Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructureViewerModel	32	29	21	0.00%	Show methods
StructureViewerModel.StructureData	57	9	7	0.00%	Show methods

Class StructureViewerModel

Class StructureViewerModel	Line # 32	Total Statements 29	Complexity 21	TOTAL Coverage 0.00%
StructureViewerModel(int,int,int,int,boolean,boolean,boolean,String,String)   StructureViewerModel(int,int,int,int,boolean,boolean,boolean,String,String)	111111	9.09	1.01	0.0 0.00%
getX() : int   getX() : int	126126	1.01	1.01	0.0 0.00%
setX(int) : void   setX(int) : void	131131	1.01	1.01	0.0 0.00%
getY() : int   getY() : int	136136	1.01	1.01	0.0 0.00%
setY(int) : void   setY(int) : void	141141	1.01	1.01	0.0 0.00%
getWidth() : int   getWidth() : int	146146	1.01	1.01	0.0 0.00%
setWidth(int) : void   setWidth(int) : void	151151	1.01	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	156156	1.01	1.01	0.0 0.00%
setHeight(int) : void   setHeight(int) : void	161161	1.01	1.01	0.0 0.00%
isAlignWithPanel() : boolean   isAlignWithPanel() : boolean	166166	1.01	1.01	0.0 0.00%
setAlignWithPanel(boolean) : void   setAlignWithPanel(boolean) : void	171171	1.01	1.01	0.0 0.00%
isColourWithAlignPanel() : boolean   isColourWithAlignPanel() : boolean	176176	1.01	1.01	0.0 0.00%
setColourWithAlignPanel(boolean) : void   setColourWithAlignPanel(boolean) : void	181181	1.01	1.01	0.0 0.00%
isColourByViewer() : boolean   isColourByViewer() : boolean	186186	1.01	1.01	0.0 0.00%
setColourByViewer(boolean) : void   setColourByViewer(boolean) : void	191191	1.01	1.01	0.0 0.00%
getStateData() : String   getStateData() : String	196196	1.01	1.01	0.0 0.00%
setStateData(String) : void   setStateData(String) : void	201201	1.01	1.01	0.0 0.00%
getFileData() : Map<File, StructureData>   getFileData() : Map<File, StructureData>	206206	1.01	1.01	0.0 0.00%
setFileData(Map<File, StructureData>) : void   setFileData(Map<File, StructureData>) : void	211211	1.01	1.01	0.0 0.00%
getViewId() : String   getViewId() : String	216216	1.01	1.01	0.0 0.00%
getType() : String   getType() : String	221221	1.01	1.01	0.0 0.00%

 

Class StructureViewerModel.StructureData

Class StructureViewerModel.StructureData	Line # 57	Total Statements 9	Complexity 7	TOTAL Coverage 0.00%
StructureData(String,String)   StructureData(String,String)	7373	3.03	1.01	0.0 0.00%
getFilePath() : String   getFilePath() : String	8080	1.01	1.01	0.0 0.00%
setFilePath(String) : void   setFilePath(String) : void	8585	1.01	1.01	0.0 0.00%
getPdbId() : String   getPdbId() : String	9090	1.01	1.01	0.0 0.00%
setPdbId(String) : void   setPdbId(String) : void	9595	1.01	1.01	0.0 0.00%
getSeqList() : List<SequenceI>   getSeqList() : List<SequenceI>	100100	1.01	1.01	0.0 0.00%
setSeqList(List<SequenceI>) : void   setSeqList(List<SequenceI>) : void	105105	1.01	1.01	0.0 0.00%

 

