Merge branch 'master' into HEAD

* master: (171 commits)
  updating version number for vignette changes
  adding required library
  fixing method definitions
  revised workflow for annotating a MRexperiment
  using demoMgDb instead of greengenes13.5MgDb
  adding usage and value documentation
  remove cyclic dependency with greengenes13.5MgDb, added demoMgDb
  using travis script to install bioconductor packages
  adding environment
  adding appveyor for checking windows build
  adding examples for data documentation files
  adding shortread to import for mgQuery data
  adding ShortRead dependency for mgQuery
  removing import due to import conflicts with combine and %>%
  removing import due to import conflicts with combine and %>%
  excluding regression tests for travis-ci build
  removing greengenes13.5MgDb depdencency for submission
  removing greengenes13.5MgDb depdencency for submission
  uncommented regression tests
  revisions based on BiocCheck run
  ...

Conflicts:
	.Rbuildignore
	.gitignore
	DESCRIPTION
	R/demoMgDb.R
	R/metagenomeAnnotation-class.R
	R/mgDb-class.R
	README.md
	man/annotate-MgDb-method.Rd
	man/get_demoMgDb.Rd
	man/select-MgDb-method.Rd
	vignettes/Example_16S_Annotation_Workflow.Rmd
	vignettes/Exploring_a_MgDb.Rmd

From: nate-d-olson <nolson@nist.gov>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeFeatures@109500 bc3139a8-67e5-0310-9ffc-ced21a209358

.Rbuildignore

@@ -2,3 +2,6 @@
 ^\.Rproj\.user$
 ^packrat/
 ^\.Rprofile$
+^data-raw$
+^\.travis\.yml$
+^appveyor\.yml$

.gitignore

@@ -2,3 +2,5 @@
 .Rhistory
 .RData
 packrat/lib*/
+inst/doc
+scratch.R

.travis.yml

@@ -0,0 +1,41 @@
+# Sample .travis.yml for R projects
+language: c
+
+sudo: required
+before_install:
+  - curl -OL http://raw.github.com/lcolladotor/r-travis/master/scripts/travis-tool.sh
+  - chmod 755 ./travis-tool.sh
+  - ./travis-tool.sh bootstrap
+
+install:
+  - ./travis-tool.sh install_bioc ShortRead
+  - ./travis-tool.sh install_r testthat
+  - ./travis-tool.sh install_r knitr
+  - ./travis-tool.sh install_r rmarkdown
+  - ./travis-tool.sh install_r dplyr
+  - ./travis-tool.sh install_r stringr
+  - ./travis-tool.sh install_r lazyeval
+  - ./travis-tool.sh install_r RSQLite
+  - ./travis-tool.sh install_r magrittr
+  - ./travis-tool.sh install_r covr
+  - ./travis-tool.sh install_bioc_deps
+
+script: ./travis-tool.sh run_tests
+
+on_failure:
+  - ./travis-tool.sh dump_logs
+
+after_script:
+  - ./travis-tool.sh dump_logs_by_extension "timings"
+  - ./travis-tool.sh dump_sysinfo
+
+after_success:
+  - Rscript -e 'covr::codecov()'
+
+env:
+  global:
+    - R_BUILD_ARGS="--no-build-vignettes --no-manual --no-resave-data"
+    - R_CHECK_ARGS=" --no-build-vignettes --no-manual --timings"
+    - R_CHECK_TIME="TRUE"
+    - R_CHECK_TESTS="TRUE"
+    - _R_CHECK_FORCE_SUGGESTS_="FALSE"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metagenomeFeatures
 Title: Exploration of marker-gene sequence taxonomic annotations
-Version: 0.99.3
+Version: 0.99.4
 Author: Nathan D. Olson, Joseph Nathaniel Paulson, Hector Corrada Bravo
 Maintainer: Nathan D. Olson <nolson@umiacs.umd.edu>
 Description: metagenomeFeatures was developed for use in exploring the
@@ -23,4 +23,4 @@ URL: https://github.com/HCBravoLab/metagenomeFeatures
 BugReports: https://github.com/HCBravoLab/metagenomeFeatures/issues
 biocViews: Microbiome, Metagenomics, Annotation, Infrastructure,
         Sequencing, Software
-NeedsCompilation: no
+NeedsCompilation: no

