1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.io

File ClustalFile.java

 

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../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

52
93
6
1
269
214
37
0.4
15.5
6
6.17

Classes

Class
Line #
Actions
ClustalFile 34 93 37
0.82119282.1%
 

Contributing tests

This file is covered by 6 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    package jalview.io;
22   
23    import jalview.datamodel.AlignmentAnnotation;
24    import jalview.datamodel.Sequence;
25    import jalview.datamodel.SequenceI;
26    import jalview.util.Format;
27   
28    import java.io.IOException;
29    import java.util.HashMap;
30    import java.util.Map;
31    import java.util.StringTokenizer;
32    import java.util.Vector;
33   
 
34    public class ClustalFile extends AlignFile
35    {
36   
 
37  37 toggle public ClustalFile()
38    {
39    }
40   
 
41  2 toggle public ClustalFile(String inFile, DataSourceType sourceType)
42    throws IOException
43    {
44  2 super(inFile, sourceType);
45    }
46   
 
47  1 toggle public ClustalFile(FileParse source) throws IOException
48    {
49  1 super(source);
50    }
51   
 
52  40 toggle @Override
53    public void initData()
54    {
55  40 super.initData();
56    }
57   
 
58  5 toggle @Override
59    public void parse() throws IOException
60    {
61  5 int i = 0;
62  5 boolean flag = false;
63  5 boolean top = false;
64  5 StringBuffer pssecstr = new StringBuffer();
65  5 StringBuffer consstr = new StringBuffer();
66  5 Vector<String> headers = new Vector<>();
67  5 Map<String, StringBuffer> seqhash = new HashMap<>();
68  5 StringBuffer tempseq;
69  5 String line, id;
70  5 StringTokenizer str;
71   
72  5 try
73    {
74  ? while ((line = nextLine()) != null)
75    {
76  78 if (line.length() == 0)
77    {
78  8 top = true;
79    }
80  78 boolean isConservation = line.startsWith(SPACE)
81    || line.startsWith(TAB);
82  78 if (!isConservation)
83    {
84  76 str = new StringTokenizer(line);
85   
86  76 if (str.hasMoreTokens())
87    {
88  68 id = str.nextToken();
89   
90  68 if (id.equalsIgnoreCase("CLUSTAL"))
91    {
92  3 flag = true;
93    }
94    else
95    {
96  65 if (flag)
97    {
98  65 if (seqhash.containsKey(id))
99    {
100  40 tempseq = seqhash.get(id);
101    }
102    else
103    {
104  25 tempseq = new StringBuffer();
105  25 seqhash.put(id, tempseq);
106    }
107   
108  65 if (!(headers.contains(id)))
109    {
110  25 headers.addElement(id);
111    }
112   
113  65 if (str.hasMoreTokens())
114    {
115  65 tempseq.append(str.nextToken());
116    }
117  65 top = false;
118    }
119    }
120    }
121    else
122    {
123  8 flag = true;
124    }
125    }
126    else
127    {
128  2 if (line.matches("\\s+(-|\\.|\\(|\\[|\\]|\\))+"))
129    {
130  0 if (top)
131    {
132  0 pssecstr.append(line.trim());
133    }
134    else
135    {
136  0 consstr.append(line.trim());
137    }
138    }
139    }
140    }
141    } catch (IOException e)
142    {
143  2 jalview.bin.Console.errPrintln("Exception parsing clustal file " + e);
144  2 e.printStackTrace();
145    }
146   
147  5 if (flag)
148    {
149  3 this.noSeqs = headers.size();
150   
151    // Add sequences to the hash
152  28 for (i = 0; i < headers.size(); i++)
153    {
154  25 if (seqhash.get(headers.elementAt(i)) != null)
155    {
156  25 if (maxLength < seqhash.get(headers.elementAt(i)).toString()
157    .length())
158    {
159  3 maxLength = seqhash.get(headers.elementAt(i)).toString()
160    .length();
161    }
162   
163  25 Sequence newSeq = parseId(headers.elementAt(i).toString());
164  25 newSeq.setSequence(
165    seqhash.get(headers.elementAt(i).toString()).toString());
166   
167  25 seqs.addElement(newSeq);
168    }
169    else
170    {
171  0 jalview.bin.Console.errPrintln(
172    "Clustal File Reader: Can't find sequence for "
173    + headers.elementAt(i));
174    }
175    }
176  3 AlignmentAnnotation lastssa = null;
177  3 if (pssecstr.length() == maxLength)
178    {
179  0 Vector<AlignmentAnnotation> ss = new Vector<>();
180  0 AlignmentAnnotation ssa = lastssa = StockholmFile
181    .parseAnnotationRow(ss, "secondary structure",
182    pssecstr.toString());
183  0 ssa.label = "Secondary Structure";
184  0 annotations.addElement(ssa);
185    }
186  3 if (consstr.length() == maxLength)
187    {
188  0 Vector<AlignmentAnnotation> ss = new Vector<>();
189  0 AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
190    "secondary structure", consstr.toString());
191  0 ssa.label = "Consensus Secondary Structure";
192  0 if (lastssa == null || !lastssa.getRNAStruc()
193    .equals(ssa.getRNAStruc().replace('-', '.')))
194    {
195  0 annotations.addElement(ssa);
196    }
197    }
198    }
199    }
200   
 
201  37 toggle @Override
202    public String print(SequenceI[] s, boolean jvsuffix)
203    {
204  37 StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
205   
206  37 int max = 0;
207  37 int maxid = 0;
208   
209  37 int i = 0;
210   
211  238 while ((i < s.length) && (s[i] != null))
212    {
213  201 String tmp = printId(s[i], jvsuffix);
214   
215  201 max = Math.max(max, s[i].getLength());
216   
217  201 if (tmp.length() > maxid)
218    {
219  53 maxid = tmp.length();
220    }
221   
222  201 i++;
223    }
224   
225  37 if (maxid < 15)
226    {
227  34 maxid = 15;
228    }
229   
230  37 maxid++;
231   
232  37 int len = 60;
233  37 int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
234   
235  82 for (i = 0; i < nochunks; i++)
236    {
237  45 int j = 0;
238   
239  366 while ((j < s.length) && (s[j] != null))
240    {
241  321 out.append(new Format("%-" + maxid + "s")
242    .form(printId(s[j], jvsuffix) + " "));
243   
244  321 int chunkStart = i * len;
245  321 int chunkEnd = chunkStart + len;
246   
247  321 int length = s[j].getLength();
248  321 if ((chunkEnd < length) && (chunkStart < length))
249    {
250  120 out.append(s[j].getSequenceAsString(chunkStart, chunkEnd));
251    }
252    else
253    {
254  201 if (chunkStart < length)
255    {
256  201 out.append(s[j].getSequenceAsString().substring(chunkStart));
257    }
258    }
259   
260  321 out.append(newline);
261  321 j++;
262    }
263   
264  45 out.append(newline);
265    }
266   
267  37 return out.toString();
268    }
269    }