Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RNAalifoldClient	52	108	46	0.0114285711.1%	Show methods

Class RNAalifoldClient

Class RNAalifoldClient	Line # 52	Total Statements 108	Complexity 46	TOTAL Coverage 0.0114285711.1%
RNAalifoldClient(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)   RNAalifoldClient(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)	6363	8.08	1.01	0.0 0.00%
getCalcId() : String   getCalcId() : String	7676	1.01	1.01	0.0 0.00%
getAlignAnalysisUITest() : AlignAnalysisUIText   getAlignAnalysisUITest() : AlignAnalysisUIText	8484	1.01	1.01	1.0 1.0100%
getServiceActionText() : String   getServiceActionText() : String	9595	1.01	1.01	0.0 0.00%
checkValidInputSeqs(boolean,List<FastaSequence>) : boolean   checkValidInputSeqs(boolean,List<FastaSequence>) : boolean	102102	1.01	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	108108	18.018	8.08	0.0 0.00%
createAnnotationRowforScoreHolder(List<AlignmentAnnotation>,String,String,TreeSet<Score>,TreeSet<Score>) : void   createAnnotationRowforScoreHolder(List<AlignmentAnnotation>,String,String,TreeSet<Score>,TreeSet<Score>) : void	170170	14.014	3.03	0.0 0.00%
constructAnnotationFromScoreHolder(AlignmentAnnotation,String,TreeSet<Score>) : AlignmentAnnotation   constructAnnotationFromScoreHolder(AlignmentAnnotation,String,TreeSet<Score>) : AlignmentAnnotation	221221	31.031	17.017	0.0 0.00%
constructTypenameAndDescription(Score) : String[]   constructTypenameAndDescription(Score) : String[]	310310	25.025	8.08	0.0 0.00%
isContact(LinkedHashMap<Range, Float>,int) : LinkedHashMap<Range, Float>   isContact(LinkedHashMap<Range, Float>,int) : LinkedHashMap<Range, Float>	377377	5.05	3.03	0.0 0.00%
isSS(char) : char   isSS(char) : char	396396	3.03	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.011428571	jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest	1PASS

 

