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

File ParsePackedSet.java

 

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ParsePackedSet 38 105 36 157
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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.packed;
22   
23    import jalview.api.FeatureColourI;
24    import jalview.datamodel.AlignmentI;
25    import jalview.io.AppletFormatAdapter;
26    import jalview.io.FileFormatI;
27    import jalview.io.FileParse;
28    import jalview.io.FormatAdapter;
29    import jalview.io.IdentifyFile;
30    import jalview.io.packed.DataProvider.JvDataType;
31   
32    import java.io.BufferedReader;
33    import java.io.IOException;
34    import java.util.ArrayList;
35    import java.util.HashMap;
36    import java.util.List;
37   
 
38    public class ParsePackedSet
39    {
40   
41    /**
42    * return results as a series of jalview.datamodel objects suitable for
43    * display
44    *
45    * @param context
46    * - context which is updated with new data
47    * @param files
48    * - source data
49    * @return list of data objects added to context
50    * @throws Exception
51    */
 
52  0 toggle public Object[] getAlignment(JalviewDataset context,
53    Iterable<DataProvider> files) throws Exception
54    {
55  0 List<Object> rslt = new ArrayList<Object>();
56  0 if (context == null)
57    {
58  0 context = new JalviewDataset();
59    }
60  0 boolean deuniquify = false;
61  0 for (DataProvider dta : files)
62    {
63  0 Exception exerror = null;
64  0 String errmsg = null;
65  0 FileParse src = dta.getDataSource();
66  0 if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
67    {
68  0 FileFormatI fmt = null;
69  0 try
70    {
71  0 fmt = new IdentifyFile().identify(src, false);
72    } catch (Exception ex)
73    {
74  0 exerror = ex;
75  0 errmsg = "Couldn't identify alignment format.";
76    }
77   
78  0 if (fmt != null)
79    {
80    // parse the alignment
81  0 AlignmentI al = null;
82  0 try
83    {
84  0 al = new FormatAdapter().readFromFile(src, fmt);
85    } catch (Exception e)
86    {
87  0 errmsg = "Failed to parse alignment from result set";
88  0 exerror = e;
89    }
90  0 if (al != null)
91    {
92    // deuniquify and construct/merge additional dataset entries if
93    // necessary.
94  0 context.addAlignment(al);
95  0 context.updateSetModified(true);
96  0 rslt.add(al);
97  0 deuniquify = true;
98    }
99    }
100    }
101  0 if (dta.getType().equals(JvDataType.ANNOTATION))
102    {
103  0 if (!context.hasAlignments())
104    {
105  0 errmsg = "No alignment or sequence dataset to associate annotation with.";
106    // could duplicate the dataset reference here as default behaviour for
107    // sequence associated annotation ?
108    }
109  0 try
110    {
111  0 BufferedReader br;
112  0 if (src.getReader() instanceof BufferedReader)
113    {
114  0 br = (BufferedReader) src.getReader();
115    }
116    else
117    {
118  0 br = new BufferedReader(src.getReader());
119    }
120    // TODO: add columnSelection to context
121  0 if (new jalview.io.AnnotationFile().parseAnnotationFrom(
122    context.getLastAlignment(), null, br))
123    {
124  0 context.updateSetModified(true);
125    }
126    else
127    {
128  0 errmsg = "Annotation file contained no data.";
129    }
130   
131    } catch (Exception e)
132    {
133  0 errmsg = ((errmsg == null) ? "" : errmsg)
134    + "Failed to parse the annotation file associated with the alignment.";
135  0 exerror = e;
136    }
137    }
138  0 if (dta.getType().equals(JvDataType.SEQASSOCATED))
139    {
140  0 if (!context.hasSequenceAssoc())
141    {
142  0 errmsg = "No sequence to associate data with.";
143   
144    }
145  0 errmsg = "parsing of sequence associated data is not implemented";
146  0 exerror = new Exception(errmsg);
147    }
148  0 if (dta.getType().equals(JvDataType.FEATURES))
149    {
150    // check the context has a place to store feature rendering definitions,
151    // if not, create one.
152  0 if (context.featureColours == null)
153    {
154  0 context.featureColours = new HashMap<String, FeatureColourI>();
155    }
156  0 try
157    {
158  0 jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
159  0 context.updateSetModified(ff.parse(context.getLastAlignment(),
160    context.featureColours, false,
161    context.relaxedIdMatching));
162    } catch (Exception e)
163    {
164  0 errmsg = ("Failed to parse the Features file associated with the alignment.");
165  0 exerror = e;
166    }
167    }
168  0 if (dta.getType().equals(JvDataType.TREE))
169    {
170  0 try
171    {
172  0 jalview.io.NewickFile nf = new jalview.io.NewickFile(src);
173  0 if (!nf.isValid())
174    {
175  0 nf.close();
176  0 nf = null;
177    }
178    else
179    {
180    // do association to current alignment.
181   
182  0 context.addTreeFromFile(nf);
183  0 rslt.add(nf);
184  0 context.updateSetModified(true);
185    }
186    } catch (Exception e)
187    {
188  0 errmsg = ("Failed to parse the treeFile associated with the result.");
189  0 exerror = e;
190    }
191   
192    }
193  0 if (exerror != null)
194    {
195  0 if (errmsg != null && errmsg.length() > 0)
196    {
197  0 throw new IOException(errmsg, exerror);
198    }
199    else
200    {
201  0 throw new IOException(errmsg, exerror);
202    }
203    }
204    else
205    {
206  0 if (errmsg != null && errmsg.length() > 0)
207    {
208  0 throw new IOException(errmsg);
209    }
210    }
211    }
212  0 if (deuniquify)
213    {
214  0 context.getLastAlignmentSet().deuniquifyAlignment();
215    }
216  0 return rslt.toArray();
217    }
218   
219    /**
220    * simple command line test. Arguments should be one or more pairs of
221    * <DataProvider.JvDataType> <Filename> arguments. The routine will attempt to
222    * read each source in turn, and report what kind of Jalview datamodel objects
223    * would be created.
224    *
225    * @param args
226    */
 
