Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
SequenceFetcherTest	38	80	31	129	0.00%	Show methods

Class SequenceFetcherTest

Class SequenceFetcherTest	Line # 38	Total Statements 80	Complexity 31	Uncovered Elements 129	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4141	2.02	1.01	2.02	0.0 0.00%
main(String[]) : void   main(String[]) : void	5353	26.026	11.011	40.040	0.0 0.00%
testRetrieval(String,DbSourceProxy,String) : void   testRetrieval(String,DbSourceProxy,String) : void	121121	52.052	19.019	84.084	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;
22
23		import jalview.analysis.CrossRef;
24		import jalview.datamodel.Alignment;
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.DBRefSource;
27		import jalview.datamodel.SequenceI;
28		import jalview.gui.JvOptionPane;
29		import jalview.ws.seqfetcher.ASequenceFetcher;
30		import jalview.ws.seqfetcher.DbSourceProxy;
31
32		import java.util.Enumeration;
33		import java.util.List;
34		import java.util.Vector;
35
36		import org.testng.annotations.BeforeClass;
37
		0% Uncovered Elements: 129 (129) Complexity: 31 Complexity Density: 0.39
38		public class SequenceFetcherTest
39		{
40
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
41	0	@BeforeClass(alwaysRun = true)...
42		public void setUpJvOptionPane()
43		{
44	0	JvOptionPane.setInteractiveMode(false);
45	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46		}
47
48		/**
49		* simple run method to test dbsources.
50		*
51		* @param argv
52		*/
		0% Uncovered Elements: 40 (40) Complexity: 11 Complexity Density: 0.42
53	0	public static void main(String[] argv)...
54		{
55		// TODO: extracted from SequenceFetcher - convert to network dependent
56		// functional integration test with
57		// assertions
58
59	0	String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
60		+ "With no arguments, all DbSources will be queried with their test Accession number.\n"
61		+ "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
62		+ "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
63
64	0	if (argv != null && argv.length > 0)
65		{
66	0	String targs[] = new String[argv.length - 1];
67	0	System.arraycopy(argv, 1, targs, 0, targs.length);
68	0	argv = targs;
69		}
70	0	if (argv != null && argv.length > 0)
71		{
72	0	List<DbSourceProxy> sps = new SequenceFetcher()
73		.getSourceProxy(argv[0]);
74
75	0	if (sps != null)
76		{
77	0	for (DbSourceProxy sp : sps)
78		{
79	0	AlignmentI al = null;
80	0	try
81		{
82	0	testRetrieval(argv[0], sp,
83	0	argv.length > 1 ? argv[1] : sp.getTestQuery());
84		} catch (Exception e)
85		{
86	0	e.printStackTrace();
87	0	System.err.println("Error when retrieving "
88	0	+ (argv.length > 1 ? argv[1] : sp.getTestQuery())
89		+ " from " + argv[0] + "\nUsage: " + usage);
90		}
91		}
92	0	return;
93		}
94		else
95		{
96	0	System.err.println("Can't resolve " + argv[0]
97		+ " as a database name. Allowed values are :\n"
98		+ new SequenceFetcher().getSupportedDb());
99		}
100	0	System.out.println(usage);
101	0	return;
102		}
103	0	ASequenceFetcher sfetcher = new SequenceFetcher();
104	0	String[] dbSources = sfetcher.getSupportedDb();
105	0	for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
106		{
107	0	String db = dbSources[dbsource];
108		// skip me
109	0	if (db.equals(DBRefSource.PDB))
110		{
111	0	continue;
112		}
113	0	for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
114		{
115	0	testRetrieval(db, sp, sp.getTestQuery());
116		}
117		}
118
119		}
120
		0% Uncovered Elements: 84 (84) Complexity: 19 Complexity Density: 0.37
121	0	private static void testRetrieval(String db, DbSourceProxy sp,...
122		String testQuery)
123		{
124	0	AlignmentI ds = null;
125	0	Vector<Object[]> noProds = new Vector<>();
126	0	System.out.println("Source: " + sp.getDbName() + " (" + db
127		+ "): retrieving test:" + sp.getTestQuery());
128		{
129	0	AlignmentI al = null;
130	0	try
131		{
132	0	al = sp.getSequenceRecords(testQuery);
133	0	if (al != null && al.getHeight() > 0)
134		{
135	0	boolean dna = sp.isDnaCoding();
136	0	al.setDataset(null);
137	0	AlignmentI alds = al.getDataset();
138		// try and find products
139	0	CrossRef crossRef = new CrossRef(al.getSequencesArray(), alds);
140	0	List<String> types = crossRef.findXrefSourcesForSequences(dna);
141	0	if (types != null)
142		{
143	0	System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));
144	0	for (String source : types)
145		{
146	0	System.out.println("Type: " + source);
147	0	SequenceI[] prod = crossRef.findXrefSequences(source, dna)
148		.getSequencesArray();
149	0	System.out.println("Found "
150	0	+ ((prod == null) ? "no" : "" + prod.length)
151		+ " products");
152	0	if (prod != null)
153		{
154	0	for (int p = 0; p < prod.length; p++)
155		{
156	0	System.out.println("Prod " + p + ": "
157		+ prod[p].getDisplayId(true));
158		}
159		}
160		}
161		}
162		else
163		{
164	0	noProds.addElement((dna ? new Object[] { al, al }
165		: new Object[] { al }));
166		}
167
168		}
169		} catch (Exception ex)
170		{
171	0	System.out.println("ERROR:Failed to retrieve test query.");
172	0	ex.printStackTrace(System.out);
173		}
174
175	0	if (al == null)
176		{
177	0	System.out.println("ERROR:No alignment retrieved.");
178	0	StringBuffer raw = sp.getRawRecords();
179	0	if (raw != null)
180		{
181	0	System.out.println(raw.toString());
182		}
183		else
184		{
185	0	System.out.println("ERROR:No Raw results.");
186		}
187		}
188		else
189		{
190	0	System.out.println("Retrieved " + al.getHeight() + " sequences.");
191	0	if (ds == null)
192		{
193	0	ds = al.getDataset();
194		}
195		else
196		{
197	0	ds.append(al.getDataset());
198	0	al.setDataset(ds);
199		}
200		}
201	0	System.out.flush();
202	0	System.err.flush();
203		}
204	0	if (noProds.size() > 0)
205		{
206	0	Enumeration<Object[]> ts = noProds.elements();
207	0	while (ts.hasMoreElements())
208
209		{
210	0	Object[] typeSq = ts.nextElement();
211	0	boolean dna = (typeSq.length > 1);
212	0	AlignmentI al = (AlignmentI) typeSq[0];
213	0	System.out.println("Trying getProducts for "
214		+ al.getSequenceAt(0).getDisplayId(true));
215	0	System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot"));
216		// have a bash at finding the products amongst all the retrieved
217		// sequences.
218	0	SequenceI[] seqs = al.getSequencesArray();
219	0	Alignment prodal = new CrossRef(seqs, ds).findXrefSequences(null,
220		dna);
221	0	System.out.println("Found "
222	0	+ ((prodal == null) ? "no" : "" + prodal.getHeight())
223		+ " products");
224	0	if (prodal != null)
225		{
226	0	SequenceI[] prod = prodal.getSequencesArray(); // note
227		// should
228		// test
229		// rather
230		// than
231		// throw
232		// away
233		// codon
234		// mapping
235		// (if
236		// present)
237	0	for (int p = 0; p < prod.length; p++)
238		{
239	0	System.out.println("Prod " + p + ": "
240		+ prod[p].getDisplayId(true));
241		}
242		}
243		}
244		}
245		}
246		}