Add JVM methods

.github/workflows/check-standard.yaml

@@ -31,6 +31,11 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 17
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2

.github/workflows/test-coverage.yaml

@@ -17,6 +17,11 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 17
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: rPHG2
 Title: R interface to PHGv2
-Version: 0.1
+Version: 0.2
 Authors@R:
     person(
         given = "Brandon",
-        family = "Last",
+        family = "Monier",
         email = "bm646@cornell.edu",
         role = c("aut", "cre"),
         comment = c(ORCID = "0000-0001-6797-1221")
@@ -23,12 +23,16 @@ License: Apache License (>= 2) | file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
+Depends: 
+    R (>= 4.1.0)
 Imports:
     cli,
     curl,
+    GenomicRanges,
     httr,
     jsonlite,
     methods,
+    rJava,
     tibble
 Suggests: 
     testthat (>= 3.0.0)

NAMESPACE

@@ -1,23 +1,48 @@
 # Generated by roxygen2: do not edit by hand
 
+export(PHGLocalCon)
 export(PHGServerCon)
 export(brapiURL)
 export(brapiVersion)
+export(buildHaplotypeGraph)
+export(hVcfFiles)
 export(host)
 export(httProtocol)
+export(initPhg)
+export(javaMemoryAddress)
+export(javaRefObj)
+export(numberOfChromosomes)
+export(numberOfRefRanges)
+export(numberOfTaxa)
 export(phgType)
 export(port)
+export(readHapIdMetaData)
+export(readHapIdPosMetaData)
+export(readHapIds)
 export(readRefRanges)
 export(readSamples)
 export(serverInfo)
+exportClasses(HaplotypeGraph)
 exportClasses(PHGCon)
+exportClasses(PHGLocalCon)
 exportClasses(PHGServerCon)
 exportMethods(brapiURL)
 exportMethods(brapiVersion)
+exportMethods(hVcfFiles)
 exportMethods(host)
 exportMethods(httProtocol)
+exportMethods(javaMemoryAddress)
+exportMethods(javaRefObj)
+exportMethods(numberOfChromosomes)
+exportMethods(numberOfRefRanges)
+exportMethods(numberOfTaxa)
 exportMethods(phgType)
 exportMethods(port)
+exportMethods(readHapIdMetaData)
+exportMethods(readHapIdPosMetaData)
+exportMethods(readHapIds)
+exportMethods(readRefRanges)
 exportMethods(readSamples)
 exportMethods(serverInfo)
 importFrom(curl,has_internet)
+importFrom(methods,is)

NEWS

@@ -0,0 +1,22 @@
+## CHANGES IN 0.2
+* Added JVM connections via `rJava` interface
+* Added new class, `HaplotypeGraph`
+  + Wrapper for PHGv2 API Java graph object
+* Added new class, `PHGLocalCon`
+  + Interface to local hVCF database and file connections
+* Added new function `initPHG()`
+  + Initializes JVM and adds PHGv2 Java JARs to classpath
+* Added new function `readHapIds()`
+  + Reads haplotype IDs as a `character` matrix from a connection object
+* Added new function `readHapIdMetaData()`
+  + Reads ALT header metadata for each haplotype ID from a connection object
+* Added new function `readHapIdPosMetaData()`
+  + Reads ALT header positional metadata for each haplotype ID from a
+    connection object
+* Added new function `readSamples()`
+  + Reads sample IDs from a connection object
+* Added new function `readRefRanges()`
+  + Read reference range positional information as a `GRanges` object from a
+    connection object
+
+

NEWS.md

@@ -0,0 +1,22 @@
+## rPHG2 0.2
+* Added JVM connections via `rJava` interface
+* Added new class, `HaplotypeGraph`
+  + Wrapper for PHGv2 API Java graph object
+* Added new class, `PHGLocalCon`
+  + Interface to local hVCF database and file connections
+* Added new function `initPHG()`
+  + Initializes JVM and adds PHGv2 Java JARs to classpath
+* Added new function `readHapIds()`
+  + Reads haplotype IDs as a `character` matrix from a connection object
+* Added new function `readHapIdMetaData()`
+  + Reads ALT header metadata for each haplotype ID from a connection object
+* Added new function `readHapIdPosMetaData()`
+  + Reads ALT header positional metadata for each haplotype ID from a 
+    connection object
+* Added new function `readSamples()`
+  + Reads sample IDs from a connection object
+* Added new function `readRefRanges()`
+  + Read reference range positional information as a `GRanges` object from a
+    connection object
+
+

