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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
test
/
jalview
/
ws
/
jabaws
/
DisorderAnnotExportImport.java
diff --git
a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index
7bbd072
..
6bcc1da
100644
(file)
--- a/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@
-25,6
+25,7
@@
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.JvOptionPane;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.JvOptionPane;
@@
-76,7
+77,7
@@
public class DisorderAnnotExportImport
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.initLogger();
+ Console.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
while (disc.isRunning())
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
while (disc.isRunning())
@@
-89,7
+90,8
@@
public class DisorderAnnotExportImport
disc2.startDiscoverer();
while (disc2.isRunning())
{
disc2.startDiscoverer();
while (disc2.isRunning())
{
- if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("iupredws"))
+ if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
+ .contains("iupredws"))
{
iupreds.add(svc);
}
{
iupreds.add(svc);
}
@@
-97,7
+99,8
@@
public class DisorderAnnotExportImport
assertTrue("Couldn't discover any IUPred services to use to test.",
iupreds.size() > 0);
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
assertTrue("Couldn't discover any IUPred services to use to test.",
iupreds.size() > 0);
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs,
+ jalview.io.DataSourceType.FILE);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
@@
-168,30
+171,24
@@
public class DisorderAnnotExportImport
{
try
{
{
try
{
- String aligfileout = FileFormat.Pfam.getWriter(al).print(
- al.getSequencesArray(), true);
+ String aligfileout = FileFormat.Pfam.getWriter(al)
+ .print(al.getSequencesArray(), true);
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Null string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
anfileout != null);
anfileout != null);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Empty string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
anfileout.length() > "JALVIEW_ANNOTATION".length());
anfileout.length() > "JALVIEW_ANNOTATION".length());
- System.out.println("Output annotation file:\n" + anfileout
- + "\n<<EOF\n");
+ System.out.println(
+ "Output annotation file:\n" + anfileout + "\n<<EOF\n");
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
DataSourceType.PASTE, FileFormat.Pfam);
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
DataSourceType.PASTE, FileFormat.Pfam);
- assertTrue(
- "Test "
- + testname
- + "\nregenerated annotation file did not annotate alignment.",
+ assertTrue("Test " + testname
+ + "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
DataSourceType.PASTE));
new AnnotationFile().readAnnotationFile(al_new, anfileout,
DataSourceType.PASTE));
@@
-203,8
+200,7
@@
public class DisorderAnnotExportImport
{
e.printStackTrace();
}
{
e.printStackTrace();
}
- Assert.fail("Test "
- + testname
+ Assert.fail("Test " + testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}