Autogenerated literator docs for v0.1.1

docs/src/main/scala/flat/AC.scala.md

@@ -32,6 +32,7 @@ case class AC(val lines: Seq[String]) extends AnyVal {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/CC.scala.md

@@ -17,46 +17,46 @@ case class CC(val lines: Seq[String])  {
 
     topic match {
 
-      case "ALLERGEN"                       => Vector( Allergen(contents.mkString(" ")) )
+      case "ALLERGEN"                       => List( Allergen(contents.mkString(" ")) )
       case "ALTERNATIVE PRODUCTS"           => isoformBlocks(contents.tail) map isoformFromBlock
-      case "BIOPHYSICOCHEMICAL PROPERTIES"  => Vector( BiophysicochemicalProperties(contents.mkString(" ")) )
-      case "BIOTECHNOLOGY"                  => Vector( Biotechnology(contents.mkString(" ")) )
-      case "CATALYTIC ACTIVITY"             => Vector( CatalyticActivity(contents.mkString(" ")) )
-      case "CAUTION"                        => Vector( Caution(contents.mkString(" ")) )
-      case "COFACTOR"                       => Vector( Cofactor(contents.mkString(" ")) )
-      case "DEVELOPMENTAL STAGE"            => Vector( DevelopmentalStage(contents.mkString(" ")) )
-      case "DISEASE"                        => Vector( Disease(contents.mkString(" ")) )
-      case "DISRUPTION PHENOTYPE"           => Vector( DisruptionPhenotype(contents.mkString(" ")) )
-      case "DOMAIN"                         => Vector( Domain(contents.mkString(" ")) )
-      case "ENZYME REGULATION"              => Vector( EnzymeRegulation(contents.mkString(" ")) )
-      case "FUNCTION"                       => Vector( Function(contents.mkString(" ")) )
-      case "INDUCTION"                      => Vector( Induction(contents.mkString(" ")) )
-      case "INTERACTION"                    => Vector( Interaction(contents.mkString(" ")) )
-      case "MASS SPECTROMETRY"              => Vector( MassSpectrometry(contents.mkString(" ")) )
-      case "MISCELLANEOUS"                  => Vector( Miscellaneous(contents.mkString(" ")) )
-      case "PATHWAY"                        => Vector( Pathway(contents.mkString(" ")) )
-      case "PHARMACEUTICAL"                 => Vector( Pharmaceutical(contents.mkString(" ")) )
-      case "POLYMORPHISM"                   => Vector( Polymorphism(contents.mkString(" ")) )
-      case "PTM"                            => Vector( PTM(contents.mkString(" ")) )
-      case "RNA EDITING"                    => Vector( RNAEditing(contents.mkString(" ")) )
-      case "SEQUENCE CAUTION"               => Vector( SequenceCaution(contents.mkString(" ")) )
-      case "SIMILARITY"                     => Vector( Similarity(contents.mkString(" ")) )
-      case "SUBCELLULAR LOCATION"           => Vector( SubcellularLocation(contents.mkString(" ")) )
-      case "SUBUNIT"                        => Vector( Subunit(contents.mkString(" ")) )
-      case "TISSUE SPECIFICITY"             => Vector( TissueSpecificity(contents.mkString(" ")) )
-      case "TOXIC DOSE"                     => Vector( ToxicDose(contents.mkString(" ")) )
-      case "WEB RESOURCE"                   => Vector( WebResource(contents.mkString(" ")) )
+      case "BIOPHYSICOCHEMICAL PROPERTIES"  => List( BiophysicochemicalProperties(contents.mkString(" ")) )
+      case "BIOTECHNOLOGY"                  => List( Biotechnology(contents.mkString(" ")) )
+      case "CATALYTIC ACTIVITY"             => List( CatalyticActivity(contents.mkString(" ")) )
+      case "CAUTION"                        => List( Caution(contents.mkString(" ")) )
+      case "COFACTOR"                       => List( Cofactor(contents.mkString(" ")) )
+      case "DEVELOPMENTAL STAGE"            => List( DevelopmentalStage(contents.mkString(" ")) )
+      case "DISEASE"                        => List( Disease(contents.mkString(" ")) )
+      case "DISRUPTION PHENOTYPE"           => List( DisruptionPhenotype(contents.mkString(" ")) )
+      case "DOMAIN"                         => List( Domain(contents.mkString(" ")) )
+      case "ENZYME REGULATION"              => List( EnzymeRegulation(contents.mkString(" ")) )
+      case "FUNCTION"                       => List( Function(contents.mkString(" ")) )
+      case "INDUCTION"                      => List( Induction(contents.mkString(" ")) )
+      case "INTERACTION"                    => List( Interaction(contents.mkString(" ")) )
+      case "MASS SPECTROMETRY"              => List( MassSpectrometry(contents.mkString(" ")) )
+      case "MISCELLANEOUS"                  => List( Miscellaneous(contents.mkString(" ")) )
+      case "PATHWAY"                        => List( Pathway(contents.mkString(" ")) )
+      case "PHARMACEUTICAL"                 => List( Pharmaceutical(contents.mkString(" ")) )
+      case "POLYMORPHISM"                   => List( Polymorphism(contents.mkString(" ")) )
+      case "PTM"                            => List( PTM(contents.mkString(" ")) )
+      case "RNA EDITING"                    => List( RNAEditing(contents.mkString(" ")) )
+      case "SEQUENCE CAUTION"               => List( SequenceCaution(contents.mkString(" ")) )
+      case "SIMILARITY"                     => List( Similarity(contents.mkString(" ")) )
+      case "SUBCELLULAR LOCATION"           => List( SubcellularLocation(contents.mkString(" ")) )
+      case "SUBUNIT"                        => List( Subunit(contents.mkString(" ")) )
+      case "TISSUE SPECIFICITY"             => List( TissueSpecificity(contents.mkString(" ")) )
+      case "TOXIC DOSE"                     => List( ToxicDose(contents.mkString(" ")) )
+      case "WEB RESOURCE"                   => List( WebResource(contents.mkString(" ")) )
     }
   }
 
