Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SplitFrame	35	68	25	0.00%	Show methods

Class SplitFrame

Class SplitFrame	Line # 35	Total Statements 68	Complexity 25	TOTAL Coverage 0.00%
SplitFrame(AlignFrame,AlignFrame)   SplitFrame(AlignFrame,AlignFrame)	4949	4.04	3.03	0.0 0.00%
init() : void   init() : void	6363	16.016	6.06	0.0 0.00%
constructSplit() : void   constructSplit() : void	101101	8.08	1.01	0.0 0.00%
adjustLayout() : void   adjustLayout() : void	118118	16.016	8.08	0.0 0.00%
addAlignFrameComponents(AlignFrame,Panel) : void   addAlignFrameComponents(AlignFrame,Panel) : void	167167	6.06	1.01	0.0 0.00%
addToDisplay(boolean,JalviewLite) : void   addToDisplay(boolean,JalviewLite) : void	185185	6.06	1.01	0.0 0.00%
createSplitFrameWindow(boolean,JalviewLite) : void   createSplitFrameWindow(boolean,JalviewLite) : void	202202	7.07	2.02	0.0 0.00%
getComplement(AlignFrame) : AlignFrame   getComplement(AlignFrame) : AlignFrame	226226	5.05	3.03	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.appletgui;
22
23		import jalview.api.AlignmentViewPanel;
24		import jalview.api.ViewStyleI;
25		import jalview.bin.JalviewLite;
26		import jalview.datamodel.AlignmentI;
27		import jalview.structure.StructureSelectionManager;
28		import jalview.viewmodel.AlignmentViewport;
29
30		import java.awt.BorderLayout;
31		import java.awt.Dimension;
32		import java.awt.GridLayout;
33		import java.awt.Panel;
34
		0% Uncovered Elements: 108 (108) Complexity: 25 Complexity Density: 0.37
35		public class SplitFrame extends EmbmenuFrame
36		{
37		private static final long serialVersionUID = 1L;
38
39		private AlignFrame topFrame;
40
41		private AlignFrame bottomFrame;
42
43		private Panel outermost;
44
45		/**
46		* Constructs the split frame placing cdna in the top half. No 'alignment' is
47		* performed here, this should be done by the calling client if wanted.
48		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
49	0	public SplitFrame(AlignFrame af1, AlignFrame af2)...
50		{
51	0	boolean af1IsNucleotide = af1.viewport.getAlignment().isNucleotide();
52	0	topFrame = af1IsNucleotide ? af1 : af2;
53	0	bottomFrame = topFrame == af1 ? af2 : af1;
54	0	init();
55		}
56
57		/**
58		* Creates a Panel containing two Panels, and adds the first and second
59		* AlignFrame's components to each. At this stage we have not yet committed to
60		* whether the enclosing panel will be added to this frame, for display as a
61		* separate frame, or added to the applet (embedded mode).
62		*/
		0% Uncovered Elements: 26 (26) Complexity: 6 Complexity Density: 0.38
63	0	public void init()...
64		{
65	0	constructSplit();
66
67		/*
68		* Try to make and add dna/protein sequence mappings
69		*/
70	0	final AlignViewport topViewport = topFrame.viewport;
71	0	final AlignViewport bottomViewport = bottomFrame.viewport;
72	0	final AlignmentI topAlignment = topViewport.getAlignment();
73	0	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
74	0	AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
75	0	: (bottomAlignment.isNucleotide() ? bottomViewport : null);
76	0	AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
77	0	: (!bottomAlignment.isNucleotide() ? bottomViewport : null);
78
79	0	final StructureSelectionManager ssm = StructureSelectionManager
80		.getStructureSelectionManager(topViewport.applet);
81	0	ssm.registerMappings(protein.getAlignment().getCodonFrames());
82	0	topViewport.setCodingComplement(bottomViewport);
83	0	ssm.addCommandListener(cdna);
84	0	ssm.addCommandListener(protein);
85
86		/*
87		* Compute cDNA consensus on protein alignment
88		*/
89	0	protein.initComplementConsensus();
90	0	AlignmentViewPanel ap = topAlignment.isNucleotide()
91		? bottomFrame.alignPanel
92		: topFrame.alignPanel;
93	0	protein.updateConsensus(ap);
94
95	0	adjustLayout();
96		}
97
98		/**
99		*
100		*/
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
101	0	protected void constructSplit()...
102		{
103	0	setMenuBar(null);
104	0	outermost = new Panel(new GridLayout(2, 1));
105
106	0	Panel topPanel = new Panel();
107	0	Panel bottomPanel = new Panel();
108	0	outermost.add(topPanel);
109	0	outermost.add(bottomPanel);
110
111	0	addAlignFrameComponents(topFrame, topPanel);
112	0	addAlignFrameComponents(bottomFrame, bottomPanel);
113		}
114
115		/**
116		* Make any adjustments to the layout
117		*/
		0% Uncovered Elements: 28 (28) Complexity: 8 Complexity Density: 0.5
118	0	protected void adjustLayout()...
