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.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNotNull;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.Annotation;
31 import jalview.datamodel.SequenceFeature;
32 import jalview.datamodel.SequenceI;
35 import java.util.BitSet;
36 import java.util.HashMap;
39 import org.testng.annotations.Test;
41 public class StockholmFileTest
44 static String PfamFile = "examples/PF00111_seed.stk",
45 RfamFile = "examples/RF00031_folded.stk";
48 public void pfamFileIO() throws Exception
50 testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
54 public void pfamFileDataExtraction() throws Exception
56 AppletFormatAdapter af = new AppletFormatAdapter();
57 AlignmentI al = af.readFile(PfamFile, af.FILE,
58 new IdentifyFile().Identify(PfamFile, af.FILE));
60 for (SequenceI sq : al.getSequences())
62 if (sq.getPDBId() != null)
64 numpdb += sq.getPDBId().size();
68 "PF00111 seed alignment has at least 1 PDB file, but the reader found none.",
73 public void rfamFileIO() throws Exception
75 testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
79 * test alignment data in given file can be imported, exported and reimported
83 * - source datafile (IdentifyFile.identify() should work with it)
85 * - label for IO class used to write and read back in the data from
89 public static void testFileIOwithFormat(File f, String ioformat,
90 int naliannot, int nminseqann)
92 System.out.println("Reading file: " + f);
93 String ff = f.getPath();
96 AppletFormatAdapter rf = new AppletFormatAdapter();
98 Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
99 new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
101 assertNotNull("Couldn't read supplied alignment data.", al);
103 // make sure dataset is initialised ? not sure about this
104 for (int i = 0; i < al.getSequencesArray().length; ++i)
106 al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
108 String outputfile = rf.formatSequences(ioformat, al, true);
109 System.out.println("Output file in '" + ioformat + "':\n"
110 + outputfile + "\n<<EOF\n");
111 // test for consistency in io
112 Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
113 AppletFormatAdapter.PASTE, ioformat);
114 assertNotNull("Couldn't parse reimported alignment data.", al_input);
116 String identifyoutput = new IdentifyFile().Identify(outputfile,
117 AppletFormatAdapter.PASTE);
118 assertNotNull("Identify routine failed for outputformat " + ioformat,
121 "Identify routine could not recognise output generated by '"
122 + ioformat + "' writer",
123 ioformat.equals(identifyoutput));
124 testAlignmentEquivalence(al, al_input, false);
125 int numaliannot = 0, numsqswithali = 0;
126 for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
128 if (ala.sequenceRef == null)
139 assertEquals("Number of alignment annotations", naliannot,
144 "Number of sequence associated annotations wasn't at least "
145 + nminseqann, numsqswithali >= nminseqann);
147 } catch (Exception e)
150 assertTrue("Couln't format the alignment for output file.", false);
155 * assert alignment equivalence
160 * 'secondary' or generated alignment from some datapreserving
162 * @param ignoreFeatures
163 * when true, differences in seuqence feature annotation are ignored.
165 public static void testAlignmentEquivalence(AlignmentI al,
166 AlignmentI al_input, boolean ignoreFeatures)
168 assertNotNull("Original alignment was null", al);
169 assertNotNull("Generated alignment was null", al_input);
172 "Alignment dimension mismatch: originl contains "
173 + al.getHeight() + " and generated has "
174 + al_input.getHeight() + " sequences; original has "
175 + al.getWidth() + " and generated has "
176 + al_input.getWidth() + " columns.",
177 al.getHeight() == al_input.getHeight()
178 && al.getWidth() == al_input.getWidth());
180 // check Alignment annotation
181 AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
182 AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
184 // note - at moment we do not distinguish between alignment without any
185 // annotation rows and alignment with no annotation row vector
186 // we might want to revise this in future
187 int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0
188 : aa_original.length);
189 Map<Integer, java.util.BitSet> orig_groups = new HashMap<Integer, java.util.BitSet>(), new_groups = new HashMap<Integer, java.util.BitSet>();
191 if (aa_new != null && aa_original != null)
193 for (int i = 0; i < aa_original.length; i++)
195 if (aa_new.length > i)
197 assertTrue("Different alignment annotation at position " + i,
198 equalss(aa_original[i], aa_new[i]));
199 // compare graphGroup or graph properties - needed to verify JAL-1299
200 assertTrue("Graph type not identical.",
201 aa_original[i].graph == aa_new[i].graph);
202 assertTrue("Visibility not identical.",
203 aa_original[i].visible == aa_new[i].visible);
205 "Threshold line not identical.",
206 aa_original[i].threshold == null ? aa_new[i].threshold == null
207 : aa_original[i].threshold
208 .equals(aa_new[i].threshold));
209 // graphGroup may differ, but pattern should be the same
210 Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2), n_ggrp = new Integer(