R/class_all_generics.R

@@ -54,6 +54,90 @@ setGeneric("host", function(object, ...) standardGeneric("host"))
 setGeneric("httProtocol", function(object, ...) standardGeneric("httProtocol"))
 
 
+## ----
+#' @title Return hVCF files
+#'
+#' @description
+#' Returns a list of hVCF files.
+#'
+#' @param object an \code{rPHG} local connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname hVcfFiles
+#' @export
+setGeneric("hVcfFiles", function(object, ...) standardGeneric("hVcfFiles"))
+
+
+## ----
+#' @title Return \code{rJava} reference object
+#'
+#' @description
+#' Returns the \code{rJava} memory reference for a given \code{rPHG} object
+#'
+#' @param object an \code{rPHG} local or server connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname javaMemoryAddress
+#' @export
+setGeneric("javaMemoryAddress", function(object, ...) standardGeneric("javaMemoryAddress"))
+
+
+## ----
+#' @title Return \code{rJava} reference object
+#'
+#' @description
+#' Returns the \code{rJava} memory reference for a given \code{rPHG} object
+#'
+#' @param object an \code{rPHG} local or server connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname javaRefObj
+#' @export
+setGeneric("javaRefObj", function(object, ...) standardGeneric("javaRefObj"))
+
+
+## ----
+#' @title Return number of chromosomes
+#'
+#' @description
+#' Returns the number of chromosomes for a given object
+#'
+#' @param object an \code{rPHG} local or server connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname numberOfChromosomes
+#' @export
+setGeneric("numberOfChromosomes", function(object, ...) standardGeneric("numberOfChromosomes"))
+
+
+## ----
+#' @title Return number of reference ranges
+#'
+#' @description
+#' Returns the number of reference ranges for a given object
+#'
+#' @param object an \code{rPHG} local or server connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname numberOfRefRanges
+#' @export
+setGeneric("numberOfRefRanges", function(object, ...) standardGeneric("numberOfRefRanges"))
+
+
+## ----
+#' @title Return number of taxa
+#'
+#' @description
+#' Returns the number of taxa for a given object
+#'
+#' @param object an \code{rPHG} local or server connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname numberOfTaxa
+#' @export
+setGeneric("numberOfTaxa", function(object, ...) standardGeneric("numberOfTaxa"))
+
+
 ## ----
 #' @title Return type of PHG connection
 #'
@@ -82,11 +166,57 @@ setGeneric("phgType", function(object, ...) standardGeneric("phgType"))
 setGeneric("port", function(object, ...) standardGeneric("port"))
 
 
+## ----
+#' @title Return haplotype IDs
+#'
+#' @description
+#' Gets haplotype ID for given samples and reference ranges from a
+#' \code{HaplotypeGraph}
+#'
+#' @param object an \code{rPHG} local or server connection object
+#' @param nThreads Number of threads to use when evaluating haplotype IDs
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname readHapIds
+#' @export
+setGeneric("readHapIds", function(object, nThreads, ...) standardGeneric("readHapIds"))
+
+
+## ----
+#' @title Return haplotype ID metadata
+#'
+#' @description
+#' Gets haplotype ID metadata for given samples and reference ranges from a
+#' \code{HaplotypeGraph}
+#'
+#' @param object an \code{rPHG} local or server connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname readHapIdMetaData
+#' @export
+setGeneric("readHapIdMetaData", function(object, ...) standardGeneric("readHapIdMetaData"))
+
+
+## ----
+#' @title Return haplotype ID positional metadata
+#'
+#' @description
+#' Gets haplotype ID positional metadata for given samples and reference ranges
+#' from a \code{HaplotypeGraph}
+#'
+#' @param object an \code{rPHG} local or server connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname readHapIdPosMetaData
+#' @export
+setGeneric("readHapIdPosMetaData", function(object, ...) standardGeneric("readHapIdPosMetaData"))
+
+
 ## ----
 #' @title Return reference ranges
 #'
 #' @description
-#' Get reference range data for a given PHG method
+#' Get reference range data from a \code{HaplotypeGraph}
 #'
 #' @param object an \code{rPHG} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
@@ -100,7 +230,7 @@ setGeneric("readRefRanges", function(object, ...) standardGeneric("readRefRanges
 #' @title Return samples IDs
 #'
 #' @description
-#' Gets sample ID data for a given PHG method
+#' Gets sample ID data from a \code{HaplotypeGraph}
 #'
 #' @param object an \code{rPHG} local or server connection object
 #' @param ... Additional arguments, for use in specific methods