Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HmmerJSONProcessor	22	112	32	0.774193577.4%	Show methods

Class HmmerJSONProcessor

Class HmmerJSONProcessor	Line # 22	Total Statements 112	Complexity 32	TOTAL Coverage 0.774193577.4%
HmmerJSONProcessor(AlignmentI)   HmmerJSONProcessor(AlignmentI)	3434	1.01	1.01	1.0 1.0100%
parseFrom(FileParse) : void   parseFrom(FileParse) : void	3939	18.018	5.05	0.72727275 0.7272727572.7%
addStatistics(JSONObject) : void   addStatistics(JSONObject) : void	8686	4.04	1.01	1.0 1.0100%
addHit(JSONObject,long) : void   addHit(JSONObject,long) : void	129129	37.037	6.06	0.9111111 0.911111191.1%
updateView(AlignmentViewport) : void   updateView(AlignmentViewport) : void	210210	3.03	1.01	0.0 0.00%
run() : void   run() : void	274274	1.01	1.01	0.0 0.00%
addRedundantSeqGroup(SequenceI,long,long,JSONArray,boolean) : void   addRedundantSeqGroup(SequenceI,long,long,JSONArray,boolean) : void	219219	26.026	10.010	0.525 0.52552.5%
addArchGroup(SequenceI,String) : void   addArchGroup(SequenceI,String) : void	286286	10.010	2.02	1.0 1.0100%
parsePosteriorProb(String) : AlignmentAnnotation   parsePosteriorProb(String) : AlignmentAnnotation	305305	12.012	5.05	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.7741935	jalview.ws.ebi.HmmerJSONProcessTest.parseJsonResultTestjalview.ws.ebi.HmmerJSONProcessTest.parseJsonResultTest	1PASS
	0.62580645	jalview.ws.ebi.HmmerJSONProcessTest.parseHitTestjalview.ws.ebi.HmmerJSONProcessTest.parseHitTest	1PASS

 

