Skip to content

Commit 22d6696

Browse files
eparejatobeseparejatobes
committed
Autogenerated literator docs for v0.2.0
1 parent 1bb031b commit 22d6696

39 files changed

+338
-36
lines changed

‎docs/src/main/scala/entry.scala.md

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -642,13 +642,15 @@ case class Sequence(val value: String) extends AnyVal
642642

643643

644644
[test/scala/LineParsingSpeed.scala]: ../../test/scala/LineParsingSpeed.scala.md
645+
[test/scala/IsoformSequences.scala]: ../../test/scala/IsoformSequences.scala.md
645646
[test/scala/lines.scala]: ../../test/scala/lines.scala.md
646647
[test/scala/testData.scala]: ../../test/scala/testData.scala.md
647648
[test/scala/FlatFileEntry.scala]: ../../test/scala/FlatFileEntry.scala.md
648649
[test/scala/EntryParsingSpeed.scala]: ../../test/scala/EntryParsingSpeed.scala.md
649650
[test/scala/FileReadSpeed.scala]: ../../test/scala/FileReadSpeed.scala.md
650651
[test/scala/SeqOps.scala]: ../../test/scala/SeqOps.scala.md
651652
[main/scala/entry.scala]: entry.scala.md
653+
[main/scala/isoformSequences.scala]: isoformSequences.scala.md
652654
[main/scala/flat/SequenceData.scala]: flat/SequenceData.scala.md
653655
[main/scala/flat/KW.scala]: flat/KW.scala.md
654656
[main/scala/flat/ID.scala]: flat/ID.scala.md
@@ -676,4 +678,5 @@ case class Sequence(val value: String) extends AnyVal
676678
[main/scala/flat/RP.scala]: flat/RP.scala.md
677679
[main/scala/flat/lineTypes.scala]: flat/lineTypes.scala.md
678680
[main/scala/flat/RT.scala]: flat/RT.scala.md
679-
[main/scala/seqOps.scala]: seqOps.scala.md
681+
[main/scala/seqOps.scala]: seqOps.scala.md
682+
[main/scala/fasta/isoforms.scala]: fasta/isoforms.scala.md

‎docs/src/main/scala/fasta/isoforms.scala.md

Lines changed: 67 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,67 @@
1+
2+
```scala
3+
package com.bio4j.data.uniprot.fasta
4+
5+
import com.bio4j.data.uniprot.AnyIsoformSequence
6+
import ohnosequences.fastarious._, fasta._
7+
8+
case class Isoform(val fa: FASTA.Value) extends AnyVal with AnyIsoformSequence {
9+
10+
def ID: String =
11+
// the format of the id is 'sp|${id}|otherstuff'
12+
fa.getV(fasta.header).id.stripPrefix("sp|").takeWhile(_ != '|')
13+
14+
def sequence: String =
15+
fa.getV(fasta.sequence).value
16+
}
17+
18+
case object isoformSequences {
19+
20+
def fromLines(lines: Iterator[String]): Iterator[Isoform] =
21+
fasta.parseFastaDropErrors(lines) map Isoform
22+
}
23+
24+
```
25+
26+
27+
28+
29+
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
30+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
31+
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
32+
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
33+
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
34+
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
35+
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
36+
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
37+
[main/scala/entry.scala]: ../entry.scala.md
38+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
39+
[main/scala/flat/SequenceData.scala]: ../flat/SequenceData.scala.md
40+
[main/scala/flat/KW.scala]: ../flat/KW.scala.md
41+
[main/scala/flat/ID.scala]: ../flat/ID.scala.md
42+
[main/scala/flat/RC.scala]: ../flat/RC.scala.md
43+
[main/scala/flat/DT.scala]: ../flat/DT.scala.md
44+
[main/scala/flat/Entry.scala]: ../flat/Entry.scala.md
45+
[main/scala/flat/GN.scala]: ../flat/GN.scala.md
46+
[main/scala/flat/parsers.scala]: ../flat/parsers.scala.md
47+
[main/scala/flat/RG.scala]: ../flat/RG.scala.md
48+
[main/scala/flat/DR.scala]: ../flat/DR.scala.md
49+
[main/scala/flat/OG.scala]: ../flat/OG.scala.md
50+
[main/scala/flat/RL.scala]: ../flat/RL.scala.md
51+
[main/scala/flat/SQ.scala]: ../flat/SQ.scala.md
52+
[main/scala/flat/PE.scala]: ../flat/PE.scala.md
53+
[main/scala/flat/OS.scala]: ../flat/OS.scala.md
54+
[main/scala/flat/CC.scala]: ../flat/CC.scala.md
55+
[main/scala/flat/OX.scala]: ../flat/OX.scala.md
56+
[main/scala/flat/OH.scala]: ../flat/OH.scala.md
57+
[main/scala/flat/RN.scala]: ../flat/RN.scala.md
58+
[main/scala/flat/DE.scala]: ../flat/DE.scala.md
59+
[main/scala/flat/RA.scala]: ../flat/RA.scala.md
60+
[main/scala/flat/RX.scala]: ../flat/RX.scala.md
61+
[main/scala/flat/FT.scala]: ../flat/FT.scala.md
62+
[main/scala/flat/AC.scala]: ../flat/AC.scala.md
63+
[main/scala/flat/RP.scala]: ../flat/RP.scala.md
64+
[main/scala/flat/lineTypes.scala]: ../flat/lineTypes.scala.md
65+
[main/scala/flat/RT.scala]: ../flat/RT.scala.md
66+
[main/scala/seqOps.scala]: ../seqOps.scala.md
67+
[main/scala/fasta/isoforms.scala]: isoforms.scala.md

