Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AADisorderClient	49	144	38	0.00%	Show methods

Class AADisorderClient

Class AADisorderClient	Line # 49	Total Statements 144	Complexity 38	TOTAL Coverage 0.00%
AADisorderClient(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)   AADisorderClient(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)	6464	9.09	1.01	0.0 0.00%
getServiceActionText() : String   getServiceActionText() : String	7979	1.01	1.01	0.0 0.00%
checkValidInputSeqs(boolean,List<FastaSequence>) : boolean   checkValidInputSeqs(boolean,List<FastaSequence>) : boolean	8585	1.01	1.01	0.0 0.00%
<clinit>, line 98()   <clinit>, line 98()	9898	44.044	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	165165	88.088	33.033	0.0 0.00%
getCalcId() : String   getCalcId() : String	373373	1.01	1.01	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.jws2;
22
23		import jalview.api.FeatureColourI;
24		import jalview.bin.Console;
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.GraphLine;
27		import jalview.datamodel.SequenceFeature;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.AlignFrame;
30		import jalview.schemes.FeatureColour;
31		import jalview.util.ColorUtils;
32		import jalview.ws.jws2.jabaws2.Jws2Instance;
33		import jalview.ws.params.WsParamSetI;
34
35		import java.awt.Color;
36		import java.util.ArrayList;
37		import java.util.HashMap;
38		import java.util.Hashtable;
39		import java.util.Iterator;
40		import java.util.List;
41		import java.util.Map;
42
43		import compbio.data.sequence.FastaSequence;
44		import compbio.data.sequence.Range;
45		import compbio.data.sequence.Score;
46		import compbio.data.sequence.ScoreManager.ScoreHolder;
47		import compbio.metadata.Argument;
48
		0% Uncovered Elements: 200 (200) Complexity: 38 Complexity Density: 0.26
49		public class AADisorderClient extends JabawsCalcWorker
50		{
51
52		private static final String THRESHOLD = "THRESHOLD";
53
54		private static final String RANGE = "RANGE";
55
56		String typeName;
57
58		String methodName;
59
60		String groupName;
61
62		AlignFrame af;
63
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11
64	0	public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,...
65		WsParamSetI thePreset, List<Argument> paramset)
66		{
67	0	super(sh, alignFrame, thePreset, paramset);
68	0	af = alignFrame;
69	0	typeName = sh.action;
70	0	methodName = sh.serviceType;
71
72	0	submitGaps = false;
73	0	alignedSeqs = false;
74	0	nucleotidesAllowed = false;
75	0	proteinAllowed = true;
76	0	bySequence = true;
77		}
78
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
79	0	@Override...
80		public String getServiceActionText()
81		{
82	0	return "Submitting amino acid sequences for disorder prediction.";
83		}
84
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
85	0	@Override...
86		boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
87		{
88	0	return (seqs.size() > 0);
89		}
90
91		private static Map<String, Map<String, String[]>> featureMap;
92
93		private static Map<String, Map<String, Map<String, Object>>> annotMap;
94
95		private static String DONTCOMBINE = "DONTCOMBINE";
96
97		private static String INVISIBLE = "INVISIBLE";
		0% Uncovered Elements: 44 (44) Complexity: 1 Complexity Density: 0.02
98	0	static...
