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JAL-1805 test envirionment separation
[jalview.git]
/
test
/
jalview
/
analysis
/
AlignmentUtilsTests.java
diff --git
a/test/jalview/analysis/AlignmentUtilsTests.java
b/test/jalview/analysis/AlignmentUtilsTests.java
index
d44a6bc
..
61b2487
100644
(file)
--- a/
test/jalview/analysis/AlignmentUtilsTests.java
+++ b/
test/jalview/analysis/AlignmentUtilsTests.java
@@
-96,7
+96,7
@@
public class AlignmentUtilsTests
public static Sequence ts = new Sequence("short",
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
public static Sequence ts = new Sequence("short",
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
- @Test
+ @Test(groups ={ "Functional" })
public void testExpandContext()
{
AlignmentI al = new Alignment(new Sequence[] {});
public void testExpandContext()
{
AlignmentI al = new Alignment(new Sequence[] {});
@@
-150,7
+150,7
@@
public class AlignmentUtilsTests
/**
* Test that annotations are correctly adjusted by expandContext
*/
/**
* Test that annotations are correctly adjusted by expandContext
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testExpandContext_annotation()
{
AlignmentI al = new Alignment(new Sequence[]
public void testExpandContext_annotation()
{
AlignmentI al = new Alignment(new Sequence[]
@@
-240,7
+240,7
@@
public class AlignmentUtilsTests
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testGetSequencesByName() throws IOException
{
final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
public void testGetSequencesByName() throws IOException
{
final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
@@
-278,7
+278,7
@@
public class AlignmentUtilsTests
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapProteinToCdna_noXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
public void testMapProteinToCdna_noXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@
-341,7
+341,7
@@
public class AlignmentUtilsTests
/**
* Test for the alignSequenceAs method that takes two sequences and a mapping.
*/
/**
* Test for the alignSequenceAs method that takes two sequences and a mapping.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignSequenceAs_withMapping_noIntrons()
{
MapList map = new MapList(new int[]
public void testAlignSequenceAs_withMapping_noIntrons()
{
MapList map = new MapList(new int[]
@@
-387,7
+387,7
@@
public class AlignmentUtilsTests
/**
* Test for the alignSequenceAs method that takes two sequences and a mapping.
*/
/**
* Test for the alignSequenceAs method that takes two sequences and a mapping.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignSequenceAs_withMapping_withIntrons()
{
/*
public void testAlignSequenceAs_withMapping_withIntrons()
{
/*
@@
-437,7
+437,7
@@
public class AlignmentUtilsTests
/**
* Test for the case where not all of the protein sequence is mapped to cDNA.
*/
/**
* Test for the case where not all of the protein sequence is mapped to cDNA.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignSequenceAs_withMapping_withUnmappedProtein()
{
public void testAlignSequenceAs_withMapping_withUnmappedProtein()
{
@@
-487,7
+487,7
@@
public class AlignmentUtilsTests
/**
* Test for the alignSequenceAs method where we preserve gaps in introns only.
*/
/**
* Test for the alignSequenceAs method where we preserve gaps in introns only.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignSequenceAs_keepIntronGapsOnly()
{
public void testAlignSequenceAs_keepIntronGapsOnly()
{
@@
-506,7
+506,7
@@
public class AlignmentUtilsTests
* Test for the method that generates an aligned translated sequence from one
* mapping.
*/
* Test for the method that generates an aligned translated sequence from one
* mapping.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testGetAlignedTranslation_dnaLikeProtein()
{
// dna alignment will be replaced
public void testGetAlignedTranslation_dnaLikeProtein()
{
// dna alignment will be replaced
@@
-530,7
+530,7
@@
public class AlignmentUtilsTests
/**
* Test the method that realigns protein to match mapped codon alignment.
*/
/**
* Test the method that realigns protein to match mapped codon alignment.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignProteinAsDna()
{
// seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
public void testAlignProteinAsDna()
{
// seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
@@
-574,7
+574,7
@@
public class AlignmentUtilsTests
* Test the method that tests whether a CDNA sequence translates to a protein
* sequence
*/
* Test the method that tests whether a CDNA sequence translates to a protein
* sequence
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testTranslatesAs()
{
assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
public void testTranslatesAs()
{
assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
@@
-613,7
+613,7
@@
public class AlignmentUtilsTests
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapProteinToCdna_withStartAndStopCodons()
throws IOException
{
public void testMapProteinToCdna_withStartAndStopCodons()
throws IOException
{
@@
-706,7
+706,7
@@
public class AlignmentUtilsTests
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapProteinToCdna_withXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
public void testMapProteinToCdna_withXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@
-782,7
+782,7
@@
public class AlignmentUtilsTests
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapProteinToCdna_prioritiseXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
public void testMapProteinToCdna_prioritiseXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@
-832,7
+832,7
@@
public class AlignmentUtilsTests
* Test the method that shows or hides sequence annotations by type(s) and
* selection group.
*/
* Test the method that shows or hides sequence annotations by type(s) and
* selection group.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testShowOrHideSequenceAnnotations()
{
SequenceI seq1 = new Sequence("Seq1", "AAA");
public void testShowOrHideSequenceAnnotations()
{
SequenceI seq1 = new Sequence("Seq1", "AAA");
@@
-940,7
+940,7
@@
public class AlignmentUtilsTests
/**
* Tests for the method that checks if one sequence cross-references another
*/
/**
* Tests for the method that checks if one sequence cross-references another
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testHasCrossRef()
{
assertFalse(AlignmentUtils.hasCrossRef(null, null));
public void testHasCrossRef()
{
assertFalse(AlignmentUtils.hasCrossRef(null, null));
@@
-969,7
+969,7
@@
public class AlignmentUtilsTests
* Tests for the method that checks if either sequence cross-references the
* other
*/
* Tests for the method that checks if either sequence cross-references the
* other
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testHaveCrossRef()
{
assertFalse(AlignmentUtils.hasCrossRef(null, null));
public void testHaveCrossRef()
{
assertFalse(AlignmentUtils.hasCrossRef(null, null));
@@
-999,7
+999,7
@@
public class AlignmentUtilsTests
/**
* Test the method that extracts the exon-only part of a dna alignment.
*/
/**
* Test the method that extracts the exon-only part of a dna alignment.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeExonAlignment()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
public void testMakeExonAlignment()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
@@
-1094,7
+1094,7
@@
public class AlignmentUtilsTests
* already has a protein product (Uniprot translation) which in turn has an
* x-ref to the EMBLCDS record.
*/
* already has a protein product (Uniprot translation) which in turn has an
* x-ref to the EMBLCDS record.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeExonSequences()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
public void testMakeExonSequences()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
@@
-1136,7
+1136,7
@@
public class AlignmentUtilsTests
* its product mappings, for the case where there are multiple exon mappings
* to different protein products.
*/
* its product mappings, for the case where there are multiple exon mappings
* to different protein products.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeExonAlignment_multipleProteins()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
public void testMakeExonAlignment_multipleProteins()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");