Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SeqVector	45	31	11	0.00%	Show methods

Class SeqVector

Class SeqVector	Line # 45	Total Statements 31	Complexity 11	TOTAL Coverage 0.00%
SeqVector()   SeqVector()	5151	1.01	1.01	0.0 0.00%
formatForInput(RestJob) : ContentBody   formatForInput(RestJob) : ContentBody	5656	7.07	2.02	0.0 0.00%
getURLEncodedParameter() : List<String>   getURLEncodedParameter() : List<String>	7373	6.06	2.02	0.0 0.00%
getURLtokenPrefix() : String   getURLtokenPrefix() : String	8686	1.01	1.01	0.0 0.00%
configureProperty(String,String,StringBuffer) : boolean   configureProperty(String,String,StringBuffer) : boolean	9292	12.012	4.04	0.0 0.00%
getOptions() : List<OptionI>   getOptions() : List<OptionI>	122122	4.04	1.01	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.ws.rest.params;
22
23		import jalview.datamodel.AlignmentI;
24		import jalview.datamodel.SequenceI;
25		import jalview.ws.params.OptionI;
26		import jalview.ws.params.simple.Option;
27		import jalview.ws.rest.InputType;
28		import jalview.ws.rest.NoValidInputDataException;
29		import jalview.ws.rest.RestJob;
30
31		import java.io.UnsupportedEncodingException;
32		import java.util.ArrayList;
33		import java.util.Arrays;
34		import java.util.List;
35
36		import org.apache.http.entity.mime.content.ContentBody;
37		import org.apache.http.entity.mime.content.StringBody;
38
39		/**
40		* input a list of sequences separated by some separator
41		*
42		* @author JimP
43		*
44		*/
		0% Uncovered Elements: 45 (45) Complexity: 11 Complexity Density: 0.35
45		public class SeqVector extends InputType
46		{
47		String sep;
48
49		molType type;
50
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
51	0	public SeqVector()...
52		{
53	0	super(new Class[] { AlignmentI.class });
54		}
55
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
56	0	@Override...
57		public ContentBody formatForInput(RestJob rj)
58		throws UnsupportedEncodingException, NoValidInputDataException
59		{
60	0	StringBuffer idvector = new StringBuffer();
61	0	boolean list = false;
62	0	for (SequenceI seq : rj.getSequencesForInput(token, type))
63		{
64	0	if (list)
65		{
66	0	idvector.append(sep);
67		}
68	0	idvector.append(seq.getSequenceAsString());
69		}
70	0	return new StringBody(idvector.toString());
71		}
72
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
73	0	@Override...
74		public List<String> getURLEncodedParameter()
75		{
76	0	ArrayList<String> prms = new ArrayList<String>();
77	0	super.addBaseParams(prms);
78	0	prms.add("sep='" + sep + "'");
79	0	if (type != null)
80		{
81	0	prms.add("type='" + type + "'");
82		}
83	0	return prms;
84		}
85
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
86	0	@Override...
87		public String getURLtokenPrefix()
88		{
89	0	return "SEQS";
90		}
91
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.33
92	0	@Override...
93		public boolean configureProperty(String tok, String val,
94		StringBuffer warnings)
95		{
96
97	0	if (tok.startsWith("sep"))
98		{
99	0	sep = val;
100	0	return true;
101		}
102	0	if (tok.startsWith("type"))
103		{
104	0	try
105		{
106	0	type = molType.valueOf(val);
107	0	return true;
108		} catch (Exception x)
109		{
110	0	warnings.append(
111		"Invalid molecule type '" + val + "'. Must be one of (");
112	0	for (molType v : molType.values())
113		{
114	0	warnings.append(" " + v);
115		}
116	0	warnings.append(")\n");
117		}
118		}
119	0	return false;
120		}
121
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
122	0	@Override...
123		public List<OptionI> getOptions()
124		{
125	0	List<OptionI> lst = getBaseOptions();
126	0	lst.add(new Option("sep",
127		"Separator character between elements of vector", true, ",",
128		sep, Arrays.asList(new String[]
129		{ " ", ",", ";", "\t", "|" }), null));
130	0	lst.add(createMolTypeOption("type", "Sequence type", false, type,
131		molType.MIX));
132
133	0	return lst;
134		}
135
136		}