Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RNAalifoldClient	51	96	41	0.0126582281.3%	Show methods

Class RNAalifoldClient

Class RNAalifoldClient	Line # 51	Total Statements 96	Complexity 41	TOTAL Coverage 0.0126582281.3%
getCalcId() : String   getCalcId() : String	5656	1.01	1.01	0.0 0.00%
getAlignAnalysisUIText() : AlignAnalysisUIText   getAlignAnalysisUIText() : AlignAnalysisUIText	6464	1.01	1.01	1.0 1.0100%
getServiceActionText() : String   getServiceActionText() : String	7676	1.01	1.01	0.0 0.00%
RNAalifoldClient(Jws2Instance)   RNAalifoldClient(Jws2Instance)	8484	1.01	1.01	0.0 0.00%
annotationFromScoreManager(AlignmentI,Map<String, FeatureColourI>,Map<String, FeatureMatcherSetI>) : List<AlignmentAnnotation>   annotationFromScoreManager(AlignmentI,Map<String, FeatureColourI>,Map<String, FeatureMatcherSetI>) : List<AlignmentAnnotation>	8989	15.015	4.04	0.0 0.00%
createAnnotationRowforScoreHolder(AlignmentI,boolean[],List<AlignmentAnnotation>,String,String,TreeSet<Score>,TreeSet<Score>) : void   createAnnotationRowforScoreHolder(AlignmentI,boolean[],List<AlignmentAnnotation>,String,String,TreeSet<Score>,TreeSet<Score>) : void	145145	13.013	3.03	0.0 0.00%
constructAnnotationFromScoreHolder(boolean[],AlignmentAnnotation,String,TreeSet<Score>) : AlignmentAnnotation   constructAnnotationFromScoreHolder(boolean[],AlignmentAnnotation,String,TreeSet<Score>) : AlignmentAnnotation	194194	31.031	17.017	0.0 0.00%
constructTypenameAndDescription(Score) : String[]   constructTypenameAndDescription(Score) : String[]	283283	25.025	8.08	0.0 0.00%
isContact(LinkedHashMap<Range, Float>,int) : LinkedHashMap<Range, Float>   isContact(LinkedHashMap<Range, Float>,int) : LinkedHashMap<Range, Float>	350350	5.05	3.03	0.0 0.00%
isSS(char) : char   isSS(char) : char	369369	3.03	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.012658228	jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest	1PASS
	0.012658228	jalview.bin.CommandsTest2.do_network_structureOpeningArgsTestjalview.bin.CommandsTest2.do_network_structureOpeningArgsTest	1PASS
	0.012658228	jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest	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.jabaws2;
22
23		import jalview.api.FeatureColourI;
24		import jalview.datamodel.AlignmentAnnotation;
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.Annotation;
27		import jalview.datamodel.features.FeatureMatcherSetI;
28		import jalview.util.MessageManager;
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.Map;
36		import java.util.TreeSet;
37		import java.util.regex.Pattern;
38
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
44		/**
45		* Client for the JABA RNA Alifold Service
46		*
47		* @author daluke - Daniel Barton
48		*
49		*/
50
		1.3% Uncovered Elements: 156 (158) Complexity: 41 Complexity Density: 0.43
51		public class RNAalifoldClient extends JabawsAnnotationInstance
52		{
53
54		// configuration
55
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	@Override...
57		public String getCalcId()
58		{
59	0	return CALC_ID;
60		}
61
62		private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
63
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
64	4	public static AlignAnalysisUIText getAlignAnalysisUIText()...
65		{
66	4	return new AlignAnalysisUIText(
67		compbio.ws.client.Services.RNAalifoldWS.toString(),
68		jalview.ws.jws2.jabaws2.RNAalifoldClient.class, CALC_ID, true,
69		false, true, true, false, 2,
70		MessageManager.getString("label.rnalifold_calculations"),
71		MessageManager.getString("tooltip.rnalifold_calculations"),
72		MessageManager.getString("label.rnalifold_settings"),
73		MessageManager.getString("tooltip.rnalifold_settings"));
74		}
75
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
76	0	public static String getServiceActionText()...
77		{
78	0	return "Submitting RNA alignment for Secondary Structure prediction using "
79		+ "RNAalifold Service";
80		}
81
82		// instance
83
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
84	0	public RNAalifoldClient(Jws2Instance handle)...
85		{
86	0	super(handle);
87		}
88
		0% Uncovered Elements: 21 (21) Complexity: 4 Complexity Density: 0.27
89	0	@Override...
