Refactoring (renaming) 2 classes: AsyncJobRunner.java -> AsyncClusterRunner.java...

[jabaws.git] / webservices / compbio / ws / server / MafftWS.java

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index 1d02e81..17c5c6e 100644 (file)
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.java
@@ -58,15 +58,13 @@ public class MafftWS implements MsaWS<Mafft> {
        private static final LimitsManager<Mafft> limitMan = EngineUtil.getLimits(new Mafft().getType());\r
 \r
        @Override\r
-       public String align(List<FastaSequence> sequences)\r
-                       throws JobSubmissionException {\r
+       public String align(List<FastaSequence> sequences) throws JobSubmissionException {\r
                WSUtil.validateFastaInput(sequences);\r
                ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
                return WSUtil.align(sequences, confMafft, log, "align", getLimit(""));\r
        }\r
 \r
-       ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)\r
-                       throws JobSubmissionException {\r
+       ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet) throws JobSubmissionException {\r
                Mafft mafft = new Mafft();\r
                mafft.setInput(SkeletalExecutable.INPUT);\r
                mafft.setOutput(SkeletalExecutable.OUTPUT);\r
@@ -75,8 +73,7 @@ public class MafftWS implements MsaWS<Mafft> {
        }\r
 \r
        @Override\r
-       public String customAlign(List<FastaSequence> sequences,\r
-                       List<Option<Mafft>> options) throws JobSubmissionException,\r
+       public String customAlign(List<FastaSequence> sequences, List<Option<Mafft>> options) throws JobSubmissionException,\r
                        WrongParameterException {\r
                WSUtil.validateFastaInput(sequences);\r
                ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
@@ -87,9 +84,7 @@ public class MafftWS implements MsaWS<Mafft> {
        }\r
 \r
        @Override\r
-       public String presetAlign(List<FastaSequence> sequences,\r
-                       Preset<Mafft> preset) throws JobSubmissionException,\r
-                       WrongParameterException {\r
+       public String presetAlign(List<FastaSequence> sequences, Preset<Mafft> preset) throws JobSubmissionException, WrongParameterException {\r
                WSUtil.validateFastaInput(sequences);\r
                if (preset == null) {\r
                        throw new WrongParameterException("Preset must be provided!");\r
@@ -108,10 +103,9 @@ public class MafftWS implements MsaWS<Mafft> {
        public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
                WSUtil.validateJobId(jobId);\r
                AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
-               ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine\r
-                               .getResults(jobId);\r
+               ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine.getResults(jobId);\r
                Alignment al = mafft.getResults();\r
-               return new Alignment (al.getSequences(), Program.Mafft, '-');\r
+               return new Alignment(al.getSequences(), Program.Mafft, '-');\r
        }\r
 \r
        @Override\r
@@ -131,8 +125,7 @@ public class MafftWS implements MsaWS<Mafft> {
        @Override\r
        public ChunkHolder pullExecStatistics(String jobId, long position) {\r
                WSUtil.validateJobId(jobId);\r
-               String file = Configurator.getWorkDirectory(jobId) + File.separator\r
-                               + new Mafft().getError();\r
+               String file = Configurator.getWorkDirectory(jobId) + File.separator + new Mafft().getError();\r
                return WSUtil.pullFile(file, position);\r
        }\r
 \r