Classes

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

Class SeqIdVector

Class SeqIdVector	Line # 45	Total Statements 31	Complexity 11	TOTAL Coverage 0.00%
SeqIdVector()   SeqIdVector()	4747	1.01	1.01	0.0 0.00%
formatForInput(RestJob) : ContentBody   formatForInput(RestJob) : ContentBody	5959	7.07	2.02	0.0 0.00%
getURLEncodedParameter() : List<String>   getURLEncodedParameter() : List<String>	7676	6.06	2.02	0.0 0.00%
getURLtokenPrefix() : String   getURLtokenPrefix() : String	8989	1.01	1.01	0.0 0.00%
configureProperty(String,String,StringBuffer) : boolean   configureProperty(String,String,StringBuffer) : boolean	9595	12.012	4.04	0.0 0.00%
getOptions() : List<OptionI>   getOptions() : List<OptionI>	124124	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 sequence IDs separated by some separator
41		*
42		* @author JimP
43		*
44		*/
		0% Uncovered Elements: 45 (45) Complexity: 11 Complexity Density: 0.35
45		public class SeqIdVector extends InputType
46		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	public SeqIdVector()...
48		{
49	0	super(new Class[] { AlignmentI.class });
50		}
51
52		/**
53		* separator for list of sequence IDs - default is ','
54		*/
55		String sep = ",";
56
57		molType type;
58
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
59	0	@Override...
60		public ContentBody formatForInput(RestJob rj)
61		throws UnsupportedEncodingException, NoValidInputDataException
62		{
63	0	StringBuffer idvector = new StringBuffer();
64	0	boolean list = false;
65	0	for (SequenceI seq : rj.getSequencesForInput(token, type))
66		{
67	0	if (list)
68		{
69	0	idvector.append(sep);
70		}
71	0	idvector.append(seq.getName());
72		}
73	0	return new StringBody(idvector.toString());
74		}
75
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
76	0	@Override...
77		public List<String> getURLEncodedParameter()
78		{
79	0	ArrayList<String> prms = new ArrayList<String>();
80	0	super.addBaseParams(prms);
81	0	prms.add("sep='" + sep + "'");
82	0	if (type != null)
83		{
84	0	prms.add("type='" + type + "'");
85		}
86	0	return prms;
87		}
88
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
89	0	@Override...
90		public String getURLtokenPrefix()
91		{
92	0	return "SEQIDS";
93		}
94
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.33
95	0	@Override...
96		public boolean configureProperty(String tok, String val,
97		StringBuffer warnings)
98		{
99	0	if (tok.startsWith("sep"))
100		{
101	0	sep = val;
102	0	return true;
103		}
104	0	if (tok.startsWith("type"))
105		{
106	0	try
107		{
108	0	type = molType.valueOf(val);
109	0	return true;
110		} catch (Exception x)
111		{
112	0	warnings.append(
113		"Invalid molecule type '" + val + "'. Must be one of (");
114	0	for (molType v : molType.values())
115		{
116	0	warnings.append(" " + v);
117		}
118	0	warnings.append(")\n");
119		}
120		}
121	0	return false;
122		}
123
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
124	0	@Override...
125		public List<OptionI> getOptions()
126		{
127	0	List<OptionI> lst = getBaseOptions();
128	0	lst.add(new Option("sep",
129		"Separator character between elements of vector", true, ",",
130		sep, Arrays.asList(new String[]
131		{ " ", ",", ";", "\t", "|" }), null));
132	0	lst.add(createMolTypeOption("type", "Sequence type", false, type,
133		null));
134	0	return lst;
135		}
136		}