Changed scala docs

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

@@ -25,9 +25,7 @@ import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFun
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 import scala.collection.mutable.ListBuffer
 
-/**
- * Base for biopet pipeline
- */
+/** Base for biopet pipeline */
 trait BiopetQScript extends Configurable with GatkLogging {
 
   @Argument(doc = "JSON / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
@@ -36,6 +34,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
   @Argument(doc = "Config values, value should be formatted like 'key=value' or 'path:path:key=value'", fullName = "config_value", shortName = "cv", required = false)
   val configValues: List[String] = Nil
 
+  /** Output directory of pipeline */
   var outputDir: File = {
     if (config.contains("output_dir", path = Nil)) config("output_dir", path = Nil).asFile
     else new File(".")
@@ -58,9 +57,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
   /** Pipeline itself */
   def biopetScript
 
-  /**
-   * Script from queue itself, final to force some checks for each pipeline and write report
-   */
+  /** Script from queue itself, final to force some checks for each pipeline and write report */
   final def script() {
     outputDir = config("output_dir")
     outputDir = outputDir.getAbsoluteFile

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

@@ -20,9 +20,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
 
-/**
- * Wrapper around executable from Queue
- */
+/** Wrapper around executable from Queue */
 trait PipelineCommand extends MainCommand with GatkLogging {
 
   /**
@@ -31,10 +29,7 @@ trait PipelineCommand extends MainCommand with GatkLogging {
    */
   def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
 
-  /**
-   * Class can be used directly from java with -cp option
-   * @param args
-   */
+  /** Class can be used directly from java with -cp option */
   def main(args: Array[String]): Unit = {
     val argsSize = args.size
     for (t <- 0 until argsSize) {

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

@@ -20,8 +20,6 @@ import nl.lumc.sasc.biopet.core.Logging
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 
-import scala.reflect.io.Directory
-
 /**
  * This class can store nested config values
  * @param map Map with value for new config

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

@@ -19,64 +19,34 @@ import java.io.File
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 
 class ConfigValue(val requestIndex: ConfigValueIndex, val foundIndex: ConfigValueIndex, val value: Any, val default: Boolean) {
-  /**
-   * Get value as String
-   * @return value as String
-   */
+  /** Get value as String */
   def asString = any2string(value)
 
-  /**
-   * Get value as File
-   * @return value as File
-   */
+  /** Get value as File */
   def asFile = new File(any2string(value))
 
-  /**
-   * Get value as Int
-   * @return value as Int
-   */
+  /** Get value as Int */
   def asInt = any2int(value)
 
-  /**
-   * Get value as Double
-   * @return value as Double
-   */
+  /** Get value as Double */
   def asDouble = any2double(value)
 
-  /**
-   * Get value as List[Any]
-   * @return value as List[Any]
-   */
+  /** Get value as List[Any] */
   def asList = any2list(value)
 
-  /**
-   * Get value as List[File]
-   * @return value as List[File]
-   */
+  /** Get value as List[File] */
   def asFileList: List[File] = for (file <- any2stringList(value)) yield new File(file)
 
-  /**
-   * Get value as List[String]
-   * @return value as List[String]
-   */
+  /** Get value as List[String] */
   def asStringList: List[String] = any2stringList(value)
 
-  /**
-   * Get value as Map
-   * @return value as Map
-   */
+  /** Get value as Map */
   def asMap = any2map(value)
 
-  /**
-   * Get value as Boolean
-   * @return value as Boolean
-   */
+  /** Get value as Boolean */
   def asBoolean = any2boolean(value)
 
-  /**
-   * Readable output of indexes and value, just for debug
-   * @return
-   */
+  /** Readable output of indexes and value, just for debug */
   override def toString: String = {
     var output = "key = " + requestIndex.key
     output += ", value = " + value

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

@@ -15,9 +15,7 @@
  */
 package nl.lumc.sasc.biopet.core.config
 
-import nl.lumc.sasc.biopet.core.Logging
 import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
-import scala.collection.JavaConversions._
 
 trait Configurable extends ImplicitConversions {
   /** Should be object of parant object */
@@ -58,9 +56,7 @@ trait Configurable extends ImplicitConversions {
       (if (submodule != null) configPath ::: configName :: Nil else configPath)
   }
 
-  /**
-   * Class is used for retrieval of config values
-   */
+  /** Class is used for retrieval of config values */
   protected class ConfigFunctions(val defaultSample: Option[String] = None, val defaultLibrary: Option[String] = None) {
     def this(defaultSample: String, defaultLibrary: String) = {
       this(defaultSample = Some(defaultSample), defaultLibrary = Some(defaultLibrary))

