTest.backupsEnabledRollMaxTestjalview.io.BackupFilesTest.backupsEnabledRollMaxTest	1PASS

 

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 jalview.api.AlignExportSettingsI;
24		import jalview.api.AlignViewportI;
25		import jalview.io.FileFormatI;
26		import jalview.util.MessageManager;
27
28		import java.awt.BorderLayout;
29		import java.awt.FlowLayout;
30		import java.awt.event.ActionEvent;
31		import java.awt.event.ActionListener;
32		import java.awt.event.ItemEvent;
33		import java.awt.event.ItemListener;
34
35		import javax.swing.JCheckBox;
36		import javax.swing.JPanel;
37
38		/**
39		* A dialog that allows the user to specify whether to include hidden columns or
40		* sequences in an alignment export, and possibly features, annotations and
41		* groups, if applicable to the output file format
42		*/
43		@SuppressWarnings("serial")
		5% Uncovered Elements: 76 (80) Complexity: 18 Complexity Density: 0.29
44		public class AlignExportOptions extends JPanel
45		{
46		protected JCheckBox chkHiddenSeqs = new JCheckBox();
47
48		protected JCheckBox chkHiddenCols = new JCheckBox();
49
50		protected JCheckBox chkExportAnnots = new JCheckBox();
51
52		protected JCheckBox chkExportFeats = new JCheckBox();
53
54		protected JCheckBox chkExportGrps = new JCheckBox();
55
56		protected AlignExportSettingsI settings;
57
58		private boolean isComplexAlignFile;
59
60		JvOptionPane dialog;
61
62		/**
63		* A convenience method that answers true if this dialog should be shown -
64		* that is, if the alignment has any hidden rows or columns, or if the file
65		* format is one that can (optionally) represent annotations, features or
66		* groups data - else false
67		*
68		* @param viewport
69		* @param format
70		* @return
71		*/
		60% Uncovered Elements: 2 (5) Complexity: 4 Complexity Density: 1.33
72	43	public static boolean isNeeded(AlignViewportI viewport,...
73		FileFormatI format)
74		{
75	43	if (viewport.hasHiddenColumns() || viewport.hasHiddenRows()
76		|| format.isComplexAlignFile())
77		{
78	0	return true;
79		}
80	43	return false;
81		}
82
83		/**
84		* Constructor that passes in an initial set of export options. User choices
85		* in the dialog should update this object, and the <em>same</em> object
86		* should be used in any action handler set by calling
87		* <code>setResponseAction</code>.
88		*
89		* @param viewport
90		* @param format
91		* @param defaults
92		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
93	0	public AlignExportOptions(AlignViewportI viewport, FileFormatI format,...
94		AlignExportSettingsI defaults)
95		{
96	0	this.settings = defaults;
97	0	this.isComplexAlignFile = format.isComplexAlignFile();
98	0	init(viewport.hasHiddenRows(), viewport.hasHiddenColumns());
99	0	dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
100		}
101
102		/**
103		* Shows the dialog, and runs any registered response actions that correspond
104		* to user choices
105		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
106	0	public void showDialog()...
107		{
108	0	Object[] options = new Object[] { MessageManager.getString("action.ok"),
109		MessageManager.getString("action.cancel") };
110	0	dialog.showInternalDialog(this,
111		MessageManager.getString("label.export_settings"),
112		JvOptionPane.OK_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE,
113		null, options, MessageManager.getString("action.ok"));
114		}
115
116		/**
117		* Registers a Runnable action to be performed for a particular user response
118		* in the dialog
119		*
120		* @param action
121		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
122	0	public void setResponseAction(Object response, Runnable action)...
123		{
124	0	dialog.setResponseHandler(response, action);
125		}
126
127		/**
128		* Selects/deselects all enabled and shown options on 'Check all' selected or
129		* deselected
130		*
131		* @param isSelected
132		*/
		0% Uncovered Elements: 15 (15) Complexity: 1 Complexity Density: 0.07
133	0	void checkAllAction(boolean isSelected)...
