Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AADisorderClient	48	125	30	0.00%	Show methods

Class AADisorderClient

Class AADisorderClient	Line # 48	Total Statements 125	Complexity 30	TOTAL Coverage 0.00%
getServiceActionText() : String   getServiceActionText() : String	5151	1.01	1.01	0.0 0.00%
AADisorderClient(Jws2Instance)   AADisorderClient(Jws2Instance)	5959	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>	6565	79.079	27.027	0.0 0.00%
<clinit>, line 273()   <clinit>, line 273()	273273	44.044	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.jabaws2;
22
23		import jalview.analysis.AlignmentAnnotationUtils;
24		import jalview.api.FeatureColourI;
25		import jalview.bin.Cache;
26		import jalview.bin.Console;
27		import jalview.datamodel.AlignmentAnnotation;
28		import jalview.datamodel.AlignmentI;
29		import jalview.datamodel.GraphLine;
30		import jalview.datamodel.SequenceFeature;
31		import jalview.datamodel.SequenceI;
32		import jalview.datamodel.features.FeatureMatcherSetI;
33		import jalview.schemes.FeatureColour;
34		import jalview.util.ColorUtils;
35
36		import java.awt.Color;
37		import java.util.ArrayList;
38		import java.util.HashMap;
39		import java.util.Hashtable;
40		import java.util.Iterator;
41		import java.util.List;
42		import java.util.Map;
43
44		import compbio.data.sequence.Range;
45		import compbio.data.sequence.Score;
46		import compbio.data.sequence.ScoreManager.ScoreHolder;
47
		0% Uncovered Elements: 169 (169) Complexity: 30 Complexity Density: 0.24
48		public class AADisorderClient extends JabawsAnnotationInstance
49		{
50		// static configuration
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
51	0	public static String getServiceActionText()...
52		{
53	0	return "Submitting amino acid sequences for disorder prediction.";
54		}
55
56		// minSeq = 1; protein only, no gaps
57
58		// instance
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	public AADisorderClient(Jws2Instance handle)...
60		{
61	0	super(handle);
62
63		}
64
		0% Uncovered Elements: 119 (119) Complexity: 27 Complexity Density: 0.34
65	0	@Override...
66		List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
67		Map<String, FeatureColourI> featureColours,
68		Map<String, FeatureMatcherSetI> featureFilters)
69		{
70
71	0	Map<String, String[]> featureTypeMap = featureMap.get(our.getName());
72	0	Map<String, Map<String, Object>> annotTypeMap = annotMap
73		.get(our.getName());
74	0	boolean dispFeatures = false;
75	0	Map<String, SequenceFeature> fc = new Hashtable<>(),
76		fex = new Hashtable();
77	0	List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
78	0	int graphGroup = 1, lastAnnot = 0;
79
80	0	for (SequenceI seq : seqs.getSequences())
81		{
82	0	String seqId = seq.getName();
83	0	boolean sameGroup = false;
84	0	SequenceI dseq, aseq;
85	0	int base = seq.findPosition(0) - 1;
86	0	aseq = seq;
87	0	while ((dseq = seq).getDatasetSequence() != null)
88		{
89	0	seq = seq.getDatasetSequence();
90		}
91	0	ScoreHolder scores = null;
92	0	try
93		{
94	0	scores = scoremanager.getAnnotationForSequence(seqId);
95		} catch (Exception q)
96		{
97	0	Console.info("Couldn't recover disorder prediction for sequence "
98		+ seq.getName() + "(Prediction name was " + seqId + ")"
99		+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.",
100		q);
101		}
102	0	float last = Float.NaN, val = Float.NaN;
103	0	if (scores != null && scores.scores != null)
104		{
105	0	for (Score scr : scores.scores)
106		{
107
108	0	if (scr.getRanges() != null && scr.getRanges().size() > 0)
109		{
110	0	Iterator<Float> vals = scr.getScores().iterator();
111		// make features on sequence
112	0	for (Range rn : scr.getRanges())
113		{
114		// TODO: Create virtual feature settings
115	0	SequenceFeature sf;
