Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignExportOptions	45	62	18	80	0.00%	Show methods

Class AlignExportOptions

Class AlignExportOptions	Line # 45	Total Statements 62	Complexity 18	Uncovered Elements 80	TOTAL Coverage 0.00%
isNeeded(AlignViewportI,FileFormatI) : boolean   isNeeded(AlignViewportI,FileFormatI) : boolean	7373	3.03	4.04	5.05	0.0 0.00%
AlignExportOptions(AlignViewportI,FileFormatI,AlignExportSettingsI)   AlignExportOptions(AlignViewportI,FileFormatI,AlignExportSettingsI)	9494	4.04	1.01	4.04	0.0 0.00%
showDialog() : void   showDialog() : void	107107	2.02	1.01	2.02	0.0 0.00%
setResponseAction(RunResponse) : void   setResponseAction(RunResponse) : void	123123	1.01	1.01	1.01	0.0 0.00%
checkAllAction(boolean) : void   checkAllAction(boolean) : void	134134	15.015	1.01	15.015	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	169169	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	180180	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	191191	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	202202	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	212212	1.01	1.01	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	228228	1.01	1.01	1.01	0.0 0.00%
init(boolean,boolean) : void   init(boolean,boolean) : void	163163	31.031	4.04	35.035	0.0 0.00%

 

