Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JnetAnnotationMaker	31	66	42	0.00%	Show methods

Class JnetAnnotationMaker

Class JnetAnnotationMaker	Line # 31	Total Statements 66	Complexity 42	TOTAL Coverage 0.00%
add_annotation(JPredFile,AlignmentI,int,boolean) : void   add_annotation(JPredFile,AlignmentI,int,boolean) : void	3333	1.01	1.01	0.0 0.00%
add_annotation(JPredFile,AlignmentI,int,boolean,int[]) : void   add_annotation(JPredFile,AlignmentI,int,boolean,int[]) : void	5656	65.065	41.041	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 java.util.Locale;
24
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.Annotation;
28		import jalview.datamodel.SequenceI;
29		import jalview.util.MessageManager;
30
		0% Uncovered Elements: 124 (124) Complexity: 42 Complexity Density: 0.64
31		public class JnetAnnotationMaker
32		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
33	0	public static void add_annotation(JPredFile prediction, AlignmentI al,...
34		int firstSeq, boolean noMsa) throws Exception
35		{
36	0	JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa,
37		(int[]) null);
38		}
39
40		/**
41		* adds the annotation parsed by prediction to al.
42		*
43		* @param prediction
44		* JPredFile
45		* @param al
46		* AlignmentI
47		* @param firstSeq
48		* int the index of the sequence to attach the annotation to (usually
49		* zero)
50		* @param noMsa
51		* boolean
52		* @param delMap
53		* mapping from columns in JPredFile prediction to residue number in
54		* al.getSequence(firstSeq)
55		*/
		0% Uncovered Elements: 121 (121) Complexity: 41 Complexity Density: 0.63
56	0	public static void add_annotation(JPredFile prediction, AlignmentI al,...
57		int firstSeq, boolean noMsa, int[] delMap) throws Exception
58		{
59	0	int i = 0;
60	0	SequenceI[] preds = prediction.getSeqsAsArray();
61		// in the future we could search for the query
62		// sequence in the alignment before calling this function.
63	0	SequenceI seqRef = al.getSequenceAt(firstSeq);
64	0	int width = preds[0].getLength();
65	0	int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
66	0	if ((delMap != null && delMap.length > width)
67		|| (delMap == null && gapmap.length != width))
68		{
69	0	throw (new Exception(MessageManager.formatMessage(
70		"exception.number_of_residues_in_query_sequence_differ_from_prediction",
71		new String[]
72	0	{ (delMap == null ? ""
73		: MessageManager.getString("label.mapped")),
74		al.getSequenceAt(firstSeq).getName(),
75		al.getSequenceAt(firstSeq).getSequenceAsString(),
76		Integer.valueOf(width).toString() })));
77		}
78
79	0	AlignmentAnnotation annot;
80	0	Annotation[] annotations = null;
81
82	0	int existingAnnotations = 0;
83	0	if (al.getAlignmentAnnotation() != null)
84		{
85	0	existingAnnotations = al.getAlignmentAnnotation().length;
86		}
87
88	0	Annotation[] sol = new Annotation[al.getWidth()];
89	0	boolean firstsol = true;
90
91	0	while (i < preds.length)
92		{
93	0	String id = preds[i].getName().toUpperCase(Locale.ROOT);
94
95	0	if (id.startsWith("LUPAS") || id.startsWith("JNET")
96		|| id.startsWith("JPRED"))
97		{
98	0	if (id.startsWith("JNETSOL"))
99		{
100	0	float amnt = (id.endsWith("25") ? 3f
101	0	: id.endsWith("5") ? 6f : 9f);
102	0	for (int spos = 0; spos < width; spos++)
103		{
104	0	int sposw = (delMap == null) ? gapmap[spos]
105		: gapmap[delMap[spos]];
106	0	if (firstsol)
107		{
108	0	sol[sposw] = new Annotation(0f);
109		}
110	0	if (preds[i].getCharAt(spos) == 'B'
111		&& (sol[sposw].value == 0f || sol[sposw].value < amnt))
112		{
113	0	sol[sposw].value = amnt;
