Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Search	22	116	30	0.00%	Show methods

Class Search

Class Search	Line # 22	Total Statements 116	Complexity 30	TOTAL Coverage 0.00%
Search(AlignFrame,List<ArgumentI>)   Search(AlignFrame,List<ArgumentI>)	4141	1.01	1.01	0.0 0.00%
run() : void   run() : void	4646	0.00	1.01	-1.0 -1.0 -
readDomainTable(File,boolean) : void   readDomainTable(File,boolean) : void	162162	25.025	5.05	0.0 0.00%
addScoreAnnotations(String,String,SequenceI) : void   addScoreAnnotations(String,String,SequenceI) : void	214214	14.014	2.02	0.0 0.00%
buildArguments(List<String>,File,File,File) : void   buildArguments(List<String>,File,File,File) : void	245245	76.076	21.021	0.0 0.00%

 

Contributing tests

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1		package jalview.hmmer;
2
3		import jalview.analysis.SeqsetUtils.SequenceInfo;
4		import jalview.datamodel.Alignment;
5		import jalview.datamodel.AlignmentAnnotation;
6		import jalview.datamodel.AlignmentI;
7		import jalview.datamodel.SequenceI;
8		import jalview.gui.AlignFrame;
9		import jalview.util.FileUtils;
10		import jalview.util.MessageManager;
11		import jalview.ws.params.ArgumentI;
12
13		import java.io.BufferedReader;
14		import java.io.File;
15		import java.io.FileReader;
16		import java.io.IOException;
17		import java.util.Hashtable;
18		import java.util.List;
19		import java.util.Map;
20		import java.util.Scanner;
21
		0% Uncovered Elements: 169 (169) Complexity: 30 Complexity Density: 0.26
22		public abstract class Search extends HmmerCommand
23		{
24
25		static final String JACKHMMER = "jackhmmer";
26
27		static final String HMMSEARCH = "hmmsearch";
28
29		boolean realign = false;
30
31		boolean trim = false;
32
33		SequenceI[] seqs;
34
35		String databaseName;
36
37		boolean searchAlignment = true;
38
39		Map<String, SequenceInfo> sequencesHash;
40
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
41	0	public Search(AlignFrame alignFrame, List<ArgumentI> args)...
42		{
43	0	super(alignFrame, args);
44		}
45
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
46	0	@Override...
47		public void run()
48		{
49		}
50
51		/*
52		void readOutputFile(File inputTableTemp) throws IOException
53		{
54		BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
55
56
57		String line = "";
58		while (!line.startsWith("//"))
59		{
60
61		while (!line.startsWith(">> ") && !line.startsWith("//"))
62		{
63		line = br.readLine();
64		}
65
66		if (line.startsWith("//"))
67		{
68		break;
69		}
70
71		Scanner scanner = new Scanner(line);
72		String name = scanner.next();
73		name = scanner.next();
74
75		br.readLine();
76		br.readLine();
77
78		List<SequenceI> domains = new ArrayList<>();
79
80		for (SequenceI seq : seqs)
81		{
82		if (seq.getName().contains(name))
83		{
84		domains.add(seq);
85		}
86		}
87
88		if (domains.contains(getSequence()))
89		{
90		domains.remove(getSequence());
91		}
92
93		if (domains.size() > 0)
94		{
95		readOutputTable(br, domains);
96		}
97
98		line = br.readLine();
99		}
100
101		}
102
103
104		/**
105		* Reads in the scores table output by jackhmmer and adds annotation to
106		* sequences for E-value and bit score
107		*
108		* @param inputTableTemp
109		* @throws IOException
110		*/
111		/*
112		void readOutputTable(BufferedReader br, List<SequenceI> seqs) throws IOException
113		{
114		String line = br.readLine();
115
116		while (!"".equals(line) && line != null)
117		{
118		if (" ------ inclusion threshold ------".equals(line))
119		{
120		line = br.readLine();
