Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PContactPredictionFile	46	27	12	0.00%	Show methods

Class PContactPredictionFile

Class PContactPredictionFile	Line # 46	Total Statements 27	Complexity 12	TOTAL Coverage 0.00%
PContactPredictionFile(String,DataSourceType)   PContactPredictionFile(String,DataSourceType)	5050	1.01	1.01	0.0 0.00%
PContactPredictionFile(FileParse)   PContactPredictionFile(FileParse)	5757	1.01	1.01	0.0 0.00%
getContactMatrices() : List<ContactMatrix>   getContactMatrices() : List<ContactMatrix>	6666	1.01	1.01	0.0 0.00%
getType() : String   getType() : String	114114	1.01	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	120120	1.01	1.01	0.0 0.00%
getWidth() : int   getWidth() : int	128128	1.01	1.01	0.0 0.00%
parse() : void   parse() : void	8585	20.020	5.05	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	158158	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.io;
22
23		import jalview.datamodel.ContactMatrix;
24		import jalview.datamodel.SequenceI;
25
26		import java.io.IOException;
27		import java.util.ArrayList;
28		import java.util.BitSet;
29		import java.util.HashMap;
30		import java.util.List;
31		import java.util.Map;
32
33		/**
34		* A file parser for contact prediction files.
35		*
36		* An example file is the following
37		*
38		* <pre>
39		*
40		* </pre>
41		*
42		*
43		* @author jim procter
44		*
45		*/
		0% Uncovered Elements: 41 (41) Complexity: 12 Complexity Density: 0.44
46		public class PContactPredictionFile extends AlignFile
47		{
48		protected static final String CONTACT_PREDICTION = "CONTACT_PREDICTION";
49
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	public PContactPredictionFile(String inFile,...
51		DataSourceType fileSourceType) throws IOException
52		{
53	0	super(inFile, fileSourceType);
54
55		}
56
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	public PContactPredictionFile(FileParse source) throws IOException...
58		{
59	0	super(source);
60		}
61
62		Integer fWidth;
63
64		List<ContactMatrix> models = new ArrayList<ContactMatrix>();
65
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	public List<ContactMatrix> getContactMatrices()...
67		{
68	0	return models;
69		}
70
71		/*
72		* RaptorX pattern:
73		* for a contact prediction
74		* Target sequence
75		* alignment for target sequence
76		* contact matrix for sequence
77		* models generated that fit matrix
78		*/
79
80		/*
81		* TODO: create annotation rows from contact matrices.
82		* (non-Javadoc)
83		* @see jalview.io.AlignFile#parse()
84		*/
		0% Uncovered Elements: 26 (26) Complexity: 5 Complexity Density: 0.25
85	0	@Override...
86		public void parse() throws IOException
87		{
88	0	String line;
89		/*
90		* stash any header lines if we've been given a CASP-RR file
91		*/
92	0	Map<String, String> header = new HashMap<String, String>();
93	0	ContactMatrix cm = null;
94
95	0	while ((line = nextLine()) != null)
96		{
97	0	int left, right;
98	0	double strength = Float.NaN;
99	0	String parts[] = line.split("\\s+");
100
101		// check for header tokens in parts[0]
102
103		// others - stash details
104		// MODEL - start a new matrix
105		// skip comments ?
106
107	0	if (parts.length == 3) // and all are integers
108		{
109
110	0	if (cm == null)
111		{
112	0	cm = new ContactMatrix(true)
113		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
114	0	@Override...
115		public String getType()
116		{
117	0	return CONTACT_PREDICTION;
118		}
119
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
120	0	@Override...
121		public int getHeight()
122		{
123		// TODO Auto-generated method stub
124		// return maximum contact height
125	0	return 0;
126		}
127
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
128	0	@Override...
129		public int getWidth()
130		{
131		// TODO Auto-generated method stub
132		// return total number of residues with contacts
133	0	return 0;
134		}
135		};
136	0	models.add(cm);
137		}
138
139	0	try
140		{
141	0	left = Integer.parseInt(parts[0]);
142	0	right = Integer.parseInt(parts[1]);
143	0	strength = Double.parseDouble(parts[2]);
144		} catch (Exception x)
145		{
146	0	error = true;
147	0	errormessage = "Couldn't process line: " + x.getLocalizedMessage()
148		+ "\n" + line;
149	0	return;
150		}
151	0	cm.addContact(left, right, (float) strength);
152		}
153		}
154		// TODO COMPLETE
155	0	throw (new Error("Not Implemented yet."));
156		}
157
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
158	0	@Override...
159		public String print(SequenceI[] sqs, boolean jvsuffix)
160		{
161		// TODO Auto-generated method stub
162	0	return "Not valid.";
163		}
164		}