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JAL-629 Fix a test and omit an incorrect error message for structureviewer=none
improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters
author
Ben Soares
<b.soares@dundee.ac.uk>
Sat, 16 Sep 2023 15:56:54 +0000
(16:56 +0100)
committer
Ben Soares
<b.soares@dundee.ac.uk>
Sat, 16 Sep 2023 15:56:54 +0000
(16:56 +0100)
src/jalview/bin/Commands.java
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src/jalview/bin/argparser/Arg.java
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test/jalview/bin/CommandsTest2.java
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test/jalview/bin/commandsTest2.argfile1
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diff --git
a/src/jalview/bin/Commands.java
b/src/jalview/bin/Commands.java
index
0565111
..
9a85f1e
100644
(file)
--- a/
src/jalview/bin/Commands.java
+++ b/
src/jalview/bin/Commands.java
@@
-582,8
+582,11
@@
public class Commands
if (structureViewer == null)
{
if (structureViewer == null)
{
- addError("Failed to import and open structure view for file '"
- + structureFile + "'.");
+ if (!StringUtils.equalsIgnoreCase(sViewerName, "none"))
+ {
+ addError("Failed to import and open structure view for file '"
+ + structureFile + "'.");
+ }
continue;
}
try
continue;
}
try
diff --git
a/src/jalview/bin/argparser/Arg.java
b/src/jalview/bin/argparser/Arg.java
index
9bb5f38
..
b69ed61
100644
(file)
--- a/
src/jalview/bin/argparser/Arg.java
+++ b/
src/jalview/bin/argparser/Arg.java
@@
-139,7
+139,7
@@
public enum Arg
TEMPFAC(Type.STRUCTURE,
"Set the type of temperature factor. Possible values are:\n"
+ "default,\n" + "plddt.",
TEMPFAC(Type.STRUCTURE,
"Set the type of temperature factor. Possible values are:\n"
+ "default,\n" + "plddt.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
+ Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
STRUCTUREVIEWER(Type.STRUCTURE,
"Set the structure viewer to use to open the 3D structure file specified in previous --structure to name. Possible values of name are:\n"
+ "none,\n" + "jmol,\n" + "chimera,\n" + "chimerax,\n"
STRUCTUREVIEWER(Type.STRUCTURE,
"Set the structure viewer to use to open the 3D structure file specified in previous --structure to name. Possible values of name are:\n"
+ "none,\n" + "jmol,\n" + "chimera,\n" + "chimerax,\n"
@@
-148,8
+148,8
@@
public enum Arg
NOTEMPFAC(Type.STRUCTURE,
"Do not show the temperature factor annotation for the preceding --structure.",
Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this
NOTEMPFAC(Type.STRUCTURE,
"Do not show the temperature factor annotation for the preceding --structure.",
Opt.UNARY, Opt.LINKED, Opt.ALLOWMULTIID, Opt.SECRET), // keep this
- // secret
- // until it works!
+ // secret until
+ // it works!
SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
Opt.ALLOWMULTIID),
SHOWSSANNOTATIONS(Type.STRUCTURE, null, Opt.BOOLEAN, Opt.LINKED,
Opt.ALLOWMULTIID),
diff --git
a/test/jalview/bin/CommandsTest2.java
b/test/jalview/bin/CommandsTest2.java
index
d6b6f3c
..
ae14c1a
100644
(file)
--- a/
test/jalview/bin/CommandsTest2.java
+++ b/
test/jalview/bin/CommandsTest2.java
@@
-65,7
+65,8
@@
public class CommandsTest2
String[] args = cmdLine.split("\\s+");
CommandsTest.callJalviewMain(args);
String[] args = cmdLine.split("\\s+");
CommandsTest.callJalviewMain(args);
- while (Desktop.instance!=null && Desktop.instance.operationsAreInProgress())
+ while (Desktop.instance != null
+ && Desktop.instance.operationsAreInProgress())
{
try
{
{
try
{
diff --git
a/test/jalview/bin/commandsTest2.argfile1
b/test/jalview/bin/commandsTest2.argfile1
index
ea3a1be
..
85eccd9
100644
(file)
--- a/
test/jalview/bin/commandsTest2.argfile1
+++ b/
test/jalview/bin/commandsTest2.argfile1
@@
-1,9
+1,8
@@
---substitutions
--append=examples/test_fab41.result/sample.a2m
--showannotations
--showssannotations
--colour=gecos-flower
--append=examples/test_fab41.result/sample.a2m
--showannotations
--showssannotations
--colour=gecos-flower
---structure=[viewer=jmol,tempfac=plddt,paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
+--structure=[structureviewer=jmol,tempfac=plddt,paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
--structureviewer=jmol
--paematrix={dirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json
--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
--structureviewer=jmol
--paematrix={dirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json
@@
-12,7
+11,7
@@
--structureviewer=jmol
--paematrix={dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
--tempfac=plddt
--structureviewer=jmol
--paematrix={dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
--tempfac=plddt
---structure=[viewer=none]{dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
+--structure=[structureviewer=none]{dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
--paematrix={dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
--tempfac=plddt
--structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb
--paematrix={dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
--tempfac=plddt
--structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb