Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SimpleBlastFile	38	103	48	0.00%	Show methods

Class SimpleBlastFile

Class SimpleBlastFile	Line # 38	Total Statements 103	Complexity 48	TOTAL Coverage 0.00%
SimpleBlastFile()   SimpleBlastFile()	5050	0.00	1.01	-1.0 -1.0 -
SimpleBlastFile(String,DataSourceType)   SimpleBlastFile(String,DataSourceType)	5454	1.01	1.01	0.0 0.00%
SimpleBlastFile(FileParse)   SimpleBlastFile(FileParse)	6060	1.01	1.01	0.0 0.00%
initData() : void   initData() : void	6565	4.04	1.01	0.0 0.00%
parse() : void   parse() : void	7474	96.096	43.043	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	293293	1.01	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.io;
22
23		import jalview.datamodel.Sequence;
24		import jalview.datamodel.SequenceI;
25
26		import java.io.IOException;
27		import java.util.Enumeration;
28		import java.util.Hashtable;
29		import java.util.Vector;
30
31		/**
32		* parse a simple blast report. Attempt to cope with query anchored and pairwise
33		* alignments only.
34		*
35		* @author Jim Procter
36		*/
37
		0% Uncovered Elements: 171 (171) Complexity: 48 Complexity Density: 0.47
38		public class SimpleBlastFile extends AlignFile
39		{
40		/**
41		* header and footer info goes into alignment annotation.
42		*/
43		StringBuffer headerLines, footerLines;
44
45		/**
46		* hold sequence ids in order of appearance in file
47		*/
48		Vector seqids;
49
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
50	0	public SimpleBlastFile()...
51		{
52		}
53
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	public SimpleBlastFile(String inFile, DataSourceType sourceType)...
55		throws IOException
56		{
57	0	super(inFile, sourceType);
58		}
59
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
60	0	public SimpleBlastFile(FileParse source) throws IOException...
61		{
62	0	super(source);
63		}
64
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
65	0	@Override...
66		public void initData()
67		{
68	0	super.initData();
69	0	headerLines = new StringBuffer();
70	0	footerLines = new StringBuffer();
71	0	seqids = new Vector();
72		}
73
		0% Uncovered Elements: 158 (158) Complexity: 43 Complexity Density: 0.45
74	0	@Override...
75		public void parse() throws IOException
76		{
77	0	String line;
78	0	char gapc = ' '; // nominal gap character
79	0	Hashtable seqhash = new Hashtable();
80	0	boolean inAlignments = false;
81	0	int padding = -1, numcol = -1, aligcol = -1, lastcol = -1;
82	0	long qlen = 0, rstart, rend; // total number of query bases so far
83	0	boolean padseq = false;
84	0	while ((line = nextLine()) != null)
85		{
86	0	if (line.indexOf("ALIGNMENTS") == 0)
87		{
88	0	inAlignments = true;
89		}
90		else
91		{
92	0	if (inAlignments)
93		{
94	0	if (line.trim().length() == 0)
95		{
96	0	continue;
97		}
98		// parse out the sequences
99		// query anchored means that we use the query sequence as the
100		// alignment ruler
101	0	if (line.indexOf("Query") == 0)
102		{
103	0	padding = -1;
104		// reset column markers for this block
105	0	numcol = -1;
106	0	aligcol = -1;
107	0	lastcol = -1;
108		// init or reset the column positions
109	0	for (int p = 5, mLen = line.length(); p < mLen; p++)
110		{
111	0	char c = line.charAt(p);
112	0	if (c >= '0' && c <= '9')
113		{
114	0	if (numcol == -1)
115		{
116	0	numcol = p;
117		}
118	0	else if (aligcol != -1 && lastcol == -1)
119		{
120	0	lastcol = p;
121		}
122		}
123		else
124		{
125	0	if (c >= 'A' && c <= 'z')
126		{
127	0	if (aligcol == -1)
128		{
129	0	aligcol = p;
130	0	padding = -1;
131		}
132		}
133		else
134		{
135	0	if (padding == -1)
136		{
137	0	padding = p; // beginning of last stretch of whitespace
138		}
139		}
140		}
141		}
142	0	if (padding == -1)
143		{
144	0	padding = aligcol;
145		}
146		}
147	0	if (line.indexOf("Database:") > -1
148		|| (aligcol == -1 || numcol == -1 || lastcol == -1)
149		|| line.length() < lastcol)
150		{
151	0	inAlignments = false;
152		}
153		else
154		{
155		// now extract the alignment.
