Added scala docs

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

@@ -5,12 +5,22 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 /**
+ * Trait for class to let them accept into a Summary
+ *
  * Created by pjvan_thof on 2/14/15.
  */
 trait Summarizable extends Configurable {
 
+  /**
+   * Must return files to store into summary
+   * @return
+   */
   def summaryFiles: Map[String, File]
 
+  /**
+   * Must returns stats to store into summary
+   * @return
+   */
   def summaryStats: Map[String, Any]
 
   /**

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

@@ -14,16 +14,30 @@ trait SummaryQScript extends BiopetQScript {
 
   /** Key is sample/library, None is sample or library is not applicable */
   private[summary] var summarizables: Map[(String, Option[String], Option[String]), List[Summarizable]] = Map()
+
+  /** Qscripts summaries that need to be merge into this summary */
   private[summary] var summaryQScripts: List[SummaryQScript] = Nil
 
+  /** Name of the pipeline in the summary */
   var summaryName = configName
 
+  /** Must return a map with used settings for this pipeline */
   def summarySettings: Map[String, Any]
 
+  /** File to put in the summary for thie pipeline */
   def summaryFiles: Map[String, File]
 
+  /** Name of summary output file */
   def summaryFile: File
 
+  /**
+   * Add a module to summary for this pipeline
+   *
+   * Auto detect sample and library from pipeline
+   *
+   * @param summarizable summarizable to add to summary for this pipeline
+   * @param name Name of module
+   */
   def addSummarizable(summarizable: Summarizable, name: String): Unit = {
     this match {
       case tag: SampleLibraryTag => addSummarizable(summarizable, name, tag.sampleId, tag.libId)
@@ -31,19 +45,39 @@ trait SummaryQScript extends BiopetQScript {
     }
   }
 
+  /**
+   * Add a module to summary for this pipeline
+   *
+   * @param summarizable summarizable to add to summary for this pipeline
+   * @param name Name of module
+   * @param sampleId
+   */
   def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String]): Unit = {
     addSummarizable(summarizable, name, sampleId, None)
   }
 
+  /**
+   * Add a module to summary for this pipeline
+   *
+   * @param summarizable summarizable to add to summary for this pipeline
+   * @param name Name of module
+   * @param sampleId
+   * @param libraryId
+   */
   def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String], libraryId: Option[String]): Unit = {
     if (libraryId.isDefined) require(sampleId.isDefined) // Library always require a sample
     summarizables += (name, sampleId, libraryId) -> (summarizable :: summarizables.getOrElse((name, sampleId, libraryId), Nil))
   }
 
+  /**
+   * Add an other qscript to merge in output summary
+   * @param summaryQScript
+   */
   def addSummaryQScript(summaryQScript: SummaryQScript): Unit = {
     summaryQScripts :+= summaryQScript
   }
 
+  /** Add jobs to qscript to execute summary, also add checksum jobs */
   def addSummaryJobs: Unit = {
     val writeSummary = new WriteSummary(this)
 
@@ -73,11 +107,11 @@ trait SummaryQScript extends BiopetQScript {
 
     add(writeSummary)
   }
-
-  protected[summary] val executables: mutable.Map[String, (File, String)] = mutable.Map()
 }
 
 object SummaryQScript {
   import scala.collection.mutable.Map
+
+  /** Cache to have no duplicate jobs */
   protected[summary] val md5sumCache: Map[File, File] = Map()
 }
\ No newline at end of file

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

@@ -20,6 +20,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
 
   require(root.isInstanceOf[SummaryQScript], "root is not a SummaryQScript")
 
+  /** To access qscript for this summary */
   val qscript = root.asInstanceOf[SummaryQScript]
 
   @Input(doc = "deps", required = false)
@@ -43,8 +44,8 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     super.freezeFieldValues()
   }
 
+  /** Function to create summary */
   def run(): Unit = {
-
     val pipelineMap = {
       val files = parseFiles(qscript.summaryFiles)
       val settings = qscript.summarySettings
@@ -100,6 +101,12 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     }
   }
 
+  /**
+   * Convert summarizable to a summary map
+   * @param summarizable
+   * @param name
+   * @return
+   */
   def parseSummarizable(summarizable: Summarizable, name: String) = {
     val data = summarizable.summaryStats
     val files = parseFiles(summarizable.summaryFiles)
@@ -108,10 +115,20 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
       (if (files.isEmpty) Map[String, Any]() else Map("files" -> Map(name -> files)))
   }
 
+  /**
+   * Parse files map to summary map
+   * @param files
+   * @return
+   */
   def parseFiles(files: Map[String, File]): Map[String, Map[String, Any]] = {
     for ((key, file) <- files) yield key -> parseFile(file)
   }
 
+  /**
+   * parse single file summary map
+   * @param file
+   * @return
+   */
   def parseFile(file: File): Map[String, Any] = {
     val map: mutable.Map[String, Any] = mutable.Map()
     map += "path" -> file.getAbsolutePath
@@ -119,6 +136,11 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     map.toMap
   }
 
+  /**
+   * Retrive checksum from file
+   * @param checksumFile
+   * @return
+   */
   def parseChecksum(checksumFile: File): String = {
     Source.fromFile(checksumFile).getLines().toList.head.split(" ")(0)
   }