Source view

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.jws2;
22
23		import jalview.datamodel.AlignmentAnnotation;
24		import jalview.datamodel.Annotation;
25		import jalview.gui.AlignFrame;
26		import jalview.util.MessageManager;
27		import jalview.ws.jws2.jabaws2.Jws2Instance;
28		import jalview.ws.params.WsParamSetI;
29		import jalview.ws.uimodel.AlignAnalysisUIText;
30
31		import java.text.MessageFormat;
32		import java.util.ArrayList;
33		import java.util.LinkedHashMap;
34		import java.util.List;
35		import java.util.TreeSet;
36		import java.util.regex.Pattern;
37
38		import compbio.data.sequence.FastaSequence;
39		import compbio.data.sequence.RNAStructReader.AlifoldResult;
40		import compbio.data.sequence.RNAStructScoreManager;
41		import compbio.data.sequence.Range;
42		import compbio.data.sequence.Score;
43		import compbio.metadata.Argument;
44
45		/**
46		* Client for the JABA RNA Alifold Service
47		*
48		* @author daluke - Daniel Barton
49		*
50		*/
51
		1.1% Uncovered Elements: 173 (175) Complexity: 46 Complexity Density: 0.43
52		public class RNAalifoldClient extends JabawsCalcWorker
53		{
54
55		String methodName;
56
57		AlignFrame af;
58
59		// keeps track of whether the RNAalifold result includes base contact
60		// probabilities
61		boolean bpScores;
62
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
63	0	public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,...
64		WsParamSetI preset, List<Argument> paramset)
65		{
66	0	super(sh, alignFrame, preset, paramset);
67	0	af = alignFrame;
68	0	methodName = sh.serviceType;
69	0	alignedSeqs = true;
70	0	submitGaps = true;
71	0	nucleotidesAllowed = true;
72	0	proteinAllowed = false;
73	0	initViewportParams();
74		}
75
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
76	0	@Override...
77		public String getCalcId()
78		{
79	0	return CALC_ID;
80		}
81
82		private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
83
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
84	1	public static AlignAnalysisUIText getAlignAnalysisUITest()...
85		{
86	1	return new AlignAnalysisUIText(
87		compbio.ws.client.Services.RNAalifoldWS.toString(),
88		jalview.ws.jws2.RNAalifoldClient.class, CALC_ID, true, false,
89		true, MessageManager.getString("label.rnalifold_calculations"),
90		MessageManager.getString("tooltip.rnalifold_calculations"),
91		MessageManager.getString("label.rnalifold_settings"),
92		MessageManager.getString("tooltip.rnalifold_settings"));
93		}
94
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	@Override...
96		public String getServiceActionText()
97		{
98	0	return "Submitting RNA alignment for Secondary Structure prediction using "
99		+ "RNAalifold Service";
100		}
101
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
102	0	@Override...
103		boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
104		{
105	0	return (seqs.size() > 1);
106		}
107
		0% Uncovered Elements: 28 (28) Complexity: 8 Complexity Density: 0.44
108	0	@Override...
109		public void updateResultAnnotation(boolean immediate)
110		{
111
112	0	if (immediate || !calcMan.isWorking(this) && scoremanager != null)
113		{
114
115	0	List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
116
117		// Unpack the ScoreManager
118	0	List<String> structs = ((RNAStructScoreManager) scoremanager)
119		.getStructs();
120	0	List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager)
121		.getData();
122
123		// test to see if this data object contains base pair contacts
124	0	Score fscore = data.get(0).first();
125	0	this.bpScores = (fscore.getMethod()
126		.equals(AlifoldResult.contactProbabilities.toString()));
127
128		// add annotation for the consensus sequence alignment
129	0	createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
130		structs.get(0), null, null);
131
132		// Add annotations for the mfe Structure
133	0	createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
134		structs.get(1), data.get(1), null);
135
136		// decide whether to add base pair contact probability histogram
137	0	int count = 2;
138	0	if (bpScores)
139		{
140	0	createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
141		structs.get(2), data.get(0), data.get(2));
142	0	count++;
143		}
144
145		// Now loop for the rest of the Annotations (if there it isn't stochastic
146		// output
147		// only the centroid and MEA structures remain anyway)
148	0	for (int i = count; i < structs.size(); i++)
149		{
150		// The ensemble values should be displayed in the description of the
151		// first (or all?) Stochastic Backtrack Structures.
152	0	if (!data.get(i).first().getMethod()
153		.equals(AlifoldResult.ensembleValues.toString()))
154		{
155
156	0	createAnnotationRowforScoreHolder(ourAnnot, getCalcId(),
157		structs.get(i), data.get(i), null);
158		}
159		}
160
161	0	if (ourAnnot.size() > 0)
162		{
163
164	0	updateOurAnnots(ourAnnot);
165	0	ap.adjustAnnotationHeight();
166		}
167		}
168		}
169
		0% Uncovered Elements: 18 (18) Complexity: 3 Complexity Density: 0.21
170	0	protected void createAnnotationRowforScoreHolder(...
171		List<AlignmentAnnotation> ourAnnot, String calcId, String struct,
172		TreeSet<Score> data, TreeSet<Score> descriptionData)
173		{
174		/*
175		* If contactProbability information is returned from RNAalifold it is
176		* stored in the first TreeSet<Score> object corresponding to the String Id
177		* which holds the consensus alignment. The method enumeration is then
178		* updated to AlifoldResult.contactProbabilties. This line recreates the
179		* same data object as was overwritten with the contact probabilites data.
180		*/
181	0	if (data == null)
182		{
183	0	data = compbio.data.sequence.RNAStructReader
184		.newEmptyScore(AlifoldResult.consensusAlignment);
185		}
186
187	0	if (descriptionData == null)
188		{
189	0	descriptionData = data;
190		}
191
192	0	String[] typenameAndDescription = constructTypenameAndDescription(
193		descriptionData.first());
194	0	String typename = typenameAndDescription[0];
195	0	String description = typenameAndDescription[1];
196
197	0	AlignmentAnnotation annotation = alignViewport.getAlignment()
198		.findOrCreateAnnotation(typename, calcId, false, null, null);
199
200	0	constructAnnotationFromScoreHolder(annotation, struct, data);
201
202		/*