Source view

1		package jalview.ws.ebi;
2
3		import jalview.datamodel.AlignmentAnnotation;
4		import jalview.datamodel.AlignmentI;
5		import jalview.datamodel.Annotation;
6		import jalview.datamodel.SequenceFeature;
7		import jalview.datamodel.SequenceGroup;
8		import jalview.datamodel.SequenceI;
9		import jalview.io.FileParse;
10		import jalview.viewmodel.AlignmentViewport;
11
12		import java.io.IOException;
13		import java.util.ArrayList;
14		import java.util.HashMap;
15		import java.util.List;
16		import java.util.Map;
17
18		import org.json.simple.JSONArray;
19		import org.json.simple.JSONObject;
20		import org.json.simple.parser.JSONParser;
21
		77.4% Uncovered Elements: 35 (155) Complexity: 32 Complexity Density: 0.29
22		public class HmmerJSONProcessor
23		{
24		/**
25		* result to be annotated. may not be null
26		*/
27		AlignmentI resultAl;
28
29		/**
30		* viewport on the alignment. may be null at construction time
31		*/
32		AlignmentViewport viewAl = null;
33
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
34	2	public HmmerJSONProcessor(AlignmentI searchResult)...
35		{
36	2	resultAl = searchResult;
37		}
38
		72.7% Uncovered Elements: 6 (22) Complexity: 5 Complexity Density: 0.28
39	1	public void parseFrom(FileParse jsonsource) throws IOException,...
40		OutOfMemoryError
41		{
42	1	JSONParser hmmerResultParser = new JSONParser();
43	1	Object jsonResults = null;
44	1	try
45		{
46	1	jsonResults = hmmerResultParser.parse(jsonsource.getReader());
47		} catch (Exception p)
48		{
49	0	throw new IOException("While parsing from " + jsonsource.getInFile(),
50		p);
51		}
52	1	if (jsonResults == null)
53		{
54	0	throw new IOException("No data at" + jsonsource.getInFile());
55		}
56	1	if (!(jsonResults instanceof JSONObject))
57		{
58	0	throw new IOException("Unexpected JSON model at "
59		+ jsonsource.getInFile());
60		}
61	1	try
62		{
63	1	JSONObject hmmsearchr = (JSONObject) ((JSONObject) jsonResults)
64		.get("results");
65		// now process the hits
66	1	addStatistics((JSONObject) hmmsearchr.get("stats"));
67	1	JSONArray jsonArray = (JSONArray) hmmsearchr.get("hits");
68	1	long p = 1;
69	1	for (Object hit : jsonArray)
70		{
71	543	JSONObject hmmhit = (JSONObject) hit;
72	543	addHit(hmmhit, p++);
73		}
74		} catch (ClassCastException q)
75		{
76	0	throw new IOException("Unexpected JSON model content at "
77		+ jsonsource.getInFile(), q);
78		}
79		}
80
81		/**
82		*
83		* @param object
84		* - actually a JSONObject key value set of search statistics.
85		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
86	1	public void addStatistics(JSONObject stats)...
87		{
88	1	for (Object stat : stats.keySet())
89		{
90	17	String key = (String) stat;
91	17	Object val = stats.get(key);
92	17	resultAl.setProperty(key, "" + val);
93		}
94		}
95
96		// encodings for JSON keys
97		/**
98		* score becomes sequence associated AlignmentAnnotation
99		*/
100		private String[] score = { "aliId", "ali_IdCount", "bitscore", "ievalue",
101		"aliSim", "aliSimCount", "aliL", "aliSim", "ievalue", "cevalue" };
102
103		/**
104		* attrib becomes numeric or binary attribute for sequence with respect to
105		* this hmmsearch run
106		*/
107		private String[] attrib = { "bias", "oasc", "is_included", "is_reported" };
108
109		/**
110		* name of the hmmsearch query
111		*/
112		private String[] label = { "alihmmname" // (query label?)},
113		};
114
115		/**
116		* integer attributes for each
117		*/
118		private String[] ipos = { "alihmmfrom", "alihmmto" }, pos_l = {
119		"alimline", "alimodel", "alirfline" };
120
121		/**
122		* positional quantitative annotation encoded as strings.
123		*/
124		private String[] pos_nscore = { "alippline" };
125
126		//
127		// mapping of keys to types of property on sequence
128		//
		91.1% Uncovered Elements: 4 (45) Complexity: 6 Complexity Density: 0.16
129	544	public void addHit(JSONObject hmmrhit, long p)...
130		{
131	544	String sname = (String) hmmrhit.get("name");
132	544	SequenceI[] hits = resultAl.findSequenceMatch(sname);
133	544	if (hits == null)
134		{
135	0	System.err.println("No seq for " + sname);
136		}
137	544	double pvalue = (Double) hmmrhit.get("pvalue");
138
139	544	double evalue = Double.valueOf("" + hmmrhit.get("evalue"));
140	544	for (Object domainhit : ((JSONArray) hmmrhit.get("domains")))
141		{
142	588	JSONObject dhit = (JSONObject) domainhit;
143		// dhit.get(key)
144
145		// alihmmfrom,alihmmto alimodel
146	588	long alihmmfrom = (long) dhit.get("alihmmfrom"), alihmmto = (long) dhit
147		.get("alihmmto"), alisqfrom = (long) dhit.get("alisqfrom"), alisqto = (long) dhit
148		.get("alisqto");
149
150		// alisqfrom,alisqto,aliaseq
151
152		// alippline
153	588	String aliaseq = (String) dhit.get("aliaseq"), alimodel = (String) dhit
154		.get("alimodel"), ppline = (String) dhit.get("alippline");
155		//
156	588	int found = 0;
157	588	SequenceI firsthit = null;
158	588	for (SequenceI hitseq : hits)
159		{
160		// match alisqfrom,alisqto,seq
161	682	if (hitseq.getStart() == alisqfrom && hitseq.getEnd() == alisqto)
162		{
163	588	if (found == 0)
164		{
165	588	firsthit = hitseq;
166		}
167	588	found++; // annotated a sequence
