Version 1.3.3

Introduce and integrate new calcRules Fix Bug in findAdducts - annoID "parent" column has now the correct entries Intial support for ruleSet class Add Biobase dependency Add ruleSet manpage Signed-off-by: Carsten Kuhl <[email protected]> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CAMERA@66231 bc3139a8-67e5-0310-9ffc-ced21a209358
sneumann · May 29, 2012 · 6dad75c · 6dad75c
1 parent e18a552
commit 6dad75c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: CAMERA
-Version: 1.13.2
-Date: 2012-05-25
+Version: 1.13.3
+Date: 2012-05-29
 Title: Collection of annotation related methods for mass spectrometry data 
 Author: Carsten Kuhl, Ralf Tautenhahn, Steffen Neumann {ckuhl|sneumann}@ipb-halle.de, [email protected]
 Maintainer: Carsten Kuhl <[email protected]>
-Depends: R (>= 2.1.0), methods, xcms (>= 1.13.5)
+Depends: R (>= 2.1.0), methods, xcms (>= 1.13.5), Biobase
 Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph
 Suggests: faahKO, RUnit
 Enhances: Rmpi, snow

diff --git a/NAMESPACE b/NAMESPACE
@@ -12,6 +12,9 @@ importFrom("stats", "cor.test")
 importFrom("utils", "flush.console", "object.size", "read.table")
 importFrom("igraph","graph.data.frame","label.propagation.community")
 
+importClassesFrom(Biobase, "Versioned")
+importFrom(Biobase, validMsg)
+
 export("annotate","xsAnnotate","getpspectra","annotateDiffreport","getIsotopeCluster","findNeutralLossSpecs","findNeutralLoss","cleanParallel","combinexsAnnos")
 exportClasses("xsAnnotate")
 exportMethods("groupFWHM")
@@ -29,3 +32,10 @@ exportMethods("calcPC",
 exportMethods("calcCiS",
 	      "calcCaS",
 	      "calcIsotopes")
+
+exportClasses("ruleSet")
+exportMethods("setDefaultLists",
+              "readLists",
+              "setDefaultParams",
+              "setParams",
+              "generateRules")
diff --git a/R/00xsAnnotate.R b/R/00xsAnnotate.R
@@ -15,6 +15,7 @@ setClass("xsAnnotate",
                     isoID="matrix",
                     polarity="character",
                     runParallel="list"),
+         contains=c("Versioned"),
     prototype(
                     groupInfo= matrix(ncol=0,nrow=0),
                     pspectra = list(),
@@ -25,9 +26,10 @@ setClass("xsAnnotate",
                     sample=NULL,
                     xcmsSet=NULL,
                     ruleset=NULL,
-                    annoID=matrix(ncol=3,nrow=0),
-                    annoGrp=matrix(ncol=4,nrow=0),
-                    isoID=matrix(ncol=4,nrow=0),
+                    annoID=matrix(ncol=4, nrow=0),
+                    annoGrp=matrix(ncol=4, nrow=0),
+                    isoID=matrix(ncol=4, nrow=0),
                     polarity="",
-                    runParallel=NULL)
+                    runParallel=NULL,
+                    new("Versioned", versions=c(CAMERA="1.13.333")))
             );