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -21,7 +21,6 @@ import nl.lumc.sasc.biopet.core.Logging
 import nl.lumc.sasc.biopet.core.config.ConfigValue
 import argonaut._, Argonaut._
 import org.yaml.snakeyaml.Yaml
-import scala.collection.mutable
 import scalaz._, Scalaz._
 import scala.collection.JavaConversions._
 
@@ -87,11 +86,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Make json aboject from a file
-   * @param configFile Input file
-   * @return Json object
-   */
+  /** Make json aboject from a file */
   def fileToJson(configFile: File): Json = {
     logger.debug("Jsonfile: " + configFile)
     val jsonText = scala.io.Source.fromFile(configFile).mkString
@@ -103,11 +98,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert config value to map
-   * @param configFile
-   * @return Config map
-   */
+  /** Convert config value to map */
   def fileToConfigMap(configFile: File): Map[String, Any] = {
 
     val configMap = {
@@ -118,22 +109,14 @@ object ConfigUtils extends Logging {
     return configMap
   }
 
-  /**
-   * Convert a yaml file to map[String, Any]
-   * @param file Input file
-   * @return config map
-   */
+  /** Convert a yaml file to map[String, Any] */
   def yamlToMap(file: File): Map[String, Any] = {
     val yaml = new Yaml()
     val a = yaml.load(scala.io.Source.fromFile(file).reader())
     ConfigUtils.any2map(a)
   }
 
-  /**
-   * Convert json to native scala map/values
-   * @param json input json
-   * @return
-   */
+  /** Convert json to native scala map/values */
   def jsonToMap(json: Json): Map[String, Any] = {
     var output: Map[String, Any] = Map()
     if (json.isObject) {
@@ -145,11 +128,7 @@ object ConfigUtils extends Logging {
     return output
   }
 
-  /**
-   * Convert json value to native scala value
-   * @param json input json
-   * @return
-   */
+  /** Convert json value to native scala value */
   def jsonToAny(json: Json): Any = {
     if (json.isObject) return jsonToMap(json)
     else if (json.isArray) {
@@ -166,11 +145,7 @@ object ConfigUtils extends Logging {
     else throw new IllegalStateException("Config value type not supported, value: " + json)
   }
 
-  /**
-   * Convert native scala map to json
-   * @param map Input map
-   * @return
-   */
+  /** Convert native scala map to json */
   def mapToJson(map: Map[String, Any]): Json = {
     map.foldLeft(jEmptyObject)((acc, kv) => (kv._1 := {
       kv._2 match {
@@ -180,11 +155,7 @@ object ConfigUtils extends Logging {
     }) ->: acc)
   }
 
-  /**
-   * Convert native scala value to json, fall back on .toString if type is not a native scala value
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert native scala value to json, fall back on .toString if type is not a native scala value */
   def anyToJson(any: Any): Json = {
     any match {
       case j: Json      => j
@@ -202,11 +173,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert Any to String
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to String */
   def any2string(any: Any): String = {
     if (any == null) return null
     any match {
@@ -215,11 +182,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert Any to Int
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to Int */
   def any2int(any: Any): Int = {
     any match {
       case i: Int    => i
@@ -233,11 +196,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert Any to Long
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to Long */
   def any2long(any: Any): Long = {
     any match {
       case l: Double => l.toLong
@@ -251,11 +210,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert Any to Double
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to Double */
   def any2double(any: Any): Double = {
     any match {
       case d: Double => d
@@ -270,11 +225,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert Any to Float
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to Float */
   def any2float(any: Any): Float = {
     any match {
       case f: Double => f.toFloat
@@ -289,11 +240,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert Any to Boolean
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to Boolean */
   def any2boolean(any: Any): Boolean = {
     any match {
       case b: Boolean => b
@@ -309,11 +256,7 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert Any to List[Any], fallback on list with 1 value
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to List[Any], fallback on list with 1 value */
   def any2list(any: Any): List[Any] = {
     if (any == null) return null
     any match {
@@ -322,31 +265,19 @@ object ConfigUtils extends Logging {
     }
   }
 
-  /**
-   * Convert Any to List[String]
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to List[String] */
   def any2stringList(any: Any): List[String] = {
     if (any == null) return null
     any2list(any).map(_.toString)
   }
 
-  /**
-   * Convert Any to List[File]
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to List[File] */
   def any2fileList(any: Any): List[File] = {
     if (any == null) return null
     any2list(any).map(x => new File(x.toString))
   }
 
-  /**
-   * Convert Any to Map[String, Any]
-   * @param any Input Any value
-   * @return
-   */
+  /** Convert Any to Map[String, Any] */
   def any2map(any: Any): Map[String, Any] = {
     if (any == null) return null
     any match {
@@ -366,9 +297,7 @@ object ConfigUtils extends Logging {
     }).toMap
   }
 
