scicom 0.2.0-java

data/lib/JRubyR/list.rb

@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+class Renjin
+
+  class List < Renjin::RubySexp
+    include Renjin::Index
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def initialize(sexp)
+      super(sexp)
+      @iterator = @sexp.iterator()
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def names
+      R.names(self)
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def unlist
+      R.unlist(self)
+    end
+
+  end
+  
+end

data/lib/JRubyR/list_orig.rb

@@ -0,0 +1,111 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+class List < Vector
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def length
+    @sexp.length()
+  end
+
+  #----------------------------------------------------------------------------------------
+  # index can be a numeric index or a string index.
+  #----------------------------------------------------------------------------------------
+
+  def get(index)
+    RubySexp.build(@sexp.get(index))
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def [](index)
+    get(index)
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def index_of_name(name)
+    @sexp.indexOfName(name)
+  end
+
+  #----------------------------------------------------------------------------------------
+  # index can be a numeric index or a string index.
+  #----------------------------------------------------------------------------------------
+
+  def get_element_as_double(index)
+    @sexp.getElementAsDouble(index)
+  end
+
+  #----------------------------------------------------------------------------------------
+  # index can be a numeric index or a string index.
+  #----------------------------------------------------------------------------------------
+
+  def get_element_as_int(index)
+    @sexp.getElementAsInt(index)
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def get_element_as_list(name)
+    RubySexp.build(@sexp.getElementAsList(name))
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def get_element_as_vector(name)
+    RubySexp.build(@sexp.getElementAsVector(name))
+  end
+
+  #----------------------------------------------------------------------------------------
+  # Treats ruby style methods in lists as named items on the list
+  #----------------------------------------------------------------------------------------
+
+  def method_missing(symbol, *args)
+
+    name = symbol.id2name
+    name.gsub!(/__/,".")
+    # super if args.length != 0
+    if (args.length == 0)
+      # treat name as a named item of the list
+      ret = R.eval("#{r}[\"#{name}\"]")[0]
+    else
+      raise "Illegal argument for named list item #{name}"
+    end
+
+    ret
+    
+  end
+  
+end
+

data/lib/JRubyR/logical_value.rb

@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+#==========================================================================================
+#
+#==========================================================================================
+
+require 'java'
+
+class Renjin
+
+  class Logical < Renjin::Vector
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def each(&block)
+      while (@iterator.hasNext())
+        block.call((@iterator.next().getInternalValue() == 1)? true : false)
+      end
+    end
+    
+    #----------------------------------------------------------------------------------------
+    # Renjin bug? toString of a LogicalVector in Renjin is returing a LogicalVector and not
+    # a string.  Need to take care of this here.
+    # to_a converts an Enumerable to an array
+    #----------------------------------------------------------------------------------------
+    
+    def to_string
+      to_a.join(",")
+    end
+    
+  end
+  
+end

