Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JPredFile	56	115	44	0.00%	Show methods

Class JPredFile

Class JPredFile	Line # 56	Total Statements 115	Complexity 44	TOTAL Coverage 0.00%
JPredFile(Object,DataSourceType)   JPredFile(Object,DataSourceType)	8383	1.01	1.01	0.0 0.00%
JPredFile(FileParse)   JPredFile(FileParse)	8989	1.01	1.01	0.0 0.00%
setQuerySeqPosition(int) : void   setQuerySeqPosition(int) : void	100100	1.01	1.01	0.0 0.00%
getQuerySeqPosition() : int   getQuerySeqPosition() : int	110110	1.01	1.01	0.0 0.00%
getScores() : Hashtable   getScores() : Hashtable	120120	1.01	1.01	0.0 0.00%
getSymscores() : Hashtable   getSymscores() : Hashtable	130130	1.01	1.01	0.0 0.00%
initData() : void   initData() : void	138138	4.04	1.01	0.0 0.00%
parse() : void   parse() : void	150150	83.083	28.028	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	361361	1.01	1.01	0.0 0.00%
main(String[]) : void   main(String[]) : void	372372	5.05	3.03	0.0 0.00%
removeNonSequences() : void   removeNonSequences() : void	398398	16.016	5.05	0.0 0.00%

 