116	0	String[] type = featureTypeMap.get(scr.getMethod());
117	0	if (type == null)
118		{
119		// create a default type for this feature
120	0	type = new String[] {
121		typeName + " (" + scr.getMethod() + ")",
122		our.getActionText() };
123		}
124	0	if (vals.hasNext())
125		{
126	0	val = vals.next().floatValue();
127	0	sf = new SequenceFeature(type[0], type[1], base + rn.from,
128		base + rn.to, val, methodName);
129		}
130		else
131		{
132	0	sf = new SequenceFeature(type[0], type[1], base + rn.from,
133		base + rn.to, methodName);
134		}
135	0	dseq.addSequenceFeature(sf);
136		// mark feature as requiring a graduated colourscheme if has
137		// variable scores
138	0	if (!Float.isNaN(last) && !Float.isNaN(val) && last != val)
139		{
140	0	fc.put(sf.getType(), sf);
141		} else
142		{
143	0	fex.put(sf.getType(), sf);
144		}
145	0	last = val;
146	0	dispFeatures = true;
147		}
148		}
149		else
150		{
151	0	if (scr.getScores().size() == 0)
152		{
153	0	continue;
154		}
155	0	String typename, calcName;
156	0	AlignmentAnnotation annot = createAnnotationRowsForScores(
157		seqs, null, ourAnnot,
158		typename = our.getName() + " (" + scr.getMethod() + ")",
159		calcName = our.getNameURI() + "/" + scr.getMethod(),
160		aseq, base + 1, scr);
161	0	annot.graph = AlignmentAnnotation.LINE_GRAPH;
162
163	0	Map<String, Object> styleMap = (annotTypeMap == null) ? null
164		: annotTypeMap.get(scr.getMethod());
165
166	0	annot.visible = (styleMap == null
167		|| styleMap.get(INVISIBLE) == null);
168	0	double[] thrsh = (styleMap == null) ? null
169		: (double[]) styleMap.get(THRESHOLD);
170	0	float[] range = (styleMap == null) ? null
171		: (float[]) styleMap.get(RANGE);
172	0	if (range != null)
173		{
174	0	annot.graphMin = range[0];
175	0	annot.graphMax = range[1];
176		}
177	0	if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
178		{
179		{
180	0	if (!sameGroup)
181		{
182	0	graphGroup++;
183	0	sameGroup = true;
184		}
185
186	0	annot.graphGroup = graphGroup;
187		}
188		}
189
190	0	annot.description = "<html>" + our.getActionText()
191		+ " - raw scores";
192	0	if (thrsh != null)
193		{
194	0	String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
195		+ thrsh[1] + " indicates disorder";
196	0	annot.threshold = new GraphLine((float) thrsh[1], threshNote,
197		Color.red);
198	0	annot.description += "<br/>" + threshNote;
199		}
200	0	annot.description += "</html>";
201	0	Color col = ColorUtils
202		.createColourFromName(typeName + scr.getMethod());
203	0	for (int p = 0, ps = annot.annotations.length; p < ps; p++)
204		{
205	0	if (annot.annotations[p] != null)
206		{
207	0	annot.annotations[p].colour = col;
208		}
209		}
210	0	annot._linecolour = col;
211		// finally, update any dataset annotation
212	0	AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(annot,
213		typename, calcName);
214		}
215		}
216		}
217	0	if (lastAnnot + 1 == ourAnnot.size())
218		{
219		// remove singleton alignment annotation row
220	0	ourAnnot.get(lastAnnot).graphGroup = -1;
221		}
222		}
223		{
224	0	if (dispFeatures)
225		{
226		// TODO: virtual feature settings
227		// feature colours need to merged with current viewport's colours
228		// simple feature colours promoted to colour-by-score ranges using
229		// currently assigned or created feature colour
230	0	for (String ft : fex.keySet())
231		{
232	0	Color col = ColorUtils.createColourFromName(ft);
233		// set graduated color as fading to white for minimum, and
234		// autoscaling to values on alignment
235
236	0	FeatureColourI ggc;
237	0	if (fc.get(ft) != null)
238		{
239	0	ggc = new FeatureColour(col, Color.white, col,
240
241		Color.white, Float.MIN_VALUE, Float.MAX_VALUE);
242	0	ggc.setAutoScaled(true);
243		}
244		else
245		{
246	0	ggc = new FeatureColour(col);
