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jamesmorrisjamesmorris
jamesmorris
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jamesmorris
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updated the test data and tests
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-54
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2 files changed

+37
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‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankWriterTest.java‎

Lines changed: 35 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -160,69 +160,54 @@ public void testLocationJoins() throws Exception {
160160

161161
assertEquals("join1, getType()", "CDS", join1.getType());
162162
assertEquals("join1, getLocations().getStrand()", "POSITIVE", join1.getLocations().getStrand().toString());
163-
assertEquals("join1, getLocations().getSubLocations().size()", 8, join1SubLocs.size());
163+
assertEquals("join1, getLocations().getSubLocations().size()", 6, join1SubLocs.size());
164164

165-
assertEquals("join1, SubLocation 1)", 3356, join1SubLocs.get(0).getStart().getPosition().intValue());
166-
assertEquals("join1, SubLocation 1)", 3356, join1SubLocs.get(0).getEnd().getPosition().intValue());
165+
assertEquals("join1, SubLocation 1)", 1, join1SubLocs.get(0).getStart().getPosition().intValue());
166+
assertEquals("join1, SubLocation 1)", 1, join1SubLocs.get(0).getEnd().getPosition().intValue());
167167

168-
assertEquals("join1, SubLocation 2)", 3500, join1SubLocs.get(1).getStart().getPosition().intValue());
169-
assertEquals("join1, SubLocation 2)", 3792, join1SubLocs.get(1).getEnd().getPosition().intValue());
168+
assertEquals("join1, SubLocation 2)", 10, join1SubLocs.get(1).getStart().getPosition().intValue());
169+
assertEquals("join1, SubLocation 2)", 12, join1SubLocs.get(1).getEnd().getPosition().intValue());
170170

171-
assertEquals("join1, SubLocation 3)", 3793, join1SubLocs.get(2).getStart().getPosition().intValue());
172-
assertEquals("join1, SubLocation 3)", 3793, join1SubLocs.get(2).getEnd().getPosition().intValue());
171+
assertEquals("join1, SubLocation 3)", 30, join1SubLocs.get(2).getStart().getPosition().intValue());
172+
assertEquals("join1, SubLocation 3)", 30, join1SubLocs.get(2).getEnd().getPosition().intValue());
173173

174-
assertEquals("join1, SubLocation 4)", 4185, join1SubLocs.get(3).getStart().getPosition().intValue());
175-
assertEquals("join1, SubLocation 4)", 4228, join1SubLocs.get(3).getEnd().getPosition().intValue());
174+
assertEquals("join1, SubLocation 3)", 35, join1SubLocs.get(3).getStart().getPosition().intValue());
175+
assertEquals("join1, SubLocation 3)", 38, join1SubLocs.get(3).getEnd().getPosition().intValue());
176176

177-
assertEquals("join1, SubLocation 5)", 4229, join1SubLocs.get(4).getStart().getPosition().intValue());
178-
assertEquals("join1, SubLocation 5)", 4229, join1SubLocs.get(4).getEnd().getPosition().intValue());
177+
assertEquals("join1, SubLocation 5)", 43, join1SubLocs.get(4).getStart().getPosition().intValue());
178+
assertEquals("join1, SubLocation 5)", 46, join1SubLocs.get(4).getEnd().getPosition().intValue());
179179

180-
assertEquals("join1, SubLocation 6)", 4348, join1SubLocs.get(5).getStart().getPosition().intValue());
181-
assertEquals("join1, SubLocation 6)", 4676, join1SubLocs.get(5).getEnd().getPosition().intValue());
182-
183-
assertEquals("join1, SubLocation 7)", 4677, join1SubLocs.get(6).getStart().getPosition().intValue());
184-
assertEquals("join1, SubLocation 7)", 4677, join1SubLocs.get(6).getEnd().getPosition().intValue());
185-
186-
assertEquals("join1, SubLocation 8)", 4775, join1SubLocs.get(7).getStart().getPosition().intValue());
187-
assertEquals("join1, SubLocation 8)", 5094, join1SubLocs.get(7).getEnd().getPosition().intValue());
180+
assertEquals("join1, SubLocation 6)", 47, join1SubLocs.get(5).getStart().getPosition().intValue());
181+
assertEquals("join1, SubLocation 6)", 50, join1SubLocs.get(5).getEnd().getPosition().intValue());
188182