90		List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
91		Map<String, FeatureColourI> featureColours,
92		Map<String, FeatureMatcherSetI> featureFilters)
93		{
94	0	List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
95
96		// Unpack the ScoreManager
97	0	List<String> structs = ((RNAStructScoreManager) scoremanager)
98		.getStructs();
99	0	List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager)
100		.getData();
101
102		// test to see if this data object contains base pair contacts
103	0	Score fscore = data.get(0).first();
104	0	boolean bpScores = (fscore.getMethod()
105		.equals(AlifoldResult.contactProbabilities.toString()));
106
107		// add annotation for the consensus sequence alignment
108	0	createAnnotationRowforScoreHolder(seqs, null,
109		ourAnnot,
110		getCalcId(), structs.get(0), null, null);
111
112		// Add annotations for the mfe Structure
113	0	createAnnotationRowforScoreHolder(seqs, null,
114		ourAnnot,
115		getCalcId(), structs.get(1), data.get(1), null);
116
117		// decide whether to add base pair contact probability histogram
118	0	int count = 2;
119	0	if (bpScores)
120		{
121	0	createAnnotationRowforScoreHolder(seqs, null,
122		ourAnnot,
123		getCalcId(), structs.get(2), data.get(0), data.get(2));
124	0	count++;
125		}
126
127		// Now loop for the rest of the Annotations (if there it isn't stochastic
128		// output
129		// only the centroid and MEA structures remain anyway)
130	0	for (int i = count; i < structs.size(); i++)
131		{
132		// The ensemble values should be displayed in the description of the
133		// first (or all?) Stochastic Backtrack Structures.
134	0	if (!data.get(i).first().getMethod()
135		.equals(AlifoldResult.ensembleValues.toString()))
136		{
137
138	0	createAnnotationRowforScoreHolder(seqs, null, ourAnnot,
139		getCalcId(), structs.get(i), data.get(i), null);
140		}
141		}
142	0	return ourAnnot;
143		}
144
		0% Uncovered Elements: 17 (17) Complexity: 3 Complexity Density: 0.23
145	0	private static void createAnnotationRowforScoreHolder(...
146		AlignmentI alignment, boolean[] gapMap,
147		List<AlignmentAnnotation> ourAnnot, String calcId, String struct,
148		TreeSet<Score> data, TreeSet<Score> descriptionData)
149		{
150		/*
151		* If contactProbability information is returned from RNAalifold it is
152		* stored in the first TreeSet<Score> object corresponding to the String Id
153		* which holds the consensus alignment. The method enumeration is then
154		* updated to AlifoldResult.contactProbabilties. This line recreates the
155		* same data object as was overwritten with the contact probabilites data.
156		*/
157	0	if (data == null)
158		{
159	0	data = compbio.data.sequence.RNAStructReader
160		.newEmptyScore(AlifoldResult.consensusAlignment);
161		}
162
163	0	if (descriptionData == null)
164		{
165	0	descriptionData = data;
166		}
167
168	0	String[] typenameAndDescription = constructTypenameAndDescription(
169		descriptionData.first());
170	0	String typename = typenameAndDescription[0];
171	0	String description = typenameAndDescription[1];
172
173	0	AlignmentAnnotation annotation = alignment
174		.findOrCreateAnnotation(typename, calcId, false, null, null);
175
176	0	constructAnnotationFromScoreHolder(gapMap, annotation, struct, data);
177
178		/*
179		* update annotation description with the free Energy, frequency in ensemble
180		* or other data where appropriate.
181		*
182		* Doesnt deal with AlifoldResult.ensembleValues, the free energy of
183		* ensemble and frequency of mfe structure in ensemble. How to deal with
184		* these?
185		*/
186	0	annotation.description = description;
187
188	0	annotation.belowAlignment = false;
189		// annotation.showAllColLabels = true;
190	0	annotation.validateRangeAndDisplay();
191	0	ourAnnot.add(annotation);
192		}
193
		0% Uncovered Elements: 55 (55) Complexity: 17 Complexity Density: 0.55
194	0	private static AlignmentAnnotation constructAnnotationFromScoreHolder(...
