Autogenerated literator docs for v0.2.0

bio4j · Nov 9, 2016 · 22d6696 · 22d6696
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diff --git a/docs/src/main/scala/entry.scala.md b/docs/src/main/scala/entry.scala.md
@@ -642,13 +642,15 @@ case class Sequence(val value: String) extends AnyVal
 
 
 [test/scala/LineParsingSpeed.scala]: ../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: entry.scala.md
+[main/scala/isoformSequences.scala]: isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: flat/SequenceData.scala.md
 [main/scala/flat/KW.scala]: flat/KW.scala.md
 [main/scala/flat/ID.scala]: flat/ID.scala.md
@@ -676,4 +678,5 @@ case class Sequence(val value: String) extends AnyVal
 [main/scala/flat/RP.scala]: flat/RP.scala.md
 [main/scala/flat/lineTypes.scala]: flat/lineTypes.scala.md
 [main/scala/flat/RT.scala]: flat/RT.scala.md
-[main/scala/seqOps.scala]: seqOps.scala.md
+[main/scala/seqOps.scala]: seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/fasta/isoforms.scala.md b/docs/src/main/scala/fasta/isoforms.scala.md
@@ -0,0 +1,67 @@
+
+```scala
+package com.bio4j.data.uniprot.fasta
+
+import com.bio4j.data.uniprot.AnyIsoformSequence
+import ohnosequences.fastarious._, fasta._
+
+case class Isoform(val fa: FASTA.Value) extends AnyVal with AnyIsoformSequence {
+
+  def ID: String =
+    // the format of the id is 'sp|${id}|otherstuff'
+    fa.getV(fasta.header).id.stripPrefix("sp|").takeWhile(_ != '|')
+
+  def sequence: String =
+    fa.getV(fasta.sequence).value
+}
+
+case object isoformSequences {
+
+  def fromLines(lines: Iterator[String]): Iterator[Isoform] =
+    fasta.parseFastaDropErrors(lines) map Isoform
+}
+
+```
+
+
+
+
+[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
+[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
+[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
+[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
+[main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
+[main/scala/flat/SequenceData.scala]: ../flat/SequenceData.scala.md
+[main/scala/flat/KW.scala]: ../flat/KW.scala.md
+[main/scala/flat/ID.scala]: ../flat/ID.scala.md
+[main/scala/flat/RC.scala]: ../flat/RC.scala.md
+[main/scala/flat/DT.scala]: ../flat/DT.scala.md
+[main/scala/flat/Entry.scala]: ../flat/Entry.scala.md
+[main/scala/flat/GN.scala]: ../flat/GN.scala.md
+[main/scala/flat/parsers.scala]: ../flat/parsers.scala.md
+[main/scala/flat/RG.scala]: ../flat/RG.scala.md
+[main/scala/flat/DR.scala]: ../flat/DR.scala.md
+[main/scala/flat/OG.scala]: ../flat/OG.scala.md
+[main/scala/flat/RL.scala]: ../flat/RL.scala.md
+[main/scala/flat/SQ.scala]: ../flat/SQ.scala.md
+[main/scala/flat/PE.scala]: ../flat/PE.scala.md
+[main/scala/flat/OS.scala]: ../flat/OS.scala.md
+[main/scala/flat/CC.scala]: ../flat/CC.scala.md
+[main/scala/flat/OX.scala]: ../flat/OX.scala.md
+[main/scala/flat/OH.scala]: ../flat/OH.scala.md
+[main/scala/flat/RN.scala]: ../flat/RN.scala.md
+[main/scala/flat/DE.scala]: ../flat/DE.scala.md
+[main/scala/flat/RA.scala]: ../flat/RA.scala.md
+[main/scala/flat/RX.scala]: ../flat/RX.scala.md
+[main/scala/flat/FT.scala]: ../flat/FT.scala.md
+[main/scala/flat/AC.scala]: ../flat/AC.scala.md
+[main/scala/flat/RP.scala]: ../flat/RP.scala.md
+[main/scala/flat/lineTypes.scala]: ../flat/lineTypes.scala.md
+[main/scala/flat/RT.scala]: ../flat/RT.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: isoforms.scala.md
diff --git a/docs/src/main/scala/flat/AC.scala.md b/docs/src/main/scala/flat/AC.scala.md
@@ -33,13 +33,15 @@ case class AC(val lines: Seq[String]) extends AnyVal {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -67,4 +69,5 @@ case class AC(val lines: Seq[String]) extends AnyVal {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/CC.scala.md b/docs/src/main/scala/flat/CC.scala.md