227  0 toggle public static void main(String args[])
228    {
229    // make data providers from the set of keys/files
230  0 int i = 0;
231  0 List<DataProvider> dp = new ArrayList<DataProvider>();
232  0 while ((i + 1) < args.length)
233    {
234  0 String type = args[i++];
235  0 final String file = args[i++];
236  0 final JvDataType jtype = DataProvider.JvDataType
237    .valueOf(type.toUpperCase());
238  0 if (jtype != null)
239    {
240  0 final FileParse fp;
241  0 try
242    {
243  0 fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
244    } catch (Exception e)
245    {
246  0 System.err.println("Couldn't handle datasource of type " + jtype
247    + " using URI " + file);
248  0 e.printStackTrace();
249  0 return;
250    }
251  0 dp.add(new SimpleDataProvider(jtype, fp, null));
252    }
253    else
254    {
255  0 System.out.println("Couldn't parse source type token '"
256    + type.toUpperCase() + "'");
257    }
258    }
259  0 if (i < args.length)
260    {
261  0 System.out.print("** WARNING\nIgnoring unused arguments:\n");
262  0 while (i < args.length)
263    {
264  0 System.out.print(" " + args[i]);
265    }
266  0 System.out.print("\n");
267   
268    }
269  0 System.out.println("Now trying to parse set:");
270  0 JalviewDataset context;
271  0 Object[] newdm;
272  0 ParsePackedSet pps;
273  0 try
274    {
275  0 newdm = (pps = new ParsePackedSet())
276    .getAlignment(context = new JalviewDataset(), dp);
277    } catch (Exception e)
278    {
279  0 System.out.println("Test failed for these arguments.\n");
280  0 e.printStackTrace(System.out);
281  0 return;
282    }
283  0 if (newdm != null)
284    {
285  0 for (Object o : newdm)
286    {
287  0 System.out.println("Will need to create an " + o.getClass());
288    }
289   
290    // now test uniquify/deuniquify stuff
291    // uniquify alignment and write alignment, annotation, features, and trees
292    // to buffers.
293    // import with deuniquify info, and compare results to input.
294   
295    }
296    else
297    {
298  0 if (context.getLastAlignmentSet().isModified())
299    {
300  0 System.err.println(
301    "Initial alignment set was modified and any associated views should be updated.");
302    }
303    }
304    }
305    }