Clover icon

jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.io

File FormatAdapter.java

 

Coverage histogram

../../img/srcFileCovDistChart2.png
51% of files have more coverage

Code metrics

20
61
16
1
278
181
28
0.46
3.81
16
1.75

Classes

Class Line # Actions
FormatAdapter 44 61 28 78
0.1958762919.6%
 

Contributing tests

This file is covered by 86 tests. .

Source view

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.api.AlignExportSettingsI;
24    import jalview.api.AlignmentViewPanel;
25    import jalview.bin.Cache;
26    import jalview.datamodel.Alignment;
27    import jalview.datamodel.AlignmentAnnotation;
28    import jalview.datamodel.AlignmentI;
29    import jalview.datamodel.HiddenColumns;
30    import jalview.datamodel.Sequence;
31    import jalview.datamodel.SequenceGroup;
32    import jalview.datamodel.SequenceI;
33    import jalview.util.Comparison;
34   
35    import java.io.File;
36    import java.io.IOException;
37   
38    /**
39    * Additional formatting methods used by the application in a number of places.
40    *
41    * @author $author$
42    * @version $Revision$
43    */
 
44    public class FormatAdapter extends AppletFormatAdapter
45    {
 
46  1 toggle public FormatAdapter(AlignmentViewPanel viewpanel)
47    {
48  1 super(viewpanel);
49  1 init();
50    }
51   
 
52  214 toggle public FormatAdapter()
53    {
54  214 super();
55  214 init();
56    }
57   
 
58  0 toggle public FormatAdapter(AlignmentViewPanel alignPanel,
59    AlignExportSettingsI settings)
60    {
61  0 super(alignPanel, settings);
62    }
63   
 
64  215 toggle private void init()
65    {
66  215 if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
67    {
68  215 annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
69    true);
70  215 localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
71    true);
72  215 serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
73    true);
74    }
75    else
76    {
77    // disable all PDB annotation options
78  0 annotFromStructure = false;
79  0 localSecondaryStruct = false;
80  0 serviceSecondaryStruct = false;
81    }
82    }
83   
 
84  0 toggle public String formatSequences(FileFormatI format, SequenceI[] seqs,
85    String[] omitHiddenColumns, int[] exportRange)
86    {
87   
88  0 return formatSequences(format,
89    replaceStrings(seqs, omitHiddenColumns, exportRange));
90    }
91   
92    /**
93    * create sequences with each sequence string replaced with the one given in
94    * omitHiddenCOlumns
95    *
96    * @param seqs
97    * @param omitHiddenColumns
98    * @return new sequences
99    */
 
100  0 toggle public SequenceI[] replaceStrings(SequenceI[] seqs,
101    String[] omitHiddenColumns, int[] startEnd)
102    {
103  0 if (omitHiddenColumns != null)
104    {
105  0 SequenceI[] tmp = new SequenceI[seqs.length];
106   
107  0 int startRes;
108  0 int endRes;
109  0 int startIndex;
110  0 int endIndex;
111  0 for (int i = 0; i < seqs.length; i++)
112    {
113  0 startRes = seqs[i].getStart();
114  0 endRes = seqs[i].getEnd();
115  0 if (startEnd != null)
116    {
117  0 startIndex = startEnd[0];
118  0 endIndex = startEnd[1];
119    // get first non-gaped residue start position
120  0 while (Comparison.isGap(seqs[i].getCharAt(startIndex))
121    && startIndex < endIndex)
122    {
123  0 startIndex++;
124    }
125   
126    // get last non-gaped residue end position
127  0 while (Comparison.isGap(seqs[i].getCharAt(endIndex))
128    && endIndex > startIndex)
129    {
130  0 endIndex--;
131    }
132   
133  0 startRes = seqs[i].findPosition(startIndex);
134  0 endRes = seqs[i].findPosition(endIndex);
135    }
136   
137  0 tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
138    startRes, endRes);
139  0 tmp[i].setDescription(seqs[i].getDescription());
140    }
141  0 seqs = tmp;
142    }
143  0 return seqs;
144    }
145   
146    /**
147    * Format a vector of sequences as a flat alignment file. TODO: allow caller
148    * to detect errors and warnings encountered when generating output
149    *
150    *
151    * @param format
152    * @param seqs
153    * vector of sequences to write
154    *
155    * @return String containing sequences in desired format
156    */
 