168	588	AlignmentAnnotation alipp = parsePosteriorProb(ppline);
169	588	AlignmentAnnotation pval = new AlignmentAnnotation("p-value",
170		"hmmer3 pvalue", pvalue);
171	588	AlignmentAnnotation eval = new AlignmentAnnotation("e-value",
172		"hmmer3 evalue", evalue);
173	588	pval.setCalcId("HMMER3");
174	588	eval.setCalcId("HMMER3");
175	588	alipp.setCalcId("HMMER3");
176	588	hitseq.addAlignmentAnnotation(pval);
177	588	hitseq.addAlignmentAnnotation(eval);
178	588	alipp.createSequenceMapping(hitseq, hitseq.getStart(), false);
179	588	hitseq.addAlignmentAnnotation(alipp);
180	588	String arch;
181	588	hitseq.addSequenceFeature(new SequenceFeature(
182		"Pfam Domain Architecture", (hmmrhit.get("archindex"))
183		+ " " + (arch = (String) hmmrhit.get("arch")), 0,
184		0,
185	588	(hmmrhit.get("archScore") != null ? Integer
186		.valueOf((String) hmmrhit.get("archScore")) : 0f),
187		"HMMER3"));
188	588	addArchGroup(hitseq, arch);
189	588	alipp.setScore(Double.valueOf("" + dhit.get("bitscore")));
190	588	alipp.adjustForAlignment();
191	588	resultAl.addAnnotation(pval);
192	588	resultAl.addAnnotation(eval);
193	588	resultAl.addAnnotation(alipp);
194	588	alipp.validateRangeAndDisplay();
195		}
196		}
197		// look for other sequences represented by this hit and create rep groups
198		// could be in "pdbs", or ..
199	588	addRedundantSeqGroup(firsthit, alisqfrom, alisqto,
200		(JSONArray) hmmrhit.get("seqs"), true);
201		}
202		}
203
204		/**
205		* series of operations to perform for the viewpanel associated with the
206		* alignment
207		*/
208		private List<Runnable> viewOps = new ArrayList<Runnable>();
209
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
210	0	public void updateView(AlignmentViewport view)...
211		{
212	0	viewAl = view;
213	0	for (Runnable op : viewOps)
214		{
215	0	op.run();
216		}
217		}
218
		52.5% Uncovered Elements: 19 (40) Complexity: 10 Complexity Density: 0.38
219	588	private void addRedundantSeqGroup(final SequenceI firsthit,...
220		long alisqfrom, long alisqto, JSONArray others, boolean justDelete)
221		{
222	588	if (others != null)
223		{
224	231	final SequenceGroup repgroup = new SequenceGroup();
225	231	repgroup.setSeqrep(firsthit);
226	231	repgroup.addOrRemove(firsthit, false);
227	231	repgroup.setStartRes(0);
228	231	repgroup.setEndRes(resultAl.getWidth() - 1);
229	231	for (Object otherseq : others.toArray(new JSONObject[0]))
230		{
231	594	String repseq = (String) ((JSONObject) otherseq).get("dn");
232	594	SequenceI[] other = resultAl.findSequenceMatch(repseq);
233	594	if (other != null && other.length > 0)
234		{
235	573	if (justDelete)
236		{
237	573	for (SequenceI oth : other)
238		{
239	594	resultAl.deleteSequence(oth);
240		}
241	573	;
242		}
243		else
244		{
245	0	int ofound = 0;
246	0	for (SequenceI oth : other)
247		{
248	0	if (oth.getStart() == alisqfrom && oth.getEnd() == alisqto)
249		{
250	0	ofound++;
251	0	repgroup.addSequence(oth, false);
252		}
253		}
254	0	if (ofound == 0)
255		{
256	0	System.err.println("Warn - no match for redundant hit "
257		+ repseq + "/" + alisqfrom + "-" + alisqto);
258		}
259	0	if (ofound > 1)
260		{
261	0	System.err
262		.println("Warn - multiple matches for redundant hit "
263		+ repseq + "/" + alisqfrom + "-" + alisqto);
264		}
265		}
266		}
267		}
268	231	if (repgroup.getSequences().size() > 1)
269		{
270		// queue a hide operation
271	0	final HmmerJSONProcessor me = this;
272	0	viewOps.add(new Runnable()
273		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
274	0	@Override...
275		public void run()
276		{
277	0	me.viewAl.hideRepSequences(firsthit, repgroup);
278		}
279		});
280		}
281		}
282		}
283
284		Map<String, SequenceGroup> groups = new HashMap<String, SequenceGroup>();
285
		100% Uncovered Elements: 0 (12) Complexity: 2 Complexity Density: 0.2
286	588	private void addArchGroup(SequenceI seqToAdd, String groupNam)...
287		{
288	588	SequenceGroup sg = groups.get(groupNam);
289	588	if (sg == null)
290		{
291	52	sg = new SequenceGroup();
292	52	sg.setName(groupNam);
293	52	sg.addSequence(seqToAdd, false);
294	52	sg.setStartRes(0);
295	52	sg.setEndRes(resultAl.getWidth() - 1);
296	52	groups.put(groupNam, sg);
297	52	resultAl.addGroup(sg);
298		}
299		else
300		{
301	536	sg.addSequence(seqToAdd, false);
302		}
303		}
304
		100% Uncovered Elements: 0 (18) Complexity: 5 Complexity Density: 0.42
305	588	private AlignmentAnnotation parsePosteriorProb(String ppline)...
306		{
307	588	Annotation[] ae = new Annotation[ppline.length()];
308	588	int spos = 0;
309	46572	for (int i = 0, iSize = ppline.length(); i < iSize; i++)
310		{
311	45984	char pp = ppline.charAt(i);
312	45984	if (pp == '*')
313		{
314	35142	ae[spos++] = new Annotation(10f);
315		}
316		else
317		{
318	10842	if (pp >= '0' && pp <= '9')
319		{
320	10267	ae[spos++] = new Annotation(Integer.valueOf("" + pp));
321		}
322		}
323		}
324	588	AlignmentAnnotation pprob = new AlignmentAnnotation(
325		"Posterior Probability",
326		"Likelihood of HMM fit at each hit position.", ae);
327	588	pprob.graph = AlignmentAnnotation.BAR_GRAPH;
328	588	pprob.visible = false;
329	588	return pprob;
330		}
331		}