Contributing tests

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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		/**
22		* PredFile.java
23		* JalviewX / Vamsas Project
24		* JPred.seq.concise reader
25		*/
26		package jalview.io;
27
28		import java.util.Locale;
29
30		import jalview.datamodel.Alignment;
31		import jalview.datamodel.AlignmentAnnotation;
32		import jalview.datamodel.Sequence;
33		import jalview.datamodel.SequenceI;
34		import jalview.util.MessageManager;
35
36		import java.io.IOException;
37		import java.util.Hashtable;
38		import java.util.StringTokenizer;
39		import java.util.Vector;
40
41		/**
42		* Parser for the JPred/JNet concise format. This is a series of CSV lines, each
43		* line is either a sequence (QUERY), a sequence profile (align;), or jnet
44		* prediction annotation (anything else). Automagic translation happens for
45		* annotation called 'JNETPRED' (translated to Secondary Structure Prediction),
46		* or 'JNETCONF' (translates to 'Prediction Confidence'). Numeric scores are
47		* differentiated from symbolic by being parseable into a float vector. They are
48		* put in Scores. Symscores gets the others. JNetAnnotationMaker translates the
49		* data parsed by this object into annotation on an alignment. It is
50		* automatically called but can be used to transfer the annotation onto a
51		* sequence in another alignment (and insert gaps where necessary)
52		*
53		* @author jprocter
54		* @version $Revision$
55		*/
		0% Uncovered Elements: 178 (178) Complexity: 44 Complexity Density: 0.38
56		public class JPredFile extends AlignFile
57		{
58		Vector ids;
59
60		Vector conf;
61
62		Hashtable Scores; // Hash of names and score vectors
63
64		Hashtable Symscores; // indexes of symbol annotation properties in sequenceI
65
66		// vector
67
68		private int QuerySeqPosition;
69
70		/**
71		* Creates a new JPredFile object.
72		*
73		* BH allows File or String
74		*
75		* @param inFile
76		* DOCUMENT ME!
77		* @param sourceType
78		* DOCUMENT ME!
79		*
80		* @throws IOException
81		* DOCUMENT ME!
82		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	public JPredFile(Object inFile, DataSourceType sourceType)...
84		throws IOException
85		{
86	0	super(inFile, sourceType);
87		}
88
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
89	0	public JPredFile(FileParse source) throws IOException...
90		{
91	0	super(source);
92		}
93
94		/**
95		* DOCUMENT ME!
96		*
97		* @param QuerySeqPosition
98		* DOCUMENT ME!
99		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
100	0	public void setQuerySeqPosition(int QuerySeqPosition)...
101		{
102	0	this.QuerySeqPosition = QuerySeqPosition;
103		}
104
105		/**
106		* DOCUMENT ME!
107		*
108		* @return DOCUMENT ME!
109		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	public int getQuerySeqPosition()...
111		{
112	0	return QuerySeqPosition;
113		}
114
115		/**
116		* DOCUMENT ME!
117		*
118		* @return DOCUMENT ME!
119		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
120	0	public Hashtable getScores()...
121		{
122	0	return Scores;
123		}
124
125		/**
126		* DOCUMENT ME!
127		*
128		* @return DOCUMENT ME!
129		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
130	0	public Hashtable getSymscores()...
131		{
132	0	return Symscores;
133		}
134
135		/**
136		* DOCUMENT ME!
137		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
138	0	@Override...
139		public void initData()
140		{
141	0	super.initData();
142	0	Scores = new Hashtable();
143	0	ids = null;
144	0	conf = null;
145		}
146
147		/**
148		* parse a JPred concise file into a sequence-alignment like object.
149		*/
		0% Uncovered Elements: 125 (125) Complexity: 28 Complexity Density: 0.34
150	0	@Override...
151		public void parse() throws IOException
152		{
153		// JBPNote log.jalview.bin.Console.outPrintln("all read in ");
154	0	String line;
155	0	QuerySeqPosition = -1;
156	0	noSeqs = 0;
157
158	0	Vector seq_entries = new Vector();
159	0	Vector ids = new Vector();
160	0	Hashtable Symscores = new Hashtable();
161
162	0	while ((line = nextLine()) != null)
163		{
164		// Concise format allows no comments or non comma-formatted data
165	0	StringTokenizer str = new StringTokenizer(line, ":");
166	0	String id = "";
167
168	0	if (!str.hasMoreTokens())
169		{
170	0	continue;
171		}
172
173	0	id = str.nextToken();
174
175	0	String seqsym = str.nextToken();
176	0	StringTokenizer symbols = new StringTokenizer(seqsym, ",");
177
178		// decide if we have more than just alphanumeric symbols
179	0	int numSymbols = symbols.countTokens();
180
181	0	if (numSymbols == 0)
182		{
183	0	continue;
184		}
185
186	0	if (seqsym.length() != (2 * numSymbols))
187		{
188		// Set of scalars for some property
189	0	if (Scores.containsKey(id))
190		{
191	0	int i = 1;
192
193	0	while (Scores.containsKey(id + "_" + i))
194		{
195	0	i++;
196		}
197
198	0	id = id + "_" + i;
199		}
200
201	0	Vector scores = new Vector();
202
203		// Typecheck from first entry
204	0	int i = 0;
205	0	String ascore = "dead";
206
207	0	try
208		{
209		// store elements as floats...
210	0	while (symbols.hasMoreTokens())
211		{
212	0	ascore = symbols.nextToken();
213
214	0	Float score = Float.valueOf(ascore);
215	0	scores.addElement(score);
216		}
217
218	0	Scores.put(id, scores);
219		} catch (Exception e)
220		{
221		// or just keep them as strings
222	0	i = scores.size();
223
224	0	for (int j = 0; j < i; j++)
225		{
226	0	scores.setElementAt(((Float) scores.elementAt(j)).toString(),
227		j);
228		}
229
230	0	scores.addElement(ascore);
231
232	0	while (symbols.hasMoreTokens())
233		{
234	0	ascore = symbols.nextToken();
235	0	scores.addElement(ascore);
236		}
237
238	0	Scores.put(id, scores);
239		}
240		}
241	0	else if (id.equals("jnetconf"))
242		{
243		// log.debug jalview.bin.Console.outPrintln("here");
244	0	id = "Prediction Confidence";
245	0	this.conf = new Vector(numSymbols);
246
247	0	for (int i = 0; i < numSymbols; i++)
