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-2629 current hmmer commands are now executed in threads
[jalview.git]
/
test
/
jalview
/
io
/
CrossRef2xmlTests.java
diff --git
a/test/jalview/io/CrossRef2xmlTests.java
b/test/jalview/io/CrossRef2xmlTests.java
index
2063c88
..
ec5855f
100644
(file)
--- a/
test/jalview/io/CrossRef2xmlTests.java
+++ b/
test/jalview/io/CrossRef2xmlTests.java
@@
-30,6
+30,7
@@
import jalview.gui.AlignFrame;
import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import java.io.File;
import java.io.IOException;
import java.io.File;
import java.io.IOException;
@@
-38,12
+39,21
@@
import java.util.HashMap;
import java.util.List;
import org.testng.Assert;
import java.util.List;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
+ @Override
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* test store and recovery of all reachable cross refs from all reachable
* crossrefs for one or more fetched db refs. Currently, this test has a known
/**
* test store and recovery of all reachable cross refs from all reachable
* crossrefs for one or more fetched db refs. Currently, this test has a known
@@
-130,7
+140,7
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
Desktop.instance.closeAll_actionPerformed(null);
// recover stored project
af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
Desktop.instance.closeAll_actionPerformed(null);
// recover stored project
af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
- .get(first).toString(), FormatAdapter.FILE);
+ .get(first).toString(), DataSourceType.FILE);
System.out.println("Recovered view for '" + first + "' from '"
+ savedProjects.get(first).toString() + "'");
dna = af.getViewport().getAlignment().isNucleotide();
System.out.println("Recovered view for '" + first + "' from '"
+ savedProjects.get(first).toString() + "'");
dna = af.getViewport().getAlignment().isNucleotide();
@@
-168,7
+178,7
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
// perform crossref action, or retrieve stored project
List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
CrossRefAction cra = null;
// perform crossref action, or retrieve stored project
List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
CrossRefAction cra = null;
-
+
if (pass2 == 0)
{ // retrieve and show cross-refs in this thread
cra = new CrossRefAction(af, seqs, dna, db);
if (pass2 == 0)
{ // retrieve and show cross-refs in this thread
cra = new CrossRefAction(af, seqs, dna, db);
@@
-203,7
+213,7
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
// recover stored project
AlignFrame af2 = new FileLoader(false)
.LoadFileWaitTillLoaded(savedProjects.get(nextxref)
// recover stored project
AlignFrame af2 = new FileLoader(false)
.LoadFileWaitTillLoaded(savedProjects.get(nextxref)
- .toString(), FormatAdapter.FILE);
+ .toString(), DataSourceType.FILE);
System.out.println("Recovered view for '" + nextxref
+ "' from '" + savedProjects.get(nextxref).toString()
+ "'");
System.out.println("Recovered view for '" + nextxref
+ "' from '" + savedProjects.get(nextxref).toString()
+ "'");
@@
-248,7
+258,7
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
: new CrossRef(xrseqs, dataset)
.findXrefSourcesForSequences(avp
.getAlignViewport().isNucleotide());
: new CrossRef(xrseqs, dataset)
.findXrefSourcesForSequences(avp
.getAlignViewport().isNucleotide());
-
+
stringify(dbtoviewBit, savedProjects, nextxref, avp);
xrptypes.put(nextxref, _xrptypes);
stringify(dbtoviewBit, savedProjects, nextxref, avp);
xrptypes.put(nextxref, _xrptypes);
@@
-266,8
+276,8
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
{
List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
int q = 0;
{
List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
int q = 0;
- String nextnextxref = nextxref
- + " -> " + xrefdb + "{" + q + "}";
+ String nextnextxref = nextxref + " -> " + xrefdb + "{"
+ + q + "}";
if (pass3 == 0)
{
if (pass3 == 0)
{
@@
-284,8
+294,8
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
{
failedXrefMenuItems
.add("No crossrefs retrieved for '"
{
failedXrefMenuItems
.add("No crossrefs retrieved for '"
- + nextxref + "' to " + xrefdb + " via '"
- + nextaf.getTitle() + "'");
+ + nextxref + "' to " + xrefdb
+ + " via '" + nextaf.getTitle() + "'");
continue;
}
cra_views2 = cra.getXrefViews();
continue;
}
cra_views2 = cra.getXrefViews();
@@
-314,7
+324,8
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
AlignFrame af2 = new FileLoader(false)
.LoadFileWaitTillLoaded(
savedProjects.get(nextnextxref)
AlignFrame af2 = new FileLoader(false)
.LoadFileWaitTillLoaded(
savedProjects.get(nextnextxref)
- .toString(), FormatAdapter.FILE);
+ .toString(),
+ DataSourceType.FILE);
System.out.println("Recovered view for '"
+ nextnextxref + "' from '"
+ savedProjects.get(nextnextxref).toString()
System.out.println("Recovered view for '"
+ nextnextxref + "' from '"
+ savedProjects.get(nextnextxref).toString()
@@
-345,8
+356,8
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
for (AlignmentViewPanel nextavp : cra_views2)
{
for (AlignmentViewPanel nextavp : cra_views2)
{
- nextnextxref = nextxref
- + " -> " + xrefdb + "{" + q++ + "}";
+ nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
+ + "}";
// verify references for this panel
AlignmentTest.assertAlignmentDatasetRefs(
// verify references for this panel
AlignmentTest.assertAlignmentDatasetRefs(
@@
-471,8
+482,7
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
{
List<SequenceI> nonType = new ArrayList<SequenceI>();
for (SequenceI sq : alignmentViewPanel.getAlignViewport()
{
List<SequenceI> nonType = new ArrayList<SequenceI>();
for (SequenceI sq : alignmentViewPanel.getAlignViewport()
- .getAlignment()
- .getSequences())
+ .getAlignment().getSequences())
{
if (sq.isProtein() != expectProtein)
{
{
if (sq.isProtein() != expectProtein)
{
@@
-483,8
+493,7
@@
public class CrossRef2xmlTests extends Jalview2xmlBase
{
Assert.fail(message + " [ "
+ (expectProtein ? "nucleotides were " : "proteins were ")
{
Assert.fail(message + " [ "
+ (expectProtein ? "nucleotides were " : "proteins were ")
- + nonType.toString()
- + " ]");
+ + nonType.toString() + " ]");
}
}
}
}