1. gmapR
  2. R
  3. GmapParam-class.R
Browse code

allow omitting gmap arg suboptimal_score, and make that the default

Michael Lawrence authored on 29/08/2017 22:10:50
Showing 1 changed files
R/GmapParam-class.R
History View file @ faf50b5
... ... 
@@ -7,6 +7,8 @@
7 7
8 8 
 setClassUnion("GmapSnps_OR_NULL", c("GmapSnps", "NULL"))
9 9
10 
+setClassUnion("integer_OR_NULL", c("integer", "NULL"))
11 
+
10 12 
 setClass("GmapAlignerParam",
11 13 
          representation(genome = "GmapGenome",
12 14 
                         part = "character_OR_NULL",
Browse code

allow omitting gmap arg suboptimal_score, and make that the default

Michael Lawrence authored on 29/08/2017 22:10:50
Showing 1 changed files
R/GmapParam-class.R
History View file @ 4bc5367
... ... 
@@ -21,7 +21,7 @@ setClass("GmapAlignerParam",
21 21 
                         extra = "list"))
22 22
23 23 
 setClass("GmapParam",
24 
-         representation(suboptimal_score = "integer",
24 
+         representation(suboptimal_score = "integer_OR_NULL",
25 25 
                         splicing = "logical",
26 26 
                         format = "character"),
27 27 
          contains="GmapAlignerParam")
... ... 
@@ -31,7 +31,7 @@ setClass("GmapParam",
31 31 
 ###
32 32
33 33 
 GmapParam <- function(genome, unique_only = FALSE,
34 
-                      suboptimal_score = 0L, mode = "standard",
34 
+                      suboptimal_score = NULL, mode = "standard",
35 35 
                       snps = NULL,
36 36 
                       npaths = if (unique_only) 1L else 100L,
37 37 
                       quiet_if_excessive = unique_only, nofails = unique_only,
Browse code

follow renaming of union classes in S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@126394 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 01/02/2017 13:23:02
Showing 1 changed files
R/GmapParam-class.R
History View file @ e1b17d3
... ... 
@@ -5,13 +5,13 @@
5 5 
 ### High-level interface to gmap.
6 6 
 ###
7 7
8 
-setClassUnion("GmapSnpsORNULL", c("GmapSnps", "NULL"))
8 
+setClassUnion("GmapSnps_OR_NULL", c("GmapSnps", "NULL"))
9 9
10 10 
 setClass("GmapAlignerParam",
11 11 
          representation(genome = "GmapGenome",
12 
-                        part = "characterORNULL",
12 
+                        part = "character_OR_NULL",
13 13 
                         batch = "character",
14 
-                        snps = "GmapSnpsORNULL",
14 
+                        snps = "GmapSnps_OR_NULL",
15 15 
                         mode = "character",
16 16 
                         nthreads = "integer",
17 17 
                         npaths = "integer",
Browse code

add ability to call GMAP

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110840 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 23/11/2015 23:25:34
Showing 1 changed files
R/GmapParam-class.R
History View file @ ead94b3
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,60 @@
1 
+### =========================================================================
2 
+### GmapParam class
3 
+### -------------------------------------------------------------------------
4 
+###
5 
+### High-level interface to gmap.
6 
+###
7 
+
8 
+setClassUnion("GmapSnpsORNULL", c("GmapSnps", "NULL"))
9 
+
10 
+setClass("GmapAlignerParam",
11 
+         representation(genome = "GmapGenome",
12 
+                        part = "characterORNULL",
13 
+                        batch = "character",
14 
+                        snps = "GmapSnpsORNULL",
15 
+                        mode = "character",
16 
+                        nthreads = "integer",
17 
+                        npaths = "integer",
18 
+                        quiet_if_excessive = "logical",
19 
+                        nofails = "logical",
20 
+                        split_output = "logical",
21 
+                        extra = "list"))
22 
+
23 
+setClass("GmapParam",
24 
+         representation(suboptimal_score = "integer",
25 
+                        splicing = "logical",
26 
+                        format = "character"),
27 
+         contains="GmapAlignerParam")
28 
+
29 
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
30 
+### Constructor
31 
+###
32 
+
33 
+GmapParam <- function(genome, unique_only = FALSE,
34 
+                      suboptimal_score = 0L, mode = "standard",
35 
+                      snps = NULL,
36 
+                      npaths = if (unique_only) 1L else 100L,
37 
+                      quiet_if_excessive = unique_only, nofails = unique_only,
38 
+                      split_output = !unique_only,
39 
+                      splicing = TRUE,
40 
+                      nthreads = 1L, part = NULL, batch = "2",
41 
+                      format = c("gff3_gene", "gff3_match_cdna",
42 
+                          "gff3_match_est", "sampe", "samse", "psl",
43 
+                          "splicesites", "introns",
44 
+                          "map_exons", "map_ranges", "coords"),
45 
+                      ...)
46 
+{
47 
+    format <- match.arg(format)
48 
+    newGmapAlignerParam("GmapParam", genome, snps)
49 
+}
50 
+
51 
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
52 
+### Coercion
53 
+###
54 
+
55 
+setAs("GmapParam", "list", function(from) {
56 
+          to <- GmapAlignerParam_asList(from)
57 
+          to$nosplicing <- !to$splicing
58 
+          to$splicing <- NULL
59 
+          to
60 
+      })