203		* update annotation description with the free Energy, frequency in ensemble
204		* or other data where appropriate.
205		*
206		* Doesnt deal with AlifoldResult.ensembleValues, the free energy of
207		* ensemble and frequency of mfe structure in ensemble. How to deal with
208		* these?
209		*/
210	0	annotation.description = description;
211
212	0	annotation.belowAlignment = false;
213		// annotation.showAllColLabels = true;
214
215	0	alignViewport.getAlignment().validateAnnotation(annotation);
216	0	af.setMenusForViewport();
217
218	0	ourAnnot.add(annotation);
219		}
220
		0% Uncovered Elements: 55 (55) Complexity: 17 Complexity Density: 0.55
221	0	private AlignmentAnnotation constructAnnotationFromScoreHolder(...
222		AlignmentAnnotation annotation, String struct,
223		TreeSet<Score> data)
224		{
225	0	Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
226		: struct.length()];
227
228	0	if (data != null && data.size() > 1 && data.first().getMethod()
229		.equals(AlifoldResult.contactProbabilities.toString()))
230		{
231
232		// The base pair probabilities are stored in a set in scoreholder. we want
233		// a map
234	0	LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<Range, Float>();
235	0	for (Score score : data)
236		{
237		// The Score objects contain a set of size one containing the range and
238		// an ArrayList<float> of size one containing the probabilty
239	0	basePairs.put(score.getRanges().first(),
240		Float.valueOf(score.getScores().get(0)));
241		}
242
243	0	for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
244		{
245	0	if (gapMap != null)
246		{
247		// skip any gapped columns in the input data
248	0	while (!gapMap[ri])
249		{
250	0	ri++;
251		}
252		}
253		// Return all the contacts associated with position i
254	0	LinkedHashMap<Range, Float> contacts = isContact(basePairs, i + 1);
255
256	0	String description = "";
257	0	float prob = 0f;
258
259	0	if (contacts.size() == 0)
260		{
261	0	description = "No Data";
262		}
263		else
264		{
265	0	for (Range contact : contacts.keySet())
266		{
267	0	float t = contacts.get(contact);
268	0	if (t > prob)
269		{
270	0	prob = t;
271		}
272	0	description += Integer.toString(contact.from) + "->"
273		+ Integer.toString(contact.to) + ": "
274		+ Float.toString(t) + "% | ";
275		}
276		}
277
278	0	anns[ri] = new Annotation(struct.substring(i, i + 1), description,
279		isSS(struct.charAt(i)), prob);
280		}
281		}
282	0	else if (data == null || data.size() == 1)
283		{
284	0	for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
285		{
286	0	if (gapMap != null)
287		{
288		// skip any gapped columns in the input data
289	0	while (!gapMap[ri] && ri < gapMap.length)
290		{
291	0	ri++;
292		}
293	0	if (ri == gapMap.length)
294		{
295	0	break;
296		}
297		}
298	0	anns[ri] = new Annotation(struct.substring(i, i + 1), "",
299		isSS(struct.charAt(i)), Float.NaN);
300		}
301
302	0	annotation.graph = 0; // No graph
303		}
304
305	0	annotation.annotations = anns;
306
307	0	return annotation;
308		}
309
		0% Uncovered Elements: 39 (39) Complexity: 8 Complexity Density: 0.32
310	0	private String[] constructTypenameAndDescription(Score score)...
311		{
312	0	String description = "";
313	0	String typename = "";
314	0	String datatype = score.getMethod();
315
316		// Look up java switch syntax and use one here
317	0	if (datatype.equals(AlifoldResult.mfeStructure.toString()))
318		{
319
320	0	description = MessageFormat.format(
321		"Minimum Free Energy Structure. Energy: {0} = {1} + {2}",
322		score.getScores().get(0), score.getScores().get(1),
323		score.getScores().get(2));
324	0	typename = "MFE Structure";
325		}
326	0	else if (datatype
327		.equals(AlifoldResult.contactProbabilityStructure.toString()))
328		{
329	0	description = MessageFormat.format("Base Pair Contact Probabilities. "
330		+ "Energy of Ensemble: {0} Frequency of Ensemble: {1}",
331		score.getScores().get(0), score.getScores().get(1));
332	0	typename = "Contact Probabilities";
333		}
334	0	else if (datatype.equals(AlifoldResult.centroidStructure.toString()))
335		{
336	0	description = MessageFormat.format(
337		"Centroid Structure. Energy: {0} = {1} + {2}",
338		score.getScores().get(0), score.getScores().get(1),
339		score.getScores().get(2));
340	0	typename = "Centroid Structure";
341		}
342	0	else if (datatype.equals(AlifoldResult.stochBTStructure.toString()))
343		{
344	0	if (score.getScores().size() > 0)
345		{
346	0	description = MessageFormat.format("Probability: {0} Energy: {1}",
347		score.getScores().get(0), score.getScores().get(1));
348		}
349		else
350		{
351	0	description = "Stochastic Backtrack Structure";
352		}
353		}
354	0	else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
355		{
356	0	description = MessageFormat.format(
357		"Maximum Expected Accuracy Values: '{' {0} MEA={1} '}",
358		score.getScores().get(0), score.getScores().get(1));
359	0	typename = "MEA Structure";
360		}
361	0	else if (datatype.equals(AlifoldResult.consensusAlignment.toString()))
362		{
363	0	typename = "RNAalifold Consensus";
364	0	description = "Consensus Alignment Produced by RNAalifold";
365		}
366		else
367		{
368	0	typename = datatype;
369	0	description = typename;
370		}
371
372	0	return new String[] { typename, description };
373		}
374
375		// Check whether, at position i there is a base contact and return all the
376		// contacts at this position. Should be in order of descending probability.
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
377	0	private LinkedHashMap<Range, Float> isContact(...
378		LinkedHashMap<Range, Float> basePairs, int i)
379		{
380	0	LinkedHashMap<Range, Float> contacts = new LinkedHashMap<Range, Float>();
381
382	0	for (Range contact : basePairs.keySet())
383		{
384		// finds the contacts associtated with position i ordered by the natural
385		// ordering of the Scores TreeSet in ScoreManager which is, descending
386		// probability
387	0	if (contact.from == i || contact.to == i)
388		{
389	0	contacts.put(contact, basePairs.get(contact));
390		}
391		}
392
393	0	return contacts;
394		}
395
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
396	0	private char isSS(char chr)...
397		{
398	0	String regex = "\\(|\\)|\\{|\\}|\\[|\\]";
399	0	char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
400	0	return ss;
401		}
402		}