-  /**
-   * Trait for implicit conversions for ConfigValue to native scala values
-   */
+  /** Trait for implicit conversions for ConfigValue to native scala values */
   trait ImplicitConversions {
     import scala.language.implicitConversions
 
@@ -385,191 +314,115 @@ object ConfigUtils extends Logging {
       value != null && value.value != null && value.value != None
     }
 
-    /**
-     * Convert ConfigValue to File
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to File */
     implicit def configValue2file(value: ConfigValue): File = {
       if (requiredValue(value)) new File(any2string(value.value))
       else new File("")
     }
 
-    /**
-     * Convert ConfigValue to File
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to File */
     implicit def configValue2optionFile(value: ConfigValue): Option[File] = {
       if (valueExists(value)) Some(new File(any2string(value.value)))
       else None
     }
 
-    /**
-     * Convert ConfigValue to String
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to String */
     implicit def configValue2string(value: ConfigValue): String = {
       if (requiredValue(value)) any2string(value.value)
       else ""
     }
 
-    /**
-     * Convert ConfigValue to String
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to String */
     implicit def configValue2optionString(value: ConfigValue): Option[String] = {
       if (valueExists(value)) Some(any2string(value.value))
       else None
     }
 
-    /**
-     * Convert ConfigValue to Long
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Long */
     implicit def configValue2long(value: ConfigValue): Long = {
       if (requiredValue(value)) any2long(value.value)
       else 0L
     }
 
-    /**
-     * Convert ConfigValue top Option[Long]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue top Option[Long] */
     implicit def configValue2optionLong(value: ConfigValue): Option[Long] = {
       if (valueExists(value)) Option(any2long(value.value))
       else None
     }
 
-    /**
-     * Convert ConfigValue to Int
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Int */
     implicit def configValue2int(value: ConfigValue): Int = {
       if (requiredValue(value)) any2int(value.value)
       else 0
     }
 
-    /**
-     * Convert ConfigValue to Option[Int]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Option[Int] */
     implicit def configValue2optionInt(value: ConfigValue): Option[Int] = {
       if (valueExists(value)) Option(any2int(value.value))
       else None
     }
 
-    /**
-     * Convert ConfigValue to Double
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Double */
     implicit def configValue2double(value: ConfigValue): Double = {
       if (requiredValue(value)) any2double(value.value)
       else 0.0
     }
 
-    /**
-     * Convert ConfigValue to Option[Double]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Option[Double] */
     implicit def configValue2optionDouble(value: ConfigValue): Option[Double] = {
       if (valueExists(value)) Option(any2double(value.value))
       else None
     }
 
-    /**
-     * Convert ConfigValue to Float
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Float */
     implicit def configValue2float(value: ConfigValue): Float = {
       if (requiredValue(value)) any2float(value.value)
       else 0f
     }
 
-    /**
-     * Convert ConfigValue to Option[Float]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Option[Float] */
     implicit def configValue2optionFloat(value: ConfigValue): Option[Float] = {
       if (valueExists(value)) Option(any2float(value.value))
       else None
     }
 
-    /**
-     * Convert ConfigValue to Boolean
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Boolean */
     implicit def configValue2boolean(value: ConfigValue): Boolean = {
       if (requiredValue(value)) any2boolean(value.value)
       else false
     }
 
-    /**
-     * Convert ConfigValue to Option[Boolean]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Option[Boolean] */
     implicit def configValue2optionBoolean(value: ConfigValue): Option[Boolean] = {
       if (valueExists(value)) Option(any2boolean(value.value))
       else None
     }
 
-    /**
-     * Convert ConfigValue to List[Any]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to List[Any] */
     implicit def configValue2list(value: ConfigValue): List[Any] = {
       if (requiredValue(value)) any2list(value.value)
       else Nil
     }
 
-    /**
-     * Convert ConfigValue to List[String]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to List[String] */
     implicit def configValue2stringList(value: ConfigValue): List[String] = {
       if (requiredValue(value)) any2stringList(value.value)
       else Nil
     }
 
-    /**
-     * Convert ConfigValue to List[File]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to List[File] */
     implicit def configValue2fileList(value: ConfigValue): List[File] = {
       if (requiredValue(value)) any2fileList(value.value)
       else Nil
     }
 
-    /**
-     * Convert ConfigValue to Set[String]
-     * @param value Input ConfigValue
-     * @return
-     */
+    /** Convert ConfigValue to Set[String] */
     implicit def configValue2stringSet(value: ConfigValue): Set[String] = {
       if (requiredValue(value)) any2stringList(value.value).toSet
       else Set()
     }
 
-    /**
-     * Config config value to Map[String, Any]
-     * @param value Input ConfigValue
-     * @return
-     */