121		continue;
122		}
123
124		Scanner scanner = new Scanner(line);
125		scanner.next();
126		scanner.next();
127		String score = scanner.next();
128
129		scanner.next();
130
131		String evalue = scanner.next();
132
133		scanner.next();
134		scanner.next();
135		scanner.next();
136		scanner.next();
137
138		int start = scanner.nextInt();
139		int end = scanner.nextInt();
140
141		SequenceI seq = null;
142		for (SequenceI sequence : seqs)
143		{
144		if (sequence.getStart() >= start && sequence.getEnd() <= end)
145		{
146		seq = sequence;
147		break;
148		}
149		}
150
151		if (seq != null)
152		{
153		addScoreAnnotations(evalue, score, seq);
154		}
155
156		scanner.close();
157		line = br.readLine();
158		}
159		}
160		*/
161
		0% Uncovered Elements: 33 (33) Complexity: 5 Complexity Density: 0.2
162	0	void readDomainTable(File inputTableTemp, boolean includesQuery)...
163		throws IOException
164		{
165	0	BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
166
167	0	String line = br.readLine();
168	0	br.readLine();
169	0	br.readLine();
170	0	line = br.readLine();
171
172	0	int index;
173
174	0	if (includesQuery)
175		{
176	0	index = 1;
177		}
178		else
179		{
180	0	index = 0;
181		}
182	0	while (!line.startsWith("#"))
183		{
184	0	if (line.contains("inclusion threshold"))
185		{
186	0	line = br.readLine();
187	0	continue;
188		}
189
190	0	Scanner scanner = new Scanner(line);
191	0	String name = scanner.next();
192
193	0	for (int i = 0; i < 10; i++)
194		{
195	0	scanner.next();
196		}
197
198	0	String evalue = scanner.next();
199	0	scanner.next();
200	0	String score = scanner.next();
201
202	0	addScoreAnnotations(evalue, score, seqs[index]);
203	0	index++;
204
205	0	scanner.close();
206	0	line = br.readLine();
207		}
208	0	br.close();
209		}
210
211
212
213
		0% Uncovered Elements: 14 (14) Complexity: 2 Complexity Density: 0.14
214	0	void addScoreAnnotations(String eValue, String bitScore, SequenceI seq)...
215		{
216	0	String label = "Search Scores";
217	0	String description = "Full sequence bit score and E-Value";
218
219	0	try
220		{
221	0	AlignmentAnnotation annot = new AlignmentAnnotation(label,
222		description, null);
223
224	0	annot.label = label;
225	0	annot.description = description;
226
227	0	annot.setCalcId(JACKHMMER);
228
229	0	double dEValue = Double.parseDouble(eValue);
230	0	annot.setEValue(dEValue);
231
232	0	double dBitScore = Double.parseDouble(bitScore);
233	0	annot.setBitScore(dBitScore);
234
235	0	annot.setSequenceRef(seq);
236	0	seq.addAlignmentAnnotation(annot);
237
238		} catch (NumberFormatException e)
239		{
240	0	System.err.println("Error parsing " + label + " from " + eValue
241		+ " & " + bitScore);
242		}
243		}
244
		0% Uncovered Elements: 116 (116) Complexity: 21 Complexity Density: 0.28
245	0	void buildArguments(List<String> args, File searchOutputFile,...
246		File hitsAlignmentFile, File queryFile) throws IOException
247		{
248	0	args.add("--domtblout");
249	0	args.add(getFilePath(searchOutputFile, true));
250	0	args.add("-A");
251	0	args.add(getFilePath(hitsAlignmentFile, true));
252
253	0	File databaseFile = null;
254
255	0	boolean useEvalueCutoff = false;
256	0	boolean useScoreCutoff = false;
257	0	String seqReportingEvalueCutoff = null;
258	0	String domReportingEvalueCutoff = null;
259	0	String seqReportingScoreCutoff = null;
260	0	String domReportingScoreCutoff = null;
261	0	String seqInclusionEvalueCutoff = null;
262	0	String domInclusionEvalueCutoff = null;
263	0	String seqInclusionScoreCutoff = null;
