Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignExportOptions	45	60	15	0.00%	Show methods

Class AlignExportOptions

Class AlignExportOptions	Line # 45	Total Statements 60	Complexity 15	TOTAL Coverage 0.00%
isNeeded(AlignViewportI,FileFormatI) : boolean   isNeeded(AlignViewportI,FileFormatI) : boolean	7373	1.01	1.01	0.0 0.00%
AlignExportOptions(AlignViewportI,FileFormatI,AlignExportSettingsI)   AlignExportOptions(AlignViewportI,FileFormatI,AlignExportSettingsI)	9191	4.04	1.01	0.0 0.00%
showDialog() : void   showDialog() : void	104104	2.02	1.01	0.0 0.00%
setResponseAction(Object,Runnable) : void   setResponseAction(Object,Runnable) : void	120120	1.01	1.01	0.0 0.00%
checkAllAction(boolean) : void   checkAllAction(boolean) : void	131131	15.015	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	166166	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	177177	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	188188	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	199199	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	209209	1.01	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	225225	1.01	1.01	0.0 0.00%
init(boolean,boolean) : void   init(boolean,boolean) : void	160160	31.031	4.04	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 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")
		0% Uncovered Elements: 76 (76) Complexity: 15 Complexity Density: 0.25
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: 1 (1) Complexity: 1 Complexity Density: 1
73	0	public static boolean isNeeded(AlignViewportI viewport,...
74		FileFormatI format)
75		{
76	0	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		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
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		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		*/
		0% Uncovered Elements: 15 (15) Complexity: 1 Complexity Density: 0.07
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		*/
		0% Uncovered Elements: 35 (35) Complexity: 4 Complexity Density: 0.13
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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
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		}