Change the way to deal with Limits to simplify wrapper writing and enable couping...

[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 cdb159c..0c8347d 100644 (file)
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.java
@@ -50,116 +50,119 @@ import compbio.runner.msa.Mafft;
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")\r
 public class MafftWS implements MsaWS<Mafft> {\r
 \r
-    // Ask for resource injection\r
-    @Resource\r
-    WebServiceContext wsContext;\r
-\r
-    private static Logger statLog = Logger.getLogger("MafftWS-stats");\r
-\r
-    private static Logger log = Logger.getLogger(MafftWS.class);\r
-\r
-    private static final RunnerConfig<Mafft> mafftOptions = Util\r
-           .getSupportedOptions(Mafft.class);\r
-\r
-    private static final PresetManager<Mafft> mafftPresets = Util\r
-           .getPresets(Mafft.class);\r
-\r
-    @Override\r
-    public String align(List<FastaSequence> sequences)\r
-           throws JobSubmissionException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
-       return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));\r
-    }\r
-\r
-    ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)\r
-           throws JobSubmissionException {\r
-       Mafft mafft = new Mafft();\r
-       mafft.setInput("fasta.in").setOutput("fasta.out");\r
-       return Configurator.configureExecutable(mafft, dataSet);\r
-    }\r
-\r
-    @Override\r
-    public String customAlign(List<FastaSequence> sequences,\r
-           List<Option<Mafft>> options) throws JobSubmissionException,\r
-           WrongParameterException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
-       List<String> params = WSUtil.getCommands(options,\r
-               Mafft.KEY_VALUE_SEPARATOR);\r
-       log.info("Setting parameters: " + params);\r
-       confMafft.addParameters(params);\r
-       return WSUtil.align(sequences, confMafft, null, "customAlign",\r
-               getLimit(""));\r
-    }\r
-\r
-    @Override\r
-    public String presetAlign(List<FastaSequence> sequences,\r
-           Preset<Mafft> preset) throws JobSubmissionException,\r
-           WrongParameterException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       if (preset == null) {\r
-           throw new WrongParameterException("Preset must be provided!");\r
+       // Ask for resource injection\r
+       @Resource\r
+       WebServiceContext wsContext;\r
+\r
+       private static Logger statLog = Logger.getLogger("MafftWS-stats");\r
+\r
+       private static Logger log = Logger.getLogger(MafftWS.class);\r
+\r
+       private static final RunnerConfig<Mafft> mafftOptions = Util\r
+                       .getSupportedOptions(Mafft.class);\r
+\r
+       private static final PresetManager<Mafft> mafftPresets = Util\r
+                       .getPresets(Mafft.class);\r
+\r
+       private static final LimitsManager<Mafft> limitMan = compbio.runner.Util\r
+                       .getLimits(new Mafft().getType());\r
+\r
+       @Override\r
+       public String align(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
+               return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));\r
+       }\r
+\r
+       ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)\r
+                       throws JobSubmissionException {\r
+               Mafft mafft = new Mafft();\r
+               mafft.setInput("fasta.in").setOutput("fasta.out");\r
+               return Configurator.configureExecutable(mafft, dataSet);\r
+       }\r
+\r
+       @Override\r
+       public String customAlign(List<FastaSequence> sequences,\r
+                       List<Option<Mafft>> options) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
+               List<String> params = WSUtil.getCommands(options,\r
+                               Mafft.KEY_VALUE_SEPARATOR);\r
+               log.info("Setting parameters: " + params);\r
+               confMafft.addParameters(params);\r
+               return WSUtil.align(sequences, confMafft, null, "customAlign",\r
+                               getLimit(""));\r
+       }\r
+\r
+       @Override\r
+       public String presetAlign(List<FastaSequence> sequences,\r
+                       Preset<Mafft> preset) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               if (preset == null) {\r
+                       throw new WrongParameterException("Preset must be provided!");\r
+               }\r
+               ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
+               confMafft.addParameters(preset.getOptions());\r
+               // This will return default limit if a specific the limit for a\r
+               // particular preset is not found\r
+               Limit<Mafft> limit = getLimit(preset.getName());\r
+\r
+               return WSUtil.align(sequences, confMafft, null, "presetAlign", limit);\r
+       }\r
+\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       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
+               Alignment al = mafft.getResults();\r
+               // log(jobId, "getResults");\r
+               return al;\r
+       }\r
+\r
+       @Override\r
+       public Limit<Mafft> getLimit(String presetName) {\r
+               return limitMan.getLimitByName(presetName);\r
+       }\r
+\r
+       @Override\r
+       public LimitsManager<Mafft> getLimits() {\r
+               return limitMan;\r
+       }\r
+\r
+       @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
+               return WSUtil.pullFile(file, position);\r
+       }\r
+\r
+       @Override\r
+       public boolean cancelJob(String jobId) {\r
+               WSUtil.validateJobId(jobId);\r
+               return WSUtil.cancelJob(jobId);\r
+       }\r
+\r
+       @Override\r
+       public JobStatus getJobStatus(String jobId) {\r
+               WSUtil.validateJobId(jobId);\r
+               return WSUtil.getJobStatus(jobId);\r
+       }\r
+\r
+       @Override\r
+       public PresetManager<Mafft> getPresets() {\r
+               return mafftPresets;\r
+       }\r
+\r
+       @Override\r
+       public RunnerConfig<Mafft> getRunnerOptions() {\r
+               return mafftOptions;\r
        }\r
-       ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
-       confMafft.addParameters(preset.getOptions());\r
-       // This will return default limit if a specific the limit for a\r
-       // particular preset is not found\r
-       Limit<Mafft> limit = getLimit(preset.getName());\r
-\r
-       return WSUtil.align(sequences, confMafft, null, "presetAlign", limit);\r
-    }\r
-\r
-    @SuppressWarnings("unchecked")\r
-    @Override\r
-    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
-       Alignment al = mafft.getResults();\r
-       //log(jobId, "getResults");\r
-       return al;\r
-    }\r
-\r
-    @Override\r
-    public Limit<Mafft> getLimit(String presetName) {\r
-       return new Mafft().getLimit(presetName);\r
-    }\r
-\r
-    @Override\r
-    public LimitsManager<Mafft> getLimits() {\r
-       return new Mafft().getLimits();\r
-    }\r
-\r
-    @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
-       return WSUtil.pullFile(file, position);\r
-    }\r
-\r
-    @Override\r
-    public boolean cancelJob(String jobId) {\r
-       WSUtil.validateJobId(jobId);\r
-       return WSUtil.cancelJob(jobId);\r
-    }\r
-\r
-    @Override\r
-    public JobStatus getJobStatus(String jobId) {\r
-       WSUtil.validateJobId(jobId);\r
-       return WSUtil.getJobStatus(jobId);\r
-    }\r
-\r
-    @Override\r
-    public PresetManager<Mafft> getPresets() {\r
-       return mafftPresets;\r
-    }\r
-\r
-    @Override\r
-    public RunnerConfig<Mafft> getRunnerOptions() {\r
-       return mafftOptions;\r
-    }\r
 \r
 }\r