@@ -124,13 +124,15 @@ IsoId=Q15746-3; Sequence=VSP_004792, VSP_004794;
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -158,4 +160,5 @@ IsoId=Q15746-3; Sequence=VSP_004792, VSP_004794;
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/DE.scala.md b/docs/src/main/scala/flat/DE.scala.md
@@ -164,13 +164,15 @@ case object DE {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -198,4 +200,5 @@ case object DE {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/DR.scala.md b/docs/src/main/scala/flat/DR.scala.md
@@ -43,13 +43,15 @@ case class DR(val lines: Seq[String]) extends AnyVal {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -77,4 +79,5 @@ case class DR(val lines: Seq[String]) extends AnyVal {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/DT.scala.md b/docs/src/main/scala/flat/DT.scala.md
@@ -66,13 +66,15 @@ case class DT(val value: Seq[String]) {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -100,4 +102,5 @@ case class DT(val value: Seq[String]) {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/Entry.scala.md b/docs/src/main/scala/flat/Entry.scala.md
@@ -154,13 +154,15 @@ case object Entry {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -188,4 +190,5 @@ case object Entry {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/FT.scala.md b/docs/src/main/scala/flat/FT.scala.md
@@ -56,13 +56,15 @@ case class FT(val lines: Seq[String]) extends AnyVal {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -90,4 +92,5 @@ case class FT(val lines: Seq[String]) extends AnyVal {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/GN.scala.md b/docs/src/main/scala/flat/GN.scala.md
@@ -94,13 +94,15 @@ case object GN {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -128,4 +130,5 @@ case object GN {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/ID.scala.md b/docs/src/main/scala/flat/ID.scala.md
@@ -54,13 +54,15 @@ case class ID(val value: String) extends AnyVal {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -88,4 +90,5 @@ case class ID(val value: String) extends AnyVal {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/KW.scala.md b/docs/src/main/scala/flat/KW.scala.md
@@ -17,13 +17,15 @@ case class KW(val lines: Seq[String]) extends AnyVal {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -51,4 +53,5 @@ case class KW(val lines: Seq[String]) extends AnyVal {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/OG.scala.md b/docs/src/main/scala/flat/OG.scala.md
@@ -45,13 +45,15 @@ case object OG {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -79,4 +81,5 @@ case object OG {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md
diff --git a/docs/src/main/scala/flat/OH.scala.md b/docs/src/main/scala/flat/OH.scala.md
@@ -33,13 +33,15 @@ case class OH(val lines: Seq[String]) extends AnyVal {
 
 
 [test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
+[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.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
 [test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
 [test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
 [test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
 [main/scala/entry.scala]: ../entry.scala.md
+[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
 [main/scala/flat/SequenceData.scala]: SequenceData.scala.md
 [main/scala/flat/KW.scala]: KW.scala.md
 [main/scala/flat/ID.scala]: ID.scala.md
@@ -67,4 +69,5 @@ case class OH(val lines: Seq[String]) extends AnyVal {
 [main/scala/flat/RP.scala]: RP.scala.md
 [main/scala/flat/lineTypes.scala]: lineTypes.scala.md
 [main/scala/flat/RT.scala]: RT.scala.md
-[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/seqOps.scala]: ../seqOps.scala.md
+[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md