Merge pull request #2 from maize-genetics/feature/cleanup

Feature/cleanup

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rPHG
-Version: 0.1.18
+Version: 0.2.0
 Date: 2019-06-03
 Title: R front-end for the practical haplotype graph
 Authors@R: c(
@@ -47,24 +47,19 @@ Description:
     for genomic selection models. This can in turn increase predictive accuracy
     and selection intensity in a breeding program.
 License: Apache License (>= 2) | file LICENSE
-URL: https://bitbucket.org/bucklerlab/rphg/src/master/,
-    https://maize-genetics.github.io/rPHG/
+URL: https://github.com/maize-genetics/rPHG,
+    https://rphg.maizegenetics.net/
 Imports:
     cli,
-    corrplot,
     curl,
-    GenomeInfoDb,
     GenomicRanges,
     ggplot2,
     httr,
     IRanges,
     jsonlite,
-    magrittr,
     methods,
-    parallel,
     rJava,
     rlang,
-    S4Vectors,
     tibble,
     visNetwork
 Depends:

NAMESPACE

@@ -1,83 +1,76 @@
 # Generated by roxygen2: do not edit by hand
 
-export(BrapiCon)
+export(PHGLocalCon)
 export(PHGMethod)
-export(availablePHGMethods)
+export(PHGServerCon)
 export(brapiURL)
-export(getVTList)
-export(graphBuilder)
-export(numHaploPerRange)
-export(pathsForMethod)
+export(brapiVersion)
+export(buildHaplotypeGraph)
+export(calcMutualInfo)
+export(configFilePath)
+export(dbName)
+export(dbType)
+export(host)
+export(httProtocol)
+export(isDemo)
+export(javaMemoryAddress)
+export(javaRefObj)
+export(numHaploPerRefRange)
+export(numberOfChromosomes)
+export(numberOfNodes)
+export(numberOfRefRanges)
+export(numberOfTaxa)
+export(phgConObj)
+export(phgMethodId)
+export(phgMethodType)
+export(phgType)
 export(plotGraph)
 export(plotMutualInfo)
-export(plotNumHaplo)
-export(readMappingTableInfo)
-export(readMappingsForLineName)
-export(readPHGDatasetFromBrapi)
+export(port)
+export(readHaplotypeIds)
+export(readPHGDataSet)
 export(readRefRanges)
 export(readSamples)
-export(readTable)
-export(refRangeTable)
-export(referenceSets)
-export(references)
-export(searchRecombination)
-export(searchSimilarGametes)
 export(serverInfo)
 export(showPHGMethods)
 export(startLogger)
 export(taxaByNode)
-exportClasses(BrapiCon)
-exportClasses(BrapiConPHG)
+exportClasses(HaplotypeGraph)
+exportClasses(PHGCon)
 exportClasses(PHGDataSet)
-exportMethods(availablePHGMethods)
+exportClasses(PHGLocalCon)
+exportClasses(PHGMethod)
+exportClasses(PHGServerCon)
 exportMethods(brapiURL)
-exportMethods(readPHGDatasetFromBrapi)
+exportMethods(brapiVersion)
+exportMethods(calcMutualInfo)
+exportMethods(configFilePath)
+exportMethods(dbName)
+exportMethods(dbType)
+exportMethods(host)
+exportMethods(httProtocol)
+exportMethods(isDemo)
+exportMethods(javaMemoryAddress)
+exportMethods(javaRefObj)
+exportMethods(numHaploPerRefRange)
+exportMethods(numberOfChromosomes)
+exportMethods(numberOfNodes)
+exportMethods(numberOfRefRanges)
+exportMethods(numberOfTaxa)
+exportMethods(phgConObj)
+exportMethods(phgMethodId)
+exportMethods(phgMethodType)
+exportMethods(phgType)
+exportMethods(plotGraph)
+exportMethods(plotMutualInfo)
+exportMethods(port)
+exportMethods(readHaplotypeIds)
+exportMethods(readPHGDataSet)
 exportMethods(readRefRanges)
 exportMethods(readSamples)
-exportMethods(readTable)
-exportMethods(referenceSets)
-exportMethods(references)
 exportMethods(serverInfo)
-import(ggplot2)
-importFrom(GenomeInfoDb,dropSeqlevels)
-importFrom(GenomicRanges,GRanges)
-importFrom(IRanges,IRanges)
-importFrom(IRanges,subsetByOverlaps)
-importFrom(S4Vectors,DataFrame)
-importFrom(S4Vectors,metadata)
-importFrom(SummarizedExperiment,SummarizedExperiment)
-importFrom(SummarizedExperiment,as.data.frame)
-importFrom(SummarizedExperiment,assay)
-importFrom(SummarizedExperiment,assays)
-importFrom(SummarizedExperiment,ranges)
-importFrom(SummarizedExperiment,rowRanges)
-importFrom(SummarizedExperiment,seqnames)
-importFrom(cli,cli_progress_bar)
-importFrom(cli,cli_progress_done)
-importFrom(cli,cli_progress_step)
-importFrom(cli,cli_progress_update)
-importFrom(corrplot,corrplot)
+exportMethods(showPHGMethods)
+exportMethods(taxaByNode)
 importFrom(curl,has_internet)
-importFrom(httr,GET)
-importFrom(httr,content)
-importFrom(jsonlite,fromJSON)
-importFrom(magrittr,"%>%")
-importFrom(methods,new)
 importFrom(methods,setClass)
-importFrom(parallel,mclapply)
-importFrom(rJava,.jcall)
-importFrom(rJava,.jcast)
-importFrom(rJava,.jevalArray)
-importFrom(rJava,.jnew)
-importFrom(rJava,.jnull)
-importFrom(rJava,J)
-importFrom(rJava,is.jnull)
-importFrom(rJava,new)
-importFrom(rlang,.data)
-importFrom(stats,median)
-importFrom(stats,model.matrix)
 importFrom(tibble,as_tibble)
-importFrom(tibble,tibble)
-importFrom(visNetwork,visEdges)
-importFrom(visNetwork,visHierarchicalLayout)
-importFrom(visNetwork,visNetwork)