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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		import jalview.util.dialogrunner.RunResponse;
28
29		import java.awt.BorderLayout;
30		import java.awt.FlowLayout;
31		import java.awt.event.ActionEvent;
32		import java.awt.event.ActionListener;
33		import java.awt.event.ItemEvent;
34		import java.awt.event.ItemListener;
35
36		import javax.swing.JCheckBox;
37		import javax.swing.JPanel;
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")
		0% Uncovered Elements: 80 (80) Complexity: 18 Complexity Density: 0.29
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		*/
		0% Uncovered Elements: 5 (5) Complexity: 4 Complexity Density: 1.33
73	0	public static boolean isNeeded(AlignViewportI viewport,...
74		FileFormatI format)
75		{
76	0	if (viewport.hasHiddenColumns() || viewport.hasHiddenRows()
77		|| format.isComplexAlignFile())
78		{
79	0	return true;
80		}
81	0	return false;
82		}
83
84		/**
85		* Constructor that passes in an initial set of export options. User choices
86		* in the dialog should update this object, and the <em>same</em> object
87		* should be used in any action handler set by calling
88		* <code>setResponseAction</code>.
89		*
90		* @param viewport
91		* @param format
92		* @param defaults
93		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
94	0	public AlignExportOptions(AlignViewportI viewport, FileFormatI format,...
95		AlignExportSettingsI defaults)
96		{
97	0	this.settings = defaults;
98	0	this.isComplexAlignFile = format.isComplexAlignFile();
99	0	init(viewport.hasHiddenRows(), viewport.hasHiddenColumns());
100	0	dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
101		}
102
103		/**
104		* Shows the dialog, and runs any registered response actions that correspond
105		* to user choices
106		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
107	0	public void showDialog()...
108		{
109	0	Object[] options = new Object[] { MessageManager.getString("action.ok"),
110		MessageManager.getString("action.cancel") };
111	0	dialog.showInternalDialog(this,
112		MessageManager.getString("label.export_settings"),
113		JvOptionPane.OK_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE,
114		null, options, MessageManager.getString("action.ok"));
115		}
116
117		/**
118		* Registers a Runnable action to be performed for a particular user response
119		* in the dialog
120		*
121		* @param action
122		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
123	0	public void setResponseAction(RunResponse action)...
124		{
125	0	dialog.response(action);
126		}
127
128		/**
129		* Selects/deselects all enabled and shown options on 'Check all' selected or
130		* deselected
131		*
132		* @param isSelected
133		*/
		0% Uncovered Elements: 15 (15) Complexity: 1 Complexity Density: 0.07
134	0	void checkAllAction(boolean isSelected)...
135		{
136	0	boolean set = chkHiddenSeqs.isEnabled() && isSelected;
137	0	chkHiddenSeqs.setSelected(set);
138	0	settings.setExportHiddenSequences(set);
139
140	0	set = chkHiddenCols.isEnabled() && isSelected;
141	0	chkHiddenCols.setSelected(set);
142	0	settings.setExportHiddenColumns(set);
143
144	0	set = isComplexAlignFile && chkExportAnnots.isEnabled() && isSelected;
145	0	chkExportAnnots.setSelected(set);
146	0	settings.setExportAnnotations(set);
147
148	0	set = isComplexAlignFile && chkExportFeats.isEnabled() && isSelected;
149	0	chkExportFeats.setSelected(set);
150	0	settings.setExportFeatures(set);
151
152	0	set = isComplexAlignFile && chkExportGrps.isEnabled() && isSelected;
153	0	chkExportGrps.setSelected(set);
154	0	settings.setExportGroups(set);
155		}
156
157		/**
158		* Initialises the components of the display
159		*
160		* @param hasHiddenSeq
161		* @param hasHiddenCols
162		*/
		0% Uncovered Elements: 35 (35) Complexity: 4 Complexity Density: 0.13
163	0	private void init(boolean hasHiddenSeq, boolean hasHiddenCols)...
164		{
165	0	chkHiddenSeqs.setText(
166		MessageManager.getString("action.export_hidden_sequences"));
167	0	chkHiddenSeqs.addActionListener(new ActionListener()
168		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
169	0	@Override...
170		public void actionPerformed(ActionEvent e)
171		{
172	0	settings.setExportHiddenSequences(chkHiddenSeqs.isSelected());
173		}
174		});
175
176	0	chkHiddenCols.setText(
177		MessageManager.getString("action.export_hidden_columns"));
178	0	chkHiddenCols.addActionListener(new ActionListener()
179		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	@Override...
181		public void actionPerformed(ActionEvent e)
182		{
183	0	settings.setExportHiddenColumns(chkHiddenCols.isSelected());
184		}
185		});
186
187	0	chkExportAnnots
188		.setText(MessageManager.getString("action.export_annotations"));
189	0	chkExportAnnots.addActionListener(new ActionListener()
190		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
191	0	@Override...
192		public void actionPerformed(ActionEvent e)
193		{
194	0	settings.setExportAnnotations(chkExportAnnots.isSelected());
195		}
196		});
197
198	0	chkExportFeats
199		.setText(MessageManager.getString("action.export_features"));
200	0	chkExportFeats.addActionListener(new ActionListener()
201		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
202	0	@Override...
203		public void actionPerformed(ActionEvent e)
204		{
205	0	settings.setExportFeatures(chkExportFeats.isSelected());
206		}
207		});
208
209	0	chkExportGrps.setText(MessageManager.getString("action.export_groups"));
210	0	chkExportGrps.addActionListener(new ActionListener()
211		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
212	0	@Override...
213		public void actionPerformed(ActionEvent e)
214		{
215	0	settings.setExportGroups(chkExportGrps.isSelected());
216		}
217		});
218
219	0	JCheckBox chkAll = new JCheckBox(
220		MessageManager.getString("action.select_all"));
221
222	0	JPanel hiddenRegionConfPanel = new JPanel(new BorderLayout());
223	0	JPanel complexExportPanel = new JPanel(new BorderLayout());
224	0	this.setLayout(new BorderLayout());
225
226	0	chkAll.addItemListener(new ItemListener()
227		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
228	0	@Override...
229		public void itemStateChanged(ItemEvent e)
230		{
231	0	checkAllAction(chkAll.isSelected());
232		}
233		});
234
235	0	hiddenRegionConfPanel.add(chkHiddenSeqs, BorderLayout.CENTER);
236	0	hiddenRegionConfPanel.add(chkHiddenCols, BorderLayout.SOUTH);
237	0	chkHiddenSeqs.setEnabled(hasHiddenSeq);
238	0	chkHiddenCols.setEnabled(hasHiddenCols);
239
240	0	complexExportPanel.add(chkExportAnnots, BorderLayout.NORTH);
241	0	complexExportPanel.add(chkExportFeats, BorderLayout.CENTER);
242	0	complexExportPanel.add(chkExportGrps, BorderLayout.SOUTH);
243
244	0	JPanel actionPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
245	0	actionPanel.add(chkAll);
246
247	0	JPanel optionsPanel = new JPanel();
248	0	if (this.isComplexAlignFile)
249		{
250	0	optionsPanel.add(complexExportPanel);
251		}
252
253	0	if (hasHiddenSeq || hasHiddenCols)
254		{
255	0	optionsPanel.add(hiddenRegionConfPanel);
256		}
257
258	0	add(optionsPanel, BorderLayout.NORTH);
259	0	add(actionPanel, BorderLayout.SOUTH);
260		}
261		}