Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JPredFile	54	115	44	178	0.00%	Show methods

Class JPredFile

Class JPredFile	Line # 54	Total Statements 115	Complexity 44	Uncovered Elements 178	TOTAL Coverage 0.00%
JPredFile(Object,DataSourceType)   JPredFile(Object,DataSourceType)	8181	1.01	1.01	1.01	0.0 0.00%
JPredFile(FileParse)   JPredFile(FileParse)	8787	1.01	1.01	1.01	0.0 0.00%
setQuerySeqPosition(int) : void   setQuerySeqPosition(int) : void	9898	1.01	1.01	1.01	0.0 0.00%
getQuerySeqPosition() : int   getQuerySeqPosition() : int	108108	1.01	1.01	1.01	0.0 0.00%
getScores() : Hashtable   getScores() : Hashtable	118118	1.01	1.01	1.01	0.0 0.00%
getSymscores() : Hashtable   getSymscores() : Hashtable	128128	1.01	1.01	1.01	0.0 0.00%
initData() : void   initData() : void	136136	4.04	1.01	4.04	0.0 0.00%
parse() : void   parse() : void	148148	83.083	28.028	125.0125	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	359359	1.01	1.01	1.01	0.0 0.00%
main(String[]) : void   main(String[]) : void	371371	5.05	3.03	7.07	0.0 0.00%
removeNonSequences() : void   removeNonSequences() : void	396396	16.016	5.05	24.024	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 jalview.datamodel.Alignment;
29		import jalview.datamodel.AlignmentAnnotation;
30		import jalview.datamodel.Sequence;
31		import jalview.datamodel.SequenceI;
32		import jalview.util.MessageManager;
33
34		import java.io.IOException;
35		import java.util.Hashtable;
36		import java.util.StringTokenizer;
37		import java.util.Vector;
38
39		/**
40		* Parser for the JPred/JNet concise format. This is a series of CSV lines, each
41		* line is either a sequence (QUERY), a sequence profile (align;), or jnet
42		* prediction annotation (anything else). Automagic translation happens for
43		* annotation called 'JNETPRED' (translated to Secondary Structure Prediction),
44		* or 'JNETCONF' (translates to 'Prediction Confidence'). Numeric scores are
45		* differentiated from symbolic by being parseable into a float vector. They are
46		* put in Scores. Symscores gets the others. JNetAnnotationMaker translates the
47		* data parsed by this object into annotation on an alignment. It is
48		* automatically called but can be used to transfer the annotation onto a
49		* sequence in another alignment (and insert gaps where necessary)
50		*
51		* @author jprocter
52		* @version $Revision$
53		*/
		0% Uncovered Elements: 178 (178) Complexity: 44 Complexity Density: 0.38
54		public class JPredFile extends AlignFile
55		{
56		Vector ids;
57
58		Vector conf;
59
60		Hashtable Scores; // Hash of names and score vectors
61
62		Hashtable Symscores; // indexes of symbol annotation properties in sequenceI
63
64		// vector
65
66		private int QuerySeqPosition;
67
68		/**
69		* Creates a new JPredFile object.
70		*
71		* BH allows File or String
72		*
73		* @param inFile
74		* DOCUMENT ME!
75		* @param sourceType
76		* DOCUMENT ME!
77		*
78		* @throws IOException
79		* DOCUMENT ME!
80		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
81	0	public JPredFile(Object inFile, DataSourceType sourceType)...
82		throws IOException
83		{
84	0	super(inFile, sourceType);
85		}
86
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
87	0	public JPredFile(FileParse source) throws IOException...
88		{
89	0	super(source);
90		}
91
92		/**
93		* DOCUMENT ME!
94		*
95		* @param QuerySeqPosition
96		* DOCUMENT ME!
97		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
98	0	public void setQuerySeqPosition(int QuerySeqPosition)...
99		{
100	0	this.QuerySeqPosition = QuerySeqPosition;
101		}
102
103		/**
104		* DOCUMENT ME!
105		*
106		* @return DOCUMENT ME!
107		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
108	0	public int getQuerySeqPosition()...
109		{
110	0	return QuerySeqPosition;
111		}
112
113		/**
114		* DOCUMENT ME!
115		*
116		* @return DOCUMENT ME!
117		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
118	0	public Hashtable getScores()...
119		{
120	0	return Scores;
121		}
122
123		/**
124		* DOCUMENT ME!
125		*
126		* @return DOCUMENT ME!
127		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
128	0	public Hashtable getSymscores()...
129		{
130	0	return Symscores;
131		}
132
133		/**
134		* DOCUMENT ME!
135		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
136	0	@Override...
137		public void initData()
138		{
139	0	super.initData();
140	0	Scores = new Hashtable();
141	0	ids = null;
142	0	conf = null;
143		}
144
145		/**
146		* parse a JPred concise file into a sequence-alignment like object.