‎docs/src/main/scala/flat/AC.scala.md

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,13 +33,15 @@ case class AC(val lines: Seq[String]) extends AnyVal {
3333

3434

3535
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
36+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
3637
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
3738
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
3839
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
3940
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
4041
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
4142
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
4243
[main/scala/entry.scala]: ../entry.scala.md
44+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
4345
[main/scala/flat/SequenceData.scala]: SequenceData.scala.md
4446
[main/scala/flat/KW.scala]: KW.scala.md
4547
[main/scala/flat/ID.scala]: ID.scala.md
@@ -67,4 +69,5 @@ case class AC(val lines: Seq[String]) extends AnyVal {
6769
[main/scala/flat/RP.scala]: RP.scala.md
6870
[main/scala/flat/lineTypes.scala]: lineTypes.scala.md
6971
[main/scala/flat/RT.scala]: RT.scala.md
70-
[main/scala/seqOps.scala]: ../seqOps.scala.md
72+
[main/scala/seqOps.scala]: ../seqOps.scala.md
73+
[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md

‎docs/src/main/scala/flat/CC.scala.md

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -124,13 +124,15 @@ IsoId=Q15746-3; Sequence=VSP_004792, VSP_004794;
124124

125125

126126
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
127+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
127128
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
128129
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
129130
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
130131
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
131132
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
132133
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
133134
[main/scala/entry.scala]: ../entry.scala.md
135+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
134136
[main/scala/flat/SequenceData.scala]: SequenceData.scala.md
135137
[main/scala/flat/KW.scala]: KW.scala.md
136138
[main/scala/flat/ID.scala]: ID.scala.md
@@ -158,4 +160,5 @@ IsoId=Q15746-3; Sequence=VSP_004792, VSP_004794;
158160
[main/scala/flat/RP.scala]: RP.scala.md
159161
[main/scala/flat/lineTypes.scala]: lineTypes.scala.md
160162
[main/scala/flat/RT.scala]: RT.scala.md
161-
[main/scala/seqOps.scala]: ../seqOps.scala.md
163+
[main/scala/seqOps.scala]: ../seqOps.scala.md
164+
[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md

‎docs/src/main/scala/flat/DE.scala.md

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -164,13 +164,15 @@ case object DE {
164164

165165

166166
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
167+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
167168
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
168169
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
169170
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
170171
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
171172
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
172173
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
173174
[main/scala/entry.scala]: ../entry.scala.md
175+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
174176
[main/scala/flat/SequenceData.scala]: SequenceData.scala.md
175177
[main/scala/flat/KW.scala]: KW.scala.md
176178
[main/scala/flat/ID.scala]: ID.scala.md
@@ -198,4 +200,5 @@ case object DE {
198200
[main/scala/flat/RP.scala]: RP.scala.md
199201
[main/scala/flat/lineTypes.scala]: lineTypes.scala.md
200202
[main/scala/flat/RT.scala]: RT.scala.md
201-
[main/scala/seqOps.scala]: ../seqOps.scala.md
203+
[main/scala/seqOps.scala]: ../seqOps.scala.md
204+
[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md

‎docs/src/main/scala/flat/DR.scala.md

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -43,13 +43,15 @@ case class DR(val lines: Seq[String]) extends AnyVal {
4343

4444

4545
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
46+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
4647
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
4748
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
4849
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
4950
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
5051
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
5152
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
5253
[main/scala/entry.scala]: ../entry.scala.md
54+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
5355
[main/scala/flat/SequenceData.scala]: SequenceData.scala.md
5456
[main/scala/flat/KW.scala]: KW.scala.md
5557
[main/scala/flat/ID.scala]: ID.scala.md
@@ -77,4 +79,5 @@ case class DR(val lines: Seq[String]) extends AnyVal {
7779
[main/scala/flat/RP.scala]: RP.scala.md
7880
[main/scala/flat/lineTypes.scala]: lineTypes.scala.md
7981
[main/scala/flat/RT.scala]: RT.scala.md
80-
[main/scala/seqOps.scala]: ../seqOps.scala.md
82+
[main/scala/seqOps.scala]: ../seqOps.scala.md
83+
[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md

