Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JnetAnnotationMaker	29	66	42	124	0.00%	Show methods

Class JnetAnnotationMaker

Class JnetAnnotationMaker	Line # 29	Total Statements 66	Complexity 42	Uncovered Elements 124	TOTAL Coverage 0.00%
add_annotation(JPredFile,AlignmentI,int,boolean) : void   add_annotation(JPredFile,AlignmentI,int,boolean) : void	3131	1.01	1.01	1.01	0.0 0.00%
add_annotation(JPredFile,AlignmentI,int,boolean,int[]) : void   add_annotation(JPredFile,AlignmentI,int,boolean,int[]) : void	5454	65.065	41.041	121.0121	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.io;
22
23		import jalview.datamodel.AlignmentAnnotation;
24		import jalview.datamodel.AlignmentI;
25		import jalview.datamodel.Annotation;
26		import jalview.datamodel.SequenceI;
27		import jalview.util.MessageManager;
28
		0% Uncovered Elements: 124 (124) Complexity: 42 Complexity Density: 0.64
29		public class JnetAnnotationMaker
30		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
31	0	public static void add_annotation(JPredFile prediction, AlignmentI al,...
32		int firstSeq, boolean noMsa) throws Exception
33		{
34	0	JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa,
35		(int[]) null);
36		}
37
38		/**
39		* adds the annotation parsed by prediction to al.
40		*
41		* @param prediction
42		* JPredFile
43		* @param al
44		* AlignmentI
45		* @param firstSeq
46		* int the index of the sequence to attach the annotation to (usually
47		* zero)
48		* @param noMsa
49		* boolean
50		* @param delMap
51		* mapping from columns in JPredFile prediction to residue number in
52		* al.getSequence(firstSeq)
53		*/
		0% Uncovered Elements: 121 (121) Complexity: 41 Complexity Density: 0.63
54	0	public static void add_annotation(JPredFile prediction, AlignmentI al,...
55		int firstSeq, boolean noMsa, int[] delMap) throws Exception
56		{
57	0	int i = 0;
58	0	SequenceI[] preds = prediction.getSeqsAsArray();
59		// in the future we could search for the query
60		// sequence in the alignment before calling this function.
61	0	SequenceI seqRef = al.getSequenceAt(firstSeq);
62	0	int width = preds[0].getLength();
63	0	int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
64	0	if ((delMap != null && delMap.length > width)
65		|| (delMap == null && gapmap.length != width))
66		{
67	0	throw (new Exception(MessageManager.formatMessage(
68		"exception.number_of_residues_in_query_sequence_differ_from_prediction",
69		new String[]
70	0	{ (delMap == null ? ""
71		: MessageManager.getString("label.mapped")),
72		al.getSequenceAt(firstSeq).getName(),
73		al.getSequenceAt(firstSeq).getSequenceAsString(),
74		Integer.valueOf(width).toString() })));
75		}
76
77	0	AlignmentAnnotation annot;
78	0	Annotation[] annotations = null;
79
80	0	int existingAnnotations = 0;
81	0	if (al.getAlignmentAnnotation() != null)
82		{
83	0	existingAnnotations = al.getAlignmentAnnotation().length;
84		}
85
86	0	Annotation[] sol = new Annotation[al.getWidth()];
87	0	boolean firstsol = true;
88
89	0	while (i < preds.length)
90		{
91	0	String id = preds[i].getName().toUpperCase();
92
93	0	if (id.startsWith("LUPAS") || id.startsWith("JNET")
94		|| id.startsWith("JPRED"))
95		{
96	0	if (id.startsWith("JNETSOL"))
97		{
98	0	float amnt = (id.endsWith("25") ? 3f
99	0	: id.endsWith("5") ? 6f : 9f);
100	0	for (int spos = 0; spos < width; spos++)
101		{
102	0	int sposw = (delMap == null) ? gapmap[spos]
103		: gapmap[delMap[spos]];
104	0	if (firstsol)
105		{
106	0	sol[sposw] = new Annotation(0f);
107		}
108	0	if (preds[i].getCharAt(spos) == 'B'
109		&& (sol[sposw].value == 0f || sol[sposw].value < amnt))
110		{
111	0	sol[sposw].value = amnt;
112		}
113		}
