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JAL-1761 need to pass molecule type when generating superposition commands
author
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 15 Feb 2022 16:55:17 +0000
(16:55 +0000)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 15 Feb 2022 16:55:50 +0000
(16:55 +0000)
test/jalview/ext/jmol/JmolCommandsTest.java
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test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
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test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
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diff --git
a/test/jalview/ext/jmol/JmolCommandsTest.java
b/test/jalview/ext/jmol/JmolCommandsTest.java
index
21f7e19
..
64899d3
100644
(file)
--- a/
test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/
test/jalview/ext/jmol/JmolCommandsTest.java
@@
-199,7
+199,7
@@
public class JmolCommandsTest
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, false); // doesn't matter for Jmol whether nuc or protein
assertEquals(command.size(), 1);
String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
assertEquals(command.size(), 1);
String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
diff --git
a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index
6880985
..
a5933d2
100644
(file)
--- a/
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@
-203,7
+203,7
@@
public class ChimeraCommandsTest
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign, false);
// qualifier to restrict match to CA and no altlocs
String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
String refSpec = "#1:12-14.A,18.B,22-23.B";
// qualifier to restrict match to CA and no altlocs
String carbonAlphas = "@CA&~@.B-Z&~@.2-9";
String refSpec = "#1:12-14.A,18.B,22-23.B";
diff --git
a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
index
439401a
..
80bf042
100644
(file)
--- a/
test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
+++ b/
test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
@@
-187,7
+187,7
@@
public class ChimeraXCommandsTest
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign);
+ toAlign,false);
assertEquals(command.size(), 1);
String cmd = command.get(0).getCommand();
String refSpec = "#1/A:12-14/B:18,22-23";
assertEquals(command.size(), 1);
String cmd = command.get(0).getCommand();
String refSpec = "#1/A:12-14/B:18,22-23";