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

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3750 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/IDEAS.txt b/IDEAS.txt
index f9f65fd..bab0292 100644 (file)
--- a/IDEAS.txt
+++ b/IDEAS.txt
@@ -1,5 +1,5 @@
 FUTURE TODO\r
 FUTURE TODO\r

-Registry for jalview WS - gives list of web services providers\r
+\r

 Registry for jalview WS - gives list of web services providers\r
  - checks the status of the web services\r
  - web service providers gives list of available WS\r
 Registry for jalview WS - gives list of web services providers\r
  - checks the status of the web services\r
  - web service providers gives list of available WS\r

@@ -26,7 +26,17 @@ FUTURE TASKS
 Prepare HMM profile for the user alignment and call jnet - instead of jpred. \r
 JPRED REWRITING Wrap Jpred\r
 Wrap scanPS    \r
 Prepare HMM profile for the user alignment and call jnet - instead of jpred. \r
 JPRED REWRITING Wrap Jpred\r
 Wrap scanPS    \r

-Look at SIFTS at EBI \r
+\r
+CBS soft: \r
+Transmembrane regions\r
+Phosphorilation sites\r
+Glycozilation sites\r
+Signal P\r
+\r
+They all have SOAP WS...\r
+ \r
+CDD domains\r
+PFAM domains\r

  \r
 JPRED IMPROVEMENTS\r
 1) Make sure PSIBLAST does not generate large output (e.g. one approach is to stop on the first iteration\r
  \r
 JPRED IMPROVEMENTS\r
 1) Make sure PSIBLAST does not generate large output (e.g. one approach is to stop on the first iteration\r

diff --git a/TODO.txt b/TODO.txt
index 0acbf85..d7ae747 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -9,9 +9,9 @@ Exception in thread "main" java.lang.NullPointerException
        at compbio.ws.client.Jws2Client.<init>(Jws2Client.java:179)\r
        at compbio.ws.client.Jws2Client.main(Jws2Client.java:483)\r
        \r
        at compbio.ws.client.Jws2Client.<init>(Jws2Client.java:179)\r
        at compbio.ws.client.Jws2Client.main(Jws2Client.java:483)\r
        \r

-       \r
-Need to pass predicted ranges to the client too - some are not straightforward to devise. \r
-This may require changes to SequenceAnnotation\r
+ScoreManager should output scores properly \r
+\r
+Check the WS input and reject it on submission rather then of access with error message\r

 \r
 Globprot need a proper reference to bio python and sav_gol binaries -> they should be \r
 somehow taken from disembl. \r
 \r
 Globprot need a proper reference to bio python and sav_gol binaries -> they should be \r
 somehow taken from disembl. \r

diff --git a/engine/compbio/engine/client/SkeletalExecutable.java b/engine/compbio/engine/client/SkeletalExecutable.java
index dbdb4f5..b289f6c 100644 (file)
--- a/engine/compbio/engine/client/SkeletalExecutable.java
+++ b/engine/compbio/engine/client/SkeletalExecutable.java
@@ -27,246 +27,251 @@ import org.apache.log4j.Logger;
 \r
 import compbio.engine.client.CommandBuilder.Parameter;\r
 import compbio.engine.conf.PropertyHelperManager;\r
 \r
 import compbio.engine.client.CommandBuilder.Parameter;\r
 import compbio.engine.conf.PropertyHelperManager;\r

+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitsManager;\r

 import compbio.util.PropertyHelper;\r
 import compbio.util.Util;\r
 \r
 public abstract class SkeletalExecutable<T> implements Executable<T> {\r
 \r
 import compbio.util.PropertyHelper;\r
 import compbio.util.Util;\r
 \r
 public abstract class SkeletalExecutable<T> implements Executable<T> {\r
 \r

-    protected static final PropertyHelper ph = PropertyHelperManager\r
-           .getPropertyHelper();\r
+       protected static final PropertyHelper ph = PropertyHelperManager\r
+                       .getPropertyHelper();\r

 \r
 \r

-    private static Logger log = Logger.getLogger(SkeletalExecutable.class);\r
+       private static Logger log = Logger.getLogger(SkeletalExecutable.class);\r

 \r
 \r

-    protected String inputFile = "input.txt";\r
-    protected String outputFile = "output.txt";\r
-    protected String errorFile = "error.txt";\r
+       // Cache for Limits information\r
+       private LimitsManager<T> limits;\r

 \r
 \r

-    private boolean isInputSet = false;\r
-    private boolean isOutputSet = false;\r
-    private boolean isErrorSet = false;\r
+       protected String inputFile = "input.txt";\r
+       protected String outputFile = "output.txt";\r
+       protected String errorFile = "error.txt";\r

 \r
 \r

-    /**\r
-     * This has to allow duplicate parameters as different options may have the\r
-     * same value e.g. Muscle -weight1 clustalw -weight2 clustalw\r
-     */\r
-    protected CommandBuilder<T> cbuilder;\r
+       private boolean isInputSet = false;\r
+       private boolean isOutputSet = false;\r
+       private boolean isErrorSet = false;\r

 \r
 \r

-    public SkeletalExecutable() {\r
-       cbuilder = new CommandBuilder<T>(" ");\r
-    }\r
+       /**\r
+        * This has to allow duplicate parameters as different options may have the\r
+        * same value e.g. Muscle -weight1 clustalw -weight2 clustalw\r
+        */\r
+       protected CommandBuilder<T> cbuilder;\r
+\r
+       public SkeletalExecutable() {\r
+               cbuilder = new CommandBuilder<T>(" ");\r
+       }\r

 \r
 \r

-    public SkeletalExecutable(String parameterKeyValueDelimiter) {\r
-       assert parameterKeyValueDelimiter != null;\r
-       cbuilder = new CommandBuilder<T>(parameterKeyValueDelimiter);\r
-    }\r
+       public SkeletalExecutable(String parameterKeyValueDelimiter) {\r
+               assert parameterKeyValueDelimiter != null;\r
+               cbuilder = new CommandBuilder<T>(parameterKeyValueDelimiter);\r
+       }\r

 \r
 \r

-    public SkeletalExecutable<T> setInput(String inFile) {\r
-       if (compbio.util.Util.isEmpty(inFile)) {\r
-           throw new IllegalArgumentException("Input file must not be NULL");\r
+       public SkeletalExecutable<T> setInput(String inFile) {\r
+               if (compbio.util.Util.isEmpty(inFile)) {\r
+                       throw new IllegalArgumentException("Input file must not be NULL");\r
+               }\r
+               this.inputFile = inFile;\r
+               this.isInputSet = true;\r
+               return this;\r

        }\r
        }\r

-       this.inputFile = inFile;\r
-       this.isInputSet = true;\r
-       return this;\r
-    }\r
-\r
-    public SkeletalExecutable<T> setOutput(String outFile) {\r
-       if (compbio.util.Util.isEmpty(outFile)\r
-               || PathValidator.isAbsolutePath(outFile)) {\r
-           throw new IllegalArgumentException(\r
-                   "Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
-                           + outFile);\r
+\r
+       public SkeletalExecutable<T> setOutput(String outFile) {\r
+               if (compbio.util.Util.isEmpty(outFile)\r
+                               || PathValidator.isAbsolutePath(outFile)) {\r
+                       throw new IllegalArgumentException(\r
+                                       "Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
+                                                       + outFile);\r
+               }\r
+               this.outputFile = outFile;\r
+               this.isOutputSet = true;\r
+               return this;\r

        }\r
        }\r

-       this.outputFile = outFile;\r
-       this.isOutputSet = true;\r
-       return this;\r
-    }\r
-\r
-    public SkeletalExecutable<T> setError(String errFile) {\r
-       if (compbio.util.Util.isEmpty(errFile)\r
-               || PathValidator.isAbsolutePath(errFile)) {\r
-           throw new IllegalArgumentException(\r
-                   "Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
-                           + errFile);\r
+\r
+       public SkeletalExecutable<T> setError(String errFile) {\r
+               if (compbio.util.Util.isEmpty(errFile)\r
+                               || PathValidator.isAbsolutePath(errFile)) {\r
+                       throw new IllegalArgumentException(\r
+                                       "Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
+                                                       + errFile);\r
+               }\r
+               this.errorFile = errFile;\r
+               this.isErrorSet = true;\r
+               return this;\r
+       }\r
+\r
+       @Override\r
+       public CommandBuilder<T> getParameters(ExecProvider provider) {\r
+               /*\r
+                * Prevent modification of the parameters unintentionally. This is\r
+                * important to preserve executable parameters intact as engine could\r
+                * add things into the array as it see fit. For instance\r
+                * ExecutableWrapper (part of local engines) add command line as the\r
+                * first element of an array.\r
+                */\r
+               paramValueUpdater();\r
+               return cbuilder;\r
+       }\r
+\r
+       @Override\r
+       public Executable<T> addParameters(List<String> parameters) {\r
+               cbuilder.addParams(parameters);\r
+               return this;\r
+       }\r
+\r
+       public Executable<T> setParameter(String parameter) {\r
+               cbuilder.setParam(parameter);\r
+               return this;\r

        }\r
        }\r

-       this.errorFile = errFile;\r
-       this.isErrorSet = true;\r
-       return this;\r
-    }\r
-\r
-    @Override\r
-    public CommandBuilder<T> getParameters(ExecProvider provider) {\r
-       /*\r
-        * Prevent modification of the parameters unintentionally. This is\r
-        * important to preserve executable parameters intact as engine could\r
-        * add things into the array as it see fit. For instance\r
-        * ExecutableWrapper (part of local engines) add command line as the\r
-        * first element of an array.\r
+\r
+       /**\r
+        * This is a generic method of changing values of the parameters with\r
+        * properties\r
+        * \r
+        * This method iterates via commands for an executable finding matches from\r
+        * the Executable.properties file and replacing values in CommandBuilder\r
+        * with a combination of value from CommandBuilder to merge path from\r
+        * properties\r

         */\r
         */\r

-       paramValueUpdater();\r
-       return cbuilder;\r
-    }\r
-\r
-    @Override\r
-    public Executable<T> addParameters(List<String> parameters) {\r
-       cbuilder.addParams(parameters);\r
-       return this;\r
-    }\r
-\r
-    public Executable<T> setParameter(String parameter) {\r
-       cbuilder.setParam(parameter);\r
-       return this;\r
-    }\r
-\r
-    /**\r
-     * This is a generic method of changing values of the parameters with\r
-     * properties\r
-     * \r
-     * This method iterates via commands for an executable finding matches from\r
-     * the Executable.properties file and replacing values in CommandBuilder\r
-     * with a combination of value from CommandBuilder to merge path from\r
-     * properties\r
-     */\r
-    void paramValueUpdater() {\r
-       for (Parameter command : cbuilder.getCommandList()) {\r
-           if (command.value == null) {\r
-               continue;\r
-           }\r
-           String propertyPath = compbio.engine.client.Util.getExecProperty(\r
-                   command.name + ".path", getType());\r
-           if (Util.isEmpty(propertyPath)) {\r
-               continue;\r
-           }\r
-           if (new File(command.value).isAbsolute()) {\r
-               // Matrix can be found so no actions necessary\r
-               // This method has been called already and the matrix name\r
-               // is modified to contain full path // no further actions is\r
-               // necessary\r
-               continue;\r
-           }\r
-           String absMatrixPath = compbio.engine.client.Util\r
-                   .convertToAbsolute(propertyPath);\r
-           command.value = absMatrixPath + File.separator + command.value;\r
-           cbuilder.setParam(command);\r
+       void paramValueUpdater() {\r
+               for (Parameter command : cbuilder.getCommandList()) {\r
+                       if (command.value == null) {\r
+                               continue;\r
+                       }\r
+                       String propertyPath = compbio.engine.client.Util.getExecProperty(\r
+                                       command.name + ".path", getType());\r
+                       if (Util.isEmpty(propertyPath)) {\r
+                               continue;\r
+                       }\r
+                       if (new File(command.value).isAbsolute()) {\r
+                               // Matrix can be found so no actions necessary\r
+                               // This method has been called already and the matrix name\r
+                               // is modified to contain full path // no further actions is\r
+                               // necessary\r
+                               continue;\r
+                       }\r
+                       String absMatrixPath = compbio.engine.client.Util\r
+                                       .convertToAbsolute(propertyPath);\r
+                       command.value = absMatrixPath + File.separator + command.value;\r
+                       cbuilder.setParam(command);\r
+               }\r

        }\r
        }\r

-    }\r
-\r
-    /**\r
-     * This method cannot really tell whether the files has actually been\r
-     * created or not. It must be overridden as required.\r
-     * \r
-     * @see compbio.engine.client.Executable#getCreatedFiles()\r
-     */\r
-    @Override\r
-    public List<String> getCreatedFiles() {\r
-       return Arrays.asList(getOutput(), getError());\r
-    }\r
-\r
-    @Override\r
-    public String getInput() {\r
-       return inputFile;\r
-    }\r
-\r
-    protected boolean isInputSet() {\r
-       return isInputSet;\r
-    }\r
-\r
-    protected boolean isOutputSet() {\r
-       return isOutputSet;\r
-    }\r
-\r
-    protected boolean isErrorSet() {\r
-       return isErrorSet;\r
-    }\r
-\r
-    @Override\r
-    public String getOutput() {\r
-       return outputFile;\r
-    }\r
-\r
-    @Override\r
-    public String getError() {\r
-       return errorFile;\r
-    }\r
-\r
-    @Override\r
-    public String toString() {\r
-       String value = "Input: " + this.getInput() + "\n";\r
-       value += "Output: " + this.getOutput() + "\n";\r
-       value += "Error: " + this.getError() + "\n";\r
-       value += "Class: " + this.getClass() + "\n";\r
-       value += "Params: " + cbuilder + "\n";\r
-       return value;\r
-    }\r
-\r
-    @Override\r
-    public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {\r
-       if (!compbio.util.Util.isEmpty(rconfig.getOutput())) {\r
-           setOutput(rconfig.getOutput());\r
+\r
+       /**\r
+        * This method cannot really tell whether the files has actually been\r
+        * created or not. It must be overridden as required.\r
+        * \r
+        * @see compbio.engine.client.Executable#getCreatedFiles()\r
+        */\r
+       @Override\r
+       public List<String> getCreatedFiles() {\r
+               return Arrays.asList(getOutput(), getError());\r

