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
forester as submodule with InternalFrame + start of distance conversion
[jalview.git]
/
test
/
jalview
/
io
/
gff
/
GffTests.java
diff --git
a/test/jalview/io/gff/GffTests.java
b/test/jalview/io/gff/GffTests.java
index
221f612
..
393f2ce
100644
(file)
--- a/
test/jalview/io/gff/GffTests.java
+++ b/
test/jalview/io/gff/GffTests.java
@@
-33,11
+33,13
@@
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
import java.util.List;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
import org.testng.annotations.Test;
/**
@@
-47,6
+49,14
@@
import org.testng.annotations.Test;
*/
public class GffTests
{
*/
public class GffTests
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the case where we load a protein ('query') sequence, then exonerateGff
* describing its mapping to cDNA, and then a DNA sequence including the
/**
* Test the case where we load a protein ('query') sequence, then exonerateGff
* describing its mapping to cDNA, and then a DNA sequence including the
@@
-57,7
+67,7
@@
public class GffTests
{
String proteinSeq = ">prot1/10-16\nYCWRSGA";
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
{
String proteinSeq = ">prot1/10-16\nYCWRSGA";
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
- proteinSeq, FormatAdapter.PASTE);
+ proteinSeq, DataSourceType.PASTE);
/*
* exonerate GFF output mapping residues 11-15 (CWRSG)
/*
* exonerate GFF output mapping residues 11-15 (CWRSG)
@@
-65,7
+75,7
@@
public class GffTests
*/
String exonerateGff = "##gff-version 2\n"
+ "prot1\tprotein2genome\tsimilarity\t11\t15\t99\t-\t.\talignment_id 0 ; Target dna1 ; Align 11 24 5";
*/
String exonerateGff = "##gff-version 2\n"
+ "prot1\tprotein2genome\tsimilarity\t11\t15\t99\t-\t.\talignment_id 0 ; Target dna1 ; Align 11 24 5";
- af.loadJalviewDataFile(exonerateGff, FormatAdapter.PASTE, null, null);
+ af.loadJalviewDataFile(exonerateGff, DataSourceType.PASTE, null, null);
/*
* check we have a mapping from prot1 to SequenceDummy 'dna1'
/*
* check we have a mapping from prot1 to SequenceDummy 'dna1'