Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructuresFile	19	55	24	0.00%	Show methods

Class StructuresFile

Class StructuresFile	Line # 19	Total Statements 55	Complexity 24	TOTAL Coverage 0.00%
StructuresFile(AlignmentI,String)   StructuresFile(AlignmentI,String)	3636	2.02	1.01	0.0 0.00%
isSuperpose() : boolean   isSuperpose() : boolean	4242	1.01	1.01	0.0 0.00%
setSuperpose(boolean) : void   setSuperpose(boolean) : void	4747	1.01	1.01	0.0 0.00%
getViewerid() : String   getViewerid() : String	5252	1.01	1.01	0.0 0.00%
setViewerid(String) : void   setViewerid(String) : void	5757	1.01	1.01	0.0 0.00%
getViewerType() : ViewerType   getViewerType() : ViewerType	6262	1.01	1.01	0.0 0.00%
setViewerType(ViewerType) : void   setViewerType(ViewerType) : void	6767	1.01	1.01	0.0 0.00%
getStructureLines() : List<StructureLine>   getStructureLines() : List<StructureLine>	7272	1.01	1.01	0.0 0.00%
setStructureLines(List<StructureLine>) : void   setStructureLines(List<StructureLine>) : void	7777	1.01	1.01	0.0 0.00%
parseStructuresFile(File) : List<StructureLine>   parseStructuresFile(File) : List<StructureLine>	8282	32.032	8.08	0.0 0.00%
getSeqs() : SequenceI[]   getSeqs() : SequenceI[]	146146	2.02	1.01	0.0 0.00%
getPdbEntries() : PDBEntry[]   getPdbEntries() : PDBEntry[]	152152	2.02	1.01	0.0 0.00%
getArgVal(Arg,String) : String   getArgVal(Arg,String) : String	158158	4.04	2.02	0.0 0.00%
getArgBoolean(Arg,String) : Boolean   getArgBoolean(Arg,String) : Boolean	169169	5.05	3.03	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.bin.argparser;
2
3		import java.io.File;
4		import java.util.ArrayList;
5		import java.util.List;
6
7		import jalview.bin.Cache;
8		import jalview.bin.Console;
9		import jalview.datamodel.AlignmentI;
10		import jalview.datamodel.PDBEntry;
11		import jalview.datamodel.SequenceI;
12		import jalview.gui.AssociatePdbFileWithSeq;
13		import jalview.gui.Desktop;
14		import jalview.gui.StructureChooser;
15		import jalview.gui.StructureViewer.ViewerType;
16		import jalview.io.AppletFormatAdapter;
17		import jalview.io.DataSourceType;
18
		0% Uncovered Elements: 89 (89) Complexity: 24 Complexity Density: 0.44
19		public class StructuresFile
20		{
21		private boolean superpose = Cache
22		.getDefault(StructureChooser.AUTOSUPERIMPOSE, true);
23
24		private String viewerid = null;
25
26		private ViewerType viewerType = ViewerType.JMOL;
27
28		private List<StructureLine> structureLines;
29
30		private List<SequenceI> seqs = new ArrayList<>();
31
32		private List<PDBEntry> pdbs = new ArrayList<>();
33
34		private AlignmentI alignment;
35
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
36	0	public StructuresFile(AlignmentI al, String filename)...
37		{
38	0	alignment = al;
39	0	setStructureLines(parseStructuresFile(new File(filename)));
40		}
41
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
42	0	public boolean isSuperpose()...
43		{
44	0	return superpose;
45		}
46
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	public void setSuperpose(boolean superpose)...
48		{
49	0	this.superpose = superpose;
50		}
51
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	public String getViewerid()...
53		{
54	0	return viewerid;
55		}
56
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	public void setViewerid(String viewerid)...
58		{
59	0	this.viewerid = viewerid;
60		}
61
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	public ViewerType getViewerType()...
63		{
64	0	return viewerType;
65		}
66
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	public void setViewerType(ViewerType viewerType)...
68		{
69	0	this.viewerType = viewerType;
70		}
71
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	public List<StructureLine> getStructureLines()...
73		{
74	0	return structureLines;
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	public void setStructureLines(List<StructureLine> structureLines)...
78		{
79	0	this.structureLines = structureLines;
80		}
81
		0% Uncovered Elements: 46 (46) Complexity: 8 Complexity Density: 0.25
82	0	public List<StructureLine> parseStructuresFile(File structuresFile)...
83		{
84	0	if (!structuresFile.exists())
85		{
86	0	String message = Arg.STRUCTURESFILE.argString() + ArgParser.EQUALS
87		+ "\"" + structuresFile.getPath()
88		+ "\": File does not exist.";
89	0	Console.warn(message);
90	0	return null;
91		}
92	0	List<String> lines = ArgParser.readArgFile(structuresFile);
93	0	List<StructureLine> structurelines = new ArrayList<>();
94	0	if (lines != null)
95		{
96	0	for (String line : lines)
97		{
98	0	if (line.startsWith(ArgParser.DOUBLEDASH))
99		{
100	0	String val = getArgVal(Arg.VIEWERID, line);
101	0	if (val != null)
102		{
103	0	setViewerid(val);
104	0	continue;
105		}
106	0	val = getArgVal(Arg.STRUCTUREVIEWER, line);
107	0	if (val != null)
108		{
109	0	setViewerType(ViewerType.getFromString(val));
110	0	continue;
111		}
112	0	Boolean b = getArgBoolean(Arg.SUPERPOSE, line);
113	0	if (b != null)
114		{
115	0	setSuperpose(b);
116	0	continue;
117		}
118		}
119	0	StructureLine sl = new StructureLine(line);
120	0	structurelines.add(sl);
121	0	String structureLocationRef = sl.getSource();
122	0	DataSourceType structureLocationType = AppletFormatAdapter
123		.checkProtocol(structureLocationRef);
124	0	if (DataSourceType.FILE.equals(structureLocationType))
125		{
126	0	structureLocationRef = new File(structureLocationRef)
127		.getAbsolutePath();
128		}
129	0	SequenceI seq = alignment.findName(sl.getSeqid());
130
131		// TODO get global or subval values for TFT and notempfac
132
133	0	PDBEntry pdbEntry = AssociatePdbFileWithSeq
134		.associatePdbWithSeq(structureLocationRef,
135		structureLocationType, seq, false, Desktop.getInstance(),
136		null, null, false);
137
138	0	pdbs.add(pdbEntry);
139	0	seqs.add(seq);
140
141		}
142		}
143	0	return structurelines;
144		}
145
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
146	0	public SequenceI[] getSeqs()...
147		{
148	0	SequenceI[] array = new SequenceI[seqs.size()];
149	0	return seqs.toArray(array);
150		}
151
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
152	0	public PDBEntry[] getPdbEntries()...
153		{
154	0	PDBEntry[] array = new PDBEntry[pdbs.size()];
155	0	return pdbs.toArray(array);
156		}
157
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
158	0	private static String getArgVal(Arg a, String line)...
159		{
160	0	String s = new StringBuilder(a.argString()).append(ArgParser.EQUALS)
161		.toString();
162	0	if (line.startsWith(s))
163		{
164	0	return line.substring(s.length());
165		}
166	0	return null;
167		}
168
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
169	0	private static Boolean getArgBoolean(Arg a, String line)...
170		{
171	0	if (line.equals(a.argString()))
172		{
173	0	return true;
174		}
175	0	if (line.equals(a.negateArgString()))
176		{
177	0	return false;
178		}
179	0	return null;
180		}
181
182		}