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JAL-2154 catch insertion of duplicate CDS after retrieve cross-references with Alignm...
[jalview.git]
/
test
/
jalview
/
io
/
CrossRef2xmlTests.java
diff --git
a/test/jalview/io/CrossRef2xmlTests.java
b/test/jalview/io/CrossRef2xmlTests.java
index
838aa7a
..
080bda8
100644
(file)
--- a/
test/jalview/io/CrossRef2xmlTests.java
+++ b/
test/jalview/io/CrossRef2xmlTests.java
@@
-77,7
+77,8
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
List<String> keyseq = new ArrayList<String>();
HashMap<String, File> savedProjects = new HashMap<String, File>();
List<String> keyseq = new ArrayList<String>();
HashMap<String, File> savedProjects = new HashMap<String, File>();
- for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
+ for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
+ { "UNIPROT", "P01731" } })
{
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
{
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
@@
-113,6
+114,9
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
.getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ pass3 + "): Fetch " + first + ":");
AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
.getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ pass3 + "): Fetch " + first + ":");
+ AlignmentTest.assertDatasetIsNormalised(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Fetch " + first + ":");
dna = af.getViewport().getAlignment().isNucleotide();
retral = af.getViewport().getAlignment();
dataset = retral.getDataset();
dna = af.getViewport().getAlignment().isNucleotide();
retral = af.getViewport().getAlignment();
dataset = retral.getDataset();
@@
-136,6
+140,9
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
.getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ pass3 + "): Recover " + first + ":");
AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
.getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ pass3 + "): Recover " + first + ":");
+ AlignmentTest.assertDatasetIsNormalised(af.getViewport()
+ .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
+ + pass3 + "): Recover " + first + ":");
}
}
@@
-228,6
+235,10
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
"Pass (" + pass1 + "," + pass2 + "," + pass3
+ "): before start of pass3: " + nextxref
+ ":");
"Pass (" + pass1 + "," + pass2 + "," + pass3
+ "): before start of pass3: " + nextxref
+ ":");
+ AlignmentTest.assertDatasetIsNormalised(avp.getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
@@
-340,6
+351,10
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
nextavp.getAlignment(), "" + "Pass (" + pass1
+ "," + pass2 + "): For "
+ nextnextxref + ":");
nextavp.getAlignment(), "" + "Pass (" + pass1
+ "," + pass2 + "): For "
+ nextnextxref + ":");
+ AlignmentTest.assertDatasetIsNormalised(
+ nextavp.getAlignment(), "" + "Pass (" + pass1
+ + "," + pass2 + "): For "
+ + nextnextxref + ":");
stringify(dbtoviewBit, savedProjects, nextnextxref,
nextavp);
stringify(dbtoviewBit, savedProjects, nextnextxref,
nextavp);