147		*/
		0% Uncovered Elements: 125 (125) Complexity: 28 Complexity Density: 0.34
148	0	@Override...
149		public void parse() throws IOException
150		{
151		// JBPNote log.System.out.println("all read in ");
152	0	String line;
153	0	QuerySeqPosition = -1;
154	0	noSeqs = 0;
155
156	0	Vector seq_entries = new Vector();
157	0	Vector ids = new Vector();
158	0	Hashtable Symscores = new Hashtable();
159
160	0	while ((line = nextLine()) != null)
161		{
162		// Concise format allows no comments or non comma-formatted data
163	0	StringTokenizer str = new StringTokenizer(line, ":");
164	0	String id = "";
165
166	0	if (!str.hasMoreTokens())
167		{
168	0	continue;
169		}
170
171	0	id = str.nextToken();
172
173	0	String seqsym = str.nextToken();
174	0	StringTokenizer symbols = new StringTokenizer(seqsym, ",");
175
176		// decide if we have more than just alphanumeric symbols
177	0	int numSymbols = symbols.countTokens();
178
179	0	if (numSymbols == 0)
180		{
181	0	continue;
182		}
183
184	0	if (seqsym.length() != (2 * numSymbols))
185		{
186		// Set of scalars for some property
187	0	if (Scores.containsKey(id))
188		{
189	0	int i = 1;
190
191	0	while (Scores.containsKey(id + "_" + i))
192		{
193	0	i++;
194		}
195
196	0	id = id + "_" + i;
197		}
198
199	0	Vector scores = new Vector();
200
201		// Typecheck from first entry
202	0	int i = 0;
203	0	String ascore = "dead";
204
205	0	try
206		{
207		// store elements as floats...
208	0	while (symbols.hasMoreTokens())
209		{
210	0	ascore = symbols.nextToken();
211
212	0	Float score = new Float(ascore);
213	0	scores.addElement(score);
214		}
215
216	0	Scores.put(id, scores);
217		} catch (Exception e)
218		{
219		// or just keep them as strings
220	0	i = scores.size();
221
222	0	for (int j = 0; j < i; j++)
223		{
224	0	scores.setElementAt(((Float) scores.elementAt(j)).toString(),
225		j);
226		}
227
228	0	scores.addElement(ascore);
229
230	0	while (symbols.hasMoreTokens())
231		{
232	0	ascore = symbols.nextToken();
233	0	scores.addElement(ascore);
234		}
235
236	0	Scores.put(id, scores);
237		}
238		}
239	0	else if (id.equals("jnetconf"))
240		{
241		// log.debug System.out.println("here");
242	0	id = "Prediction Confidence";
243	0	this.conf = new Vector(numSymbols);
244
245	0	for (int i = 0; i < numSymbols; i++)
246		{
247	0	conf.setElementAt(symbols.nextToken(), i);
248		}
249		}
250		else
251		{
252		// Sequence or a prediction string (rendered as sequence)
253	0	StringBuffer newseq = new StringBuffer();
254
255	0	for (int i = 0; i < numSymbols; i++)
256		{
257	0	newseq.append(symbols.nextToken());
258		}
259
260	0	if (id.indexOf(";") > -1)
261		{
262	0	seq_entries.addElement(newseq);
263
264	0	int i = 1;
265	0	String name = id.substring(id.indexOf(";") + 1);
266
267	0	while (ids.lastIndexOf(name) > -1)
268		{
269	0	name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
270		}
271
272	0	if (QuerySeqPosition == -1)
273		{
274	0	QuerySeqPosition = ids.size();
275		}
276	0	ids.addElement(name);
277	0	noSeqs++;
278		}
279		else
280		{
281	0	if (id.equals("JNETPRED"))
282		{
283	0	id = "Predicted Secondary Structure";
284		}
285
286	0	seq_entries.addElement(newseq.toString());
287	0	ids.addElement(id);
288	0	Symscores.put(id, new Integer(ids.size() - 1));
289		}
290		}
291		}
292		/*
293		* leave it to the parser user to actually check this. if (noSeqs < 1) {
294		* throw new IOException( "JpredFile Parser: No sequence in the
295		* prediction!"); }
296		*/
297
298	0	maxLength = seq_entries.elementAt(0).toString().length();
299
300	0	for (int i = 0; i < ids.size(); i++)
301		{
302		// Add all sequence like objects
303	0	Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
304		seq_entries.elementAt(i).toString(), 1,
305		seq_entries.elementAt(i).toString().length());
306
307	0	if (maxLength != seq_entries.elementAt(i).toString().length())
308		{
309	0	throw new IOException(MessageManager.formatMessage(
310		"exception.jpredconcide_entry_has_unexpected_number_of_columns",
311		new String[]
312		{ ids.elementAt(i).toString() }));
313		}
314
315	0	if ((newSeq.getName().startsWith("QUERY")