        }\r
        }\r

-       if (!compbio.util.Util.isEmpty(rconfig.getError())) {\r
-           setError(rconfig.getError());\r
+\r
+       @Override\r
+       public String getInput() {\r
+               return inputFile;\r

        }\r
        }\r

-       if (!compbio.util.Util.isEmpty(rconfig.getInput())) {\r
-           setInput(rconfig.getInput());\r
+\r
+       protected boolean isInputSet() {\r
+               return isInputSet;\r

        }\r
        }\r

-       this.cbuilder = (CommandBuilder<T>) rconfig.getParameters();\r
-       return this;\r
-    }\r
-\r
-    @Override\r
-    public boolean equals(Object obj) {\r
-       if (obj == null) {\r
-           return false;\r
+\r
+       protected boolean isOutputSet() {\r
+               return isOutputSet;\r

        }\r
        }\r

-       if (!(obj instanceof SkeletalExecutable<?>)) {\r
-           return false;\r
+\r
+       protected boolean isErrorSet() {\r
+               return isErrorSet;\r

        }\r
        }\r

-       SkeletalExecutable<?> exec = (SkeletalExecutable<?>) obj;\r
-       if (!Util.isEmpty(this.inputFile) && !Util.isEmpty(exec.inputFile)) {\r
-           if (!this.inputFile.equals(exec.inputFile)) {\r
-               return false;\r
-           }\r
+\r
+       @Override\r
+       public String getOutput() {\r
+               return outputFile;\r

        }\r
        }\r

-       if (!Util.isEmpty(this.outputFile) && !Util.isEmpty(exec.outputFile)) {\r
-           if (!this.outputFile.equals(exec.outputFile)) {\r
-               return false;\r
-           }\r
+\r
+       @Override\r
+       public String getError() {\r
+               return errorFile;\r

        }\r
        }\r

-       if (!Util.isEmpty(this.errorFile) && !Util.isEmpty(exec.errorFile)) {\r
-           if (!this.errorFile.equals(exec.errorFile)) {\r
-               return false;\r
-           }\r
+\r
+       @Override\r
+       public String toString() {\r
+               String value = "Input: " + this.getInput() + "\n";\r
+               value += "Output: " + this.getOutput() + "\n";\r
+               value += "Error: " + this.getError() + "\n";\r
+               value += "Class: " + this.getClass() + "\n";\r
+               value += "Params: " + cbuilder + "\n";\r
+               return value;\r

        }\r
        }\r

-       if (!this.cbuilder.equals(exec.cbuilder)) {\r
-           return false;\r
+\r
+       @Override\r
+       public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {\r
+               if (!compbio.util.Util.isEmpty(rconfig.getOutput())) {\r
+                       setOutput(rconfig.getOutput());\r
+               }\r
+               if (!compbio.util.Util.isEmpty(rconfig.getError())) {\r
+                       setError(rconfig.getError());\r
+               }\r
+               if (!compbio.util.Util.isEmpty(rconfig.getInput())) {\r
+                       setInput(rconfig.getInput());\r
+               }\r
+               this.cbuilder = (CommandBuilder<T>) rconfig.getParameters();\r
+               return this;\r
+       }\r
+\r
+       @Override\r
+       public boolean equals(Object obj) {\r
+               if (obj == null) {\r
+                       return false;\r
+               }\r
+               if (!(obj instanceof SkeletalExecutable<?>)) {\r
+                       return false;\r
+               }\r
+               SkeletalExecutable<?> exec = (SkeletalExecutable<?>) obj;\r
+               if (!Util.isEmpty(this.inputFile) && !Util.isEmpty(exec.inputFile)) {\r
+                       if (!this.inputFile.equals(exec.inputFile)) {\r
+                               return false;\r
+                       }\r
+               }\r
+               if (!Util.isEmpty(this.outputFile) && !Util.isEmpty(exec.outputFile)) {\r
+                       if (!this.outputFile.equals(exec.outputFile)) {\r
+                               return false;\r
+                       }\r
+               }\r
+               if (!Util.isEmpty(this.errorFile) && !Util.isEmpty(exec.errorFile)) {\r
+                       if (!this.errorFile.equals(exec.errorFile)) {\r
+                               return false;\r
+                       }\r
+               }\r
+               if (!this.cbuilder.equals(exec.cbuilder)) {\r
+                       return false;\r
+               }\r
+               return true;\r
+       }\r
+\r
+       @Override\r
+       public int hashCode() {\r
+               int code = inputFile.hashCode();\r
+               code += outputFile.hashCode();\r
+               code += errorFile.hashCode();\r
+               code *= this.cbuilder.hashCode();\r
+               return code;\r
+       }\r
+\r
+       public String getClusterSettings() {\r
+               String settings = ph.getProperty(getType().getSimpleName()\r
+                               .toLowerCase() + ".cluster.settings");\r
+               return settings == null ? "" : settings;\r

        }\r
        }\r

-       return true;\r
-    }\r
-\r
-    @Override\r
-    public int hashCode() {\r
-       int code = inputFile.hashCode();\r
-       code += outputFile.hashCode();\r
-       code += errorFile.hashCode();\r
-       code *= this.cbuilder.hashCode();\r
-       return code;\r
-    }\r
-\r
-    public String getClusterSettings() {\r
-       String settings = ph.getProperty(getType().getSimpleName()\r
-               .toLowerCase()\r
-               + ".cluster.settings");\r
-       return settings == null ? "" : settings;\r
-    }\r
-\r
-    /**\r
+\r
+       /**\r

         * \r
         * @return number of cpus to use on the cluster or 0 if the value is\r
         *         undefined\r
         */\r
        public static int getClusterCpuNum(Class<? extends Executable<?>> type) {\r
                int cpus = 0;\r
         * \r
         * @return number of cpus to use on the cluster or 0 if the value is\r
         *         undefined\r
         */\r
        public static int getClusterCpuNum(Class<? extends Executable<?>> type) {\r
                int cpus = 0;\r

-               String cpuNum = ph.getProperty(type.getSimpleName().toLowerCase()+ ".cluster.cpunum");\r
+               String cpuNum = ph.getProperty(type.getSimpleName().toLowerCase()\r
+                               + ".cluster.cpunum");\r

                if (compbio.util.Util.isEmpty(cpuNum)) {\r
                        return 0;\r
                }\r
                if (compbio.util.Util.isEmpty(cpuNum)) {\r
                        return 0;\r
                }\r

@@ -274,20 +279,55 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
                        cpus = Integer.parseInt(cpuNum);\r
                } catch (NumberFormatException e) {\r
                        // safe to ignore\r
                        cpus = Integer.parseInt(cpuNum);\r
                } catch (NumberFormatException e) {\r
                        // safe to ignore\r

-                       log\r
-                       .debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: "\r
+                       log.debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: "\r

                                        + cpuNum);\r
                        return 0;\r
                }\r
                if (cpus < 1 || cpus > 100) {\r
                        throw new InvalidParameterException(\r
                                        "Number of cpu for cluster execution must be within 1 and 100! "\r
                                        + cpuNum);\r
                        return 0;\r
                }\r
                if (cpus < 1 || cpus > 100) {\r
                        throw new InvalidParameterException(\r
                                        "Number of cpu for cluster execution must be within 1 and 100! "\r

-                                       + "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is "\r
-                                       + cpus);\r
+                                                       + "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is "\r
+                                                       + cpus);\r

                }\r
                return cpus;\r
        }\r
 \r
                }\r
                return cpus;\r
        }\r
 \r

-    public abstract Class<? extends Executable<?>> getType();\r
+       @Override\r
+       public Limit<T> getLimit(String presetName) {\r
+\r
+               if (limits == null) {\r
+                       limits = getLimits();\r
+               }\r
+\r
+               Limit<T> limit = null;\r
+               if (limits != null) {\r
+                       // this returns default limit if preset is undefined!\r
+                       limit = limits.getLimitByName(presetName);\r
+               }\r
+               // If limit is not defined for a particular preset, then return default\r
+               // limit\r
+               if (limit == null) {\r
+                       log.debug("Limit for the preset " + presetName\r
+                                       + " is not found. Using default");\r
+                       limit = limits.getDefaultLimit();\r
+               }\r
+               return limit;\r
+       }\r
+\r
+       @Override\r
+       public LimitsManager<T> getLimits() {\r
+               synchronized (SkeletalExecutable.class) {\r
+                       if (limits == null) {\r
+                               limits = compbio.runner.Util.getLimits(this.getType());\r
+                       }\r
+               }\r
+               return limits;\r
+       }\r
+\r
+       /**\r
+        * \r
+        * @return subclasses must return their type\r
+        */\r
+       public abstract Class<Executable<T>> getType();\r

 \r
 }\r
 \r
 }\r

diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/Util.java
index 2f040aa..189ded7 100644 (file)
--- a/runner/compbio/runner/Util.java
+++ b/runner/compbio/runner/Util.java
@@ -67,19 +67,15 @@ public final class Util {
         *         separate options options.add(option); } return options; }\r
         */\r
 \r
         *         separate options options.add(option); } return options; }\r
         */\r
 \r

-       public static <T> LimitsManager<T> getLimits(\r
-                       Class<? extends Executable<T>> clazz) {\r
-               LimitsManager<T> limits = null;\r
+       public static <T> LimitsManager<T> getLimits(Class<Executable<T>> clazz) {\r
+               LimitsManager<T> limits = new LimitsManager<T>();\r

                try {\r
                        limits = ConfExecutable.getRunnerLimits(clazz);\r
                try {\r
                        limits = ConfExecutable.getRunnerLimits(clazz);\r

-                       if (limits == null) {\r
-                               return null;\r
-                       }\r

                } catch (FileNotFoundException e) {\r
                        log.warn(\r
                                        "No limits are found for " + clazz + " executable! "\r
                                                        + e.getLocalizedMessage(), e.getCause());\r
                } catch (FileNotFoundException e) {\r
                        log.warn(\r
                                        "No limits are found for " + clazz + " executable! "\r
                                                        + e.getLocalizedMessage(), e.getCause());\r

-                       return null;\r
+                       // its ok, limit may not be initialized\r

                } catch (IOException e) {\r
                        log.warn("IO exception while attempting to read limits for "\r
                                        + clazz + " executable! " + e.getLocalizedMessage(),\r
                } catch (IOException e) {\r
                        log.warn("IO exception while attempting to read limits for "\r
                                        + clazz + " executable! " + e.getLocalizedMessage(),\r

diff --git a/runner/compbio/runner/conservation/AACon.java b/runner/compbio/runner/conservation/AACon.java
index fd76e55..366b95f 100644 (file)
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -30,10 +30,7 @@ import compbio.data.sequence.SequenceUtil;
 import compbio.engine.client.CommandBuilder;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.engine.client.CommandBuilder;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.metadata.ResultNotAvailableException;\r

-import compbio.runner.Util;\r

 \r
 /**\r
  * Command line\r
 \r
 /**\r
  * Command line\r

@@ -55,9 +52,6 @@ public class AACon extends SkeletalExecutable<AACon> {
 \r
        private final String ncorePrm = "-t=";\r
 \r
 \r
        private final String ncorePrm = "-t=";\r
 \r

-       // Cache for Limits information\r
-       private static LimitsManager<AACon> limits;\r
-\r

        public static final String KEY_VALUE_SEPARATOR = "=";\r
        public static final String STAT_FILE = "stat.txt";\r
 \r
        public static final String KEY_VALUE_SEPARATOR = "=";\r
        public static final String STAT_FILE = "stat.txt";\r
 \r

@@ -128,40 +122,10 @@ public class AACon extends SkeletalExecutable<AACon> {
                return this;\r
        }\r
 \r
                return this;\r
        }\r
 \r

+       @SuppressWarnings("unchecked")\r

        @Override\r
        @Override\r

-       public Limit<AACon> getLimit(String presetName) {\r
-               if (limits == null) {\r
-                       limits = getLimits();\r
-               }\r
-               Limit<AACon> limit = null;\r
-               if (limits != null) {\r
-                       // this returns default limit if preset is undefined!\r
-                       limit = limits.getLimitByName(presetName);\r
-               }\r
-               // If limit is not defined for a particular preset, then return default\r
-               // limit\r
-               if (limit == null) {\r
-                       log.debug("Limit for the preset " + presetName\r
-                                       + " is not found. Using default");\r
-                       limit = limits.getDefaultLimit();\r
-               }\r
-               return limit;\r
-       }\r
-\r
-       @Override\r
-       public LimitsManager<AACon> getLimits() {\r
-               // synchronise on static field\r
-               synchronized (log) {\r
-                       if (limits == null) {\r
-                               limits = Util.getLimits(this.getClass());\r
-                       }\r
-               }\r
-               return limits;\r
-       }\r
-\r
-       @Override\r
-       public Class<? extends Executable<?>> getType() {\r
-               return this.getClass();\r
+       public Class<Executable<AACon>> getType() {\r
+               return (Class<Executable<AACon>>) this.getClass();\r