   private def commentBlocks(commentLines: Seq[String]): Seq[Seq[String]] =
-    commentLines.foldLeft[Seq[Seq[String]]](Vector()){ (acc: Seq[Seq[String]], line: String) =>
+    commentLines.foldLeft[collection.mutable.Buffer[Seq[String]]](new collection.mutable.UnrolledBuffer[Seq[String]]){ (acc: collection.mutable.Buffer[Seq[String]], line: String) =>
       // extra lines for a comment
       if(line startsWith "    ") {
         acc.updated(acc.length - 1, acc.last :+ line.trim)
       }
       else {
-        acc :+ Vector(line.stripPrefix("-!-").trim)
+        acc += List(line.stripPrefix("-!-").trim)
       }
     }
 ```
@@ -87,12 +87,12 @@ The input here has lines **already trimmed**.
   private def isoformBlocks(altProdLines: Seq[String]): Seq[Seq[String]] =
     altProdLines
       .dropWhile(altProdLine => !altProdLine.startsWith("Name="))
-      .foldLeft(Seq[Seq[String]]()){ (acc: Seq[Seq[String]], line: String) =>
+      .foldLeft(new collection.mutable.UnrolledBuffer[Seq[String]]()){ (acc: collection.mutable.UnrolledBuffer[Seq[String]], line: String) =>
       // same iso
       if(!(line startsWith "Name="))
         acc.updated(acc.length - 1, acc.last :+ line.trim)
       else
-        acc :+ Vector(line.trim)
+        acc += List(line.trim)
     }
 ```
 
@@ -123,6 +123,7 @@ IsoId=Q15746-3; Sequence=VSP_004792, VSP_004794;
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/DE.scala.md

@@ -163,6 +163,7 @@ case object DE {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/DR.scala.md