247		}
248	0	featureColours.put(ft, ggc);
249		}
250
251		}
252	0	return ourAnnot;
253		}
254		}
255
256		private static final String THRESHOLD = "THRESHOLD";
257
258		private static final String RANGE = "RANGE";
259
260		String typeName;
261
262		String methodName;
263
264		String groupName;
265
266		private static Map<String, Map<String, String[]>> featureMap;
267
268		private static Map<String, Map<String, Map<String, Object>>> annotMap;
269
270		private static String DONTCOMBINE = "DONTCOMBINE";
271
272		private static String INVISIBLE = "INVISIBLE";
		0% Uncovered Elements: 44 (44) Complexity: 1 Complexity Density: 0.02
273	0	static...
274		{
275		// TODO: turn this into some kind of configuration file that's a bit easier
276		// to edit
277	0	featureMap = new HashMap<>();
278	0	Map<String, String[]> fmap;
279	0	featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
280		fmap = new HashMap<>());
281	0	fmap.put("Glob",
282		new String[]
283		{ "Globular Domain", "Predicted globular domain" });
284	0	featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
285		fmap = new HashMap<>());
286	0	featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
287		fmap = new HashMap<>());
288	0	fmap.put("REM465", new String[] { "REM465", "Missing density" });
289	0	fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
290	0	fmap.put("COILS", new String[] { "COILS", "Random coil" });
291	0	featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
292		fmap = new HashMap<>());
293	0	fmap.put("GlobDoms",
294		new String[]
295		{ "Globular Domain", "Predicted globular domain" });
296	0	fmap.put("Disorder",
297		new String[]
298		{ "Protein Disorder", "Probable unstructured peptide region" });
299	0	Map<String, Map<String, Object>> amap;
300	0	annotMap = new HashMap<>();
301	0	annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
302		amap = new HashMap<>());
303	0	amap.put("Dydx", new HashMap<String, Object>());
304	0	amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
305	0	amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
306	0	amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
307
308	0	amap.put("SmoothedScore", new HashMap<String, Object>());
309	0	amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
310	0	amap.put("RawScore", new HashMap<String, Object>());
311	0	amap.get("RawScore").put(INVISIBLE, INVISIBLE);
312	0	annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
313		amap = new HashMap<>());
314	0	amap.put("COILS", new HashMap<String, Object>());
315	0	amap.put("HOTLOOPS", new HashMap<String, Object>());
316	0	amap.put("REM465", new HashMap<String, Object>());
317	0	amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
318	0	amap.get("COILS").put(RANGE, new float[] { 0, 1 });
319
320	0	amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
321	0	amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
322	0	amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
323	0	amap.get("REM465").put(RANGE, new float[] { 0, 1 });
324
325	0	annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
326		amap = new HashMap<>());
327	0	amap.put("Long", new HashMap<String, Object>());
328	0	amap.put("Short", new HashMap<String, Object>());
329	0	amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
330	0	amap.get("Long").put(RANGE, new float[] { 0, 1 });
331	0	amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
332	0	amap.get("Short").put(RANGE, new float[] { 0, 1 });
333	0	annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
334		amap = new HashMap<>());
335	0	amap.put("JRonn", new HashMap<String, Object>());
336	0	amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
337	0	amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
338		}
339
340		}