}
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
- .getProperty("user.home")
- + File.separatorChar
+ .getProperty("user.home") + File.separatorChar
+ ".sifts_downloads" + File.separatorChar;
private String testPDBId = "1a70";
private SiftsClient siftsClient = null;
- SequenceI testSeq = new Sequence(
- "P00221",
+ SequenceI testSeq = new Sequence("P00221",
"MAAT..TTTMMG..MATTFVPKPQAPPMMAALPSNTGR..SLFGLKT.GSR..GGRMTMA"
+ "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD"
- + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", 1, 147);
+ + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.",
+ 1, 147);
int u = SiftsClient.UNASSIGNED;
// SIFTs entries are updated weekly - so use saved SIFTs file to enforce
// test reproducibility
new SiftsSettings();
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
- "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+ SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setMapWithSifts(true);
SiftsSettings.setCacheThresholdInDays("2");
SiftsSettings.setFailSafePIDThreshold("70");
PDBfile pdbFile;
- pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
- + testPDBId + ".pdb", DataSourceType.FILE);
+ pdbFile = new PDBfile(false, false, false,
+ "test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
siftsClient = new SiftsClient(pdbFile);
}
try
{
- HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
- "A", testSeq, null);
+ HashMap<Integer, int[]> actualMapping = siftsClient
+ .getGreedyMapping("A", testSeq, null);
Assert.assertEquals(testSeq.getStart(), 1);
Assert.assertEquals(testSeq.getEnd(), 147);
// Can't do Assert.assertEquals(actualMapping, expectedMapping);
}
@Test(
- groups = { "Network" },
+ groups =
+ { "Network" },
expectedExceptions = IllegalArgumentException.class)
private void getAtomIndexNullTest()
{
}
- @Test(
-groups = { "Network" },
- expectedExceptions = SiftsException.class)
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
private void populateAtomPositionsNullTest1()
throws IllegalArgumentException, SiftsException
{
siftsClient.populateAtomPositions(null, null);
}
- @Test(
-groups = { "Network" },
- expectedExceptions = SiftsException.class)
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
private void populateAtomPositionsNullTest2()
throws IllegalArgumentException, SiftsException
{
Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
}
- @Test(
-groups = { "Network" },
- expectedExceptions = SiftsException.class)
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
public void getValidSourceDBRefExceptionTest() throws SiftsException
{
SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
siftsClient.getValidSourceDBRef(invalidTestSeq);
}
- @Test(
-groups = { "Network" },
- expectedExceptions = SiftsException.class)
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
public void getValidSourceDBRefExceptionXTest() throws SiftsException
{
SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
public void getSiftsStructureMappingTest() throws SiftsException
{
Assert.assertTrue(SiftsSettings.isMapWithSifts());
- StructureMapping strucMapping = siftsClient.getSiftsStructureMapping(
- testSeq, testPDBId, "A");
+ StructureMapping strucMapping = siftsClient
+ .getSiftsStructureMapping(testSeq, testPDBId, "A");
String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
- + "Method: SIFTS\n\n"
- + "P00221 : 51 - 147 Maps to \n"
+ + "Method: SIFTS\n\n" + "P00221 : 51 - 147 Maps to \n"
+ "1A70|A : 1 - 97\n\n"
+ "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
+ " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
while (it.hasNext())
{
Map.Entry<Integer, int[]> pair = it.next();
- Assert.assertTrue(strucMapping.getMapping()
- .containsKey(pair.getKey()));
+ Assert.assertTrue(
+ strucMapping.getMapping().containsKey(pair.getKey()));
Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
pair.getValue());
}
}
@Test(groups = { "Network" })
- public void getEntityByMostOptimalMatchedIdTest1() throws IOException,
- SiftsException
+ public void getEntityByMostOptimalMatchedIdTest1()
+ throws IOException, SiftsException
{
SiftsClient siftsClientX = null;
PDBfile pdbFile;
- pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
- + ".pdb", DataSourceType.FILE);
+ pdbFile = new PDBfile(false, false, false,
+ "test/jalview/io/2nq2" + ".pdb", DataSourceType.FILE);
siftsClientX = new SiftsClient(pdbFile);
Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
Assert.assertEquals(entityA.getEntityId(), "A");
}
@Test(groups = { "Network" })
- public void getEntityByMostOptimalMatchedIdTest2() throws IOException,
- SiftsException
+ public void getEntityByMostOptimalMatchedIdTest2()
+ throws IOException, SiftsException
{
// This test is for a SIFTS file in which entity A should map to chain P for
// the given PDB Id. All the other chains shouldn't be mapped as there are
@Test(groups = { "Network" })
public void getLeadingIntegerFromString()
{
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("1234abcd", -1), 1234);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("1234", -1),
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234abcd", -1),
+ 1234);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234", -1),
1234);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("abcd1234", -1), -1);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("None", -1), -1);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("Null", -1), -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd1234", -1),
+ -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("None", -1), -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("Null", -1), -1);
}
}