        }\r
 \r
        public static String getStatFile() {\r
        }\r
 \r
        public static String getStatFile() {\r

diff --git a/runner/compbio/runner/disorder/Disembl.java b/runner/compbio/runner/disorder/Disembl.java
index 6b014ba..37cb2c1 100644 (file)
--- a/runner/compbio/runner/disorder/Disembl.java
+++ b/runner/compbio/runner/disorder/Disembl.java
@@ -28,8 +28,6 @@ import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r

@@ -62,9 +60,6 @@ public class Disembl extends SkeletalExecutable<Disembl>
 \r
        private static Logger log = Logger.getLogger(Disembl.class);\r
 \r
 \r
        private static Logger log = Logger.getLogger(Disembl.class);\r
 \r

-       // Cache for Limits information\r
-       private static LimitsManager<Disembl> limits;\r
-\r

        public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
 \r
        /**\r
        public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
 \r
        /**\r

@@ -117,41 +112,10 @@ public class Disembl extends SkeletalExecutable<Disembl>
                return this;\r
        }\r
 \r
                return this;\r
        }\r
 \r

+       @SuppressWarnings("unchecked")\r

        @Override\r
        @Override\r

-       public Limit<Disembl> getLimit(String presetName) {\r
-               if (limits == null) {\r
-                       limits = getLimits();\r
-               }\r
-\r
-               Limit<Disembl> limit = null;\r
-               if (limits != null) {\r
-                       // this returns default limit if preset is undefined!\r
-                       limit = limits.getLimitByName(presetName);\r
-               }\r
-               // If limit is not defined for a particular preset, then return default\r
-               // limit\r
-               if (limit == null) {\r
-                       log.debug("Limit for the preset " + presetName\r
-                                       + " is not found. Using default");\r
-                       limit = limits.getDefaultLimit();\r
-               }\r
-               return limit;\r
-       }\r
-\r
-       @Override\r
-       public LimitsManager<Disembl> getLimits() {\r
-               // synchronise on static field\r
-               synchronized (log) {\r
-                       if (limits == null) {\r
-                               limits = Util.getLimits(this.getClass());\r
-                       }\r
-               }\r
-               return limits;\r
-       }\r
-\r
-       @Override\r
-       public Class<? extends Executable<?>> getType() {\r
-               return this.getClass();\r
+       public Class<Executable<Disembl>> getType() {\r
+               return (Class<Executable<Disembl>>) this.getClass();\r

        }\r
 \r
 }\r
        }\r
 \r
 }\r

diff --git a/runner/compbio/runner/disorder/GlobPlot.java b/runner/compbio/runner/disorder/GlobPlot.java
index ce08077..a5b887a 100644 (file)
--- a/runner/compbio/runner/disorder/GlobPlot.java
+++ b/runner/compbio/runner/disorder/GlobPlot.java
@@ -28,8 +28,6 @@ import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r

@@ -55,9 +53,6 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
 \r
        private static Logger log = Logger.getLogger(GlobPlot.class);\r
 \r
 \r
        private static Logger log = Logger.getLogger(GlobPlot.class);\r
 \r

-       // Cache for Limits information\r
-       private static LimitsManager<GlobPlot> limits;\r
-\r

        public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
 \r
        /* The parameter list there must not contain same values! */\r
        public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
 \r
        /* The parameter list there must not contain same values! */\r

@@ -103,41 +98,10 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
                return this;\r
        }\r
 \r
                return this;\r
        }\r
 \r

+       @SuppressWarnings("unchecked")\r

        @Override\r
        @Override\r

-       public Limit<GlobPlot> getLimit(String presetName) {\r
-               if (limits == null) {\r
-                       limits = getLimits();\r
-               }\r
-\r
-               Limit<GlobPlot> limit = null;\r
-               if (limits != null) {\r
-                       // this returns default limit if preset is undefined!\r
-                       limit = limits.getLimitByName(presetName);\r
-               }\r
-               // If limit is not defined for a particular preset, then return default\r
-               // limit\r
-               if (limit == null) {\r
-                       log.debug("Limit for the preset " + presetName\r
-                                       + " is not found. Using default");\r
-                       limit = limits.getDefaultLimit();\r
-               }\r
-               return limit;\r
-       }\r
-\r
-       @Override\r
-       public LimitsManager<GlobPlot> getLimits() {\r
-               // synchronise on static field\r
-               synchronized (log) {\r
-                       if (limits == null) {\r
-                               limits = Util.getLimits(this.getClass());\r
-                       }\r
-               }\r
-               return limits;\r
-       }\r
-\r
-       @Override\r
-       public Class<? extends Executable<?>> getType() {\r
-               return this.getClass();\r
+       public Class<Executable<GlobPlot>> getType() {\r
+               return (Class<Executable<GlobPlot>>) this.getClass();\r

        }\r
 \r
 }\r
        }\r
 \r
 }\r

diff --git a/runner/compbio/runner/disorder/Jronn.java b/runner/compbio/runner/disorder/Jronn.java
index 617d3bb..3f668e3 100644 (file)
--- a/runner/compbio/runner/disorder/Jronn.java
+++ b/runner/compbio/runner/disorder/Jronn.java
@@ -34,8 +34,6 @@ import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.CommandBuilder;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.engine.client.CommandBuilder;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r

@@ -59,9 +57,6 @@ public class Jronn extends SkeletalExecutable<Jronn> {
 \r
        private final String ncorePrm = "-n=";\r
 \r
 \r
        private final String ncorePrm = "-n=";\r
 \r

-       // Cache for Limits information\r
-       private static LimitsManager<Jronn> limits;\r
-\r

        public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
        public static final String STAT_FILE = "stat.txt";\r
 \r
        public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
        public static final String STAT_FILE = "stat.txt";\r
 \r

@@ -132,40 +127,10 @@ public class Jronn extends SkeletalExecutable<Jronn> {
                return this;\r
        }\r
 \r
                return this;\r
        }\r
 \r

+       @SuppressWarnings("unchecked")\r

        @Override\r
        @Override\r

-       public Limit<Jronn> getLimit(String presetName) {\r
-               if (limits == null) {\r
-                       limits = getLimits();\r
-               }\r
-               Limit<Jronn> limit = null;\r
-               if (limits != null) {\r
-                       // this returns default limit if preset is undefined!\r
-                       limit = limits.getLimitByName(presetName);\r
-               }\r
-               // If limit is not defined for a particular preset, then return default\r
-               // limit\r
-               if (limit == null) {\r
-                       log.debug("Limit for the preset " + presetName\r
-                                       + " is not found. Using default");\r
-                       limit = limits.getDefaultLimit();\r
-               }\r
-               return limit;\r
-       }\r
-\r
-       @Override\r
-       public LimitsManager<Jronn> getLimits() {\r
-               // synchronise on static field\r
-               synchronized (log) {\r
-                       if (limits == null) {\r
-                               limits = Util.getLimits(this.getClass());\r
-                       }\r
-               }\r
-               return limits;\r
-       }\r
-\r
-       @Override\r
-       public Class<? extends Executable<?>> getType() {\r
-               return this.getClass();\r
+       public Class<Executable<Jronn>> getType() {\r
+               return (Class<Executable<Jronn>>) this.getClass();\r

        }\r
 \r
        public static String getStatFile() {\r
        }\r
 \r
        public static String getStatFile() {\r

diff --git a/runner/compbio/runner/msa/ClustalW.java b/runner/compbio/runner/msa/ClustalW.java
index 7aff01c..88f6358 100644 (file)
--- a/runner/compbio/runner/msa/ClustalW.java
+++ b/runner/compbio/runner/msa/ClustalW.java
@@ -29,130 +29,93 @@ import compbio.data.sequence.Alignment;
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 public class ClustalW extends SkeletalExecutable<ClustalW> {\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 public class ClustalW extends SkeletalExecutable<ClustalW> {\r
 \r

-    private static Logger log = Logger.getLogger(ClustalW.class);\r
-    private static final String EXEC_STAT_FILE = "stat.log";\r
-    private static final String TREE_FILE_EXT = ".dnd";\r
-\r
-    public static final String KEY_VALUE_SEPARATOR = "=";\r
-\r
-    // Cache for Limits information\r
-    private static LimitsManager<ClustalW> limits;\r
-\r
-    public ClustalW() {\r
-       super(KEY_VALUE_SEPARATOR);\r
-       addParameters(Arrays.asList("-OUTORDER=ALIGNED", "-QUIET", "-STATS="\r
-               + EXEC_STAT_FILE));\r
-       // set default in, outs and err files\r
-       this.setInput(super.inputFile);\r
-       this.setOutput(super.outputFile);\r
-       this.setError(super.errorFile);\r
-    }\r
-\r
-    @Override\r
-    public ClustalW setOutput(String outFile) {\r
-       super.setOutput(outFile);\r
-       cbuilder.setParam("-OUTFILE=" + outFile);\r
-       return this;\r
-    }\r
-\r
-    @Override\r
-    public ClustalW setInput(String inFile) {\r
-       super.setInput(inFile);\r
-       cbuilder.setParam("-INFILE=" + inFile);\r
-       return this;\r
-    }\r
-\r
-    @SuppressWarnings("unchecked")\r
-    public Alignment getResults(String workDirectory)\r
-           throws ResultNotAvailableException {\r
-       try {\r
-           return Util.readClustalFile(workDirectory, getOutput());\r
-       } catch (FileNotFoundException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (IOException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (UnknownFileFormatException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (NullPointerException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       }\r
-    }\r
-\r
-    @Override\r
-    public List<String> getCreatedFiles() {\r
-       return Arrays.asList(getOutput(), EXEC_STAT_FILE,\r
-               convertInputNameToTreeName());\r
-    }\r
-\r
-    /*\r
-     * Clustal output tree with same name as input file but .dnd extension e.g.\r
-     * this methods do similar conversion TO122.fasta -> TO122.dnd or\r
-     * TO122.fasta.in -> TO122.fasta.dnd It does not seems that there is any\r
-     * limits on the name length\r
-     * \r
-     * @return\r
-     */\r
-    private String convertInputNameToTreeName() {\r
-       assert super.getInput() != null;\r
-       int dotIdx = getInput().lastIndexOf(".");\r
-       String treeFileName = "";\r
-       if (dotIdx > 0) {\r
-           treeFileName = getInput().substring(0, dotIdx);\r
+       private static Logger log = Logger.getLogger(ClustalW.class);\r
+       private static final String EXEC_STAT_FILE = "stat.log";\r
+       private static final String TREE_FILE_EXT = ".dnd";\r
+\r
+       public static final String KEY_VALUE_SEPARATOR = "=";\r
+\r
+       public ClustalW() {\r
+               super(KEY_VALUE_SEPARATOR);\r
+               addParameters(Arrays.asList("-OUTORDER=ALIGNED", "-QUIET", "-STATS="\r
+                               + EXEC_STAT_FILE));\r
+               // set default in, outs and err files\r
+               this.setInput(super.inputFile);\r
+               this.setOutput(super.outputFile);\r
+               this.setError(super.errorFile);\r

        }\r
        }\r

-       return treeFileName + TREE_FILE_EXT;\r
-    }\r

 \r
 \r

-    public static String getStatFile() {\r
-       return EXEC_STAT_FILE;\r
-    }\r
+       @Override\r
+       public ClustalW setOutput(String outFile) {\r
+               super.setOutput(outFile);\r
+               cbuilder.setParam("-OUTFILE=" + outFile);\r
+               return this;\r
+       }\r

 \r
 \r

-    @Override\r
-    public Limit<ClustalW> getLimit(String presetName) {\r
+       @Override\r
+       public ClustalW setInput(String inFile) {\r
+               super.setInput(inFile);\r
+               cbuilder.setParam("-INFILE=" + inFile);\r
+               return this;\r
+       }\r

 \r
 \r

-       if (limits == null) {\r
-           limits = getLimits();\r
+       @SuppressWarnings("unchecked")\r
+       public Alignment getResults(String workDirectory)\r
+                       throws ResultNotAvailableException {\r
+               try {\r
+                       return Util.readClustalFile(workDirectory, getOutput());\r
+               } catch (FileNotFoundException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (IOException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (UnknownFileFormatException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (NullPointerException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               }\r

        }\r
 \r
        }\r
 \r

-       Limit<ClustalW> limit = null;\r
-       if (limits != null) {\r
-           // this returns default limit if preset is undefined!\r
-           limit = limits.getLimitByName(presetName);\r
+       @Override\r
+       public List<String> getCreatedFiles() {\r
+               return Arrays.asList(getOutput(), EXEC_STAT_FILE,\r
+                               convertInputNameToTreeName());\r

        }\r
        }\r

-       // If limit is not defined for a particular preset, then return default\r
-       // limit\r
-       if (limit == null) {\r
-           log.debug("Limit for the preset " + presetName\r
-                   + " is not found. Using default");\r
-           limit = limits.getDefaultLimit();\r
+\r
+       /*\r
+        * Clustal output tree with same name as input file but .dnd extension e.g.\r
+        * this methods do similar conversion TO122.fasta -> TO122.dnd or\r
+        * TO122.fasta.in -> TO122.fasta.dnd It does not seems that there is any\r
+        * limits on the name length\r
+        * \r
+        * @return\r
+        */\r
+       private String convertInputNameToTreeName() {\r
+               assert super.getInput() != null;\r
+               int dotIdx = getInput().lastIndexOf(".");\r
+               String treeFileName = "";\r
+               if (dotIdx > 0) {\r
+                       treeFileName = getInput().substring(0, dotIdx);\r
+               }\r
+               return treeFileName + TREE_FILE_EXT;\r