119		{
120	0	AlignmentViewport cdna = topFrame.getAlignViewport().getAlignment()
121		.isNucleotide() ? topFrame.viewport : bottomFrame.viewport;
122	0	AlignmentViewport protein = cdna == topFrame.viewport
123		? bottomFrame.viewport
124		: topFrame.viewport;
125
126		/*
127		* Ensure sequence ids are the same width for good alignment.
128		*/
129		// TODO should do this via av.getViewStyle/setViewStyle
130		// however at present av.viewStyle is not set in IdPanel.fontChanged
131	0	int w1 = topFrame.alignPanel.idPanel.idCanvas.getWidth();
132	0	int w2 = bottomFrame.alignPanel.idPanel.idCanvas.getWidth();
133	0	int w3 = Math.max(w1, w2);
134	0	if (w1 != w3)
135		{
136	0	Dimension d = topFrame.alignPanel.idPanel.idCanvas.getSize();
137	0	topFrame.alignPanel.idPanel.idCanvas
138		.setSize(new Dimension(w3, d.height));
139		}
140	0	if (w2 != w3)
141		{
142	0	Dimension d = bottomFrame.alignPanel.idPanel.idCanvas.getSize();
143	0	bottomFrame.alignPanel.idPanel.idCanvas
144		.setSize(new Dimension(w3, d.height));
145		}
146
147		/*
148		* Scale protein to either 1 or 3 times character width of dna
149		*/
150	0	if (protein != null && cdna != null)
151		{
152	0	ViewStyleI vs = protein.getViewStyle();
153	0	int scale = vs.isScaleProteinAsCdna() ? 3 : 1;
154	0	vs.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
155	0	protein.setViewStyle(vs);
156		}
157		}
158
159		/**
160		* Add the menu bar, alignment panel and status bar from the AlignFrame to the
161		* panel. The menu bar is a panel 'reconstructed' from the AlignFrame's frame
162		* menu bar. This allows each half of the SplitFrame to have its own menu bar.
163		*
164		* @param af
165		* @param panel
166		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
167	0	private void addAlignFrameComponents(AlignFrame af, Panel panel)...
168		{
169	0	panel.setLayout(new BorderLayout());
170	0	Panel menuPanel = af.makeEmbeddedPopupMenu(af.getMenuBar(), true,
171		false);
172	0	panel.add(menuPanel, BorderLayout.NORTH);
173	0	panel.add(af.statusBar, BorderLayout.SOUTH);
174	0	panel.add(af.alignPanel, BorderLayout.CENTER);
175
176	0	af.setSplitFrame(this);
177		}
178
179		/**
180		* Display the content panel either as a new frame or embedded in the applet.
181		*
182		* @param embedded
183		* @param applet
184		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
185	0	public void addToDisplay(boolean embedded, JalviewLite applet)...
186		{
187	0	createSplitFrameWindow(embedded, applet);
188	0	validate();
189	0	topFrame.alignPanel.adjustAnnotationHeight();
190	0	topFrame.alignPanel.paintAlignment(true, true);
191	0	bottomFrame.alignPanel.adjustAnnotationHeight();
192	0	bottomFrame.alignPanel.paintAlignment(true, true);
193		}
194
195		/**
196		* Either show the content panel in this frame as a new frame, or (if
197		* embed=true) add it to the applet container instead.
198		*
199		* @param embed
200		* @param applet
201		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
202	0	protected void createSplitFrameWindow(boolean embed, JalviewLite applet)...
203		{
204	0	if (embed)
205		{
206	0	applet.add(outermost);
207	0	applet.validate();
208		}
209		else
210		{
211	0	this.add(outermost);
212	0	int width = Math.max(topFrame.frameWidth, bottomFrame.frameWidth);
213	0	int height = topFrame.frameHeight + bottomFrame.frameHeight;
214	0	jalview.bin.JalviewLite.addFrame(this, this.getTitle(), width,
215		height);
216		}
217		}
218
219		/**
220		* Returns the contained AlignFrame complementary to the one given (or null if
221		* no match to top or bottom component).
222		*
223		* @param af
224		* @return
225		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
226	0	public AlignFrame getComplement(AlignFrame af)...
227		{
228	0	if (topFrame == af)
229		{
230	0	return bottomFrame;
231		}
232	0	else if (bottomFrame == af)
233		{
234	0	return topFrame;
235		}
236	0	return null;
237		}
238		}