R/demoMgDb.R

@@ -1,7 +1,7 @@
 #' Example MgDb-class object
 #'
 #' Example \link[=MgDb]{MgDb-class} object with 249 entries from the Greengenes 13.5 database.
-#' @return MgDb-class
+#' @return MgDb-class object
 #' @export
 #' @examples
 #'  get_demoMgDb()

R/metagenomeAnnotation-class.R

@@ -100,4 +100,7 @@ setMethod("split_by", "metagenomeAnnotation",
           }
 )
 # mgTree - generates a tree from annotated dataframe
+<<<<<<< HEAD
 
+=======
+>>>>>>> master

R/mgDb-class.R

@@ -43,7 +43,6 @@ MgDb <- setRefClass("MgDb",
                              metadata <<- metadata
                          }))
 
-<<<<<<< HEAD
 ## MgDb Validity ---------------------------------------------------------------
 setValidity("MgDb", function(object) {
     msg <- NULL
@@ -56,26 +55,10 @@ setValidity("MgDb", function(object) {
                      "'taxa' slot must contain a tbl_sqlite object",
                      sep = "\n")
     if(!("metadata" %in% ls(object)) || !is(object$metadata, "list"))
-=======
-### Metadata - Need to change namespace to not export - Not exported.
-# DB_TYPE_NAME <- "Db type"
-# DB_TYPE_VALUE <- "MgDb"  # same as the name of the class
-# DB_SCHEMA_VERSION <- "1.0"
-
-## MgDb Validity ---------------------------------------------------------------
-setValidity("MgDb", function(object) {
-    msg <- NULL
-    if(!("seq" %in% ls(object)) || !is(object@seq, "ShortRead"))
-        msg <- paste(msg, "'seq' slot must contain a ShortRead object with sequence data", sep = "\n")
-    if(!("taxa" %in% ls(object)) || !is(object@taxa, "tbl_sqlite"))
-        msg <- paste(msg, "'taxa' slot must contain a tbl_sqlite object with taxonomy data", sep = "\n")
-    if(!("metadata" %in% ls(object)) || !is(object@metadata, "list"))
->>>>>>> initial commit
         msg <- paste(msg, "'metadata' slot must contain a list", sep = "\n")
     if (is.null(msg)) TRUE else msg
 })
 
-<<<<<<< HEAD
 ################################################################################
 ################################################################################
 ##
@@ -105,26 +88,10 @@ setMethod("show", "MgDb",
             print("Sequence Data:")
             print(object$seq)
             print("Taxonomy Data:")
-=======
-## MgDb Methods ----------------------------------------------------------------
-## General Methods
-setMethod("show", "MgDb",
-          function(object){
-            cat(class(object), "object:\n")
-            print("Metadata\n")
-            metadata <-object$metadata
-                for(i in names(metadata)){
-                    cat("|", i, ": ", metadata[[i]], "\n", sep = "")
-                }
-            print("Sequence Data:\n")
-            print(object$seq)
-            print("Taxonomy Data:\n")
->>>>>>> initial commit
             print(object$taxa)
         }
 )
 
-<<<<<<< HEAD
 ### ============================================================================
 ##
 ##                              MgDb select method
@@ -143,40 +110,6 @@ setMethod("show", "MgDb",
     if(keytype !=  "Keys"){
         level_id <- rep(tolower(stringr::str_sub(string = keytype,
                                              start = 1,end = 1)), length(keys))
-=======
-##
-##
-## Methods to generate metagenomeAnnotation object %%TODO%% modify features to
-## include additional information about metagenomeAnnotation class, specifically
-## filter command and other approriate metadata, e.g. method used for mapping
-MgDb$methods(annotate = function(object, ...){
-                filtered_db <- select(object, type = "both", ...)
-                MgDb$new(taxa = filtered_db[[1]],
-                          seq = filtered_db[[2]],
-                          features = object$metadata)
-            }
-)
-
-## select methods --------------------------------------------------------------
-## use ShortRead Object filters
-.select.seq <- function(x, ...){
-    return
-}
-
-#' Function for querying the marker gene taxonomy database.
-#' @param ids sequence ids to select
-#' @param columns quoted vector of table columns returned, all returned by default
-#' @param sqlite database connection, see src_sqlite in dplyr
-#' @param dbtable database table name, defaults to tree.
-#' @return generates database, function does not return anything
-.select.taxa<- function(keys, keytype,
-                        columns="all"){
-
-    # selecting desired rows
-    if(keytype !=  "Keys"){
-        level_id <- tolower(stringr::str_sub(string = keytype,
-                                             start = 1,end = 1))
->>>>>>> initial commit
         keys <- stringr::str_c(level_id,keys,sep = "__")
     }
     if(length(keys) == 1){
@@ -197,7 +130,6 @@ MgDb$methods(annotate = function(object, ...){
     return(select_tbl %>% dplyr::collect())
 }
 