        }\r
        }\r

-       return limit;\r
-    }\r
-\r
-    @Override\r
-    public LimitsManager<ClustalW> getLimits() {\r
-       // synchronise on static field\r
-       synchronized (log) {\r
-           if (limits == null) {\r
-               limits = Util.getLimits(this.getClass());\r
-           }\r
+\r
+       public static String getStatFile() {\r
+               return EXEC_STAT_FILE;\r

        }\r
        }\r

-       return limits;\r
-    }\r

 \r
 \r

-    @Override\r
-    public Class<? extends Executable<?>> getType() {\r
-       return this.getClass();\r
-    }\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Class<Executable<ClustalW>> getType() {\r
+               return (Class<Executable<ClustalW>>) this.getClass();\r
+       }\r

 \r
 }\r
 \r
 }\r

diff --git a/runner/compbio/runner/msa/Mafft.java b/runner/compbio/runner/msa/Mafft.java
index 2e8a9fc..ee0e5cb 100644 (file)
--- a/runner/compbio/runner/msa/Mafft.java
+++ b/runner/compbio/runner/msa/Mafft.java
@@ -30,125 +30,90 @@ import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r

-public class Mafft extends SkeletalExecutable<Mafft> implements\r
-       PipedExecutable<Mafft> {\r
+public class Mafft extends SkeletalExecutable<Mafft>\r
+               implements\r
+                       PipedExecutable<Mafft> {\r

 \r
 \r

-    private static Logger log = Logger.getLogger(Mafft.class);\r
+       private static Logger log = Logger.getLogger(Mafft.class);\r

 \r
 \r

-    // Cache for Limits information\r
-    private static LimitsManager<Mafft> limits;\r
+       private static String autoOption = "--auto";\r

 \r
 \r

-    private static String autoOption = "--auto";\r
+       private final String MATRIX_PAR_NAME = "--aamatrix";\r

 \r
 \r

-    private final String MATRIX_PAR_NAME = "--aamatrix";\r
+       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r

 \r
 \r

-    public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
-\r
-    public Mafft() {\r
-       // remove default input to prevent it to appear in the parameters list\r
-       // that could happen if the parameters are set first\r
-       // super.setInput("");\r
-       addParameters(Arrays.asList("--clustalout", autoOption));\r
-    }\r
-\r
-    @SuppressWarnings("unchecked")\r
-    public Alignment getResults(String workDirectory)\r
-           throws ResultNotAvailableException {\r
-       try {\r
-           return Util.readClustalFile(workDirectory, getOutput());\r
-       } catch (FileNotFoundException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (IOException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (UnknownFileFormatException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (NullPointerException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
+       public Mafft() {\r
+               // remove default input to prevent it to appear in the parameters list\r
+               // that could happen if the parameters are set first\r
+               // super.setInput("");\r
+               addParameters(Arrays.asList("--clustalout", autoOption));\r

        }\r
        }\r

-    }\r
-\r
-    @Override\r
-    public Mafft setInput(String inFile) {\r
-       super.setInput(inFile);\r
-       cbuilder.setLast(inFile);\r
-       return this;\r
-    }\r

 \r
 \r

-    /**\r
-     * Mafft input must always be the last parameter!\r
-     */\r
-    @Override\r
-    public Mafft addParameters(List<String> parameters) {\r
-       cbuilder.addParams(parameters);\r
-       cbuilder.removeParam(autoOption);\r
-       return this;\r
-    }\r
-\r
-    @Override\r
-    public Limit<Mafft> getLimit(String presetName) {\r
-       if (limits == null) {\r
-           limits = getLimits();\r
+       @SuppressWarnings("unchecked")\r
+       public Alignment getResults(String workDirectory)\r
+                       throws ResultNotAvailableException {\r
+               try {\r
+                       return Util.readClustalFile(workDirectory, getOutput());\r
+               } catch (FileNotFoundException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (IOException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (UnknownFileFormatException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (NullPointerException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               }\r

        }\r
 \r
        }\r
 \r

-       Limit<Mafft> limit = null;\r
-       if (limits != null) {\r
-           // this returns default limit if preset is undefined!\r
-           limit = limits.getLimitByName(presetName);\r
-       }\r
-       // If limit is not defined for a particular preset, then return default\r
-       // limit\r
-       if (limit == null) {\r
-           log.debug("Limit for the preset " + presetName\r
-                   + " is not found. Using default");\r
-           limit = limits.getDefaultLimit();\r
+       @Override\r
+       public Mafft setInput(String inFile) {\r
+               super.setInput(inFile);\r
+               cbuilder.setLast(inFile);\r
+               return this;\r

        }\r
        }\r

-       return limit;\r
-    }\r

 \r
 \r

-    @Override\r
-    public LimitsManager<Mafft> getLimits() {\r
-       // synchronise on static field\r
-       synchronized (log) {\r
-           if (limits == null) {\r
-               limits = Util.getLimits(this.getClass());\r
-           }\r
+       /**\r
+        * Mafft input must always be the last parameter!\r
+        */\r
+       @Override\r
+       public Mafft addParameters(List<String> parameters) {\r
+               cbuilder.addParams(parameters);\r
+               cbuilder.removeParam(autoOption);\r
+               return this;\r

        }\r
        }\r

-       return limits;\r
-    }\r

 \r
 \r

-    @Override\r
-    public Class<? extends Executable<?>> getType() {\r
-       return this.getClass();\r
-    }\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Class<Executable<Mafft>> getType() {\r
+               return (Class<Executable<Mafft>>) this.getClass();\r
+       }\r

 \r
 \r

-    /*\r
-     * @Override public List<String> getParameters(\r
-     * compbio.runner.Executable.ExecProvider provider) { for (int i = 0; i <\r
-     * param.size(); i++) { String par = param.get(i); if\r
-     * (isMatrixParameter(par)) { String matrixName = getValue(i); if (new\r
-     * File(matrixName).isAbsolute()) { // Matrix can be found so no actions\r
-     * necessary // This method has been called already and the matrix name //\r
-     * is modified to contain full path // no further actions is necessary\r
-     * break; } String matrixPath = Util.getExecProperty("matrix.path", this);\r
-     * String absMatrixPath = Util.convertToAbsolute(matrixPath); param.remove(i\r
-     * + 1); param.remove(i); super.addParameter(MATRIX_PAR_NAME);\r
-     * super.addParameter(absMatrixPath + File.separator + matrixName); break; }\r
-     * } return super.getParameters(provider); }\r
-     * \r
-     * boolean isMatrixParameter(String parameter) { assert\r
-     * !compbio.util.Util.isEmpty(parameter); if\r
-     * (parameter.toUpperCase().startsWith(MATRIX_PAR_NAME)) { return true; }\r
-     * return false; }\r
-     * \r
-     * String getValue(int i) { return param.get(i + 1); }\r
-     */\r
+       /*\r
+        * @Override public List<String> getParameters(\r
+        * compbio.runner.Executable.ExecProvider provider) { for (int i = 0; i <\r
+        * param.size(); i++) { String par = param.get(i); if\r
+        * (isMatrixParameter(par)) { String matrixName = getValue(i); if (new\r
+        * File(matrixName).isAbsolute()) { // Matrix can be found so no actions\r
+        * necessary // This method has been called already and the matrix name //\r
+        * is modified to contain full path // no further actions is necessary\r
+        * break; } String matrixPath = Util.getExecProperty("matrix.path", this);\r
+        * String absMatrixPath = Util.convertToAbsolute(matrixPath); param.remove(i\r
+        * + 1); param.remove(i); super.addParameter(MATRIX_PAR_NAME);\r
+        * super.addParameter(absMatrixPath + File.separator + matrixName); break; }\r
+        * } return super.getParameters(provider); }\r
+        * \r
+        * boolean isMatrixParameter(String parameter) { assert\r
+        * !compbio.util.Util.isEmpty(parameter); if\r
+        * (parameter.toUpperCase().startsWith(MATRIX_PAR_NAME)) { return true; }\r
+        * return false; }\r
+        * \r
+        * String getValue(int i) { return param.get(i + 1); }\r
+        */\r

 }\r
 }\r

diff --git a/runner/compbio/runner/msa/Muscle.java b/runner/compbio/runner/msa/Muscle.java
index d220d16..c37b73a 100644 (file)
--- a/runner/compbio/runner/msa/Muscle.java
+++ b/runner/compbio/runner/msa/Muscle.java
@@ -31,125 +31,88 @@ import compbio.data.sequence.Alignment;
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 public class Muscle extends SkeletalExecutable<Muscle> {\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 public class Muscle extends SkeletalExecutable<Muscle> {\r
 \r

-    /*\r
-     * Tell JAXB to ignore this while marshalling\r
-     */\r
-    @XmlTransient\r
-    private static Logger log = Logger.getLogger(Muscle.class);\r
-\r
-    // Cache for Limits information\r
-    private static LimitsManager<Muscle> limits;\r
+       /*\r
+        * Tell JAXB to ignore this while marshalling\r
+        */\r
+       @XmlTransient\r
+       private static Logger log = Logger.getLogger(Muscle.class);\r

 \r
 \r

-    private static final String EXEC_STAT_FILE = "stat.log";\r
+       private static final String EXEC_STAT_FILE = "stat.log";\r

 \r
 \r

-    public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r

 \r
 \r

-    /**\r
-     * Default options are\r
-     * \r
-     * -clwstrict - write output in clustal format\r
-     * \r
-     * @param workDirectory\r
-     */\r
-    public Muscle() {\r
-       /*\r
-        * The –quiet command-line option disables writing progress messages to\r
-        * standard error. If the –verbose command-line option is specified, a\r
-        * progress message will be written to the log file when each iteration\r
-        * completes. So –quiet and –verbose are not contradictory."-quiet",\r
-        * "-verbose"\r
+       /**\r
+        * Default options are\r
+        * \r
+        * -clwstrict - write output in clustal format\r
+        * \r
+        * @param workDirectory\r

         */\r
         */\r

-       addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose"));\r
-       cbuilder.setParam("-log", EXEC_STAT_FILE);\r
-    }\r
-\r
-    @Override\r
-    public Muscle setOutput(String outFile) {\r
-       super.setOutput(outFile);\r
-       cbuilder.setParam("-out", outFile);\r
-       return this;\r
-    }\r
-\r
-    @Override\r
-    public Muscle setInput(String inFile) {\r
-       super.setInput(inFile);\r
-       cbuilder.setParam("-in", inFile);\r
-       return this;\r
-    }\r
-\r
-    @SuppressWarnings("unchecked")\r
-    @Override\r
-    public Alignment getResults(String workDirectory)\r
-           throws ResultNotAvailableException {\r
-       try {\r
-           return Util.readClustalFile(workDirectory, getOutput());\r
-       } catch (FileNotFoundException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (IOException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (UnknownFileFormatException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (NullPointerException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
+       public Muscle() {\r
+               /*\r
+                * The –quiet command-line option disables writing progress messages to\r
+                * standard error. If the –verbose command-line option is specified, a\r
+                * progress message will be written to the log file when each iteration\r
+                * completes. So –quiet and –verbose are not contradictory."-quiet",\r
+                * "-verbose"\r
+                */\r
+               addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose"));\r
+               cbuilder.setParam("-log", EXEC_STAT_FILE);\r

        }\r
        }\r

-    }\r
-\r
-    @Override\r
-    public List<String> getCreatedFiles() {\r
-       return Arrays.asList(getOutput(), EXEC_STAT_FILE);\r
-    }\r

 \r
 \r

-    public static String getStatFile() {\r
-       return EXEC_STAT_FILE;\r
-    }\r
-\r
-    @Override\r
-    public Limit<Muscle> getLimit(String presetName) {\r
+       @Override\r
+       public Muscle setOutput(String outFile) {\r
+               super.setOutput(outFile);\r
+               cbuilder.setParam("-out", outFile);\r
+               return this;\r
+       }\r

 \r
 \r

-       if (limits == null) {\r
-           limits = getLimits();\r
+       @Override\r
+       public Muscle setInput(String inFile) {\r
+               super.setInput(inFile);\r
+               cbuilder.setParam("-in", inFile);\r
+               return this;\r

        }\r
 \r
        }\r
 \r

-       Limit<Muscle> limit = null;\r
-       if (limits != null) {\r
-           // this returns default limit if preset is undefined!\r
-           limit = limits.getLimitByName(presetName);\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Alignment getResults(String workDirectory)\r
+                       throws ResultNotAvailableException {\r
+               try {\r
+                       return Util.readClustalFile(workDirectory, getOutput());\r
+               } catch (FileNotFoundException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (IOException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (UnknownFileFormatException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (NullPointerException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               }\r

        }\r
        }\r

-       // If limit is not defined for a particular preset, then return default\r
-       // limit\r
-       if (limit == null) {\r
-           log.debug("Limit for the preset " + presetName\r
-                   + " is not found. Using default");\r
-           limit = limits.getDefaultLimit();\r
+\r
+       @Override\r
+       public List<String> getCreatedFiles() {\r
+               return Arrays.asList(getOutput(), EXEC_STAT_FILE);\r

        }\r
        }\r

-       return limit;\r
-    }\r
-\r
-    @Override\r
-    public LimitsManager<Muscle> getLimits() {\r
-       // synchronise on static field\r
-       synchronized (log) {\r
-           if (limits == null) {\r
-               limits = Util.getLimits(this.getClass());\r
-           }\r
+\r
+       public static String getStatFile() {\r
+               return EXEC_STAT_FILE;\r