114	0	firstsol = false;
115		}
116		else
117		{
118		// some other kind of annotation
119	0	annotations = new Annotation[al.getWidth()];
120		/*
121		* if (delMap!=null) { for (int j=0; j<annotations.length; j++)
122		* annotations[j] = new Annotation("","",'',0); }
123		*/
124	0	if (id.equals("JNETPRED") || id.equals("JNETPSSM")
125		|| id.equals("JNETFREQ") || id.equals("JNETHMM")
126		|| id.equals("JNETALIGN") || id.equals("JPRED"))
127		{
128	0	if (delMap == null)
129		{
130	0	for (int j = 0; j < width; j++)
131		{
132	0	annotations[gapmap[j]] = new Annotation("", "",
133		preds[i].getCharAt(j), 0);
134		}
135		}
136		else
137		{
138	0	for (int j = 0; j < width; j++)
139		{
140	0	annotations[gapmap[delMap[j]]] = new Annotation("", "",
141		preds[i].getCharAt(j), 0);
142		}
143		}
144		}
145	0	else if (id.equals("JNETCONF"))
146		{
147	0	if (delMap == null)
148		{
149	0	for (int j = 0; j < width; j++)
150		{
151	0	float value = new Float(preds[i].getCharAt(j) + "")
152		.floatValue();
153	0	annotations[gapmap[j]] = new Annotation(
154		preds[i].getCharAt(j) + "", "",
155		preds[i].getCharAt(j), value);
156		}
157		}
158		else
159		{
160	0	for (int j = 0; j < width; j++)
161		{
162	0	float value = new Float(preds[i].getCharAt(j) + "")
163		.floatValue();
164	0	annotations[gapmap[delMap[j]]] = new Annotation(
165		preds[i].getCharAt(j) + "", "",
166		preds[i].getCharAt(j), value);
167		}
168		}
169		}
170		else
171		{
172	0	if (delMap == null)
173		{
174	0	for (int j = 0; j < width; j++)
175		{
176	0	annotations[gapmap[j]] = new Annotation(
177		preds[i].getCharAt(j) + "", "", ' ', 0);
178		}
179		}
180		else
181		{
182	0	for (int j = 0; j < width; j++)
183		{
184	0	annotations[gapmap[delMap[j]]] = new Annotation(
185		preds[i].getCharAt(j) + "", "", ' ', 0);
186		}
187		}
188		}
189
190	0	if (id.equals("JNETCONF"))
191		{
192	0	annot = new AlignmentAnnotation(preds[i].getName(),
193		"JPred Output", annotations, 0f, 10f,
194		AlignmentAnnotation.BAR_GRAPH);
195		}
196		else
197		{
198	0	annot = new AlignmentAnnotation(preds[i].getName(),
199		"JPred Output", annotations);
200		}
201
202	0	if (seqRef != null)
203		{
204	0	annot.createSequenceMapping(seqRef, 1, true);
205	0	seqRef.addAlignmentAnnotation(annot);
206		}
207
208	0	al.addAnnotation(annot);
209	0	al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
210		- existingAnnotations - 1);
211		}
212	0	if (noMsa)
213		{
214	0	al.deleteSequence(preds[i]);
215		}
216		}
217
218	0	i++;
219		}
220	0	if (!firstsol)
221		{
222		// add the solvent accessibility
223	0	annot = new AlignmentAnnotation("Jnet Burial",
224		"<html>Prediction of Solvent Accessibility<br/>levels are<ul><li>0 - Exposed</li><li>3 - 25% or more S.A. accessible</li><li>6 - 5% or more S.A. accessible</li><li>9 - Buried (<5% exposed)</li></ul>",
225		sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH);
226
227	0	annot.validateRangeAndDisplay();
228	0	if (seqRef != null)
229		{
230	0	annot.createSequenceMapping(seqRef, 1, true);
231	0	seqRef.addAlignmentAnnotation(annot);
232		}
233	0	al.addAnnotation(annot);
234	0	al.setAnnotationIndex(annot,
235		al.getAlignmentAnnotation().length - existingAnnotations - 1);
236		}
237		// Hashtable scores = prediction.getScores();
238
239		/*
240		* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),
241		* "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
242		*
243		* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),
244		* "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
245		*
246		* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),
247		* "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
248		*/
249
250		}
251		}