99		{
100		// TODO: turn this into some kind of configuration file that's a bit easier
101		// to edit
102	0	featureMap = new HashMap<>();
103	0	Map<String, String[]> fmap;
104	0	featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
105		fmap = new HashMap<>());
106	0	fmap.put("Glob",
107		new String[]
108		{ "Globular Domain", "Predicted globular domain" });
109	0	featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
110		fmap = new HashMap<>());
111	0	featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
112		fmap = new HashMap<>());
113	0	fmap.put("REM465", new String[] { "REM465", "Missing density" });
114	0	fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
115	0	fmap.put("COILS", new String[] { "COILS", "Random coil" });
116	0	featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
117		fmap = new HashMap<>());
118	0	fmap.put("GlobDoms",
119		new String[]
120		{ "Globular Domain", "Predicted globular domain" });
121	0	fmap.put("Disorder",
122		new String[]
123		{ "Protein Disorder", "Probable unstructured peptide region" });
124	0	Map<String, Map<String, Object>> amap;
125	0	annotMap = new HashMap<>();
126	0	annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
127		amap = new HashMap<>());
128	0	amap.put("Dydx", new HashMap<String, Object>());
129	0	amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
130	0	amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
131	0	amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
132
133	0	amap.put("SmoothedScore", new HashMap<String, Object>());
134	0	amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
135	0	amap.put("RawScore", new HashMap<String, Object>());
136	0	amap.get("RawScore").put(INVISIBLE, INVISIBLE);
137	0	annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
138		amap = new HashMap<>());
139	0	amap.put("COILS", new HashMap<String, Object>());
140	0	amap.put("HOTLOOPS", new HashMap<String, Object>());
141	0	amap.put("REM465", new HashMap<String, Object>());
142	0	amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
143	0	amap.get("COILS").put(RANGE, new float[] { 0, 1 });
144
145	0	amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
146	0	amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
147	0	amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
148	0	amap.get("REM465").put(RANGE, new float[] { 0, 1 });
149
150	0	annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
151		amap = new HashMap<>());
152	0	amap.put("Long", new HashMap<String, Object>());
153	0	amap.put("Short", new HashMap<String, Object>());
154	0	amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
155	0	amap.get("Long").put(RANGE, new float[] { 0, 1 });
156	0	amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
157	0	amap.get("Short").put(RANGE, new float[] { 0, 1 });
158	0	annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
159		amap = new HashMap<>());
160	0	amap.put("JRonn", new HashMap<String, Object>());
161	0	amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
162	0	amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
163		}
164
		0% Uncovered Elements: 138 (138) Complexity: 33 Complexity Density: 0.38
165	0	@Override...
166		public void updateResultAnnotation(boolean immediate)
167		{
168
169	0	if (immediate || !calcMan.isWorking(this) && scoremanager != null)
170		{
171	0	Map<String, String[]> featureTypeMap = featureMap
172		.get(service.serviceType);
173	0	Map<String, Map<String, Object>> annotTypeMap = annotMap
174		.get(service.serviceType);
175	0	boolean dispFeatures = false;
176	0	Map<String, Object> fc = new Hashtable<>();
177	0	List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
178		/**
179		* grouping for any annotation rows created
180		*/
181	0	int graphGroup = 1;
182	0	if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
183		{
184	0	for (AlignmentAnnotation ala : alignViewport.getAlignment()
185		.getAlignmentAnnotation())
186		{
187	0	if (ala.graphGroup > graphGroup)
188		{
189	0	graphGroup = ala.graphGroup;
190		}
191		}
192		}
193
194	0	for (String seqId : seqNames.keySet())
195		{
196	0	boolean sameGroup = false;
197	0	SequenceI dseq, aseq, seq = seqNames.get(seqId);
198	0	int base = seq.findPosition(start) - 1;
199	0	aseq = seq;
200	0	while ((dseq = seq).getDatasetSequence() != null)
201		{
202	0	seq = seq.getDatasetSequence();
203		}
204	0	ScoreHolder scores = null;
205	0	try
206		{
207	0	scores = scoremanager.getAnnotationForSequence(seqId);
208		} catch (Exception q)
209		{
210	0	Console.info("Couldn't recover disorder prediction for sequence "
211		+ seq.getName() + "(Prediction name was " + seqId + ")"
212		+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
213		}
214	0	float last = Float.NaN, val = Float.NaN;