        }\r
        }\r

-       return limits;\r
-    }\r

 \r
 \r

-    @Override\r
-    public Class<? extends Executable<?>> getType() {\r
-       return this.getClass();\r
-    }\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Class<Executable<Muscle>> getType() {\r
+               return (Class<Executable<Muscle>>) this.getClass();\r
+       }\r

 \r
 }\r
 \r
 }\r

diff --git a/runner/compbio/runner/msa/Probcons.java b/runner/compbio/runner/msa/Probcons.java
index ea9fa1d..2df7f92 100644 (file)
--- a/runner/compbio/runner/msa/Probcons.java
+++ b/runner/compbio/runner/msa/Probcons.java
@@ -30,102 +30,69 @@ import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r

-public class Probcons extends SkeletalExecutable<Probcons> implements\r
-       PipedExecutable<Probcons> {\r
+public class Probcons extends SkeletalExecutable<Probcons>\r
+               implements\r
+                       PipedExecutable<Probcons> {\r

 \r
 \r

-    private static Logger log = Logger.getLogger(Probcons.class);\r
+       private static Logger log = Logger.getLogger(Probcons.class);\r

 \r
 \r

-    // Cache for Limits information\r
-    private static LimitsManager<Probcons> limits;\r
-    private final static String ANNOTATION = "annotation.txt";\r
+       private final static String ANNOTATION = "annotation.txt";\r

 \r
 \r

-    public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r

 \r
 \r

-    /**\r
-     * \r
-     * @param workDirectory\r
-     */\r
-    public Probcons() {\r
-       addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
-       /*\r
-        * Could either have probabilities or the alignment, but not both "-t",\r
-        * "probabilities"\r
+       /**\r
+        * \r
+        * @param workDirectory\r

         */\r
         */\r

-    }\r
-\r
-    @SuppressWarnings("unchecked")\r
-    @Override\r
-    public Alignment getResults(String workDirectory)\r
-           throws ResultNotAvailableException {\r
-       try {\r
-           return Util.readClustalFile(workDirectory, getOutput());\r
-       } catch (FileNotFoundException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (IOException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (UnknownFileFormatException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
-       } catch (NullPointerException e) {\r
-           log.error(e.getMessage(), e.getCause());\r
-           throw new ResultNotAvailableException(e);\r
+       public Probcons() {\r
+               addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
+               /*\r
+                * Could either have probabilities or the alignment, but not both "-t",\r
+                * "probabilities"\r
+                */\r

        }\r
        }\r

-    }\r
-\r
-    @Override\r
-    public List<String> getCreatedFiles() {\r
-       return Arrays.asList(getOutput(), ANNOTATION, getError());\r
-    }\r
-\r
-    @Override\r
-    public Probcons setInput(String inFile) {\r
-       String input = getInput();\r
-       super.setInput(inFile);\r
-       // TODO replace with setLast\r
-       cbuilder.setParam(inFile);\r
-       return this;\r
-    }\r

 \r
 \r

-    @Override\r
-    public Limit<Probcons> getLimit(String presetName) {\r
-       if (limits == null) {\r
-           limits = getLimits();\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Alignment getResults(String workDirectory)\r
+                       throws ResultNotAvailableException {\r
+               try {\r
+                       return Util.readClustalFile(workDirectory, getOutput());\r
+               } catch (FileNotFoundException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (IOException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (UnknownFileFormatException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               } catch (NullPointerException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               }\r

        }\r
        }\r

-       Limit<Probcons> limit = null;\r
-       if (limits != null) {\r
-           // this returns default limit if preset is undefined!\r
-           limit = limits.getLimitByName(presetName);\r
-       }\r
-       // If limit is not defined for a particular preset, then return default\r
-       // limit\r
-       if (limit == null) {\r
-           log.debug("Limit for the preset " + presetName\r
-                   + " is not found. Using default");\r
-           limit = limits.getDefaultLimit();\r
+\r
+       @Override\r
+       public List<String> getCreatedFiles() {\r
+               return Arrays.asList(getOutput(), ANNOTATION, getError());\r

        }\r
        }\r

-       return limit;\r
-    }\r

 \r
 \r

-    @Override\r
-    public LimitsManager<Probcons> getLimits() {\r
-       // synchronise on static field\r
-       synchronized (log) {\r
-           if (limits == null) {\r
-               limits = Util.getLimits(this.getClass());\r
-           }\r
+       @Override\r
+       public Probcons setInput(String inFile) {\r
+               String input = getInput();\r
+               super.setInput(inFile);\r
+               // TODO replace with setLast\r
+               cbuilder.setParam(inFile);\r
+               return this;\r

        }\r
        }\r

-       return limits;\r
-    }\r

 \r
 \r

-    @Override\r
-    public Class<? extends Executable<?>> getType() {\r
-       return this.getClass();\r
-    }\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Class<Executable<Probcons>> getType() {\r
+               return (Class<Executable<Probcons>>) this.getClass();\r
+       }\r

 }\r
 }\r

diff --git a/runner/compbio/runner/msa/Tcoffee.java b/runner/compbio/runner/msa/Tcoffee.java
index 949c4f1..3b35875 100644 (file)
--- a/runner/compbio/runner/msa/Tcoffee.java
+++ b/runner/compbio/runner/msa/Tcoffee.java
@@ -20,7 +20,6 @@ package compbio.runner.msa;
 \r
 import java.io.FileNotFoundException;\r
 import java.io.IOException;\r
 \r
 import java.io.FileNotFoundException;\r
 import java.io.IOException;\r

-import java.security.InvalidParameterException;\r

 import java.util.Arrays;\r
 import java.util.List;\r
 \r
 import java.util.Arrays;\r
 import java.util.List;\r
 \r

@@ -34,22 +33,19 @@ import compbio.engine.client.Executable;
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.engine.conf.PropertyHelperManager;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.engine.conf.PropertyHelperManager;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 import compbio.util.PropertyHelper;\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 import compbio.util.PropertyHelper;\r
 \r

-public class Tcoffee extends SkeletalExecutable<Tcoffee> implements\r
-PipedExecutable<Tcoffee>, ClusterNativeSpecExecutable<Tcoffee> {\r
+public class Tcoffee extends SkeletalExecutable<Tcoffee>\r
+               implements\r
+                       PipedExecutable<Tcoffee>,\r
+                       ClusterNativeSpecExecutable<Tcoffee> {\r

 \r
        private static Logger log = Logger.getLogger(Tcoffee.class);\r
 \r
        private static PropertyHelper ph = PropertyHelperManager\r
 \r
        private static Logger log = Logger.getLogger(Tcoffee.class);\r
 \r
        private static PropertyHelper ph = PropertyHelperManager\r

-       .getPropertyHelper();\r
-\r
-       // Cache for Limits information\r
-       private static LimitsManager<Tcoffee> limits;\r
+                       .getPropertyHelper();\r

 \r
        public static final String KEY_VALUE_SEPARATOR = "=";\r
 \r
 \r
        public static final String KEY_VALUE_SEPARATOR = "=";\r
 \r

@@ -88,7 +84,7 @@ PipedExecutable<Tcoffee>, ClusterNativeSpecExecutable<Tcoffee> {
        @SuppressWarnings("unchecked")\r
        @Override\r
        public Alignment getResults(String workDirectory)\r
        @SuppressWarnings("unchecked")\r
        @Override\r
        public Alignment getResults(String workDirectory)\r

-       throws ResultNotAvailableException {\r
+                       throws ResultNotAvailableException {\r

                try {\r
                        return Util.readClustalFile(workDirectory, getOutput());\r
                } catch (FileNotFoundException e) {\r
                try {\r
                        return Util.readClustalFile(workDirectory, getOutput());\r
                } catch (FileNotFoundException e) {\r

@@ -141,45 +137,13 @@ PipedExecutable<Tcoffee>, ClusterNativeSpecExecutable<Tcoffee> {
        }\r
 \r
        @Override\r
        }\r
 \r
        @Override\r

-       public Limit<Tcoffee> getLimit(String presetName) {\r
-               if (limits == null) {\r
-                       limits = getLimits();\r
-               }\r
-\r
-               Limit<Tcoffee> limit = null;\r
-               if (limits != null) {\r
-                       // this returns default limit if preset is undefined!\r
-                       limit = limits.getLimitByName(presetName);\r
-               }\r
-               // If limit is not defined for a particular preset, then return default\r
-               // limit\r
-               if (limit == null) {\r
-                       log.debug("Limit for the preset " + presetName\r
-                                       + " is not found. Using default");\r
-                       limit = limits.getDefaultLimit();\r
-               }\r
-               return limit;\r
-       }\r
-\r
-       @Override\r
-       public LimitsManager<Tcoffee> getLimits() {\r
-               // synchronise on static field\r
-               synchronized (log) {\r
-                       if (limits == null) {\r
-                               limits = Util.getLimits(this.getClass());\r
-                       }\r
-               }\r
-               return limits;\r
-       }\r
-\r
-       @Override\r

        public String getNativeSpecs() {\r
                return getClusterSettings();\r
        }\r
 \r
        public String getNativeSpecs() {\r
                return getClusterSettings();\r
        }\r
 \r

-\r
+       @SuppressWarnings("unchecked")\r

        @Override\r
        @Override\r

-       public Class<? extends Executable<?>> getType() {\r
-               return this.getClass();\r
+       public Class<Executable<Tcoffee>> getType() {\r
+               return (Class<Executable<Tcoffee>>) this.getClass();\r

        }\r
 }\r
        }\r
 }\r

diff --git a/runner/compbio/runner/psiblast/PsiBlast.java b/runner/compbio/runner/psiblast/PsiBlast.java
index 8299d6d..c51df24 100644 (file)
--- a/runner/compbio/runner/psiblast/PsiBlast.java
+++ b/runner/compbio/runner/psiblast/PsiBlast.java
@@ -20,42 +20,29 @@ package compbio.runner.psiblast;
 \r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 \r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r

-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r

 import compbio.metadata.ResultNotAvailableException;\r
 \r
 public class PsiBlast extends SkeletalExecutable<PsiBlast> {\r
 \r
 import compbio.metadata.ResultNotAvailableException;\r
 \r
 public class PsiBlast extends SkeletalExecutable<PsiBlast> {\r
 \r

-    public PsiBlast() {\r
+       public PsiBlast() {\r

 \r
 \r

-    }\r
+       }\r

 \r
 \r

-    void getSupportedDatabases() {\r
+       void getSupportedDatabases() {\r

 \r
 \r

-    }\r
+       }\r

 \r
 \r

-    @Override\r
-    public <V> V getResults(String directory)\r
-           throws ResultNotAvailableException {\r
-       // TODO Auto-generated method stub\r
-       return null;\r
-    }\r
+       @Override\r
+       public <V> V getResults(String directory)\r
+                       throws ResultNotAvailableException {\r
+               // TODO Auto-generated method stub\r
+               return null;\r
+       }\r

 \r
 \r

-    @Override\r
-    public Limit<PsiBlast> getLimit(String presetName) {\r
-       // TODO Auto-generated method stub\r
-       return null;\r
-    }\r
-\r
-    @Override\r
-    public LimitsManager<PsiBlast> getLimits() {\r
-       // TODO Auto-generated method stub\r
-       return null;\r
-    }\r
-\r
-    @Override\r
-    public Class<? extends Executable<?>> getType() {\r
-       return this.getClass();\r
-    }\r
+       @Override\r
+       public Class<Executable<PsiBlast>> getType() {\r
+               // TODO Auto-generated method stub\r
+               return null;\r
+       }\r

 \r
 }\r
 \r
 }\r

diff --git a/testsrc/compbio/metadata/AllTestSuit.java b/testsrc/compbio/metadata/AllTestSuit.java
index 633e30b..794565a 100644 (file)
--- a/testsrc/compbio/metadata/AllTestSuit.java
+++ b/testsrc/compbio/metadata/AllTestSuit.java
@@ -33,21 +33,21 @@ public class AllTestSuit {
        public static final RunnerConfig<ClustalW> CLUSTAL_PARAMETERS = Util\r
                        .getSupportedOptions(ClustalW.class);\r
        public static final LimitsManager<ClustalW> CLUSTAL_LIMITS = Util\r
        public static final RunnerConfig<ClustalW> CLUSTAL_PARAMETERS = Util\r
                        .getSupportedOptions(ClustalW.class);\r
        public static final LimitsManager<ClustalW> CLUSTAL_LIMITS = Util\r

-                       .getLimits(ClustalW.class);\r
+                       .getLimits(new ClustalW().getType());\r

 \r
        public static final PresetManager<Tcoffee> TCOFFEE_PRESETS = Util\r
                        .getPresets(Tcoffee.class);\r
        public static final RunnerConfig<Tcoffee> TCOFFEE_PARAMETERS = Util\r
                        .getSupportedOptions(Tcoffee.class);\r
        public static final LimitsManager<Tcoffee> TCOFFEE_LIMITS = Util\r
 \r
        public static final PresetManager<Tcoffee> TCOFFEE_PRESETS = Util\r
                        .getPresets(Tcoffee.class);\r
        public static final RunnerConfig<Tcoffee> TCOFFEE_PARAMETERS = Util\r
                        .getSupportedOptions(Tcoffee.class);\r
        public static final LimitsManager<Tcoffee> TCOFFEE_LIMITS = Util\r

-                       .getLimits(Tcoffee.class);\r
+                       .getLimits(new Tcoffee().getType());\r