211 aa_new[i].graphGroup + 2);
212 BitSet orig_g = orig_groups.get(o_ggrp), new_g = new_groups
216 orig_groups.put(o_ggrp, orig_g = new BitSet());
220 new_groups.put(n_ggrp, new_g = new BitSet());
222 assertTrue("Graph Group pattern differs at annotation " + i,
223 orig_g.equals(new_g));
229 System.err.println("No matching annotation row for "
230 + aa_original[i].toString());
235 "Generated and imported alignment have different annotation sets ("
236 + aa_new_size + " != " + aa_original_size + ")",
237 aa_new_size == aa_original_size);
239 // check sequences, annotation and features
240 SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
241 seq_original = al.getSequencesArray();
242 SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
243 seq_new = al_input.getSequencesArray();
244 SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
245 AlignmentAnnotation annot_original, annot_new;
247 for (int i = 0; i < al.getSequencesArray().length; i++)
249 String name = seq_original[i].getName();
250 int start = seq_original[i].getStart();
251 int end = seq_original[i].getEnd();
252 System.out.println("Check sequence: " + name + "/" + start + "-"
255 // search equal sequence
256 for (int in = 0; in < al_input.getSequencesArray().length; in++)
258 if (name.equals(seq_new[in].getName())
259 && start == seq_new[in].getStart()
260 && end == seq_new[in].getEnd())
262 String ss_original = seq_original[i].getSequenceAsString();
263 String ss_new = seq_new[in].getSequenceAsString();
264 assertTrue("The sequences " + name + "/" + start + "-" + end
265 + " are not equal", ss_original.equals(ss_new));
268 "Sequence Features were not equivalent"
269 + (ignoreFeatures ? " ignoring." : ""),
271 || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
272 .getSequenceFeatures() == null)
273 || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
274 .getSequenceFeatures() != null));
275 // compare sequence features
276 if (seq_original[i].getSequenceFeatures() != null
277 && seq_new[in].getSequenceFeatures() != null)
279 System.out.println("There are feature!!!");
280 sequenceFeatures_original = new SequenceFeature[seq_original[i]
281 .getSequenceFeatures().length];
282 sequenceFeatures_original = seq_original[i]
283 .getSequenceFeatures();
284 sequenceFeatures_new = new SequenceFeature[seq_new[in]
285 .getSequenceFeatures().length];
286 sequenceFeatures_new = seq_new[in].getSequenceFeatures();
288 assertTrue("different number of features", seq_original[i]
289 .getSequenceFeatures().length == seq_new[in]
290 .getSequenceFeatures().length);
292 for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
294 assertTrue("Different features",
295 sequenceFeatures_original[feat]
296 .equals(sequenceFeatures_new[feat]));
299 // compare alignment annotation
300 if (al.getSequenceAt(i).getAnnotation() != null
301 && al_input.getSequenceAt(in).getAnnotation() != null)
303 for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
305 if (al.getSequenceAt(i).getAnnotation()[j] != null
306 && al_input.getSequenceAt(in).getAnnotation()[j] != null)
308 annot_original = al.getSequenceAt(i).getAnnotation()[j];
309 annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
310 assertTrue("Different annotation elements",
311 equalss(annot_original, annot_new));
315 else if (al.getSequenceAt(i).getAnnotation() == null
316 && al_input.getSequenceAt(in).getAnnotation() == null)
318 System.out.println("No annotations");
320 else if (al.getSequenceAt(i).getAnnotation() != null
321 && al_input.getSequenceAt(in).getAnnotation() == null)
323 assertTrue("Annotations differed between sequences ("
324 + al.getSequenceAt(i).getName() + ") and ("
325 + al_input.getSequenceAt(i).getName() + ")", false);
334 * compare annotations
336 private static boolean equalss(AlignmentAnnotation annot_or,
337 AlignmentAnnotation annot_new)
339 if (annot_or.annotations.length != annot_new.annotations.length)
341 System.err.println("Different lengths for annotation row elements: "
342 + annot_or.annotations.length + "!="
343 + annot_new.annotations.length);
346 for (int i = 0; i < annot_or.annotations.length; i++)
348 Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
349 if (an_or != null && an_new != null)
351 if (!an_or.displayCharacter.trim().equals(
352 an_new.displayCharacter.trim())
353 || !("" + an_or.secondaryStructure).trim().equals(
354 ("" + an_new.secondaryStructure).trim())
355 || (an_or.description != an_new.description && (an_or.description == null
356 || an_new.description == null || !an_or.description
357 .equals(an_new.description))))
359 System.err.println("Annotation Element Mismatch\nElement " + i
360 + " in original: " + annot_or.annotations[i].toString()
361 + "\nElement " + i + " in new: "
362 + annot_new.annotations[i].toString());
366 else if (annot_or.annotations[i] == null
367 && annot_new.annotations[i] == null)
373 System.err.println("Annotation Element Mismatch\nElement "
376 + (annot_or.annotations[i] == null ? "is null"
377 : annot_or.annotations[i].toString())
381 + (annot_new.annotations[i] == null ? "is null"
382 : annot_new.annotations[i].toString()));