Moved getThreads to BiopetCommandLineFunction

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -9,11 +9,7 @@ import scala.util.matching.Regex
 import nl.lumc.sasc.biopet.core.config._
 
 abstract class BiopetCommandLineFunction extends CommandLineFunction with Configurable {
-//  val globalConfig: Config
   analysisName = getClass.getSimpleName
-//  protected var config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName.toLowerCase), globalConfig)
-//  logger.debug("config passed for " + analysisName)
-//  logger.debug("config for " + analysisName + ": " + config)
   
   @Input(doc="deps", required=false)
   var deps: List[File] = Nil
@@ -35,11 +31,6 @@ abstract class BiopetCommandLineFunction extends CommandLineFunction with Config
   protected def afterGraph {
   }
   
-//  def setConfig(name:String) {
-//    analysisName = name
-//    config = Config.mergeConfigs(config.getAsConfig(analysisName.toLowerCase), config)
-//  }
-    
   override def freezeFieldValues() {
     checkExecuteble
     afterGraph
@@ -115,4 +106,18 @@ abstract class BiopetCommandLineFunction extends CommandLineFunction with Config
     logger.warn("Version command: '" + versionCommand + "' give a exit code 0 but no version was found, executeble oke?")
     return "N/A"
   }
+  
+  def getThreads(default:Int) : Int = {
+    val maxThreads: Int = config("maxthreads", 8)
+    val threads: Int = config("threads", default)
+    if (maxThreads > threads) return threads
+    else return maxThreads
+  }
+  
+  def getThreads(default:Int, module:String) : Int = {
+    val maxThreads: Int = config("maxthreads", 8, module)
+    val threads: Int = config("threads", default, module)
+    if (maxThreads > threads) return threads
+    else return maxThreads
+  }
 }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

@@ -28,21 +28,6 @@ trait Configurable extends Logging {
   implicit def configValue2stringList(value:ConfigValue) = Configurable.any2stringList(value.value)
   implicit def configValue2stringSet(value:ConfigValue) = Configurable.any2stringList(value.value).toSet
   implicit def configValue2map(value:ConfigValue) = Configurable.any2map(value.value)
-  
-  
-  def getThreads(default:Int) : Int = {
-    val maxThreads: Int = config("maxthreads", 8)
-    val threads: Int = config("threads", default)
-    if (maxThreads > threads) return threads
-    else return maxThreads
-  }
-  
-  def getThreads(default:Int, module:String) : Int = {
-    val maxThreads: Int = config("maxthreads", 8, module)
-    val threads: Int = config("threads", default, module)
-    if (maxThreads > threads) return threads
-    else return maxThreads
-  }
 }
 
 object Configurable extends Logging {