 \r
        public static final PresetManager<Muscle> MUSCLE_PRESETS = Util\r
                        .getPresets(Muscle.class);\r
        public static final RunnerConfig<Muscle> MUSCLE_PARAMETERS = Util\r
                        .getSupportedOptions(Muscle.class);\r
        public static final LimitsManager<Muscle> MUSCLE_LIMITS = Util\r
 \r
        public static final PresetManager<Muscle> MUSCLE_PRESETS = Util\r
                        .getPresets(Muscle.class);\r
        public static final RunnerConfig<Muscle> MUSCLE_PARAMETERS = Util\r
                        .getSupportedOptions(Muscle.class);\r
        public static final LimitsManager<Muscle> MUSCLE_LIMITS = Util\r

-                       .getLimits(Muscle.class);\r
+                       .getLimits(new Muscle().getType());\r

 \r
        public final static String test_group_cluster = "cluster";\r
        public final static String test_group_runner = "runner";\r
 \r
        public final static String test_group_cluster = "cluster";\r
        public final static String test_group_runner = "runner";\r

diff --git a/webservices/compbio/ws/client/MetadataHelper.java b/webservices/compbio/ws/client/MetadataHelper.java
index d69c3c1..f0539dc 100644 (file)
--- a/webservices/compbio/ws/client/MetadataHelper.java
+++ b/webservices/compbio/ws/client/MetadataHelper.java
@@ -3,6 +3,7 @@ package compbio.ws.client;
 import static compbio.ws.client.Constraints.pseparator;\r
 \r
 import java.util.ArrayList;\r
 import static compbio.ws.client.Constraints.pseparator;\r
 \r
 import java.util.ArrayList;\r

+import java.util.Collections;\r

 import java.util.List;\r
 \r
 import compbio.data.msa.Metadata;\r
 import java.util.List;\r
 \r
 import compbio.data.msa.Metadata;\r

@@ -27,7 +28,11 @@ public class MetadataHelper {
         */\r
        static <T> List<Option<T>> getParametersList(Metadata<T> msaws) {\r
                assert msaws != null;\r
         */\r
        static <T> List<Option<T>> getParametersList(Metadata<T> msaws) {\r
                assert msaws != null;\r

-               return msaws.getRunnerOptions().getArguments();\r
+               RunnerConfig<T> config = msaws.getRunnerOptions();\r
+               if (config == null) {\r
+                       return Collections.emptyList();\r
+               }\r
+               return config.getArguments();\r

        }\r
 \r
        /**\r
        }\r
 \r
        /**\r

diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java
index 095bc4e..ac7435d 100644 (file)
--- a/webservices/compbio/ws/server/AAConWS.java
+++ b/webservices/compbio/ws/server/AAConWS.java
@@ -51,6 +51,9 @@ public class AAConWS implements SequenceAnnotation<AACon> {
        private static final PresetManager<AACon> aaconPresets = Util\r
                        .getPresets(AACon.class);\r
 \r
        private static final PresetManager<AACon> aaconPresets = Util\r
                        .getPresets(AACon.class);\r
 \r

+       private static final LimitsManager<AACon> limitMan = compbio.runner.Util\r
+                       .getLimits(new AACon().getType());\r
+\r

        ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                AACon aacon = new AACon();\r
        ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                AACon aacon = new AACon();\r

@@ -81,12 +84,12 @@ public class AAConWS implements SequenceAnnotation<AACon> {
 \r
        @Override\r
        public Limit<AACon> getLimit(String presetName) {\r
 \r
        @Override\r
        public Limit<AACon> getLimit(String presetName) {\r

-               return new AACon().getLimit(presetName);\r
+               return limitMan.getLimitByName(presetName);\r

        }\r
 \r
        @Override\r
        public LimitsManager<AACon> getLimits() {\r
        }\r
 \r
        @Override\r
        public LimitsManager<AACon> getLimits() {\r

-               return new AACon().getLimits();\r
+               return limitMan;\r

        }\r
 \r
        @Override\r
        }\r
 \r
        @Override\r

diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java
index 4b38157..f13136a 100644 (file)
--- a/webservices/compbio/ws/server/ClustalWS.java
+++ b/webservices/compbio/ws/server/ClustalWS.java
@@ -52,152 +52,152 @@ import compbio.ws.client.Services;
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")\r
 public class ClustalWS implements MsaWS<ClustalW> {\r
 \r
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")\r
 public class ClustalWS implements MsaWS<ClustalW> {\r
 \r

-    // Ask for resource injection\r
-    @Resource\r
-    private WebServiceContext wsContext;\r
+       // Ask for resource injection\r
+       @Resource\r
+       private WebServiceContext wsContext;\r

 \r
 \r

-    private static Logger log = Logger.getLogger(ClustalWS.class);\r
+       private static Logger log = Logger.getLogger(ClustalWS.class);\r

 \r
 \r

-    private static volatile WSLogger logger;\r
+       private static volatile WSLogger logger;\r

 \r
 \r

-    private static final RunnerConfig<ClustalW> clustalOptions = Util\r
-           .getSupportedOptions(ClustalW.class);\r
+       private static final RunnerConfig<ClustalW> clustalOptions = Util\r
+                       .getSupportedOptions(ClustalW.class);\r

 \r
 \r

-    private static final PresetManager<ClustalW> clustalPresets = Util\r
-           .getPresets(ClustalW.class);\r
+       private static final PresetManager<ClustalW> clustalPresets = Util\r
+                       .getPresets(ClustalW.class);\r

 \r
 \r

-    /*\r
-     * Initialise the logger. This cannot be done in the constructor as the\r
-     * WebServiceContext is not available at the object construction time\r
-     */\r
-    private WSLogger getLogger() {\r
-       if (logger == null) {\r
-           synchronized (ClustalWS.class) {\r
+       private static final LimitsManager<ClustalW> limitMan = compbio.runner.Util\r
+                       .getLimits(new ClustalW().getType());\r
+\r
+       /*\r
+        * Initialise the logger. This cannot be done in the constructor as the\r
+        * WebServiceContext is not available at the object construction time\r
+        */\r
+       private WSLogger getLogger() {\r

                if (logger == null) {\r
                if (logger == null) {\r

-                   logger = WSLogger.getStatLogger(Services.ClustalWS,\r
-                           wsContext);\r
+                       synchronized (ClustalWS.class) {\r
+                               if (logger == null) {\r
+                                       logger = WSLogger.getStatLogger(Services.ClustalWS,\r
+                                                       wsContext);\r
+                               }\r
+                       }\r

                }\r
                }\r

-           }\r
+               return logger;\r
+       }\r
+\r
+       @Override\r
+       public String align(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
+               return WSUtil.align(sequences, confClust, getLogger(), "align",\r
+                               getLimit(""));\r
+       }\r
+\r
+       ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)\r
+                       throws JobSubmissionException {\r
+               ClustalW clustal = new ClustalW();\r
+               ConfiguredExecutable<ClustalW> confClust = Configurator\r
+                               .configureExecutable(clustal, dataSet);\r
+               return confClust;\r
+       }\r
+\r
+       @Override\r
+       public String presetAlign(List<FastaSequence> sequences,\r
+                       Preset<ClustalW> preset) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               if (preset == null) {\r
+                       throw new WrongParameterException("Preset must be provided!");\r
+               }\r
+               Limit<ClustalW> limit = getLimit(preset.getName());\r
+               ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
+               confClust.addParameters(preset.getOptions());\r
+               return WSUtil.align(sequences, confClust, getLogger(), "presetAlign",\r
+                               limit);\r
+       }\r
+\r
+       @Override\r
+       public String customAlign(List<FastaSequence> sequences,\r
+                       List<Option<ClustalW>> options) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
+               List<String> params = WSUtil.getCommands(options,\r
+                               ClustalW.KEY_VALUE_SEPARATOR);\r
+               confClust.addParameters(params);\r
+               log.info("Setting parameters: " + params);\r
+               return WSUtil.align(sequences, confClust, getLogger(), "customAlign",\r
+                               getLimit(""));\r
+       }\r
+\r
+       @Override\r
+       public RunnerConfig<ClustalW> getRunnerOptions() {\r
+               Timer timer = Timer.getMilliSecondsTimer();\r
+               getLogger().logAll(timer, "getRunnerOptions");\r
+               return clustalOptions;\r

        }\r
        }\r

-       return logger;\r
-    }\r
-\r
-    @Override\r
-    public String align(List<FastaSequence> sequences)\r
-           throws JobSubmissionException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
-       return WSUtil.align(sequences, confClust, getLogger(), "align",\r
-               getLimit(""));\r
-    }\r
-\r
-    ConfiguredExecutable<ClustalW> init(List<FastaSequence> dataSet)\r
-           throws JobSubmissionException {\r
-       ClustalW clustal = new ClustalW();\r
-       ConfiguredExecutable<ClustalW> confClust = Configurator\r
-               .configureExecutable(clustal, dataSet);\r
-       return confClust;\r
-    }\r
-\r
-    @Override\r
-    public String presetAlign(List<FastaSequence> sequences,\r
-           Preset<ClustalW> preset) throws JobSubmissionException,\r
-           WrongParameterException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       if (preset == null) {\r
-           throw new WrongParameterException("Preset must be provided!");\r
+\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
+               Timer timer = Timer.getMilliSecondsTimer();\r
+               WSUtil.validateJobId(jobId);\r
+               AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+               ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine\r
+                               .getResults(jobId);\r
+               Alignment al = clustal.getResults();\r
+               getLogger().log(timer, "getResults", jobId);\r
+               return al;\r
+       }\r
+\r
+       @Override\r
+       public Limit<ClustalW> getLimit(String presetName) {\r
+               Timer timer = Timer.getMilliSecondsTimer();\r
+               Limit<ClustalW> limit = limitMan.getLimitByName(presetName);\r
+               getLogger().logAll(timer, "getLimit");\r
+               return limit;\r
+       }\r
+       @Override\r
+       public LimitsManager<ClustalW> getLimits() {\r
+               return limitMan;\r
+       }\r
+\r
+       @Override\r
+       public boolean cancelJob(String jobId) {\r
+               Timer timer = Timer.getMilliSecondsTimer();\r
+               WSUtil.validateJobId(jobId);\r
+               boolean result = WSUtil.cancelJob(jobId);\r
+               getLogger().logFine(timer, "Cancel");\r
+               return result;\r
+       }\r
+\r
+       @Override\r
+       public JobStatus getJobStatus(String jobId) {\r
+               Timer timer = Timer.getMilliSecondsTimer();\r
+               WSUtil.validateJobId(jobId);\r
+               JobStatus status = WSUtil.getJobStatus(jobId);\r
+               getLogger().logFine(timer, "getJobStatus");\r
+               return status;\r
+       }\r
+\r
+       @Override\r
+       public PresetManager<ClustalW> getPresets() {\r
+               Timer timer = Timer.getMilliSecondsTimer();\r
+               getLogger().logAll(timer, "pullExecStatistics");\r
+               return clustalPresets;\r
+       }\r
+\r
+       @Override\r
+       public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+               Timer timer = Timer.getMilliSecondsTimer();\r
+               WSUtil.validateJobId(jobId);\r
+               String file = Configurator.getWorkDirectory(jobId) + File.separator\r
+                               + ClustalW.getStatFile();\r
+               ChunkHolder cholder = WSUtil.pullFile(file, position);\r
+               getLogger().logFine(timer, "pullExecStatistics");\r
+               return cholder;\r

        }\r
        }\r

-       Limit<ClustalW> limit = getLimit(preset.getName());\r
-       ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
-       confClust.addParameters(preset.getOptions());\r
-       return WSUtil.align(sequences, confClust, getLogger(), "presetAlign",\r
-               limit);\r
-    }\r
-\r
-    @Override\r
-    public String customAlign(List<FastaSequence> sequences,\r
-           List<Option<ClustalW>> options) throws JobSubmissionException,\r
-           WrongParameterException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<ClustalW> confClust = init(sequences);\r
-       List<String> params = WSUtil.getCommands(options,\r
-               ClustalW.KEY_VALUE_SEPARATOR);\r
-       confClust.addParameters(params);\r
-       log.info("Setting parameters: " + params);\r
-       return WSUtil.align(sequences, confClust, getLogger(), "customAlign",\r
-               getLimit(""));\r
-    }\r
-\r
-    @Override\r
-    public RunnerConfig<ClustalW> getRunnerOptions() {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       getLogger().logAll(timer, "getRunnerOptions");\r
-       return clustalOptions;\r
-    }\r
-\r
-    @SuppressWarnings("unchecked")\r
-    @Override\r
-    public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       WSUtil.validateJobId(jobId);\r
-       AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
-       ConfiguredExecutable<ClustalW> clustal = (ConfiguredExecutable<ClustalW>) asyncEngine\r
-               .getResults(jobId);\r
-       Alignment al = clustal.getResults();\r
-       getLogger().log(timer, "getResults", jobId);\r
-       return al;\r
-    }\r
-\r
-    @Override\r
-    public Limit<ClustalW> getLimit(String presetName) {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       Limit<ClustalW> limit = new ClustalW().getLimit(presetName);\r
-       getLogger().logAll(timer, "getLimit");\r
-       return limit;\r
-    }\r
-\r
-    @Override\r
-    public LimitsManager<ClustalW> getLimits() {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       LimitsManager<ClustalW> limits = new ClustalW().getLimits();\r
-       getLogger().logAll(timer, "getLimits");\r
-       return limits;\r
-    }\r
-\r
-    @Override\r
-    public boolean cancelJob(String jobId) {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       WSUtil.validateJobId(jobId);\r
-       boolean result = WSUtil.cancelJob(jobId);\r
-       getLogger().logFine(timer, "Cancel");\r
-       return result;\r
-    }\r
-\r
-    @Override\r
-    public JobStatus getJobStatus(String jobId) {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       WSUtil.validateJobId(jobId);\r
-       JobStatus status = WSUtil.getJobStatus(jobId);\r
-       getLogger().logFine(timer, "getJobStatus");\r
-       return status;\r
-    }\r
-\r
-    @Override\r
-    public PresetManager<ClustalW> getPresets() {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       getLogger().logAll(timer, "pullExecStatistics");\r
-       return clustalPresets;\r
-    }\r
-\r
-    @Override\r
-    public ChunkHolder pullExecStatistics(String jobId, long position) {\r
-       Timer timer = Timer.getMilliSecondsTimer();\r
-       WSUtil.validateJobId(jobId);\r
-       String file = Configurator.getWorkDirectory(jobId) + File.separator\r
-               + ClustalW.getStatFile();\r
-       ChunkHolder cholder = WSUtil.pullFile(file, position);\r
-       getLogger().logFine(timer, "pullExecStatistics");\r
-       return cholder;\r
-    }\r