189183
//qualifiers
190184
assertEquals("join1, getType()", "Joined feature", join1.getQualifiers().get("standard_name").get(0).getValue());
191185

192186
//Join 2
193187
FeatureInterface<AbstractSequence<NucleotideCompound>, NucleotideCompound> join2 = features.get(1);
194-
List<Location> join2SubLocs = join1.getLocations().getSubLocations();
195-
196-
assertEquals("join1, getType()", "CDS", join2.getType());
197-
assertEquals("join1, getLocations().getStrand()", "NEGATIVE", join2.getLocations().getStrand().toString());
198-
assertEquals("join1, getLocations().getSubLocations().size()", 8, join2SubLocs.size());
188+
List<Location> join2SubLocs = join2.getLocations().getSubLocations();
199189

200-
assertEquals("join2, SubLocation 1)", 3356, join2SubLocs.get(0).getStart().getPosition().intValue());
201-
assertEquals("join2, SubLocation 1)", 3356, join2SubLocs.get(0).getEnd().getPosition().intValue());
190+
assertEquals("join2, getType()", "CDS", join2.getType());
191+
assertEquals("join2, getLocations().getStrand()", "NEGATIVE", join2.getLocations().getStrand().toString());
192+
assertEquals("join2, getLocations().getSubLocations().size()", 5, join2SubLocs.size());
202193

203-
assertEquals("join2, SubLocation 2)", 3500, join2SubLocs.get(1).getStart().getPosition().intValue());
204-
assertEquals("join2, SubLocation 2)", 3792, join2SubLocs.get(1).getEnd().getPosition().intValue());
194+
assertEquals("join2, SubLocation 1)", 33, join2SubLocs.get(0).getStart().getPosition().intValue());
195+
assertEquals("join2, SubLocation 1)", 33, join2SubLocs.get(0).getEnd().getPosition().intValue());
205196

206-
assertEquals("join2, SubLocation 3)", 3793, join2SubLocs.get(2).getStart().getPosition().intValue());
207-
assertEquals("join2, SubLocation 3)", 3793, join2SubLocs.get(2).getEnd().getPosition().intValue());
197+
assertEquals("join2, SubLocation 2)", 35, join2SubLocs.get(1).getStart().getPosition().intValue());
198+
assertEquals("join2, SubLocation 2)", 37, join2SubLocs.get(1).getEnd().getPosition().intValue());
208199

209-
assertEquals("join2, SubLocation 4)", 4185, join2SubLocs.get(3).getStart().getPosition().intValue());
210-
assertEquals("join2, SubLocation 4)", 4228, join2SubLocs.get(3).getEnd().getPosition().intValue());
200+
assertEquals("join2, SubLocation 3)", 41, join2SubLocs.get(2).getStart().getPosition().intValue());
201+
assertEquals("join2, SubLocation 3)", 43, join2SubLocs.get(2).getEnd().getPosition().intValue());
211202

212-
assertEquals("join2, SubLocation 5)", 4229, join2SubLocs.get(4).getStart().getPosition().intValue());
213-
assertEquals("join2, SubLocation 5)", 4229, join2SubLocs.get(4).getEnd().getPosition().intValue());
214-
215-
assertEquals("join2, SubLocation 6)", 4348, join2SubLocs.get(5).getStart().getPosition().intValue());
216-
assertEquals("join2, SubLocation 6)", 4676, join2SubLocs.get(5).getEnd().getPosition().intValue());
217-
218-
assertEquals("join2, SubLocation 7)", 4677, join2SubLocs.get(6).getStart().getPosition().intValue());
219-
assertEquals("join2, SubLocation 7)", 4677, join2SubLocs.get(6).getEnd().getPosition().intValue());
203+
assertEquals("join2, SubLocation 4)", 44, join2SubLocs.get(3).getStart().getPosition().intValue());
204+
assertEquals("join2, SubLocation 4)", 46, join2SubLocs.get(3).getEnd().getPosition().intValue());
220205