195		boolean[] gapMap, AlignmentAnnotation annotation, String struct,
196		TreeSet<Score> data)
197		{
198	0	Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
199		: struct.length()];
200
201	0	if (data != null && data.size() > 1 && data.first().getMethod()
202		.equals(AlifoldResult.contactProbabilities.toString()))
203		{
204
205		// The base pair probabilities are stored in a set in scoreholder. we want
206		// a map
207	0	LinkedHashMap<Range, Float> basePairs = new LinkedHashMap<>();
208	0	for (Score score : data)
209		{
210		// The Score objects contain a set of size one containing the range and
211		// an ArrayList<float> of size one containing the probabilty
212	0	basePairs.put(score.getRanges().first(),
213		Float.valueOf(score.getScores().get(0)));
214		}
215
216	0	for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
217		{
218	0	if (gapMap != null)
219		{
220		// skip any gapped columns in the input data
221	0	while (!gapMap[ri])
222		{
223	0	ri++;
224		}
225		}
226		// Return all the contacts associated with position i
227	0	LinkedHashMap<Range, Float> contacts = isContact(basePairs, i + 1);
228
229	0	String description = "";
230	0	float prob = 0f;
231
232	0	if (contacts.size() == 0)
233		{
234	0	description = "No Data";
235		}
236		else
237		{
238	0	for (Range contact : contacts.keySet())
239		{
240	0	float t = contacts.get(contact);
241	0	if (t > prob)
242		{
243	0	prob = t;
244		}
245	0	description += Integer.toString(contact.from) + "->"
246		+ Integer.toString(contact.to) + ": "
247		+ Float.toString(t) + "% | ";
248		}
249		}
250
251	0	anns[ri] = new Annotation(struct.substring(i, i + 1), description,
252		isSS(struct.charAt(i)), prob);
253		}
254		}
255	0	else if (data == null || data.size() == 1)
256		{
257	0	for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
258		{
259	0	if (gapMap != null)
260		{
261		// skip any gapped columns in the input data
262	0	while (!gapMap[ri] && ri < gapMap.length)
263		{
264	0	ri++;
265		}
266	0	if (ri == gapMap.length)
267		{
268	0	break;
269		}
270		}
271	0	anns[ri] = new Annotation(struct.substring(i, i + 1), "",
272		isSS(struct.charAt(i)), Float.NaN);
273		}
274
275	0	annotation.graph = 0; // No graph
276		}
277
278	0	annotation.annotations = anns;
279
280	0	return annotation;
281		}
282
		0% Uncovered Elements: 39 (39) Complexity: 8 Complexity Density: 0.32
283	0	private static String[] constructTypenameAndDescription(Score score)...
284		{
285	0	String description = "";
286	0	String typename = "";
287	0	String datatype = score.getMethod();
288
289		// Look up java switch syntax and use one here
290	0	if (datatype.equals(AlifoldResult.mfeStructure.toString()))
291		{
292
293	0	description = MessageFormat.format(
294		"Minimum Free Energy Structure. Energy: {0} = {1} + {2}",
295		score.getScores().get(0), score.getScores().get(1),
296		score.getScores().get(2));
297	0	typename = "MFE Structure";
298		}
299	0	else if (datatype
300		.equals(AlifoldResult.contactProbabilityStructure.toString()))
301		{
302	0	description = MessageFormat.format("Base Pair Contact Probabilities. "
303		+ "Energy of Ensemble: {0} Frequency of Ensemble: {1}",
304		score.getScores().get(0), score.getScores().get(1));
305	0	typename = "Contact Probabilities";
306		}
307	0	else if (datatype.equals(AlifoldResult.centroidStructure.toString()))
308		{
309	0	description = MessageFormat.format(
310		"Centroid Structure. Energy: {0} = {1} + {2}",
311		score.getScores().get(0), score.getScores().get(1),
312		score.getScores().get(2));
313	0	typename = "Centroid Structure";
314		}
315	0	else if (datatype.equals(AlifoldResult.stochBTStructure.toString()))
316		{
317	0	if (score.getScores().size() > 0)
318		{
319	0	description = MessageFormat.format("Probability: {0} Energy: {1}",
320		score.getScores().get(0), score.getScores().get(1));
321		}
322		else
323		{
324	0	description = "Stochastic Backtrack Structure";
325		}
326		}
327	0	else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
328		{
329	0	description = MessageFormat.format(
330		"Maximum Expected Accuracy Values: '{' {0} MEA={1} '}",
331		score.getScores().get(0), score.getScores().get(1));
332	0	typename = "MEA Structure";
333		}
334	0	else if (datatype.equals(AlifoldResult.consensusAlignment.toString()))
335		{
336	0	typename = "RNAalifold Consensus";
337	0	description = "Consensus Alignment Produced by RNAalifold";
338		}
339		else
340		{
341	0	typename = datatype;
342	0	description = typename;
343		}
344
345	0	return new String[] { typename, description };
346		}
347
348		// Check whether, at position i there is a base contact and return all the
349		// contacts at this position. Should be in order of descending probability.
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
350	0	private static LinkedHashMap<Range, Float> isContact(...
351		LinkedHashMap<Range, Float> basePairs, int i)
352		{
353	0	LinkedHashMap<Range, Float> contacts = new LinkedHashMap<>();
354
355	0	for (Range contact : basePairs.keySet())
356		{
357		// finds the contacts associtated with position i ordered by the natural
358		// ordering of the Scores TreeSet in ScoreManager which is, descending
359		// probability
360	0	if (contact.from == i || contact.to == i)
361		{
362	0	contacts.put(contact, basePairs.get(contact));
363		}
364		}
365
366	0	return contacts;
367		}
368
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
369	0	private static char isSS(char chr)...
370		{
371	0	String regex = "\\(|\\)|\\{|\\}|\\[|\\]";
372	0	char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
373	0	return ss;
374		}
375
376		}