data/lib/JRubyR/rbsexp.rb

@@ -0,0 +1,386 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require_relative "attributes"
+
+#==========================================================================================
+#
+#==========================================================================================
+
+class Renjin
+
+  module Index
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def [](*index)
+      index = parse(index)
+      R.eval("#{r}[#{index}]")
+    end
+        
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def []=(*index, value)
+      index = parse(index)
+      value = R.parse(value)
+      R.eval("#{r}[#{index}] = #{value}")
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def parse(index)
+
+      params = Array.new
+
+      index.each do |i|
+        if (i.is_a? Array)
+          params << i
+        else
+          params << R.parse(i)
+        end
+      end
+      
+      ps = String.new
+      params.each_with_index do |p, i|
+        ps << "," if i > 0
+        ps << ((p == "NULL")? "" : p.to_s)
+      end
+
+      ps
+
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def method_missing(symbol, *args)
+      
+      name = symbol.id2name
+      name.gsub!(/__/,".")
+      
+      # super if args.length != 0
+      if name =~ /(.*)=$/
+        super if args.length != 1
+        # p "#{r}$#{$1} = #{args[0].r}"
+        # ret = R.eval("#{r}[\"#{name}\"] = #{args[0].r}")
+        ret = R.eval("#{r}$#{$1} = #{args[0].r}")
+      elsif (name == "_")
+        method = "%#{args.shift.to_s}%"
+        arg2 = R.parse(*args)
+        ret = R.eval("#{r} #{method} #{arg2}")
+      elsif (args.length == 0)
+        # treat name as a named item of the list
+        if (R.eval("\"#{name}\" %in% names(#{r})").gt)
+          ret = R.eval("#{r}[[\"#{name}\"]]")
+        else
+          ret = R.eval("#{name}(#{r})") if ret == nil 
+        end
+      elsif (args.length > 0)
+        # p "#{name}(#{r}, #{R.parse(*args)})"
+        ret = R.eval("#{name}(#{r}, #{R.parse(*args)})")
+      else
+        raise "Illegal argument for named list item #{name}"
+      end
+      
+      ret
+      
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def length
+      R.length(R.eval("#{r}")).gz
+    end
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def each(&block)
+      while (@iterator.hasNext())
+        block.call(@iterator.next())
+      end
+    end
+
+  end
+
+  #==========================================================================================
+  #
+  #==========================================================================================
+
+  module RBSexp
+    include_package "org.renjin"
+    include_package "java.lang"
+    
+    attr_reader :sexp
+    attr_reader :rvar
+    attr_reader :attr
+    attr_accessor :scope
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def destroy
+      
+      if (@rvar != nil)
+        @sexp = R.direct_eval("#{@rvar}")
+        # change value in the scope
+        if (@scope)
+          R.direct_eval("#{scope[0]}(#{scope[1].r}, \"#{scope[2]}\") = #{@rvar}")
+          # @scope = nil
+        end
+        R.direct_eval("rm('#{@rvar}')")
+        @rvar = nil
+        
+      end
+      
+    end
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def r
+      
+      if (@rvar == nil)
+        @rvar = "sc_#{SecureRandom.hex(8)}"
+        (@sexp == nil)? R.assign(@rvar, self) : R.assign(@rvar, @sexp)
+        # Whenever a variable is injected in Renjin, it is also added to the Renjin stack.
+        # After eval, every injected variable is removed from Renjin making sure that we
+        # do not have memory leak.
+        Renjin.stack << self
+      end
+      
+      @rvar
+      
+    end
+
+    #----------------------------------------------------------------------------------------
+    # * @return true if this RubySexp already points to a sexp in R environment
+    #----------------------------------------------------------------------------------------
+    
+    def sexp?
+      sexp != nil
+    end
+    
+    #----------------------------------------------------------------------------------------
+    # 
+    #----------------------------------------------------------------------------------------
+    
+    def unbind
+      @scope = nil
+    end
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def typeof
+      R.typeof(R.eval("#{r}"))
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def rclass
+      R.rclass(R.eval("#{r}"))
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def print
+      R.eval("print(#{r})")
+    end
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def pp
+      print
+    end
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def nrow
+      R.nrow(self)
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def ncol
+      R.ncol(self)
+    end
+
+  end
+  
+end
+
+#==========================================================================================
+# Make a Ruby Array into a RBSexp
+#==========================================================================================
+
+class Array
+  include Renjin::RBSexp
+end
+
+#==========================================================================================
+#
+#==========================================================================================
+
+class Renjin
+
+  class RubySexp
+    include Renjin::RBSexp
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def initialize(sexp)
+
+      @sexp = sexp
+      @rvar = nil
+      @attr = Attributes.new(self)
+
+    end
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def to_string
+      R.eval("toString(#{r})")
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def fassign(function, value)
+      R.fassign(self, function, value)
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def self.build(sexp)
+      
+      if (sexp.instance_of? Java::OrgRenjinPrimitivesSequence::IntSequence)
+        res = Renjin::Sequence.new(sexp)
+      elsif (sexp.instance_of? Java::OrgRenjinSexp::Null)
+        res = nil
+      elsif (sexp.instance_of? Java::OrgRenjinSexp::ListVector)
+        res = Renjin::List.new(sexp)
+      elsif (sexp.instance_of? Java::OrgRenjinSexp::LogicalArrayVector)
+        res = Renjin::Logical.new(sexp)
+      elsif (sexp.instance_of? Java::OrgRenjinSexp::Environment)
+        res = Renjin::Environment.new(sexp)
+      elsif (sexp.is_a? Java::OrgRenjinSexp::ComplexVector)
+        res = Renjin::ComplexVector.new(sexp)
+      elsif (sexp.is_a? Java::OrgRenjinSexp::Vector)
+        res = Renjin::Vector.new(sexp)
+      elsif (sexp.is_a? Java::OrgRenjinSexp::Closure)
+        res = Renjin::Closure.new(sexp)
+      # elsif (sexp.is_a? Java::OrgRenjinPrimitives::R$primitive$sum)
+        # res = Renjin::Primitive.new(sexp)
+      else
+        p "sexp type needs to be specialized"
+        p sexp
+        res = Renjin::RubySexp.new(sexp)
+      end
+      
+      return res
+      
+    end
+    
+  end
+
+end
+
+require_relative 'ruby_classes'
+require_relative 'vector'
+require_relative 'sequence'
+require_relative 'list'
+require_relative 'function'
+require_relative 'logical_value'
+require_relative 'environment'
+
+
+=begin    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def set_sexp(sexp)
+      @sexp = sexp
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def method_missing(symbol, *args)
+      
+      name = symbol.id2name
+      name.gsub!(/__/,".")
+      
+      # super if args.length != 0
+      if name =~ /(.*)=$/
+        super if args.length != 1
+        args = R.parse(*args)
+        ret = R.eval("#{r}[[\"#{name}\"]] = #{args}")
+      elsif (args.length == 0)
+        # treat name as a named item of the list
+        ret = R.eval("#{r}[[\"#{name}\"]]")
+      elsif (name == "_")
+        method = "%#{args.shift.to_s}%"
+        arg2 = R.parse(*args)
+        ret = R.eval("#{r} #{method} #{arg2}")
+      else
+        raise "Illegal argument for named list item #{name}"
+      end
+      
+      ret
+      
+    end
+
+=end