134		{
135	0	boolean set = chkHiddenSeqs.isEnabled() && isSelected;
136	0	chkHiddenSeqs.setSelected(set);
137	0	settings.setExportHiddenSequences(set);
138
139	0	set = chkHiddenCols.isEnabled() && isSelected;
140	0	chkHiddenCols.setSelected(set);
141	0	settings.setExportHiddenColumns(set);
142
143	0	set = isComplexAlignFile && chkExportAnnots.isEnabled() && isSelected;
144	0	chkExportAnnots.setSelected(set);
145	0	settings.setExportAnnotations(set);
146
147	0	set = isComplexAlignFile && chkExportFeats.isEnabled() && isSelected;
148	0	chkExportFeats.setSelected(set);
149	0	settings.setExportFeatures(set);
150
151	0	set = isComplexAlignFile && chkExportGrps.isEnabled() && isSelected;
152	0	chkExportGrps.setSelected(set);
153	0	settings.setExportGroups(set);
154		}
155
156		/**
157		* Initialises the components of the display
158		*
159		* @param hasHiddenSeq
160		* @param hasHiddenCols
161		*/
		0% Uncovered Elements: 35 (35) Complexity: 4 Complexity Density: 0.13
162	0	private void init(boolean hasHiddenSeq, boolean hasHiddenCols)...
163		{
164	0	chkHiddenSeqs.setText(
165		MessageManager.getString("action.export_hidden_sequences"));
166	0	chkHiddenSeqs.addActionListener(new ActionListener()
167		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
168	0	@Override...
169		public void actionPerformed(ActionEvent e)
170		{
171	0	settings.setExportHiddenSequences(chkHiddenSeqs.isSelected());
172		}
173		});
174
175	0	chkHiddenCols.setText(
176		MessageManager.getString("action.export_hidden_columns"));
177	0	chkHiddenCols.addActionListener(new ActionListener()
178		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
179	0	@Override...
180		public void actionPerformed(ActionEvent e)
181		{
182	0	settings.setExportHiddenColumns(chkHiddenCols.isSelected());
183		}
184		});
185
186	0	chkExportAnnots
187		.setText(MessageManager.getString("action.export_annotations"));
188	0	chkExportAnnots.addActionListener(new ActionListener()
189		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
190	0	@Override...
191		public void actionPerformed(ActionEvent e)
192		{
193	0	settings.setExportAnnotations(chkExportAnnots.isSelected());
194		}
195		});
196
197	0	chkExportFeats
198		.setText(MessageManager.getString("action.export_features"));
199	0	chkExportFeats.addActionListener(new ActionListener()
200		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
201	0	@Override...
202		public void actionPerformed(ActionEvent e)
203		{
204	0	settings.setExportFeatures(chkExportFeats.isSelected());
205		}
206		});
207
208	0	chkExportGrps.setText(MessageManager.getString("action.export_groups"));
209	0	chkExportGrps.addActionListener(new ActionListener()
210		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
211	0	@Override...
212		public void actionPerformed(ActionEvent e)
213		{
214	0	settings.setExportGroups(chkExportGrps.isSelected());
215		}
216		});
217
218	0	JCheckBox chkAll = new JCheckBox(
219		MessageManager.getString("action.select_all"));
220
221	0	JPanel hiddenRegionConfPanel = new JPanel(new BorderLayout());
222	0	JPanel complexExportPanel = new JPanel(new BorderLayout());
223	0	this.setLayout(new BorderLayout());
224
225	0	chkAll.addItemListener(new ItemListener()
226		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
227	0	@Override...
228		public void itemStateChanged(ItemEvent e)
229		{
230	0	checkAllAction(chkAll.isSelected());
231		}
232		});
233
234	0	hiddenRegionConfPanel.add(chkHiddenSeqs, BorderLayout.CENTER);
235	0	hiddenRegionConfPanel.add(chkHiddenCols, BorderLayout.SOUTH);
236	0	chkHiddenSeqs.setEnabled(hasHiddenSeq);
237	0	chkHiddenCols.setEnabled(hasHiddenCols);
238
239	0	complexExportPanel.add(chkExportAnnots, BorderLayout.NORTH);
240	0	complexExportPanel.add(chkExportFeats, BorderLayout.CENTER);
241	0	complexExportPanel.add(chkExportGrps, BorderLayout.SOUTH);
242
243	0	JPanel actionPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
244	0	actionPanel.add(chkAll);
245
246	0	JPanel optionsPanel = new JPanel();
247	0	if (this.isComplexAlignFile)
248		{
249	0	optionsPanel.add(complexExportPanel);
250		}
251
252	0	if (hasHiddenSeq || hasHiddenCols)
253		{
254	0	optionsPanel.add(hiddenRegionConfPanel);
255		}
256
257	0	add(optionsPanel, BorderLayout.NORTH);
258	0	add(actionPanel, BorderLayout.SOUTH);
259		}
260		}