Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParamStores	15	193	5	0.00%	Show methods

Class ParamStores

Class ParamStores	Line # 15	Total Statements 193	Complexity 5	TOTAL Coverage 0.00%
<clinit>, line 22()   <clinit>, line 22()	2222	189.0189	2.02	0.0 0.00%
resolveURL(URL,String) : URL   resolveURL(URL,String) : URL	269269	3.03	2.02	0.0 0.00%
newPhmmerDatastore(URL,ParamManager) : ParamDatastoreI   newPhmmerDatastore(URL,ParamManager) : ParamDatastoreI	280280	1.01	1.01	0.0 0.00%

 

Contributing tests

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1		package jalview.ws2.client.ebi;
2
3		import jalview.ws.params.ArgumentI;
4		import jalview.ws.params.ParamDatastoreI;
5		import jalview.ws.params.ParamManager;
6		import jalview.ws.params.simple.*;
7		import jalview.ws2.params.SimpleParamDatastore;
8
9		import java.net.MalformedURLException;
10		import java.net.URL;
11		import java.util.ArrayList;
12		import java.util.Collections;
13		import java.util.List;
14
		0% Uncovered Elements: 196 (196) Complexity: 5 Complexity Density: 0.03
15		class ParamStores
16		{
17		static final List<ArgumentI> phmmerParameters;
18
19		/**
20		* Set up phmmer parameters list.
21		*/
		0% Uncovered Elements: 189 (189) Complexity: 2 Complexity Density: 0.01
22	0	static...
23		{
24	0	var parameters = new ArrayList<ArgumentI>();
25	0	URL baseURL;
26	0	try
27		{
28	0	baseURL = new URL( "https://www.ebi.ac.uk/Tools/services/rest/hmmer3_phmmer/");
29		} catch (MalformedURLException e)
30		{
31	0	throw new ExceptionInInitializerError(e);
32		}
33		{
34	0	var builder = StringParameter.newBuilder();
35	0	builder.setName("cut-offs");
36	0	builder.setLabel("Cut-offs");
37	0	builder.setDescription("Set the method of controlling which target sequences match your query.");
38	0	builder.setRequired(true);
39	0	builder.setValue("E");
40	0	builder.setDefaultValue("E");
41	0	builder.setPossibleValues(List.of("E", "T"));
42	0	builder.setDisplayValues(List.of("E-values", "Bit scores"));
43	0	parameters.add(builder.build());
44		}
45		{
46	0	var builder = DoubleParameter.newBuilder();
47	0	builder.setName("incE");
48	0	builder.setLabel("Significance E-values[Sequence]");
49	0	builder.setDescription("Significance E-values[Sequence]");
50	0	builder.setRequired(false);
51	0	builder.setValue(0.01);
52	0	builder.setDefaultValue(0.01);
53	0	builder.setMin(0.);
54	0	builder.setMax(10.);
55	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incE"));
56	0	parameters.add(builder.build());
57		}
58		{
59	0	var builder = DoubleParameter.newBuilder();
60	0	builder.setName("incdomE");
61	0	builder.setLabel("Significance E-values[Hit]");
62	0	builder.setDescription("Significance E-values[Hit]");
63	0	builder.setRequired(false);
64	0	builder.setValue(0.03);
65	0	builder.setDefaultValue(0.03);
66	0	builder.setMin(0.);
67	0	builder.setMax(10.);
68	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incdomE"));
69	0	parameters.add(builder.build());
70		}
71		{
72	0	var builder = DoubleParameter.newBuilder();
73	0	builder.setName("E");
74	0	builder.setLabel("Report E-values[Sequence]");
75	0	builder.setDescription("Report E-values[Sequence]");
76	0	builder.setRequired(false);
77	0	builder.setValue(1.0);
78	0	builder.setDefaultValue(1.0);
79	0	builder.setMin(0.);
80	0	builder.setMax(10.);
81	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/E"));
82	0	parameters.add(builder.build());
83		}
84		{
85	0	var builder = DoubleParameter.newBuilder();
86	0	builder.setName("domE");
87	0	builder.setLabel("Report E-values[Hit]");
88	0	builder.setDescription("Report E-values[Hit]");
89	0	builder.setRequired(false);
90	0	builder.setValue(1.0);
91	0	builder.setDefaultValue(1.0);
92	0	builder.setMin(0.);
93	0	builder.setMax(10.);
94	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/domE"));