215	0	int lastAnnot = ourAnnot.size();
216	0	if (scores != null && scores.scores != null)
217		{
218	0	for (Score scr : scores.scores)
219		{
220
221	0	if (scr.getRanges() != null && scr.getRanges().size() > 0)
222		{
223	0	Iterator<Float> vals = scr.getScores().iterator();
224		// make features on sequence
225	0	for (Range rn : scr.getRanges())
226		{
227
228	0	SequenceFeature sf;
229	0	String[] type = featureTypeMap.get(scr.getMethod());
230	0	if (type == null)
231		{
232		// create a default type for this feature
233	0	type = new String[] {
234		typeName + " (" + scr.getMethod() + ")",
235		service.getActionText() };
236		}
237	0	if (vals.hasNext())
238		{
239	0	val = vals.next().floatValue();
240	0	sf = new SequenceFeature(type[0], type[1], base + rn.from,
241		base + rn.to, val, methodName);
242		}
243		else
244		{
245	0	sf = new SequenceFeature(type[0], type[1], base + rn.from,
246		base + rn.to, methodName);
247		}
248	0	dseq.addSequenceFeature(sf);
249	0	if (last != val && !Float.isNaN(last))
250		{
251	0	fc.put(sf.getType(), sf);
252		}
253	0	last = val;
254	0	dispFeatures = true;
255		}
256		}
257		else
258		{
259	0	if (scr.getScores().size() == 0)
260		{
261	0	continue;
262		}
263	0	String typename, calcName;
264	0	AlignmentAnnotation annot = createAnnotationRowsForScores(
265		ourAnnot,
266		typename = service.serviceType + " ("
267		+ scr.getMethod() + ")",
268		calcName = service.getServiceTypeURI() + "/"
269		+ scr.getMethod(),
270		aseq, base + 1, scr);
271	0	annot.graph = AlignmentAnnotation.LINE_GRAPH;
272
273	0	Map<String, Object> styleMap = (annotTypeMap == null) ? null
274		: annotTypeMap.get(scr.getMethod());
275
276	0	annot.visible = (styleMap == null
277		|| styleMap.get(INVISIBLE) == null);
278	0	double[] thrsh = (styleMap == null) ? null
279		: (double[]) styleMap.get(THRESHOLD);
280	0	float[] range = (styleMap == null) ? null
281		: (float[]) styleMap.get(RANGE);
282	0	if (range != null)
283		{
284	0	annot.graphMin = range[0];
285	0	annot.graphMax = range[1];
286		}
287	0	if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
288		{
289		{
290	0	if (!sameGroup)
291		{
292	0	graphGroup++;
293	0	sameGroup = true;
294		}
295
296	0	annot.graphGroup = graphGroup;
297		}
298		}
299
300	0	annot.description = "<html>" + service.getActionText()
301		+ " - raw scores";
302	0	if (thrsh != null)
303		{
304	0	String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
305		+ thrsh[1] + " indicates disorder";
306	0	annot.threshold = new GraphLine((float) thrsh[1],
307		threshNote, Color.red);
308	0	annot.description += "<br/>" + threshNote;
309		}
310	0	annot.description += "</html>";
311	0	Color col = ColorUtils
312		.createColourFromName(typeName + scr.getMethod());
313	0	for (int p = 0, ps = annot.annotations.length; p < ps; p++)
314		{
315	0	if (annot.annotations[p] != null)
316		{
317	0	annot.annotations[p].colour = col;
318		}
319		}
320	0	annot._linecolour = col;
321		// finally, update any dataset annotation
322	0	replaceAnnotationOnAlignmentWith(annot, typename, calcName,
323		aseq);
324		}
325		}
326		}
327	0	if (lastAnnot + 1 == ourAnnot.size())
328		{
329		// remove singleton alignment annotation row
330	0	ourAnnot.get(lastAnnot).graphGroup = -1;
331		}
332		}
333		{
334	0	if (dispFeatures)
335		{
336	0	jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
337		.cloneFeatureRenderer();
338	0	for (String ft : fc.keySet())
339		{
340	0	FeatureColourI gc = fr.getFeatureStyle(ft);
341	0	if (gc.isSimpleColour())
342		{
343		// set graduated color as fading to white for minimum, and
344		// autoscaling to values on alignment
345	0	FeatureColourI ggc = new FeatureColour(gc.getColour(),
346		Color.white, gc.getColour(), Color.white,
347		Float.MIN_VALUE, Float.MAX_VALUE);
348	0	ggc.setAutoScaled(true);
349	0	fr.setColour(ft, ggc);
350		}
351		}
352		// TODO: JAL-1150 - create sequence feature settings API for defining
353		// styles and enabling/disabling feature overlay on alignment panel
354	0	((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
355	0	if (af.alignPanel == ap)
356		{
357		// only do this if the alignFrame is currently showing this view.
358	0	af.setShowSeqFeatures(true);
359		}
360		}
361	0	if (ourAnnot.size() > 0)
362		{
363		// Modify the visible annotation on the alignment viewport with the
364		// new alignment annotation rows created.
365	0	updateOurAnnots(ourAnnot);
366	0	ap.adjustAnnotationHeight();
367	0	ap.paintAlignment(true, true);
368		}
369		}
370		}
371		}
372
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
373	0	@Override...
374		public String getCalcId()
375		{
376		// Disorder predictions are not dynamically updated so we return null
377	0	return null;
378		}
379
380		}