114		}
115		}
116	0	firstsol = false;
117		}
118		else
119		{
120		// some other kind of annotation
121	0	annotations = new Annotation[al.getWidth()];
122		/*
123		* if (delMap!=null) { for (int j=0; j<annotations.length; j++)
124		* annotations[j] = new Annotation("","",'',0); }
125		*/
126	0	if (id.equals("JNETPRED") || id.equals("JNETPSSM")
127		|| id.equals("JNETFREQ") || id.equals("JNETHMM")
128		|| id.equals("JNETALIGN") || id.equals("JPRED"))
129		{
130	0	if (delMap == null)
131		{
132	0	for (int j = 0; j < width; j++)
133		{
134	0	annotations[gapmap[j]] = new Annotation("", "",
135		preds[i].getCharAt(j), 0);
136		}
137		}
138		else
139		{
140	0	for (int j = 0; j < width; j++)
141		{
142	0	annotations[gapmap[delMap[j]]] = new Annotation("", "",
143		preds[i].getCharAt(j), 0);
144		}
145		}
146		}
147	0	else if (id.equals("JNETCONF"))
148		{
149	0	if (delMap == null)
150		{
151	0	for (int j = 0; j < width; j++)
152		{
153	0	float value = Float.valueOf(preds[i].getCharAt(j) + "")
154		.floatValue();
155	0	annotations[gapmap[j]] = new Annotation(
156		preds[i].getCharAt(j) + "", "",
157		preds[i].getCharAt(j), value);
158		}
159		}
160		else
161		{
162	0	for (int j = 0; j < width; j++)
163		{
164	0	float value = Float.valueOf(preds[i].getCharAt(j) + "")
165		.floatValue();
166	0	annotations[gapmap[delMap[j]]] = new Annotation(
167		preds[i].getCharAt(j) + "", "",
168		preds[i].getCharAt(j), value);
169		}
170		}
171		}
172		else
173		{
174	0	if (delMap == null)
175		{
176	0	for (int j = 0; j < width; j++)
177		{
178	0	annotations[gapmap[j]] = new Annotation(
179		preds[i].getCharAt(j) + "", "", ' ', 0);
180		}
181		}
182		else
183		{
184	0	for (int j = 0; j < width; j++)
185		{
186	0	annotations[gapmap[delMap[j]]] = new Annotation(
187		preds[i].getCharAt(j) + "", "", ' ', 0);
188		}
189		}
190		}
191
192	0	if (id.equals("JNETCONF"))
193		{
194	0	annot = new AlignmentAnnotation(preds[i].getName(),
195		"JPred Output", annotations, 0f, 10f,
196		AlignmentAnnotation.BAR_GRAPH);
197		}
198		else
199		{
200	0	annot = new AlignmentAnnotation(preds[i].getName(),
201		"JPred Output", annotations);
202		}
203
204	0	if (seqRef != null)
205		{
206	0	annot.createSequenceMapping(seqRef, 1, true);
207	0	seqRef.addAlignmentAnnotation(annot);
208		}
209
210	0	al.addAnnotation(annot);
211	0	al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
212		- existingAnnotations - 1);
213		}
214	0	if (noMsa)
215		{
216	0	al.deleteSequence(preds[i]);
217		}
218		}
219
220	0	i++;
221		}
222	0	if (!firstsol)
223		{
224		// add the solvent accessibility
225	0	annot = new AlignmentAnnotation("Jnet Burial",
226		"<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>",
227		sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH);
228
229	0	annot.validateRangeAndDisplay();
230	0	if (seqRef != null)
231		{
232	0	annot.createSequenceMapping(seqRef, 1, true);
233	0	seqRef.addAlignmentAnnotation(annot);
234		}
235	0	al.addAnnotation(annot);
236	0	al.setAnnotationIndex(annot,
237		al.getAlignmentAnnotation().length - existingAnnotations - 1);
238		}
239		// Hashtable scores = prediction.getScores();
240
241		/*
242		* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),
243		* "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
244		*
245		* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),
246		* "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
247		*
248		* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),
249		* "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
250		*/
251
252		}
253		}