2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.io.packed;
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;
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 import java.util.Locale;
39 public class ParsePackedSet
43 * return results as a series of jalview.datamodel objects suitable for
47 * - context which is updated with new data
50 * @return list of data objects added to context
53 public Object[] getAlignment(JalviewDataset context,
54 Iterable<DataProvider> files) throws Exception
56 List<Object> rslt = new ArrayList<Object>();
59 context = new JalviewDataset();
61 boolean deuniquify = false;
62 for (DataProvider dta : files)
64 Exception exerror = null;
66 FileParse src = dta.getDataSource();
67 if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
69 FileFormatI fmt = null;
72 fmt = new IdentifyFile().identify(src, false);
73 } catch (Exception ex)
76 errmsg = "Couldn't identify alignment format.";
81 // parse the alignment
85 al = new FormatAdapter().readFromFile(src, fmt);
88 errmsg = "Failed to parse alignment from result set";
93 // deuniquify and construct/merge additional dataset entries if
95 context.addAlignment(al);
96 context.updateSetModified(true);
102 if (dta.getType().equals(JvDataType.ANNOTATION))
104 if (!context.hasAlignments())
106 errmsg = "No alignment or sequence dataset to associate annotation with.";
107 // could duplicate the dataset reference here as default behaviour for
108 // sequence associated annotation ?
113 if (src.getReader() instanceof BufferedReader)
115 br = (BufferedReader) src.getReader();
119 br = new BufferedReader(src.getReader());
121 // TODO: add columnSelection to context
122 if (new jalview.io.AnnotationFile().parseAnnotationFrom(
123 context.getLastAlignment(), null, br))
125 context.updateSetModified(true);
129 errmsg = "Annotation file contained no data.";
132 } catch (Exception e)
134 errmsg = ((errmsg == null) ? "" : errmsg)
135 + "Failed to parse the annotation file associated with the alignment.";
139 if (dta.getType().equals(JvDataType.SEQASSOCATED))
141 if (!context.hasSequenceAssoc())
143 errmsg = "No sequence to associate data with.";
146 errmsg = "parsing of sequence associated data is not implemented";
147 exerror = new Exception(errmsg);
149 if (dta.getType().equals(JvDataType.FEATURES))
151 // check the context has a place to store feature rendering definitions,
152 // if not, create one.
153 if (context.featureColours == null)
155 context.featureColours = new HashMap<String, FeatureColourI>();
159 jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
160 context.updateSetModified(ff.parse(context.getLastAlignment(),
161 context.featureColours, false,
162 context.relaxedIdMatching));
163 } catch (Exception e)
165 errmsg = ("Failed to parse the Features file associated with the alignment.");
169 if (dta.getType().equals(JvDataType.TREE))
173 jalview.io.NewickFile nf = new jalview.io.NewickFile(src);
181 // do association to current alignment.
183 context.addTreeFromFile(nf);
185 context.updateSetModified(true);
187 } catch (Exception e)
189 errmsg = ("Failed to parse the treeFile associated with the result.");
196 if (errmsg != null && errmsg.length() > 0)
198 throw new IOException(errmsg, exerror);
202 throw new IOException(errmsg, exerror);
207 if (errmsg != null && errmsg.length() > 0)
209 throw new IOException(errmsg);
215 context.getLastAlignmentSet().deuniquifyAlignment();
217 return rslt.toArray();
221 * simple command line test. Arguments should be one or more pairs of
222 * <DataProvider.JvDataType> <Filename> arguments. The routine will attempt to
223 * read each source in turn, and report what kind of Jalview datamodel objects
228 public static void main(String args[])
230 // make data providers from the set of keys/files
232 List<DataProvider> dp = new ArrayList<DataProvider>();
233 while ((i + 1) < args.length)
235 String type = args[i++];
236 final String file = args[i++];
237 final JvDataType jtype = DataProvider.JvDataType
238 .valueOf(type.toUpperCase(Locale.ROOT));
244 fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
245 } catch (Exception e)
247 System.err.println("Couldn't handle datasource of type " + jtype
248 + " using URI " + file);
252 dp.add(new SimpleDataProvider(jtype, fp, null));
256 System.out.println("Couldn't parse source type token '"
257 + type.toUpperCase(Locale.ROOT) + "'");
262 System.out.print("** WARNING\nIgnoring unused arguments:\n");
263 while (i < args.length)
265 System.out.print(" " + args[i]);
267 System.out.print("\n");
270 System.out.println("Now trying to parse set:");
271 JalviewDataset context;
276 newdm = (pps = new ParsePackedSet())
277 .getAlignment(context = new JalviewDataset(), dp);
278 } catch (Exception e)
280 System.out.println("Test failed for these arguments.\n");
281 e.printStackTrace(System.out);
286 for (Object o : newdm)
288 System.out.println("Will need to create an " + o.getClass());
291 // now test uniquify/deuniquify stuff
292 // uniquify alignment and write alignment, annotation, features, and trees
294 // import with deuniquify info, and compare results to input.
299 if (context.getLastAlignmentSet().isModified())
302 "Initial alignment set was modified and any associated views should be updated.");