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paolopavanpaolopavan
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raw type checking fixes
1 parent 83152ed commit 3703042

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Lines changed: 11 additions & 9 deletions

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‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,8 @@
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import org.biojava.nbio.core.sequence.features.Qualifier;
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import org.biojava.nbio.core.sequence.location.template.AbstractLocation;
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import org.biojava.nbio.core.sequence.template.AbstractSequence;
33+
import org.biojava.nbio.core.sequence.template.Compound;
34+
import org.biojava.nbio.core.sequence.template.Sequence;
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import org.junit.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
@@ -238,7 +240,7 @@ private ProteinSequence readGenbankProteinResource(final String resource) throws
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239241
private AbstractSequence<?> readUnknownGenbankResource(final String resource) throws IOException, CompoundNotFoundException {
240242
InputStream inputStream = getClass().getResourceAsStream(resource);
241-
GenbankSequenceParser genbankParser = new GenbankSequenceParser();
243+
GenbankSequenceParser<AbstractSequence<Compound>, Compound> genbankParser = new GenbankSequenceParser<>();
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BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream));
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String seqString = genbankParser.getSequence(bufferedReader, 0);
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String compoundSet = genbankParser.getCompoundType().getClass().getSimpleName();
@@ -268,48 +270,48 @@ public void testNcbiExpandedAccessionFormats() throws IOException, CompoundNotFo
268270
public void testLegacyLocusCompatable() throws IOException, CompoundNotFoundException {
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270272
// Testing opening a genbank file with uppercase units, strand and topology
271-
AbstractSequence header0 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io/uppercase_locus0.gb");
273+
AbstractSequence<? extends Compound> header0 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io/uppercase_locus0.gb");
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assertEquals("ABC12.3_DE 7071 BP DS-DNA CIRCULAR SYN 22-JUL-1994", header0.getOriginalHeader());
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assertEquals("ABC12.3_DE", header0.getAccession().getID());
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assertEquals("DNACompoundSet", header0.getCompoundSet().getClass().getSimpleName());
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276278
// Testing uppercase SS strand
277-
AbstractSequence header1 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus1.gb");
279+
AbstractSequence<? extends Compound> header1 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus1.gb");
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assertEquals("ABC12.3_DE 7071 BP SS-DNA CIRCULAR SYN 13-JUL-1994", header1.getOriginalHeader());
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assertEquals("ABC12.3_DE", header1.getAccession().getID());
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assertEquals("DNACompoundSet", header0.getCompoundSet().getClass().getSimpleName());
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282284
// Testing uppercase MS strand
283-
AbstractSequence header2 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus2.gb");
285+
AbstractSequence<? extends Compound> header2 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus2.gb");
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assertEquals("ABC12.3_DE 7071 BP MS-DNA CIRCULAR SYN 13-JUL-1994", header2.getOriginalHeader());
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assertEquals("ABC12.3_DE", header2.getAccession().getID());
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assertEquals("DNACompoundSet", header0.getCompoundSet().getClass().getSimpleName());
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// Testing uppercase LINEAR topology
289-
AbstractSequence header3 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus3.gb");
291+
AbstractSequence<? extends Compound> header3 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus3.gb");
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assertEquals("ABC12.3_DE 7071 BP DNA LINEAR SYN 22-JUL-1994", header3.getOriginalHeader());
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assertEquals("ABC12.3_DE", header3.getAccession().getID());
292294
assertEquals("DNACompoundSet", header0.getCompoundSet().getClass().getSimpleName());
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// Testing uppercase units with no strand or topology
295-
AbstractSequence header4 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus4.gb");
297+
AbstractSequence<? extends Compound> header4 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus4.gb");
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assertEquals("ABC12.3_DE 7071 BP RNA SYN 13-JUL-1994", header4.getOriginalHeader());
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assertEquals("ABC12.3_DE", header4.getAccession().getID());
298300
assertEquals("RNACompoundSet", header4.getCompoundSet().getClass().getSimpleName());
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300302
// Testing uppercase units with no strand, topology, division or date
301-
AbstractSequence header5 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus5.gb");
303+
AbstractSequence<? extends Compound> header5 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus5.gb");
302304
assertEquals("ABC12.3_DE 7071 BP DNA", header5.getOriginalHeader());
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assertEquals("ABC12.3_DE", header5.getAccession().getID());
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305307
// Testing uppercase units with no strand, molecule type, topology, division or date
306-
AbstractSequence header6 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus6.gb");
308+
AbstractSequence<? extends Compound> header6 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus6.gb");
307309
assertEquals("ABC12.3_DE 7071 BP", header6.getOriginalHeader());
308310
assertEquals("ABC12.3_DE", header6.getAccession().getID());
309311
assertEquals("DNACompoundSet", header0.getCompoundSet().getClass().getSimpleName());
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311313
// Testing uppercase protein units
312-
AbstractSequence header7 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus7.gb");
314+
AbstractSequence<? extends Compound> header7 = readUnknownGenbankResource("/org/biojava/nbio/core/sequence/io//uppercase_locus7.gb");
313315
assertEquals("ABC12.3_DE 7071 AA Protein", header7.getOriginalHeader());
314316
assertEquals("ABC12.3_DE", header7.getAccession().getID());
315317
assertEquals("AminoAcidCompoundSet", header7.getCompoundSet().getClass().getSimpleName());

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