git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (from parent 1:
0b656c6
)
JAL-1270 more fix for failing Functional test
author
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Wed, 13 Apr 2016 14:39:19 +0000
(15:39 +0100)
committer
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Wed, 13 Apr 2016 14:39:19 +0000
(15:39 +0100)
src/MCview/PDBChain.java
patch
|
blob
|
history
test/MCview/PDBChainTest.java
patch
|
blob
|
history
test/jalview/ext/jmol/JmolParserTest.java
patch
|
blob
|
history
test/jalview/structure/Mapping.java
patch
|
blob
|
history
test/jalview/structure/StructureSelectionManagerTest.java
patch
|
blob
|
history
diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
108ccf1
..
3b84ee3
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-394,9
+394,12
@@
public class PDBChain
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ char r = ResidueProperties
+ .getSingleCharacterCode(ResidueProperties
+ .getCanonicalAminoAcid(tmpat.resName));
+ seq.append(r == '0' ? 'X' : r);
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
}
else
{
}
else
{
diff --git
a/test/MCview/PDBChainTest.java
b/test/MCview/PDBChainTest.java
index
9255e5a
..
ff745ac
100644
(file)
--- a/
test/MCview/PDBChainTest.java
+++ b/
test/MCview/PDBChainTest.java
@@
-32,6
+32,7
@@
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TaylorColourScheme;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TaylorColourScheme;
+import jalview.structure.StructureViewSettings;
import java.awt.Color;
import java.util.Vector;
import java.awt.Color;
import java.util.Vector;
@@
-55,6
+56,7
@@
public class PDBChainTest
public void setUp()
{
System.out.println("setup");
public void setUp()
{
System.out.println("setup");
+ StructureViewSettings.setShowSeqFeatures(true);
c = new PDBChain("1GAQ", "A");
}
c = new PDBChain("1GAQ", "A");
}
diff --git
a/test/jalview/ext/jmol/JmolParserTest.java
b/test/jalview/ext/jmol/JmolParserTest.java
index
a68f7c8
..
7ac1579
100644
(file)
--- a/
test/jalview/ext/jmol/JmolParserTest.java
+++ b/
test/jalview/ext/jmol/JmolParserTest.java
@@
-50,7
+50,8
@@
public class JmolParserTest
* 1QCF is the full PDB file including headers, HETATM etc
*/
String[] testFile = new String[] { "./examples/1GAQ.txt",
* 1QCF is the full PDB file including headers, HETATM etc
*/
String[] testFile = new String[] { "./examples/1GAQ.txt",
- "./test/jalview/ext/jmol/1xyz.pdb" };
+ "./test/jalview/ext/jmol/1xyz.pdb",
+ "./test/jalview/ext/jmol/1qcf.pdb" };
//@formatter:off
// a modified and very cut-down extract of 4UJ4
//@formatter:off
// a modified and very cut-down extract of 4UJ4
diff --git
a/test/jalview/structure/Mapping.java
b/test/jalview/structure/Mapping.java
index
1630110
..
8674ed8
100644
(file)
--- a/
test/jalview/structure/Mapping.java
+++ b/
test/jalview/structure/Mapping.java
@@
-250,6
+250,7
@@
public class Mapping
@Test(groups = { "Functional" })
public void compareTransferredToRefPDBAnnot() throws Exception
{
@Test(groups = { "Functional" })
public void compareTransferredToRefPDBAnnot() throws Exception
{
+ StructureViewSettings.setShowSeqFeatures(true);
AlignFrame ref = new FileLoader(false)
.LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
jalview.io.FormatAdapter.FILE);
AlignFrame ref = new FileLoader(false)
.LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
jalview.io.FormatAdapter.FILE);
diff --git
a/test/jalview/structure/StructureSelectionManagerTest.java
b/test/jalview/structure/StructureSelectionManagerTest.java
index
3529375
..
999d158
100644
(file)
--- a/
test/jalview/structure/StructureSelectionManagerTest.java
+++ b/
test/jalview/structure/StructureSelectionManagerTest.java
@@
-43,6
+43,7
@@
public class StructureSelectionManagerTest
@BeforeMethod(alwaysRun = true)
public void setUp()
{
@BeforeMethod(alwaysRun = true)
public void setUp()
{
+ StructureViewSettings.setShowSeqFeatures(true);
ssm = new StructureSelectionManager();
}
ssm = new StructureSelectionManager();
}