Contributing 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.datamodel;
22
23		import java.io.File;
24		import java.util.ArrayList;
25		import java.util.HashMap;
26		import java.util.List;
27		import java.util.Map;
28
29		/**
30		* A data bean to hold stored data about a structure viewer.
31		*/
		0% Uncovered Elements: 50 (50) Complexity: 21 Complexity Density: 0.72
32		public class StructureViewerModel
33		{
34		private int x;
35
36		private int y;
37
38		private int width;
39
40		private int height;
41
42		private boolean alignWithPanel;
43
44		private boolean colourWithAlignPanel;
45
46		private boolean colourByViewer;
47
48		private String stateData = "";
49
50		private String viewId;
51
52		// CHIMERA or JMOL (for projects from Jalview 2.9 on)
53		private String type;
54
55		private Map<File, StructureData> fileData = new HashMap<File, StructureData>();
56
		0% Uncovered Elements: 16 (16) Complexity: 7 Complexity Density: 0.78
57		public class StructureData
58		{
59		private String filePath;
60
61		private String pdbId;
62
63		private List<SequenceI> seqList;
64
65		// TODO and possibly a list of chains?
66
67		/**
68		* Constructor given structure file path and id.
69		*
70		* @param pdbFile
71		* @param id
72		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
73	0	public StructureData(String pdbFile, String id)...
74		{
75	0	this.filePath = pdbFile;
76	0	this.pdbId = id;
77	0	this.seqList = new ArrayList<SequenceI>();
78		}
79
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
80	0	public String getFilePath()...
81		{
82	0	return filePath;
83		}
84
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
85	0	protected void setFilePath(String filePath)...
86		{
87	0	this.filePath = filePath;
88		}
89
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
90	0	public String getPdbId()...
91		{
92	0	return pdbId;
93		}
94
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	protected void setPdbId(String pdbId)...
96		{
97	0	this.pdbId = pdbId;
98		}
99
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
100	0	public List<SequenceI> getSeqList()...
101		{
102	0	return seqList;
103		}
104
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	protected void setSeqList(List<SequenceI> seqList)...
106		{
107	0	this.seqList = seqList;
108		}
109		}
110
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11
111	0	public StructureViewerModel(int x, int y, int width, int height,...
112		boolean alignWithPanel, boolean colourWithAlignPanel,
113		boolean colourByViewer, String viewId, String type)
114		{
115	0	this.x = x;
116	0	this.y = y;
117	0	this.width = width;
118	0	this.height = height;
119	0	this.alignWithPanel = alignWithPanel;
120	0	this.colourWithAlignPanel = colourWithAlignPanel;
121	0	this.colourByViewer = colourByViewer;
122	0	this.viewId = viewId;
123	0	this.type = type;
124		}
125
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
126	0	public int getX()...
127		{
128	0	return x;
129		}
130
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	protected void setX(int x)...
132		{
133	0	this.x = x;
134		}
135
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
136	0	public int getY()...
137		{
138	0	return y;
139		}
140
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
141	0	protected void setY(int y)...
142		{
143	0	this.y = y;
144		}
145
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
146	0	public int getWidth()...
147		{
148	0	return width;
149		}
150
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	protected void setWidth(int width)...
152		{
153	0	this.width = width;
154		}
155
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
156	0	public int getHeight()...
157		{
158	0	return height;
159		}
160
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
161	0	public void setHeight(int height)...
162		{
163	0	this.height = height;
164		}
165
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
166	0	public boolean isAlignWithPanel()...
167		{
168	0	return alignWithPanel;
169		}
170
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
171	0	public void setAlignWithPanel(boolean alignWithPanel)...
172		{
173	0	this.alignWithPanel = alignWithPanel;
174		}
175
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
176	0	public boolean isColourWithAlignPanel()...
177		{
178	0	return colourWithAlignPanel;
179		}
180
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
181	0	public void setColourWithAlignPanel(boolean colourWithAlignPanel)...
182		{
183	0	this.colourWithAlignPanel = colourWithAlignPanel;
184		}
185
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
186	0	public boolean isColourByViewer()...
187		{
188	0	return colourByViewer;
189		}
190
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
191	0	public void setColourByViewer(boolean colourByViewer)...
192		{
193	0	this.colourByViewer = colourByViewer;
194		}
195
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
196	0	public String getStateData()...
197		{
198	0	return stateData;
199		}
200
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
201	0	public void setStateData(String stateData)...
202		{
203	0	this.stateData = stateData;
204		}
205
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
206	0	public Map<File, StructureData> getFileData()...
207		{
208	0	return fileData;
209		}
210
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
211	0	protected void setFileData(Map<File, StructureData> fileData)...
212		{
213	0	this.fileData = fileData;
214		}
215
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
216	0	public String getViewId()...
217		{
218	0	return this.viewId;
219		}
220
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
221	0	public String getType()...
222		{
223	0	return this.type;
224		}
225		}