From 0f73a668ad9aa4905b4c90948af0ede97b544c90 Mon Sep 17 00:00:00 2001 From: Daniel Barton Date: Sat, 31 Aug 2013 11:54:03 +0100 Subject: [PATCH] Parameter bug fixed, Jalview will now run some parameters --- conf/Executable.properties | 2 +- conf/settings/RNAalifoldOptionsOnly.xml | 75 ----------------------- conf/settings/RNAalifoldParameters.xml | 10 +-- webservices/compbio/ws/client/Jws2Client.java | 3 - webservices/compbio/ws/server/RNAalifoldWS.java | 2 +- webservices/compbio/ws/server/WSUtil.java | 2 - 6 files changed, 7 insertions(+), 87 deletions(-) delete mode 100644 conf/settings/RNAalifoldOptionsOnly.xml diff --git a/conf/Executable.properties b/conf/Executable.properties index ba9b4a7..333477e 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -199,5 +199,5 @@ aacon.presets.file=conf/settings/AAConPresets.xml ##### RNAALIFOLD CONFIGURATION ###### local.rnaalifold.bin.windows=binaries/windows/ViennaRNA/RNAalifold.exe local.rnaalifold.bin=binaries/src/ViennaRNA/Progs/RNAalifold -rnaalifold.parameters.file=conf/settings/RNAalifoldOptionsOnly.xml +rnaalifold.parameters.file=conf/settings/RNAalifoldParameters.xml diff --git a/conf/settings/RNAalifoldOptionsOnly.xml b/conf/settings/RNAalifoldOptionsOnly.xml deleted file mode 100644 index 7f8ef44..0000000 --- a/conf/settings/RNAalifoldOptionsOnly.xml +++ /dev/null @@ -1,75 +0,0 @@ - - - compbio.runner.structure.RNAalifold - - Endgaps - Score pairs with endgaps same as gap-gap pairs - -E - - - Most Informative Sequence - Ouput Set of nucleotides with frequency > average - --mis - - - Partition Function - Output partition function and probability matrix - -p - - - Circular - Assume circular RNA molecule - -c - - - - G-Quadruplex - Incorporate G-Quadruplex formation into prediction algorithm - -g - - - d2 - dangling energies will be added for the bases adjacent to a helix on both sides - -d2 - - - No LP - Produce Structures without lonely pairs - --noLP - - - No GU - Do not allow GU pairs - --noGU - - - No Closing GU - Do not allow GU pairs at the end of sequences - --noClosingGU - - - old - Use old energy evaluation, treating gaps as characters - --old - - - Ribosum Scoring - Use Ribosum Scoring Matrix - -r - - - d2 - - Dangling energies are added for the bases adjacent to a helix on both sides - - -d2 - - - MEA Structure - Maximum Expected Accuracy Structure - --MEA - - - - - \ No newline at end of file diff --git a/conf/settings/RNAalifoldParameters.xml b/conf/settings/RNAalifoldParameters.xml index e79c44c..a234019 100644 --- a/conf/settings/RNAalifoldParameters.xml +++ b/conf/settings/RNAalifoldParameters.xml @@ -80,7 +80,7 @@ Float 0 - 100 + 10 @@ -90,7 +90,7 @@ 0.000001 Float - 0.0000000000001 + 0.00000001 1.0 @@ -102,7 +102,7 @@ Float -274 - 1000000 + 5000 @@ -114,7 +114,7 @@ Float 0 - 100000 + 100 @@ -125,7 +125,7 @@ Float 0 - 100000 + 100 diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java index 7b781a2..5a72802 100644 --- a/webservices/compbio/ws/client/Jws2Client.java +++ b/webservices/compbio/ws/client/Jws2Client.java @@ -173,9 +173,6 @@ public class Jws2Client { ScoreManager result = analize(inputFile, ((SequenceAnnotation) msaws), preset, customOptions); - // A System.out.println just for testing! - System.out.println(result.toString()); - IOHelper.writeOut(writer, result); } else if (service.getServiceType() == MsaWS.class) { alignment = align(inputFile, (MsaWS) msaws, preset, diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java index 91081c4..33208a0 100644 --- a/webservices/compbio/ws/server/RNAalifoldWS.java +++ b/webservices/compbio/ws/server/RNAalifoldWS.java @@ -53,7 +53,7 @@ public class RNAalifoldWS extends SequenceAnnotationService ConfiguredExecutable confRNAalifold = init(sequences); List params = WSUtil.getCommands(options, - AACon.KEY_VALUE_SEPARATOR); + RNAalifold.KEY_VALUE_SEPARATOR); confRNAalifold.addParameters(params); return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit("")); diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java index e46c2d9..da4182c 100644 --- a/webservices/compbio/ws/server/WSUtil.java +++ b/webservices/compbio/ws/server/WSUtil.java @@ -150,8 +150,6 @@ public final class WSUtil { // This line is different from the above method compbio.runner.Util.writeClustalInput(sequences, confExec, '-'); AsyncExecutor engine = Configurator.getAsyncEngine(confExec); - System.out.println("Job Command: + " - + confExec.getParameters()); String jobId = engine.submitJob(confExec); reportUsage(confExec, log); return jobId; -- 1.7.10.2