95	0	parameters.add(builder.build());
96		}
97		{
98	0	var builder = DoubleParameter.newBuilder();
99	0	builder.setName("incT");
100	0	builder.setLabel("Significance bit scores[Sequence]");
101	0	builder.setDescription("Significance bit scores[Sequence]");
102	0	builder.setRequired(false);
103	0	builder.setValue(25.0);
104	0	builder.setDefaultValue(25.0);
105	0	builder.setMin(0.);
106	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incT"));
107	0	parameters.add(builder.build());
108		}
109		{
110	0	var builder = DoubleParameter.newBuilder();
111	0	builder.setName("incdomT");
112	0	builder.setLabel("Significance bit scores[Hit]");
113	0	builder.setDescription("Significance bit scores[Hit]");
114	0	builder.setRequired(false);
115	0	builder.setValue(22.0);
116	0	builder.setDefaultValue(22.0);
117	0	builder.setMin(0.);
118	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incdomT"));
119	0	parameters.add(builder.build());
120		}
121		{
122	0	var builder = DoubleParameter.newBuilder();
123	0	builder.setName("T");
124	0	builder.setLabel("Report bit scores[Sequence]");
125	0	builder.setDescription("Report bit scores[Sequence]");
126	0	builder.setRequired(false);
127	0	builder.setValue(7.0);
128	0	builder.setDefaultValue(7.0);
129	0	builder.setMin(0.);
130	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/T"));
131	0	parameters.add(builder.build());
132		}
133		{
134	0	var builder = DoubleParameter.newBuilder();
135	0	builder.setName("domT");
136	0	builder.setLabel("Report bit scores[Hit]");
137	0	builder.setDescription("Report bit scores[Hit]");
138	0	builder.setRequired(false);
139	0	builder.setValue(5.0);
140	0	builder.setDefaultValue(5.0);
141	0	builder.setMin(0.);
142	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/domT"));
143	0	parameters.add(builder.build());
144		}
145		{
146	0	var builder = DoubleParameter.newBuilder();
147	0	builder.setName("popen");
148	0	builder.setLabel("Gap Penalties[open]");
149	0	builder.setDescription("Gap Penalties[open]");
150	0	builder.setRequired(false);
151	0	builder.setValue(0.02);
152	0	builder.setDefaultValue(0.02);
153	0	builder.setMin(0.);
154	0	builder.setMax(0.5);
155	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/popen"));
156	0	parameters.add(builder.build());
157		}
158		{
159	0	var builder = DoubleParameter.newBuilder();
160	0	builder.setName("pextend");
161	0	builder.setLabel("Gap Penalties[extend]");
162	0	builder.setDescription("Gap Penalties[extend]");
163	0	builder.setRequired(false);
164	0	builder.setValue(0.4);
165	0	builder.setDefaultValue(0.4);
166	0	builder.setMin(0.);
167	0	builder.setMax(1.);
168	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/pextend"));
169	0	parameters.add(builder.build());
170		}
171		{
172	0	var builder = StringParameter.newBuilder();
173	0	builder.setName("mx");
174	0	builder.setLabel("Gap Penalties[Substitution scoring matrix]");
175	0	builder.setDescription("Gap Penalties[Substitution scoring matrix]");
176	0	builder.setRequired(false);
177	0	builder.setValue("BLOSUM62");
178	0	builder.setDefaultValue("BLOSUM62");
179	0	builder.setPossibleValues(List.of("BLOSUM45", "BLOSUM62", "BLOSUM90", "PAM30", "PAM70"));
180	0	builder.setDisplayValues(List.of("BLOSUM45", "BLOSUM62", "BLOSUM90", "PAM30", "PAM70"));
181	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/mx"));
182	0	parameters.add(builder.build());
183		}
184		{
185	0	var builder = BooleanOption.newBuilder();
186	0	builder.setName("nobias");
187	0	builder.setLabel("No bias filter");
188	0	builder.setDescription(
189		"The '--nobias' option turns off (bypasses) the biased composition filter which is on by default.");
190	0	builder.setRequired(false);
191	0	builder.setValue(false);
192	0	builder.setDefaultValue(false);
193	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/nobias"));
194	0	parameters.add(builder.build());
195		}
196		{
197	0	var builder = BooleanOption.newBuilder();
198	0	builder.setName("compressedout");
199	0	builder.setLabel("Compressed Output");
200	0	builder.setDescription(
201		"By default it runs hmm2c plus post-processing (default output), whereas with compressedout, it gets compressed output only.");
202	0	builder.setRequired(false);
203	0	builder.setValue(false);
204	0	builder.setDefaultValue(false);
205	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/compressedout"));
206	0	parameters.add(builder.build());
207		}
208		{
209	0	var builder = BooleanOption.newBuilder();
210	0	builder.setName("alignView");
211	0	builder.setLabel("Output Alignment");
212	0	builder.setDescription("Output alignment in result");
213	0	builder.setRequired(false);
214	0	builder.setValue(true);
215	0	builder.setDefaultValue(true);
216	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/alignView"));
217	0	parameters.add(builder.build());
218		}
219		{
220	0	var builder = StringParameter.newBuilder();
221	0	builder.setName("database");
222	0	builder.setLabel("Sequence Database");
223	0	builder.setDescription("Sequence Database Selection");
224	0	builder.setRequired(true);
225	0	builder.setValue("uniprotkb");
226	0	builder.setDefaultValue("uniprotkb");
227	0	builder.setPossibleValues(List.of("swissprot", "uniprotrefprot", "uniprotkb", "pdb", "rp75", "rp55", "rp35", "rp15", "ensembl", "merops", "qfo", "chembl"));
228	0	builder.setDisplayValues(List.of("SwissProt", "Reference Proteomes", "UniProtKB", "PDB", "rp75", "rp55", "rp35", "rp15", "Ensembl", "MEROPS", "Quest for Orthologs", "ChEMBL"));
229	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/database"));
230	0	parameters.add(builder.build());
231		}
232		{
233	0	var builder = DoubleParameter.newBuilder();
234	0	builder.setName("evalue");
235	0	builder.setLabel("Expectation Value Threshold");
236	0	builder.setDescription(
237		"Expectation value cut-off for reporting target profiles in the per-target output.");
238	0	builder.setRequired(false);
239	0	builder.setValue(0.01);
240	0	builder.setDefaultValue(0.01);
241	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/evalue"));
242	0	parameters.add(builder.build());
243		}
244		// {
245		// var builder = StringParameter.newBuilder();
246		// builder.setName("sequence");
247		// builder.setLabel("Input Sequence");
248		// builder.setDescription(
249		// "The input sequence can be entered directly into this form. The sequence can be be in FASTA or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.");
250		// builder.setRequired(false);
251		//
252		// builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/sequence"));
253		// parameters.add(builder.build());
254		// }
255		{
256	0	var builder = IntegerParameter.newBuilder();
257	0	builder.setName("nhits");
258	0	builder.setLabel("Number of Hits Displayed");
259	0	builder.setDescription("Number of hits to be displayed.");
260	0	builder.setRequired(false);
261	0	builder.setValue(100);
262	0	builder.setDefaultValue(100);
263	0	builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/nhits"));
264	0	parameters.add(builder.build());
265		}
266	0	phmmerParameters = Collections.unmodifiableList(parameters);
267		}
268
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
269	0	private static URL resolveURL(URL base, String spec)...
270		{
271	0	try
272		{
273	0	return new URL(base, spec);
274		} catch (MalformedURLException e)
275		{
276	0	throw new ExceptionInInitializerError(e);
277		}
278		}
279
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
280	0	public static ParamDatastoreI newPhmmerDatastore(URL url, ParamManager manager)...
281		{
282	0	return new SimpleParamDatastore(url, phmmerParameters,
283		Collections.emptyList(), manager);
284		}
285		}