 \r
 }\r
 \r
 }\r

diff --git a/webservices/compbio/ws/server/DisemblWS.java b/webservices/compbio/ws/server/DisemblWS.java
index 2eac30d..7970579 100644 (file)
--- a/webservices/compbio/ws/server/DisemblWS.java
+++ b/webservices/compbio/ws/server/DisemblWS.java
@@ -47,6 +47,9 @@ public class DisemblWS implements SequenceAnnotation<Disembl> {
        private static final PresetManager<Disembl> disemblPresets = Util\r
                        .getPresets(Disembl.class);\r
 \r
        private static final PresetManager<Disembl> disemblPresets = Util\r
                        .getPresets(Disembl.class);\r
 \r

+       private static final LimitsManager<Disembl> limitMan = compbio.runner.Util\r
+                       .getLimits(new Disembl().getType());\r
+\r

        ConfiguredExecutable<Disembl> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                Disembl disembl = new Disembl();\r
        ConfiguredExecutable<Disembl> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                Disembl disembl = new Disembl();\r

@@ -68,12 +71,12 @@ public class DisemblWS implements SequenceAnnotation<Disembl> {
 \r
        @Override\r
        public Limit<Disembl> getLimit(String presetName) {\r
 \r
        @Override\r
        public Limit<Disembl> getLimit(String presetName) {\r

-               return new Disembl().getLimit(presetName);\r
+               return limitMan.getLimitByName(presetName);\r

        }\r
 \r
        @Override\r
        public LimitsManager<Disembl> getLimits() {\r
        }\r
 \r
        @Override\r
        public LimitsManager<Disembl> getLimits() {\r

-               return new Disembl().getLimits();\r
+               return limitMan;\r

        }\r
 \r
        @Override\r
        }\r
 \r
        @Override\r

diff --git a/webservices/compbio/ws/server/GlobPlotWS.java b/webservices/compbio/ws/server/GlobPlotWS.java
index cf266b0..a77dfa2 100644 (file)
--- a/webservices/compbio/ws/server/GlobPlotWS.java
+++ b/webservices/compbio/ws/server/GlobPlotWS.java
@@ -47,6 +47,9 @@ public class GlobPlotWS implements SequenceAnnotation<GlobPlot> {
        private static final PresetManager<GlobPlot> globPlotPresets = Util\r
                        .getPresets(GlobPlot.class);\r
 \r
        private static final PresetManager<GlobPlot> globPlotPresets = Util\r
                        .getPresets(GlobPlot.class);\r
 \r

+       private static final LimitsManager<GlobPlot> limitMan = compbio.runner.Util\r
+                       .getLimits(new GlobPlot().getType());\r
+\r

        ConfiguredExecutable<GlobPlot> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                GlobPlot globPlot = new GlobPlot();\r
        ConfiguredExecutable<GlobPlot> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                GlobPlot globPlot = new GlobPlot();\r

@@ -68,12 +71,12 @@ public class GlobPlotWS implements SequenceAnnotation<GlobPlot> {
 \r
        @Override\r
        public Limit<GlobPlot> getLimit(String presetName) {\r
 \r
        @Override\r
        public Limit<GlobPlot> getLimit(String presetName) {\r

-               return new GlobPlot().getLimit(presetName);\r
+               return limitMan.getLimitByName(presetName);\r

        }\r
 \r
        @Override\r
        public LimitsManager<GlobPlot> getLimits() {\r
        }\r
 \r
        @Override\r
        public LimitsManager<GlobPlot> getLimits() {\r

-               return new GlobPlot().getLimits();\r
+               return limitMan;\r

        }\r
 \r
        @Override\r
        }\r
 \r
        @Override\r

diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
index e9070d5..5a4b136 100644 (file)
--- a/webservices/compbio/ws/server/JronnWS.java
+++ b/webservices/compbio/ws/server/JronnWS.java
@@ -49,6 +49,9 @@ public class JronnWS implements SequenceAnnotation<Jronn> {
        private static final PresetManager<Jronn> jronnPresets = Util\r
                        .getPresets(Jronn.class);\r
 \r
        private static final PresetManager<Jronn> jronnPresets = Util\r
                        .getPresets(Jronn.class);\r
 \r

+       private static final LimitsManager<Jronn> limitMan = compbio.runner.Util\r
+                       .getLimits(new Jronn().getType());\r
+\r

        ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                Jronn jronn = new Jronn();\r
        ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                Jronn jronn = new Jronn();\r

@@ -70,12 +73,12 @@ public class JronnWS implements SequenceAnnotation<Jronn> {
 \r
        @Override\r
        public Limit<Jronn> getLimit(String presetName) {\r
 \r
        @Override\r
        public Limit<Jronn> getLimit(String presetName) {\r

-               return new Jronn().getLimit(presetName);\r
+               return limitMan.getLimitByName(presetName);\r

        }\r
 \r
        @Override\r
        public LimitsManager<Jronn> getLimits() {\r
        }\r
 \r
        @Override\r
        public LimitsManager<Jronn> getLimits() {\r

-               return new Jronn().getLimits();\r
+               return limitMan;\r

        }\r
 \r
        @Override\r
        }\r
 \r
        @Override\r

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
 @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
        }\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
 \r
 }\r

diff --git a/webservices/compbio/ws/server/MuscleWS.java b/webservices/compbio/ws/server/MuscleWS.java
index e626f94..c0de308 100644 (file)
--- a/webservices/compbio/ws/server/MuscleWS.java
+++ b/webservices/compbio/ws/server/MuscleWS.java
@@ -50,115 +50,118 @@ import compbio.runner.msa.Muscle;
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")\r
 public class MuscleWS implements MsaWS<Muscle> {\r
 \r
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")\r
 public class MuscleWS implements MsaWS<Muscle> {\r
 \r

-    // Ask for resource injection\r
-    @Resource\r
-    WebServiceContext wsContext;\r
-\r
-    private static Logger statLog = Logger.getLogger("MuscleWS-stats");\r
-\r
-    private static Logger log = Logger.getLogger(MuscleWS.class);\r
-\r
-    private static final RunnerConfig<Muscle> muscleOptions = Util\r
-           .getSupportedOptions(Muscle.class);\r
-\r
-    private static final PresetManager<Muscle> musclePresets = Util\r
-           .getPresets(Muscle.class);\r
-\r
-    @Override\r
-    public String align(List<FastaSequence> sequences)\r
-           throws JobSubmissionException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
-       return WSUtil.align(sequences, confMuscle, null, "align", getLimit(""));\r
-    }\r
-\r
-    ConfiguredExecutable<Muscle> init(List<FastaSequence> sequences)\r
-           throws JobSubmissionException {\r
-       Muscle muscle = new Muscle();\r
-       muscle.setInput("fasta.in").setOutput("fasta.out");\r
-       return Configurator.configureExecutable(muscle, sequences);\r
-    }\r
-\r
-    @Override\r
-    public String customAlign(List<FastaSequence> sequences,\r
-           List<Option<Muscle>> options) throws JobSubmissionException,\r
-           WrongParameterException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
-       // Could not do that! Space separated values\r
-       // will all be treated as keys! thus duplicates removed\r
-       // String params = cbuilder.getCommand();\r
-       List<String> params = WSUtil.getCommands(options,\r
-               Muscle.KEY_VALUE_SEPARATOR);\r
-       confMuscle.addParameters(params);\r
-       return WSUtil.align(sequences, confMuscle, null, "customAlign",\r
-               getLimit(""));\r
-    }\r
-\r
-    @Override\r
-    public String presetAlign(List<FastaSequence> sequences,\r
-           Preset<Muscle> 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("MuscleWS-stats");\r
+\r
+       private static Logger log = Logger.getLogger(MuscleWS.class);\r
+\r
+       private static final RunnerConfig<Muscle> muscleOptions = Util\r
+                       .getSupportedOptions(Muscle.class);\r
+\r
+       private static final PresetManager<Muscle> musclePresets = Util\r
+                       .getPresets(Muscle.class);\r
+\r
+       private static final LimitsManager<Muscle> limitMan = compbio.runner.Util\r
+                       .getLimits(new Muscle().getType());\r
+\r
+       @Override\r
+       public String align(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
+               return WSUtil.align(sequences, confMuscle, null, "align", getLimit(""));\r
+       }\r
+\r
+       ConfiguredExecutable<Muscle> init(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               Muscle muscle = new Muscle();\r
+               muscle.setInput("fasta.in").setOutput("fasta.out");\r
+               return Configurator.configureExecutable(muscle, sequences);\r
+       }\r
+\r
+       @Override\r
+       public String customAlign(List<FastaSequence> sequences,\r
+                       List<Option<Muscle>> options) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
+               // Could not do that! Space separated values\r
+               // will all be treated as keys! thus duplicates removed\r
+               // String params = cbuilder.getCommand();\r
+               List<String> params = WSUtil.getCommands(options,\r
+                               Muscle.KEY_VALUE_SEPARATOR);\r
+               confMuscle.addParameters(params);\r
+               return WSUtil.align(sequences, confMuscle, null, "customAlign",\r
+                               getLimit(""));\r
+       }\r
+\r
+       @Override\r
+       public String presetAlign(List<FastaSequence> sequences,\r
+                       Preset<Muscle> preset) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               if (preset == null) {\r
+                       throw new WrongParameterException("Preset must be provided!");\r
+               }\r
+               ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
+               confMuscle.addParameters(preset.getOptions());\r
+               Limit<Muscle> limit = getLimit(preset.getName());\r
+               return WSUtil.align(sequences, confMuscle, 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<Muscle> muscle = (ConfiguredExecutable<Muscle>) asyncEngine\r
+                               .getResults(jobId);\r
+               Alignment al = muscle.getResults();\r
+               // log(jobId, "getResults");\r
+               return al;\r
+       }\r
+\r
+       @Override\r
+       public Limit<Muscle> getLimit(String presetName) {\r
+               return limitMan.getLimitByName(presetName);\r
+       }\r
+\r
+       @Override\r
+       public LimitsManager<Muscle> 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
+                               + Muscle.getStatFile();\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<Muscle> getPresets() {\r
+               return musclePresets;\r
+       }\r
+\r
+       @Override\r
+       public RunnerConfig<Muscle> getRunnerOptions() {\r
+               return muscleOptions;\r

        }\r
        }\r

-       ConfiguredExecutable<Muscle> confMuscle = init(sequences);\r
-       confMuscle.addParameters(preset.getOptions());\r
-       Limit<Muscle> limit = getLimit(preset.getName());\r
-       return WSUtil.align(sequences, confMuscle, 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<Muscle> muscle = (ConfiguredExecutable<Muscle>) asyncEngine\r
-               .getResults(jobId);\r
-       Alignment al = muscle.getResults();\r
-       //log(jobId, "getResults");\r
-       return al;\r
-    }\r
-\r
-    @Override\r
-    public Limit<Muscle> getLimit(String presetName) {\r
-       return new Muscle().getLimit(presetName);\r
-    }\r
-\r
-    @Override\r
-    public LimitsManager<Muscle> getLimits() {\r
-       return new Muscle().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
-               + Muscle.getStatFile();\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<Muscle> getPresets() {\r
-       return musclePresets;\r
-    }\r
-\r
-    @Override\r
-    public RunnerConfig<Muscle> getRunnerOptions() {\r
-       return muscleOptions;\r
-    }\r

 \r
 }\r
 \r
 }\r

diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java
index 8060be6..85e8a70 100644 (file)
--- a/webservices/compbio/ws/server/ProbconsWS.java
+++ b/webservices/compbio/ws/server/ProbconsWS.java
@@ -50,113 +50,116 @@ import compbio.runner.msa.Probcons;
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")\r
 public class ProbconsWS implements MsaWS<Probcons> {\r
 \r
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")\r
 public class ProbconsWS implements MsaWS<Probcons> {\r
 \r

