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JAL-653 test for GFF file recognition and alignment import
author
Jim Procter
<jprocter@issues.jalview.org>
Sun, 7 Jun 2015 18:04:31 +0000
(19:04 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Sun, 7 Jun 2015 18:04:31 +0000
(19:04 +0100)
test/jalview/io/Gff3tests.java
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diff --git
a/test/jalview/io/Gff3tests.java
b/test/jalview/io/Gff3tests.java
index
8c4a40d
..
30cb451
100644
(file)
--- a/
test/jalview/io/Gff3tests.java
+++ b/
test/jalview/io/Gff3tests.java
@@
-41,7
+41,15
@@
public class Gff3tests
}
@Test
}
@Test
- public void simpleGff3() throws IOException
+ public void simpleGff3FileIdentify()
+ {
+ Assert.assertEquals("Didn't recognise file correctly.",
+ IdentifyFile.GFF3File,
+ new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
+ }
+
+ @Test
+ public void simpleGff3FileClass() throws IOException
{
AlignmentI dataset = new Alignment(new SequenceI[]
{});
{
AlignmentI dataset = new Alignment(new SequenceI[]
{});
@@
-54,6
+62,17
@@
public class Gff3tests
}
@Test
}
@Test
+ public void simpleGff3FileLoader() throws IOException
+ {
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ simpleGff3file, null);
+ Assert.assertTrue(
+ "Didn't read the alignment into an alignframe from Gff3 File",
+ af != null);
+ checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
+ }
+
+ @Test
public void simpleGff3RelaxedIdMatching() throws IOException
{
AlignmentI dataset = new Alignment(new SequenceI[]
public void simpleGff3RelaxedIdMatching() throws IOException
{
AlignmentI dataset = new Alignment(new SequenceI[]
@@
-67,6
+86,16
@@
public class Gff3tests
checkDatasetfromSimpleGff3(dataset);
}
checkDatasetfromSimpleGff3(dataset);
}
+ @Test
+ public void readGff3File() throws IOException
+ {
+ Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
+ Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
+ gff3reader.addProperties(dataset);
+ checkDatasetfromSimpleGff3(dataset);
+
+ }
+
private void checkDatasetfromSimpleGff3(AlignmentI dataset)
{
Assert.assertEquals("no sequences extracted from GFF3 file", 2,
private void checkDatasetfromSimpleGff3(AlignmentI dataset)
{
Assert.assertEquals("no sequences extracted from GFF3 file", 2,
@@
-97,6
+126,10
@@
public class Gff3tests
Assert.assertEquals("Wrong number of features", 0, seq2
.getSequenceFeatures() == null ? 0
: seq2.getSequenceFeatures().length);
Assert.assertEquals("Wrong number of features", 0, seq2
.getSequenceFeatures() == null ? 0
: seq2.getSequenceFeatures().length);
+ Assert.assertTrue(
+ "Expected at least one CDNA/Protein mapping for seq1",
+ dataset.getCodonFrame(seq1) != null
+ && dataset.getCodonFrame(seq1).size() > 0);
}
// @Test
}
// @Test