‎docs/src/main/scala/flat/DT.scala.md

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -66,13 +66,15 @@ case class DT(val value: Seq[String]) {
6666

6767

6868
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
69+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
6970
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
7071
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
7172
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
7273
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
7374
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
7475
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
7576
[main/scala/entry.scala]: ../entry.scala.md
77+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
7678
[main/scala/flat/SequenceData.scala]: SequenceData.scala.md
7779
[main/scala/flat/KW.scala]: KW.scala.md
7880
[main/scala/flat/ID.scala]: ID.scala.md
@@ -100,4 +102,5 @@ case class DT(val value: Seq[String]) {
100102
[main/scala/flat/RP.scala]: RP.scala.md
101103
[main/scala/flat/lineTypes.scala]: lineTypes.scala.md
102104
[main/scala/flat/RT.scala]: RT.scala.md
103-
[main/scala/seqOps.scala]: ../seqOps.scala.md
105+
[main/scala/seqOps.scala]: ../seqOps.scala.md
106+
[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md

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

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -154,13 +154,15 @@ case object Entry {
154154

155155

156156
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
157+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
157158
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
158159
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
159160
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
160161
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
161162
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
162163
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
163164
[main/scala/entry.scala]: ../entry.scala.md
165+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
164166
[main/scala/flat/SequenceData.scala]: SequenceData.scala.md
165167
[main/scala/flat/KW.scala]: KW.scala.md
166168
[main/scala/flat/ID.scala]: ID.scala.md
@@ -188,4 +190,5 @@ case object Entry {
188190
[main/scala/flat/RP.scala]: RP.scala.md
189191
[main/scala/flat/lineTypes.scala]: lineTypes.scala.md
190192
[main/scala/flat/RT.scala]: RT.scala.md
191-
[main/scala/seqOps.scala]: ../seqOps.scala.md
193+
[main/scala/seqOps.scala]: ../seqOps.scala.md
194+
[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md

‎docs/src/main/scala/flat/FT.scala.md

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -56,13 +56,15 @@ case class FT(val lines: Seq[String]) extends AnyVal {
5656

5757

5858
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
59+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
5960
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
6061
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
6162
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
6263
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
6364
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
6465
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
6566
[main/scala/entry.scala]: ../entry.scala.md
67+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
6668
[main/scala/flat/SequenceData.scala]: SequenceData.scala.md
6769
[main/scala/flat/KW.scala]: KW.scala.md
6870
[main/scala/flat/ID.scala]: ID.scala.md
@@ -90,4 +92,5 @@ case class FT(val lines: Seq[String]) extends AnyVal {
9092
[main/scala/flat/RP.scala]: RP.scala.md
9193
[main/scala/flat/lineTypes.scala]: lineTypes.scala.md
9294
[main/scala/flat/RT.scala]: RT.scala.md
93-
[main/scala/seqOps.scala]: ../seqOps.scala.md
95+
[main/scala/seqOps.scala]: ../seqOps.scala.md
96+
[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md

‎docs/src/main/scala/flat/GN.scala.md

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -94,13 +94,15 @@ case object GN {
9494

9595

9696
[test/scala/LineParsingSpeed.scala]: ../../../test/scala/LineParsingSpeed.scala.md
97+
[test/scala/IsoformSequences.scala]: ../../../test/scala/IsoformSequences.scala.md
9798
[test/scala/lines.scala]: ../../../test/scala/lines.scala.md
9899
[test/scala/testData.scala]: ../../../test/scala/testData.scala.md
99100
[test/scala/FlatFileEntry.scala]: ../../../test/scala/FlatFileEntry.scala.md
100101
[test/scala/EntryParsingSpeed.scala]: ../../../test/scala/EntryParsingSpeed.scala.md
101102
[test/scala/FileReadSpeed.scala]: ../../../test/scala/FileReadSpeed.scala.md
102103
[test/scala/SeqOps.scala]: ../../../test/scala/SeqOps.scala.md
103104
[main/scala/entry.scala]: ../entry.scala.md
105+
[main/scala/isoformSequences.scala]: ../isoformSequences.scala.md
104106
[main/scala/flat/SequenceData.scala]: SequenceData.scala.md
105107
[main/scala/flat/KW.scala]: KW.scala.md
106108
[main/scala/flat/ID.scala]: ID.scala.md
@@ -128,4 +130,5 @@ case object GN {
128130
[main/scala/flat/RP.scala]: RP.scala.md
129131
[main/scala/flat/lineTypes.scala]: lineTypes.scala.md
130132
[main/scala/flat/RT.scala]: RT.scala.md
131-
[main/scala/seqOps.scala]: ../seqOps.scala.md
133+
[main/scala/seqOps.scala]: ../seqOps.scala.md
134+
[main/scala/fasta/isoforms.scala]: ../fasta/isoforms.scala.md

0 commit comments

Comments
 (0)