221-
assertEquals("join2, SubLocation 8)", 4775, join2SubLocs.get(7).getStart().getPosition().intValue());
222-
assertEquals("join2, SubLocation 8)", 5094, join2SubLocs.get(7).getEnd().getPosition().intValue());
206+
assertEquals("join2, SubLocation 5)", 47, join2SubLocs.get(4).getStart().getPosition().intValue());
207+
assertEquals("join2, SubLocation 5)", 50, join2SubLocs.get(4).getEnd().getPosition().intValue());
223208

224209
//qualifiers
225-
assertEquals("join1, getType()", "Joined feature on complement", join2.getQualifiers().get("standard_name").get(0).getValue());
210+
assertEquals("join2, getType()", "Joined feature on complement", join2.getQualifiers().get("standard_name").get(0).getValue());
226211

227212
// Now write the joins back to a file using the GenbankWriterHelper
228213
ByteArrayOutputStream fragwriter = new ByteArrayOutputStream();
@@ -231,7 +216,7 @@ public void testLocationJoins() throws Exception {
231216
Arrays.asList(sequence));
232217
fragwriter.close();
233218

234-
//System.out.println(fragwriter.toString().replaceAll("\r\n", "\n"));
219+
System.out.println(fragwriter.toString().replaceAll("\r\n", "\n"));
235220

236221
// Read the output file and test that no information is lost
237222
InputStream readerInputStream = new ByteArrayInputStream(fragwriter.toByteArray());
@@ -242,17 +227,17 @@ public void testLocationJoins() throws Exception {
242227
// Check the output matches the original sequence feature
243228
for (int i=0; i < features.size(); i++ ) {
244229
assertEquals("getFeatures(), getType()", features.get(i).getType(), newFeatures.get(i).getType());
245-
assertEquals("getFeatures(), getLocations()", features.get(i).getLocations(), newFeatures.get(i).getLocations());
230+
assertEquals("getFeatures(), getStart()", features.get(i).getLocations().getStart(), newFeatures.get(i).getLocations().getStart());
231+
assertEquals("getFeatures(), getEnd()", features.get(i).getLocations().getEnd(), newFeatures.get(i).getLocations().getEnd());
246232
assertEquals("getFeatures(), getStrand()", features.get(i).getLocations().getStrand(), newFeatures.get(i).getLocations().getStrand());
247233

248234
List<Location> subLocations = features.get(i).getLocations().getSubLocations();
249235
List<Location> newSubLocations = newFeatures.get(i).getLocations().getSubLocations();
250236
assertEquals("getSubLocations()", subLocations.size(), newSubLocations.size());
251-
252-
assertEquals("getSubLocations()", subLocations, newSubLocations);
253-
254-
for (int j=0; j < subLocations.size(); j++ ) {
255-
assertEquals("getSubLocations()", subLocations.get(j).toString(), newSubLocations.get(j).toString());
237+
for (int j=0; j < subLocations.size(); j++ ) {
238+
assertEquals("getSubLocations(), getStart()", subLocations.get(j).getStart(), newSubLocations.get(j).getStart());
239+
assertEquals("getSubLocations(), getEnd()", subLocations.get(j).getEnd(), newSubLocations.get(j).getEnd());
240+
assertEquals("getSubLocations(), getStrand()", subLocations.get(j).getStrand(), newSubLocations.get(j).getStrand());
256241
}
257242

258243
Map<String, List<Qualifier>> qualifiers = features.get(i).getQualifiers();

‎biojava-core/src/test/resources/with_joins.gb‎

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,9 @@ VERSION .
55
KEYWORDS .
66
SOURCE .
77
FEATURES Location/Qualifiers
8-
CDS join(1,10..12,30,41..42,43..46,
9-
47..50)
8+
CDS join(1,10..12,30,35..38,43..46,47..50)
109
/standard_name="Joined feature"
11-
CDS complement(join(33,35..37,41..42,
12-
43..46,47..50))
10+
CDS complement(join(33,35..37,41..43,44..46,47..50))
1311
/standard_name="Joined feature on complement"
1412
ORIGIN
1513
1 acgg

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