316		|| newSeq.getName().startsWith("align;"))
317		&& (QuerySeqPosition == -1))
318		{
319	0	QuerySeqPosition = seqs.size();
320		}
321
322	0	seqs.addElement(newSeq);
323		}
324	0	if (seqs.size() > 0 && QuerySeqPosition > -1)
325		{
326		// try to make annotation for a prediction only input (default if no
327		// alignment is given and prediction contains a QUERY or align;sequence_id
328		// line)
329	0	Alignment tal = new Alignment(this.getSeqsAsArray());
330	0	try
331		{
332	0	JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition,
333		true);
334		} catch (Exception e)
335		{
336	0	tal = null;
337	0	IOException ex = new IOException(MessageManager.formatMessage(
338		"exception.couldnt_parse_concise_annotation_for_prediction",
339		new String[]
340		{ e.getMessage() }));
341	0	e.printStackTrace(); // java 1.1 does not have :
342		// ex.setStackTrace(e.getStackTrace());
343	0	throw ex;
344		}
345	0	this.annotations = new Vector();
346	0	AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
347	0	for (int aai = 0; aan != null && aai < aan.length; aai++)
348		{
349	0	annotations.addElement(aan[aai]);
350		}
351		}
352		}
353
354		/**
355		* print
356		*
357		* @return String
358		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
359	0	@Override...
360		public String print(SequenceI[] sqs, boolean jvsuffix)
361		{
362	0	return "Not Supported";
363		}
364
365		/**
366		* DOCUMENT ME!
367		*
368		* @param args
369		* DOCUMENT ME!
370		*/
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
371	0	public static void main(String[] args)...
372		{
373	0	try
374		{
375	0	JPredFile jpred = new JPredFile(args[0], DataSourceType.FILE);
376
377	0	for (int i = 0; i < jpred.seqs.size(); i++)
378		{
379	0	System.out.println(((Sequence) jpred.seqs.elementAt(i)).getName()
380		+ "\n"
381		+ ((Sequence) jpred.seqs.elementAt(i)).getSequenceAsString()
382		+ "\n");
383		}
384		} catch (java.io.IOException e)
385		{
386	0	System.err.println("Exception " + e);
387		// e.printStackTrace(); not java 1.1 compatible!
388		}
389		}
390
391		Vector annotSeqs = null;
392
393		/**
394		* removeNonSequences
395		*/
		0% Uncovered Elements: 24 (24) Complexity: 5 Complexity Density: 0.31
396	0	public void removeNonSequences()...
397		{
398	0	if (annotSeqs != null)
399		{
400	0	return;
401		}
402	0	annotSeqs = new Vector();
403	0	Vector newseqs = new Vector();
404	0	int i = 0;
405	0	int j = seqs.size();
406	0	for (; i < QuerySeqPosition; i++)
407		{
408	0	annotSeqs.addElement(seqs.elementAt(i));
409		}
410		// check that no stray annotations have been added at the end.
411		{
412	0	SequenceI sq = seqs.elementAt(j - 1);
413	0	if (sq.getName().toUpperCase().startsWith("JPRED"))
414		{
415	0	annotSeqs.addElement(sq);
416	0	seqs.removeElementAt(--j);
417		}
418		}
419	0	for (; i < j; i++)
420		{
421	0	newseqs.addElement(seqs.elementAt(i));
422		}
423
424	0	seqs.removeAllElements();
425	0	seqs = newseqs;
426		}
427		}
428
429		/*
430		* StringBuffer out = new StringBuffer();
431		*
432		* out.append("START PRED\n"); for (int i = 0; i < s[0].sequence.length(); i++)
433		* { out.append(s[0].sequence.substring(i, i + 1) + " ");
434		* out.append(s[1].sequence.substring(i, i + 1) + " ");
435		* out.append(s[1].score[0].elementAt(i) + " ");
436		* out.append(s[1].score[1].elementAt(i) + " ");
437		* out.append(s[1].score[2].elementAt(i) + " ");
438		* out.append(s[1].score[3].elementAt(i) + " ");
439		*
440		* out.append("\n"); } out.append("END PRED\n"); return out.toString(); }
441		*
442		* public static void main(String[] args) { try { BLCFile blc = new
443		* BLCFile(args[0], "File"); DrawableSequence[] s = new
444		* DrawableSequence[blc.seqs.size()]; for (int i = 0; i < blc.seqs.size(); i++)
445		* { s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i)); } String
446		* out = BLCFile.print(s);
447		*
448		* AlignFrame af = new AlignFrame(null, s); af.resize(700, 500); af.show();
449		* System.out.println(out); } catch (java.io.IOException e) {
450		* System.out.println("Exception " + e); } } }
451		*/