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Coverage Report

  1. Project Clover database Mon Nov 11 2024 15:14:12 GMT
  2. Package jalview.io

File SimpleBlastFile.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

62
103
6
1
298
232
48
0.47
17.17
6
8

Classes

Class Line # Actions
SimpleBlastFile 38 103 48
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   
 
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   
 
50  0 toggle public SimpleBlastFile()
51    {
52    }
53   
 
54  0 toggle public SimpleBlastFile(String inFile, DataSourceType sourceType)
55    throws IOException
56    {
57  0 super(inFile, sourceType);
58    }
59   
 
60  0 toggle public SimpleBlastFile(FileParse source) throws IOException
61    {
62  0 super(source);
63    }
64   
 
65  0 toggle @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   
 
74  0 toggle @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   
 
293  0 toggle @Override
294    public String print(SequenceI[] sqs, boolean jvsuffix)
295    {
296  0 return new String("Not Implemented.");
297    }
298    }