157  0 toggle public String formatSequences(FileFormatI format, SequenceI[] seqs)
158    {
159  0 boolean withSuffix = getCacheSuffixDefault(format);
160  0 return format.getWriter(null).print(seqs, withSuffix);
161    }
162   
 
163  1 toggle public boolean getCacheSuffixDefault(FileFormatI format)
164    {
165  1 return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
166    true);
167    }
168   
 
169  0 toggle public String formatSequences(FileFormatI format, AlignmentI alignment,
170    String[] omitHidden, int[] exportRange, HiddenColumns hidden)
171    {
172  0 return formatSequences(format, alignment, omitHidden, exportRange,
173    getCacheSuffixDefault(format), hidden, null);
174    }
175   
176    /**
177    * hack function to replace sequences with visible sequence strings before
178    * generating a string of the alignment in the given format.
179    *
180    * @param format
181    * @param alignment
182    * @param omitHidden
183    * sequence strings to write out in order of sequences in alignment
184    * @param colSel
185    * defines hidden columns that are edited out of annotation
186    * @return string representation of the alignment formatted as format
187    */
 
188  0 toggle public String formatSequences(FileFormatI format, AlignmentI alignment,
189    String[] omitHidden, int[] exportRange, boolean suffix,
190    HiddenColumns hidden)
191    {
192  0 return formatSequences(format, alignment, omitHidden, exportRange,
193    suffix, hidden, null);
194    }
195   
 
196  0 toggle public String formatSequences(FileFormatI format, AlignmentI alignment,
197    String[] omitHidden, int[] exportRange, boolean suffix,
198    HiddenColumns hidden, SequenceGroup selgp)
199    {
200  0 if (omitHidden != null)
201    {
202    // TODO consider using AlignmentView to prune to visible region
203    // TODO prune sequence annotation and groups to visible region
204    // TODO: JAL-1486 - set start and end for output correctly. basically,
205    // AlignmentView.getVisibleContigs does this.
206  0 Alignment alv = new Alignment(replaceStrings(
207    alignment.getSequencesArray(), omitHidden, exportRange));
208  0 AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
209  0 if (ala != null)
210    {
211  0 for (int i = 0; i < ala.length; i++)
212    {
213  0 AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
214  0 if (selgp != null)
215    {
216  0 na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
217    hidden);
218    }
219    else
220    {
221  0 na.makeVisibleAnnotation(hidden);
222    }
223  0 alv.addAnnotation(na);
224    }
225    }
226  0 return this.formatSequences(format, alv, suffix);
227    }
228  0 return this.formatSequences(format, alignment, suffix);
229    }
230   
 
231  201 toggle @Override
232    public AlignmentI readFile(String file, DataSourceType sourceType,
233    FileFormatI fileFormat) throws IOException
234    {
235  201 AlignmentI al = super.readFile(file, sourceType, fileFormat);
236  201 return al;
237    }
238   
 
239  0 toggle public AlignmentI readFile(File file, DataSourceType sourceType,
240    FileFormatI fileFormat) throws IOException
241    {
242  0 AlignmentI al = super.readFile(file, null, sourceType, fileFormat);
243  0 return al;
244    }
245   
 
246  0 toggle @Override
247    public AlignmentI readFromFile(FileParse source, FileFormatI format)
248    throws IOException
249    {
250  0 AlignmentI al = super.readFromFile(source, format);
251  0 return al;
252    }
253   
254    /**
255    * Create a flat file representation of a given view or selected region of a
256    * view
257    *
258    * @param format
259    * @param ap
260    * alignment panel originating the view
261    * @return String containing flat file
262    */
 
263  1 toggle public String formatSequences(FileFormatI format, AlignmentViewPanel ap,
264    boolean selectedOnly)
265    {
266  1 return formatSequences(format, getCacheSuffixDefault(format), ap,
267    selectedOnly);
268    }
269   
 
270  0 toggle public AlignmentI readFromFile(AlignmentFileReaderI source,
271    FileFormatI format) throws IOException
272    {
273  0 FileParse fp = new FileParse(source.getInFile(),
274    source.getDataSourceType());
275  0 return readFromFile(fp, format);
276    }
277   
278    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.