264	0	String domInclusionScoreCutoff = null;
265	0	databaseName = "Alignment";
266
267	0	if (params != null)
268		{
269	0	for (ArgumentI arg : params)
270		{
271	0	String name = arg.getName();
272
273	0	if (MessageManager.getString(REPORTING_CUTOFF_KEY).equals(name))
274		{
275	0	if (MessageManager.getString(CUTOFF_EVALUE)
276		.equals(arg.getValue()))
277		{
278	0	useEvalueCutoff = true;
279		}
280	0	else if (MessageManager.getString(CUTOFF_SCORE)
281		.equals(arg.getValue()))
282		{
283	0	useScoreCutoff = true;
284		}
285		}
286	0	else if (MessageManager.getString(REPORTING_SEQ_EVALUE_KEY)
287		.equals(name))
288		{
289	0	seqReportingEvalueCutoff = arg.getValue();
290		}
291	0	else if (MessageManager.getString(REPORTING_SEQ_SCORE_KEY)
292		.equals(name))
293		{
294	0	seqReportingScoreCutoff = arg.getValue();
295		}
296	0	else if (MessageManager.getString(REPORTING_DOM_EVALUE_KEY)
297		.equals(name))
298		{
299	0	domReportingEvalueCutoff = arg.getValue();
300		}
301	0	else if (MessageManager.getString(REPORTING_DOM_SCORE_KEY)
302		.equals(name))
303		{
304	0	domReportingScoreCutoff = arg.getValue();
305		}
306	0	else if (MessageManager.getString(INCLUSION_SEQ_EVALUE_KEY)
307		.equals(name))
308		{
309	0	seqInclusionEvalueCutoff = arg.getValue();
310		}
311	0	else if (MessageManager.getString(INCLUSION_SEQ_SCORE_KEY)
312		.equals(name))
313		{
314	0	seqInclusionScoreCutoff = arg.getValue();
315		}
316	0	else if (MessageManager.getString(INCLUSION_DOM_EVALUE_KEY)
317		.equals(name))
318		{
319	0	domInclusionEvalueCutoff = arg.getValue();
320		}
321	0	else if (MessageManager.getString(INCLUSION_DOM_SCORE_KEY)
322		.equals(name))
323		{
324	0	domInclusionScoreCutoff = arg.getValue();
325		}
326	0	else if (MessageManager.getString(DATABASE_KEY).equals(name))
327		{
328	0	databaseFile = new File(arg.getValue());
329	0	if (!arg.getValue().isEmpty())
330		{
331	0	searchAlignment = false;
332		}
333		}
334	0	else if (MessageManager.getString(NUMBER_OF_ITERATIONS)
335		.equals(name))
336		{
337	0	if (!arg.getValue().isEmpty())
338		{
339	0	args.add("-N");
340	0	args.add(arg.getValue());
341		}
342		}
343		}
344		}
345
346	0	if (useEvalueCutoff)
347		{
348	0	args.add("-E");
349	0	args.add(seqReportingEvalueCutoff);
350	0	args.add("--domE");
351	0	args.add(domReportingEvalueCutoff);
352
353	0	args.add("--incE");
354	0	args.add(seqInclusionEvalueCutoff);
355	0	args.add("--incdomE");
356	0	args.add(domInclusionEvalueCutoff);
357		}
358	0	else if (useScoreCutoff)
359		{
360	0	args.add("-T");
361	0	args.add(seqReportingScoreCutoff);
362	0	args.add("--domT");
363	0	args.add(domReportingScoreCutoff);
364
365	0	args.add("--incT");
366	0	args.add(seqInclusionEvalueCutoff);
367	0	args.add("--incdomT");
368	0	args.add(domInclusionEvalueCutoff);
369		}
370
371		// if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
372		// .equals(dbPath))
373	0	if (searchAlignment)
374		{
375		/*
376		* no external database specified for search, so
377		* export current alignment as 'database' to search
378		*/
379	0	databaseFile = FileUtils.createTempFile("database", ".sto");
380	0	AlignmentI al = af.getViewport().getAlignment();
381	0	AlignmentI copy = new Alignment(al);
382
383	0	deleteHmmSequences(copy);
384
385	0	if (searchAlignment)
386		{
387	0	sequencesHash = stashSequences(copy.getSequencesArray());
388		}
389
390	0	exportStockholm(copy.getSequencesArray(), databaseFile, null);
391		}
392
393	0	args.add(getFilePath(queryFile, true));
394	0	args.add(getFilePath(databaseFile, true));
395		}
396		}