156	0	String sqid = line.substring(0, numcol).trim();
157	0	String stindx = line.substring(numcol, aligcol).trim();
158	0	String aligseg = line.substring(aligcol, padding);
159	0	String endindx = line.substring(lastcol).trim();
160		// init start/end prior to parsing
161	0	rstart = 1; // best guess we have
162	0	rend = 0; // if zero at end of parsing, then we count non-gaps
163	0	try
164		{
165	0	rstart = Long.parseLong(stindx);
166		} catch (Exception e)
167		{
168	0	jalview.bin.Console.errPrintln(
169		"Couldn't parse '" + stindx + "' as start of row");
170		// inAlignments = false;
171		// warn for this line
172		}
173	0	try
174		{
175	0	rend = Long.parseLong(endindx);
176		} catch (Exception e)
177		{
178	0	jalview.bin.Console.errPrintln(
179		"Couldn't parse '" + endindx + "' as end of row");
180		// inAlignments = false;
181
182		// warn for this line
183		}
184	0	Vector seqentries = (Vector) seqhash.get(sqid);
185	0	if (seqentries == null)
186		{
187	0	seqentries = new Vector();
188	0	seqhash.put(sqid, seqentries);
189	0	seqids.addElement(sqid);
190		}
191
192	0	Object[] seqentry = null;
193	0	Enumeration sqent = seqentries.elements();
194	0	while (seqentry == null && sqent.hasMoreElements())
195		{
196	0	seqentry = (Object[]) sqent.nextElement();
197	0	if (((long[]) seqentry[1])[1] + 1 != rstart)
198		{
199	0	seqentry = null;
200		}
201		}
202	0	padseq = false;
203	0	if (seqentry == null)
204		{
205	0	padseq = true; // prepend gaps to new sequences in this block
206	0	seqentry = new Object[] { new StringBuffer(),
207		new long[]
208		{ rstart, rend } };
209	0	seqentries.addElement(seqentry);
210	0	seqhash.put(sqid, seqentry);
211
212		}
213	0	if (sqid.equals("Query"))
214		{
215		// update current block length in case we need to pad
216	0	qlen = ((StringBuffer) seqentry[0]).length();
217		}
218	0	StringBuffer sqs = ((StringBuffer) seqentry[0]);
219	0	if (padseq)
220		{
221	0	for (long c = sqs.length(); c < qlen; c++)
222		{
223	0	sqs.append(gapc);
224		}
225		}
226	0	sqs.append(aligseg);
227	0	if (rend > 0)
228		{
229	0	((long[]) seqentry[1])[1] = rend;
230		}
231		}
232		// end of parsing out the sequences
233		}
234		// if we haven't parsed the line as an alignment, then
235		// add to the sequence header
236	0	if (!inAlignments)
237		{
238	0	String ln = line.trim();
239		// save any header stuff for the user
240	0	if (ln.length() > 0)
241		{
242	0	StringBuffer addto = (seqhash.size() > 0) ? footerLines
243		: headerLines;
244	0	addto.append(line);
245	0	addto.append("\n");
246		}
247		}
248		}
249		}
250	0	if (seqhash.size() > 0)
251		{
252		// make the sequence vector
253	0	Enumeration seqid = seqids.elements();
254	0	while (seqid.hasMoreElements())
255		{
256	0	String idstring = (String) seqid.nextElement();
257	0	Object[] seqentry = (Object[]) seqhash.get(idstring);
258	0	try
259		{
260	0	Sequence newseq = new Sequence(idstring,
261
262		((StringBuffer) seqentry[0]).toString(),
263		(int) ((long[]) seqentry[1])[0],
264		(int) ((long[]) seqentry[1])[1]);
265	0	if (newseq.getEnd() == 0)
266		{
267		// assume there are no deletions in the sequence.
268	0	newseq.setEnd(newseq.findPosition(newseq.getLength()));
269		}
270	0	seqs.addElement(newseq);
271		} catch (Exception e)
272		{
273	0	if (warningMessage == null)
274		{
275	0	warningMessage = "";
276		}
277	0	warningMessage += "Couldn't add Sequence - ID is '" + idstring
278		+ "' : Exception was " + e.toString() + "\n";
279		}
280		}
281		// add any annotation
282	0	if (headerLines.length() > 1)
283		{
284	0	setAlignmentProperty("HEADER", headerLines.toString());
285		}
286	0	if (footerLines.length() > 1)
287		{
288	0	setAlignmentProperty("FOOTER", footerLines.toString());
289		}
290		}
291		}
292
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
293	0	@Override...
294		public String print(SequenceI[] sqs, boolean jvsuffix)
295		{
296	0	return new String("Not Implemented.");
297		}
298		}