-<<<<<<< HEAD
 ## either select by ids for taxa information
 .select <- function(mgdb, type, keys, keytype, columns){
     if(!(type %in% c("seq","taxa", "both"))){
@@ -360,7 +292,7 @@ setMethod("select", "MgDb",
 #'   "user provided", use for documenting methods used to perfom the taxonomic
 #'   assignment.
 #' @param ... additional arguments passed to select function
-#' @return metagenomeAnnotation class object
+#' @return metagenomeAnnotation-class object
 #' @note Must include either db_keys or query_df as argument.
 #' @rdname annotate-MgDb-method
 setGeneric("annotate", signature = "mgdb",
@@ -378,49 +310,4 @@ setMethod("annotate", "MgDb",
                    query_seq = NULL, mapping = "user provided ids"){
               .mgDb_annotate(mgdb, db_keys,
                              query_df, query_seq, mapping)}
-=======
-#' select function returns a filtered set of sequences or taxa based on defined
-# input ' use type = "seq" returns a ShortRead object and type = "taxa" returns a
-# filtered database not sure if we want to make the select method only generate a
-MgDb$methods(select = function(object, type, ...){
-              if(!(type %in% c("seq","taxa", "both"))){
-                  stop("type must be either 'seq' or 'taxa'")
-              }
-              if(type == "seq" || type == "both"){
-                  seq_obj <- .select.seq(object$seq, ...)
-                  if(type != "both"){
-                      return(seq_obj)
-                  }
-              }
-              if(type == "taxa"|| type == "both"){
-                  taxa_df <- .select.taxa(object$taxa, ...)
-                  if(type != "both"){
-                      return(taxa_obj)
-                  }
-              }else{
-                  taxa_df <- object$taxa
-              }
-              return(list(taxa_df, seq_df))
-          }
-)
-
-## MgDb Taxa function ----------------------------------------------------------
-
-# Select function revisions
-MgDb$methods(taxa_keys = function(object, keytype){
-                dplyr::select_(object$taxa, keytype) %>% dplyr::collect()
-          }
-)
-
-#' List of database columns.
-MgDb$methods(taxa_columns = function(object){
-        colnames(object$taxa)
-    }
-)
-
-#' Field to potentially use to query database.
-MgDb$methods(taxa_keytypes = function(object){
-        colnames(object$taxa)
-    }
->>>>>>> initial commit
 )

appveyor.yml

@@ -0,0 +1,46 @@
+# DO NOT CHANGE the "init" and "install" sections below
+
+# Download script file from GitHub
+init:
+  ps: |
+        $ErrorActionPreference = "Stop"
+        Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+        Import-Module '..\appveyor-tool.ps1'
+
+install:
+  ps: Bootstrap
+
+# Adapt as necessary starting from here
+
+build_script:
+  - travis-tool.sh install_bioc msd16s Biostrings ShortRead
+  - travis-tool.sh install_deps
+
+test_script:
+  - travis-tool.sh run_tests
+
+on_failure:
+  - travis-tool.sh dump_logs
+
+environment:
+  WARNINGS_ARE_ERRORS: 1
+  _R_CHECK_FORCE_SUGGESTS_: 0
+
+artifacts:
+  - path: '*.Rcheck\**\*.log'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.out'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.fail'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.Rout'
+    name: Logs
+
+  - path: '\*_*.tar.gz'
+    name: Bits
+
+  - path: '\*_*.zip'
+    name: Bits