@@ -20,19 +20,19 @@ Bgee; ENSMUSG00000032315; -.
 ```scala
 case class DR(val lines: Seq[String]) extends AnyVal {
 
+  @inline
   def databaseCrossReferences: Seq[DatabaseCrossReference] =
     lines map { line =>
 
-      val fragments = line.splitSegments(_==';')
-      val resourceAbbrv = fragments(0).trim
-      val id            = fragments(1).trim
+      val (firstFrag, rest1)  = line.span(_!=';')
+      val (secondFrag, rest2) = rest1.stripPrefix(";").span(_!=';')
 
       DatabaseCrossReference(
-        resource          = ResourceAbbreviation.fromString(resourceAbbrv),
-        identifier        = id,
+        resource          = ResourceAbbreviation.fromString(firstFrag.trim),
+        identifier        = secondFrag.trim
         // TODO other info?
-        otherInformation  = None,
-        isoformID         = None
+        // otherInformation  = None,
+        // isoformID         = None
       )
     }
 }
@@ -42,6 +42,7 @@ case class DR(val lines: Seq[String]) extends AnyVal {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/DT.scala.md

@@ -65,6 +65,7 @@ case class DT(val value: Seq[String]) {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/Entry.scala.md

@@ -9,16 +9,16 @@ import java.time.LocalDate
 case class Entry(
   val allLines: Seq[String]
 )
-extends AnyEntry {
+extends AnyVal with AnyEntry {
 
-  private lazy val id: ID =
+  final def id: ID =
     ID(linesOfType(LineType.ID).head)
 
   @inline
   final def identification: Identification =
     id.identification
 
-  private lazy val ac: AC =
+  final def ac: AC =
     AC(linesOfType(LineType.AC))
 
   @inline
@@ -33,21 +33,21 @@ extends AnyEntry {
     )
   }
 
-  private lazy val dt: DT =
+  final def dt: DT =
     DT(linesOfType(LineType.DT))
 
   @inline
   final def date: Date =
     dt.date
 
-  private lazy val de: DE =
+  final def de: DE =
     DE(linesOfType(LineType.DE))
 
   @inline
   final def description: Description =
     de.description
 
-  private lazy val gn: GN =
+  final def gn: GN =
     GN(linesOfType(LineType.GN))
 
   @inline
@@ -58,87 +58,92 @@ extends AnyEntry {
   final def organismSpecies: OrganismSpecies =
     ???
 
-  private lazy val og: OG =
-    OG(linesOfType(LineType.GN))
+  final def og: OG =
+    OG(linesOfType(LineType.OG))
 
-  lazy val organelles: Seq[Organelle] =
+  @inline
+  final def organelles: Seq[Organelle] =
     og.organelles
 
   @inline
   final def organismClassification: OrganismClassification =
     ???
 
-  private lazy val ox: OX =
+  final def ox: OX =
     OX(linesOfType(LineType.OX).head)
 
   @inline
   final def taxonomyCrossReference: TaxonomyCrossReference =
     ox.taxonomyCrossReference
 
-  private lazy val oh: OH =
+  final def oh: OH =
     OH(linesOfType(LineType.OH))
 
   @inline
   final def organismHost: Seq[TaxonomyCrossReference] =
     oh.taxonomyCrossReferences
 
-  private lazy val cc: CC =
+  final def cc: CC =
     CC(linesOfType(LineType.CC))
 
   @inline
   final def comments: Seq[Comment] =
     cc.comments
 
-  private lazy val dr: DR =
-    DR(linesOfType(LineType.DR))
+  final def dr: DR =
+    DR(linesOfType(LineType.DR).toList)
 
   @inline
   final def databaseCrossReferences: Seq[DatabaseCrossReference] =
     dr.databaseCrossReferences
 
-  private lazy val pe: PE =
+  final def pe: PE =
     PE(linesOfType(LineType.PE).head)
 
   @inline
   final def proteinExistence: ProteinExistence =
     pe.proteinExistence
 
-  private lazy val kw: KW =
+  final def kw: KW =
     KW(linesOfType(LineType.KW))
 
   @inline
   final def keywords: Seq[Keyword] =
     kw.keywords
 
-  private lazy val ft: FT =
+  final def ft: FT =
     FT(linesOfType(LineType.FT))
 
   @inline
   final def features: Seq[Feature] =
     ft.features
 
-  private lazy val sq: SQ =
+  final def sq: SQ =
     SQ(linesOfType(LineType.SQ).head)
 
   @inline
   final def sequenceHeader: SequenceHeader =
     sq.sequenceHeader
 
-  private lazy val sd: SequenceData =
+  final def sd: SequenceData =
     SequenceData(linesOfType(LineType.`  `))
 
   @inline
   final def sequence: Sequence =
     sd.sequence
 
-
-
-  private def linesOfType(lt: LineType) =
-    (allLines filter Line.isOfType(lt)).map(Line.contentOf)
+  @inline
+  final def linesOfType(lt: LineType) =
+    allLines
+      .dropWhile(l => !(l startsWith lt.asString))
+      .takeWhile(_ startsWith lt.asString)
+      .map(_ drop 5)
+    // allLines collect { case l if(l startsWith lt.toString) => l drop 5 }
 }
 
 case object Entry {
 
+  @inline
   def from(lns: Seq[String]): Entry =
     Entry(lns)
 }
@@ -148,6 +153,7 @@ case object Entry {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/FT.scala.md

@@ -55,6 +55,7 @@ case class FT(val lines: Seq[String]) extends AnyVal {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/GN.scala.md

@@ -93,6 +93,7 @@ case object GN {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/ID.scala.md

@@ -53,6 +53,7 @@ case class ID(val value: String) extends AnyVal {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md

docs/src/main/scala/flat/KW.scala.md

@@ -16,6 +16,7 @@ case class KW(val lines: Seq[String]) extends AnyVal {
 
 
 
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
 [test/scala/lines.scala]: ../../../test/scala/lines.scala.md
 [test/scala/testData.scala]: ../../../test/scala/testData.scala.md
 [test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md