NEWS

@@ -1,3 +1,28 @@
+## CHANGES IN VERSION 0.2.0
+* Unified workflow for both local and server instances
+* Added new class, `PHGServerCon`
+  + New object for connecting to remote public PHG servers using BrAPI
+    endpoints
+* Added new class, `PHGLocalCon`
+  + New object for connecting to local SQLite or PostgreSQL database
+    instances
+* Added new class, `HaplotypeGraph`
+  + Wrapper for PHG API Java graph object
+* Prior objects now use method dispatch for singular set of methods to return
+  relevant PHG data:
+  + `PHGMethod()`
+  + `showPHGMethods()`
+  + `readSamples()`
+  + `readRefRanges()`
+  + `readHaplotypeIds()`
+  + `readPHGDataSet()`
+* Updated summary methods:
+  + `numHaploPerRefRange()`
+  + `calcMutualInfo()`
+  + `plotGraph()`
+  + `plotMutualInfo()`
+
+
 ## CHANGES IN VERSION 0.1.18
 * Fixed `availablePHGMethods()`:
   + Now returns only method IDs for graphs with more than 100 samples in the

NEWS.md

@@ -1,3 +1,28 @@
+## rPHG 0.2.0
+* Unified workflow for both local and server instances
+* Added new class, `PHGServerCon`
+  + New object for connecting to remote public PHG servers using BrAPI 
+    endpoints
+* Added new class, `PHGLocalCon`
+  + New object for connecting to local SQLite or PostgreSQL database
+    instances
+* Added new class, `HaplotypeGraph`
+  + Wrapper for PHG API Java graph object
+* Prior objects now use method dispatch for singular set of methods to return
+  relevant PHG data:
+  + `PHGMethod()`
+  + `showPHGMethods()`
+  + `readSamples()`
+  + `readRefRanges()`
+  + `readHaplotypeIds()`
+  + `readPHGDataSet()`
+* Updated summary methods:
+  + `numHaploPerRefRange()`
+  + `calcMutualInfo()`
+  + `plotGraph()`
+  + `plotMutualInfo()`
+
+
 ## rPHG 0.1.18
 * Modified `availablePHGMethods()`:
   + Now returns only method IDs for graphs with more than 100 samples in the