-    // Ask for resource injection\r
-    @Resource\r
-    WebServiceContext wsContext;\r
-\r
-    private static Logger statLog = Logger.getLogger("ProbconsWS-stats");\r
-\r
-    private static Logger log = Logger.getLogger(ProbconsWS.class);\r
-\r
-    private static final RunnerConfig<Probcons> probconsOptions = Util\r
-           .getSupportedOptions(Probcons.class);\r
-\r
-    @Override\r
-    public String align(List<FastaSequence> sequences)\r
-           throws JobSubmissionException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
-       return WSUtil.align(sequences, confProbcons, null, "align",\r
-               getLimit(""));\r
-    }\r
-\r
-    ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
-           throws JobSubmissionException {\r
-       Probcons probcons = new Probcons();\r
-       probcons.setInput("fasta.in").setOutput("alignment.out");\r
-       return Configurator.configureExecutable(probcons, dataSet);\r
-    }\r
-\r
-    @Override\r
-    public String customAlign(List<FastaSequence> sequences,\r
-           List<Option<Probcons>> options) throws JobSubmissionException,\r
-           WrongParameterException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
-       List<String> params = WSUtil.getCommands(options,\r
-               Probcons.KEY_VALUE_SEPARATOR);\r
-       log.info("Setting parameters:" + params);\r
-       confProbcons.addParameters(params);\r
-       return WSUtil.align(sequences, confProbcons, null, "customAlign",\r
-               getLimit(""));\r
-    }\r
-\r
-    @Override\r
-    public String presetAlign(List<FastaSequence> sequences,\r
-           Preset<Probcons> 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("ProbconsWS-stats");\r
+\r
+       private static Logger log = Logger.getLogger(ProbconsWS.class);\r
+\r
+       private static final RunnerConfig<Probcons> probconsOptions = Util\r
+                       .getSupportedOptions(Probcons.class);\r
+\r
+       private static final LimitsManager<Probcons> limitMan = compbio.runner.Util\r
+                       .getLimits(new Probcons().getType());\r
+\r
+       @Override\r
+       public String align(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
+               return WSUtil.align(sequences, confProbcons, null, "align",\r
+                               getLimit(""));\r
+       }\r
+\r
+       ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
+                       throws JobSubmissionException {\r
+               Probcons probcons = new Probcons();\r
+               probcons.setInput("fasta.in").setOutput("alignment.out");\r
+               return Configurator.configureExecutable(probcons, dataSet);\r
+       }\r
+\r
+       @Override\r
+       public String customAlign(List<FastaSequence> sequences,\r
+                       List<Option<Probcons>> options) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
+               List<String> params = WSUtil.getCommands(options,\r
+                               Probcons.KEY_VALUE_SEPARATOR);\r
+               log.info("Setting parameters:" + params);\r
+               confProbcons.addParameters(params);\r
+               return WSUtil.align(sequences, confProbcons, null, "customAlign",\r
+                               getLimit(""));\r
+       }\r
+\r
+       @Override\r
+       public String presetAlign(List<FastaSequence> sequences,\r
+                       Preset<Probcons> preset) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               if (preset == null) {\r
+                       throw new WrongParameterException("Preset must be provided!");\r
+               }\r
+               ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
+               confProbcons.addParameters(preset.getOptions());\r
+               Limit<Probcons> limit = getLimit(preset.getName());\r
+               return WSUtil\r
+                               .align(sequences, confProbcons, 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<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine\r
+                               .getResults(jobId);\r
+               Alignment al = probcons.getResults();\r
+               // log(jobId, "getResults");\r
+               return al;\r
+       }\r
+\r
+       @Override\r
+       public Limit<Probcons> getLimit(String presetName) {\r
+               return limitMan.getLimitByName(presetName);\r
+       }\r
+\r
+       @Override\r
+       public LimitsManager<Probcons> getLimits() {\r
+               return limitMan;\r
+       }\r
+\r
+       @Override\r
+       public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+               WSUtil.validateJobId(jobId);\r
+               // TODO check if output is the one to return\r
+               String file = Configurator.getWorkDirectory(jobId) + File.separator\r
+                               + new Probcons().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<Probcons> getPresets() {\r
+               return null;\r
+       }\r
+\r
+       @Override\r
+       public RunnerConfig<Probcons> getRunnerOptions() {\r
+               return probconsOptions;\r

        }\r
        }\r

-       ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
-       confProbcons.addParameters(preset.getOptions());\r
-       Limit<Probcons> limit = getLimit(preset.getName());\r
-       return WSUtil\r
-               .align(sequences, confProbcons, 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<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine\r
-               .getResults(jobId);\r
-       Alignment al = probcons.getResults();\r
-       //log(jobId, "getResults");\r
-       return al;\r
-    }\r
-\r
-    @Override\r
-    public Limit<Probcons> getLimit(String presetName) {\r
-       return new Probcons().getLimit(presetName);\r
-    }\r
-\r
-    @Override\r
-    public LimitsManager<Probcons> getLimits() {\r
-       return new Probcons().getLimits();\r
-    }\r
-\r
-    @Override\r
-    public ChunkHolder pullExecStatistics(String jobId, long position) {\r
-       WSUtil.validateJobId(jobId);\r
-       // TODO check if output is the one to return\r
-       String file = Configurator.getWorkDirectory(jobId) + File.separator\r
-               + new Probcons().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<Probcons> getPresets() {\r
-       return null;\r
-    }\r
-\r
-    @Override\r
-    public RunnerConfig<Probcons> getRunnerOptions() {\r
-       return probconsOptions;\r
-    }\r

 \r
 }\r
 \r
 }\r

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index 07a1f41..d8054b4 100644 (file)
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.java
@@ -52,123 +52,127 @@ import compbio.runner.msa.Tcoffee;
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")\r
 public class TcoffeeWS implements MsaWS<Tcoffee> {\r
 \r
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")\r
 public class TcoffeeWS implements MsaWS<Tcoffee> {\r
 \r

-    // Ask for resource injection\r
-    @Resource\r
-    WebServiceContext wsContext;\r
-\r
-    private static Logger statLog = Logger.getLogger("TcoffeeWS-stats");\r
-\r
-    private static Logger log = Logger.getLogger(TcoffeeWS.class);\r
-\r
-    private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util\r
-           .getSupportedOptions(Tcoffee.class);\r
-\r
-    private static final PresetManager<Tcoffee> tcoffeePresets = Util\r
-           .getPresets(Tcoffee.class);\r
-\r
-    @Override\r
-    public String align(List<FastaSequence> sequences)\r
-           throws JobSubmissionException {\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
-       return WSUtil\r
-               .align(sequences, confTcoffee, null, "align", getLimit(""));\r
-    }\r
-\r
-    ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)\r
-    throws JobSubmissionException {\r
-       Tcoffee tcoffee = new Tcoffee();\r
-       tcoffee.setInput("fasta.in").setOutput("fasta.out");\r
-       ConfiguredExecutable<Tcoffee> confCoffee = Configurator\r
-       .configureExecutable(tcoffee, sequences);\r
-       if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {\r
-               int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(Tcoffee.class);\r
-               if (clusterCpuNum != 0) {\r
-                       tcoffee.setNCore(clusterCpuNum);\r
-               }\r
-       }\r
-       return confCoffee;\r
-    }\r
-\r
-    @Override\r
-    public String customAlign(List<FastaSequence> sequences,\r
-           List<Option<Tcoffee>> options) throws JobSubmissionException,\r
-           WrongParameterException {\r
-\r
-       WSUtil.validateFastaInput(sequences);\r
-       ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
-       List<String> params = WSUtil.getCommands(options,\r
-               Tcoffee.KEY_VALUE_SEPARATOR);\r
-       log.info("Setting parameters:" + params);\r
-       confTcoffee.addParameters(params);\r
-       return WSUtil.align(sequences, confTcoffee, null, "customAlign",\r
-               getLimit(""));\r
-    }\r
-\r
-    @Override\r
-    public String presetAlign(List<FastaSequence> sequences,\r
-           Preset<Tcoffee> 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("TcoffeeWS-stats");\r
+\r
+       private static Logger log = Logger.getLogger(TcoffeeWS.class);\r
+\r
+       private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util\r
+                       .getSupportedOptions(Tcoffee.class);\r
+\r
+       private static final PresetManager<Tcoffee> tcoffeePresets = Util\r
+                       .getPresets(Tcoffee.class);\r
+\r
+       private static final LimitsManager<Tcoffee> limitMan = compbio.runner.Util\r
+                       .getLimits(new Tcoffee().getType());\r
+\r
+       @Override\r
+       public String align(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
+               return WSUtil\r
+                               .align(sequences, confTcoffee, null, "align", getLimit(""));\r
+       }\r
+\r
+       ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               Tcoffee tcoffee = new Tcoffee();\r
+               tcoffee.setInput("fasta.in").setOutput("fasta.out");\r
+               ConfiguredExecutable<Tcoffee> confCoffee = Configurator\r
+                               .configureExecutable(tcoffee, sequences);\r
+               if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {\r
+                       int clusterCpuNum = SkeletalExecutable\r
+                                       .getClusterCpuNum(Tcoffee.class);\r
+                       if (clusterCpuNum != 0) {\r
+                               tcoffee.setNCore(clusterCpuNum);\r
+                       }\r
+               }\r
+               return confCoffee;\r
+       }\r
+\r
+       @Override\r
+       public String customAlign(List<FastaSequence> sequences,\r
+                       List<Option<Tcoffee>> options) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
+               List<String> params = WSUtil.getCommands(options,\r
+                               Tcoffee.KEY_VALUE_SEPARATOR);\r
+               log.info("Setting parameters:" + params);\r
+               confTcoffee.addParameters(params);\r
+               return WSUtil.align(sequences, confTcoffee, null, "customAlign",\r
+                               getLimit(""));\r
+       }\r
+\r
+       @Override\r
+       public String presetAlign(List<FastaSequence> sequences,\r
+                       Preset<Tcoffee> preset) throws JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               if (preset == null) {\r
+                       throw new WrongParameterException("Preset must be provided!");\r
+               }\r
+               ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
+               confTcoffee.addParameters(preset.getOptions());\r
+               Limit<Tcoffee> limit = getLimit(preset.getName());\r
+               return WSUtil.align(sequences, confTcoffee, 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<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
+                               .getResults(jobId);\r
+               Alignment al = tcoffee.getResults();\r
+               // log(jobId, "getResults");\r
+               return al;\r
+       }\r
+\r
+       @Override\r
+       public Limit<Tcoffee> getLimit(String presetName) {\r
+               return limitMan.getLimitByName(presetName);\r
+       }\r
+\r
+       @Override\r
+       public LimitsManager<Tcoffee> 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 Tcoffee().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<Tcoffee> getPresets() {\r
+               return tcoffeePresets;\r
+       }\r
+\r
+       @Override\r
+       public RunnerConfig<Tcoffee> getRunnerOptions() {\r
+               return tcoffeeOptions;\r

        }\r
        }\r

-       ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
-       confTcoffee.addParameters(preset.getOptions());\r
-       Limit<Tcoffee> limit = getLimit(preset.getName());\r
-       return WSUtil.align(sequences, confTcoffee, 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<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
-               .getResults(jobId);\r
-       Alignment al = tcoffee.getResults();\r
-       //log(jobId, "getResults");\r
-       return al;\r
-    }\r
-\r
-    @Override\r
-    public Limit<Tcoffee> getLimit(String presetName) {\r
-       return new Tcoffee().getLimit(presetName);\r
-    }\r
-\r
-    @Override\r
-    public LimitsManager<Tcoffee> getLimits() {\r
-       return new Tcoffee().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 Tcoffee().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<Tcoffee> getPresets() {\r
-       return tcoffeePresets;\r
-    }\r
-\r
-    @Override\r
-    public RunnerConfig<Tcoffee> getRunnerOptions() {\r
-       return tcoffeeOptions;\r
-    }\r

 \r
 }\r
 \r
 }\r

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index 7e45991..9895289 100644 (file)
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -38,6 +38,8 @@ import compbio.util.Timer;
 \r
 public final class WSUtil {\r
 \r
 \r
 public final class WSUtil {\r
 \r

+       private static final String CACHE_KEY = "LIMITS_CACHE";\r
+\r

        private static Logger log = Logger.getLogger(WSUtil.class);\r
 \r
        public static final void validateJobId(String jobId)\r
        private static Logger log = Logger.getLogger(WSUtil.class);\r
 \r
        public static final void validateJobId(String jobId)\r

@@ -109,4 +111,38 @@ public final class WSUtil {
                return oList;\r
        }\r
 \r
                return oList;\r
        }\r
 \r

+       /*\r
+        * UNUSED\r
+        * \r
+        * @SuppressWarnings("unchecked") static <T> LimitsManager<T>\r
+        * getLimits(Class<? extends Executable<T>> clazz, WebServiceContext\r
+        * wsContext) {\r
+        * \r
+        * String LIMIT_KEY = CACHE_KEY + clazz.getCanonicalName(); LimitsManager<T>\r
+        * limit = (LimitsManager<T>) getObjectFromApplContext( LIMIT_KEY,\r
+        * wsContext); if (limit == null) { synchronized (WSUtil.class) { limit =\r
+        * (LimitsManager<T>) getObjectFromApplContext(LIMIT_KEY, wsContext); if\r
+        * (limit == null) { limit = compbio.runner.Util\r
+        * .getLimits((Class<Executable<T>>) clazz);\r
+        * addObjectToApplContext(wsContext, LIMIT_KEY, limit); } } } return limit;\r
+        * }\r
+        * \r
+        * static void addObjectToApplContext(WebServiceContext wsContext, String\r
+        * objKey, Object obj) { assert !Util.isEmpty(objKey) :\r
+        * "Key for the object must not be empty! "; assert wsContext != null;\r
+        * \r
+        * ServletContext ctx = ((javax.servlet.ServletContext) wsContext\r
+        * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); assert ctx !=\r
+        * null; log.debug("Adding object with key '" + objKey + "' and value '" +\r
+        * obj + "' to the application context"); ctx.setAttribute(objKey, obj); }\r
+        * static Object getObjectFromApplContext(String objKey, WebServiceContext\r
+        * wsContext) { assert !Util.isEmpty(objKey) :\r
+        * "Key for the object must not be empty! "; assert wsContext != null;\r
+        * \r
+        * ServletContext ctx = ((javax.servlet.ServletContext) wsContext\r
+        * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); Object obj =\r
+        * ctx.getAttribute(objKey); log.trace("Retrieving object with key '" +\r
+        * objKey + "' and value '" + obj + "' from the application context");\r
+        * return obj; }\r
+        */\r

 }\r
 }\r