248		{
249	0	conf.setElementAt(symbols.nextToken(), i);
250		}
251		}
252		else
253		{
254		// Sequence or a prediction string (rendered as sequence)
255	0	StringBuffer newseq = new StringBuffer();
256
257	0	for (int i = 0; i < numSymbols; i++)
258		{
259	0	newseq.append(symbols.nextToken());
260		}
261
262	0	if (id.indexOf(";") > -1)
263		{
264	0	seq_entries.addElement(newseq);
265
266	0	int i = 1;
267	0	String name = id.substring(id.indexOf(";") + 1);
268
269	0	while (ids.lastIndexOf(name) > -1)
270		{
271	0	name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
272		}
273
274	0	if (QuerySeqPosition == -1)
275		{
276	0	QuerySeqPosition = ids.size();
277		}
278	0	ids.addElement(name);
279	0	noSeqs++;
280		}
281		else
282		{
283	0	if (id.equals("JNETPRED"))
284		{
285	0	id = "Predicted Secondary Structure";
286		}
287
288	0	seq_entries.addElement(newseq.toString());
289	0	ids.addElement(id);
290	0	Symscores.put(id, Integer.valueOf(ids.size() - 1));
291		}
292		}
293		}
294		/*
295		* leave it to the parser user to actually check this. if (noSeqs < 1) {
296		* throw new IOException( "JpredFile Parser: No sequence in the
297		* prediction!"); }
298		*/
299
300	0	maxLength = seq_entries.elementAt(0).toString().length();
301
302	0	for (int i = 0; i < ids.size(); i++)
303		{
304		// Add all sequence like objects
305	0	Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
306		seq_entries.elementAt(i).toString(), 1,
307		seq_entries.elementAt(i).toString().length());
308
309	0	if (maxLength != seq_entries.elementAt(i).toString().length())
310		{
311	0	throw new IOException(MessageManager.formatMessage(
312		"exception.jpredconcide_entry_has_unexpected_number_of_columns",
313		new String[]
314		{ ids.elementAt(i).toString() }));
315		}
316
317	0	if ((newSeq.getName().startsWith("QUERY")
318		|| newSeq.getName().startsWith("align;"))
319		&& (QuerySeqPosition == -1))
320		{
321	0	QuerySeqPosition = seqs.size();
322		}
323
324	0	seqs.addElement(newSeq);
325		}
326	0	if (seqs.size() > 0 && QuerySeqPosition > -1)
327		{
328		// try to make annotation for a prediction only input (default if no
329		// alignment is given and prediction contains a QUERY or align;sequence_id
330		// line)
331	0	Alignment tal = new Alignment(this.getSeqsAsArray());
332	0	try
333		{
334	0	JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition,
335		true);
336		} catch (Exception e)
337		{
338	0	tal = null;
339	0	IOException ex = new IOException(MessageManager.formatMessage(
340		"exception.couldnt_parse_concise_annotation_for_prediction",
341		new String[]
342		{ e.getMessage() }));
343	0	e.printStackTrace(); // java 1.1 does not have :
344		// ex.setStackTrace(e.getStackTrace());
345	0	throw ex;
346		}
347	0	this.annotations = new Vector();
348	0	AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
349	0	for (int aai = 0; aan != null && aai < aan.length; aai++)
350		{
351	0	annotations.addElement(aan[aai]);
352		}
353		}
354		}
355
356		/**
357		* print
358		*
359		* @return String
360		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
361	0	@Override...
362		public String print(SequenceI[] sqs, boolean jvsuffix)
363		{
364	0	return "Not Supported";
365		}
366
367		/**
368		*
369		* @param args
370		* @j2sIgnore
371		*/
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
372	0	public static void main(String[] args)...
373		{
374	0	try
375		{
376	0	JPredFile jpred = new JPredFile(args[0], DataSourceType.FILE);
377
378	0	for (int i = 0; i < jpred.seqs.size(); i++)
379		{
380	0	jalview.bin.Console
381		.outPrintln(((Sequence) jpred.seqs.elementAt(i)).getName()
382		+ "\n" + ((Sequence) jpred.seqs.elementAt(i))
383		.getSequenceAsString()
384		+ "\n");
385		}
386		} catch (java.io.IOException e)
387		{
388	0	jalview.bin.Console.errPrintln("Exception " + e);
389		// e.printStackTrace(); not java 1.1 compatible!
390		}
391		}
392
393		Vector annotSeqs = null;
394
395		/**
396		* removeNonSequences
397		*/
		0% Uncovered Elements: 24 (24) Complexity: 5 Complexity Density: 0.31
398	0	public void removeNonSequences()...
399		{
400	0	if (annotSeqs != null)
401		{
402	0	return;
403		}
404	0	annotSeqs = new Vector();
405	0	Vector newseqs = new Vector();
406	0	int i = 0;
407	0	int j = seqs.size();
408	0	for (; i < QuerySeqPosition; i++)
409		{
410	0	annotSeqs.addElement(seqs.elementAt(i));
411		}
412		// check that no stray annotations have been added at the end.
413		{
414	0	SequenceI sq = seqs.elementAt(j - 1);
415	0	if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
416		{
417	0	annotSeqs.addElement(sq);
418	0	seqs.removeElementAt(--j);
419		}
420		}
421	0	for (; i < j; i++)
422		{
423	0	newseqs.addElement(seqs.elementAt(i));
424		}
425
426	0	seqs.removeAllElements();
427	0	seqs = newseqs;
428		}
429		}
430
431		/*
432		* StringBuffer out = new StringBuffer();
433		*
434		* out.append("START PRED\n"); for (int i = 0; i < s[0].sequence.length(); i++)
435		* { out.append(s[0].sequence.substring(i, i + 1) + " ");
436		* out.append(s[1].sequence.substring(i, i + 1) + " ");
437		* out.append(s[1].score[0].elementAt(i) + " ");
438		* out.append(s[1].score[1].elementAt(i) + " ");
439		* out.append(s[1].score[2].elementAt(i) + " ");
440		* out.append(s[1].score[3].elementAt(i) + " ");
441		*
442		* out.append("\n"); } out.append("END PRED\n"); return out.toString(); }
443		*
444		* public static void main(String[] args) { try { BLCFile blc = new
445		* BLCFile(args[0], "File"); DrawableSequence[] s = new
446		* DrawableSequence[blc.seqs.size()]; for (int i = 0; i < blc.seqs.size(); i++)
447		* { s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i)); } String
448		* out = BLCFile.print(s);
449		*
450		* AlignFrame af = new AlignFrame(null, s); af.resize(700, 500); af.show();
451		* jalview.bin.Console.outPrintln(out); } catch (java.io.IOException e) {
452		* jalview.bin.Console.outPrintln("Exception " + e); } } }
453		*/