git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2189 format tests
[jalview.git]
/
test
/
jalview
/
ws
/
PDBSequenceFetcherTest.java
diff --git
a/test/jalview/ws/PDBSequenceFetcherTest.java
b/test/jalview/ws/PDBSequenceFetcherTest.java
index
d082785
..
4b9437a
100644
(file)
--- a/
test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/
test/jalview/ws/PDBSequenceFetcherTest.java
@@
-26,6
+26,7
@@
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureImportSettings;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
@@
-41,6
+42,7
@@
public class PDBSequenceFetcherTest
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
// ensure 'add annotation from structure' is selected
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
// ensure 'add annotation from structure' is selected
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
@@
-61,10
+63,7
@@
public class PDBSequenceFetcherTest
@Test(groups = { "Network" }, enabled = true)
public void testRnaSeqRetrieve() throws Exception
{
@Test(groups = { "Network" }, enabled = true)
public void testRnaSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_FORMAT",
- "PDB");
+ Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
assertTrue(response != null);
List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
assertTrue(response != null);
@@
-84,11
+83,9
@@
public class PDBSequenceFetcherTest
@Test(groups = { "Network" }, enabled = true)
public void testPdbSeqRetrieve() throws Exception
{
@Test(groups = { "Network" }, enabled = true)
public void testPdbSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("PDB");
StructureImportSettings
StructureImportSettings.setDefaultStructureFileFormat("PDB");
StructureImportSettings
- .setDefaultPDBFileParser(StructureImportSettings.JALVIEW_PARSER);
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
testRetrieveProteinSeqFromPDB();
}
testRetrieveProteinSeqFromPDB();
}
@@
-96,8
+93,6
@@
public class PDBSequenceFetcherTest
@Test(groups = { "Network" }, enabled = true)
public void testmmCifSeqRetrieve() throws Exception
{
@Test(groups = { "Network" }, enabled = true)
public void testmmCifSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
testRetrieveProteinSeqFromPDB();
}
StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
testRetrieveProteinSeqFromPDB();
}