bio-incanter 0.1.0

data/lib/bio-incanter.rb

@@ -0,0 +1,108 @@
+require 'java'
+
+jars_dir = File.join(File.dirname(__FILE__), 'java')
+for jar in Dir["#{jars_dir}/*.jar"]
+  require jar
+end
+
+#require for customer class
+require 'pie_chart/pie_chart.rb'
+require 'area_chart/area_chart.rb'
+require 'bar_chart/bar_chart.rb'
+require 'bland_altman/bland_altman.rb'
+require 'box_plot/box_plot.rb'
+require 'function_plot/function_plot.rb'
+require 'histogram/histogram.rb'
+require 'line_chart/line_chart.rb'
+require 'qq_plot/qq_plot.rb'
+require 'scatter_plot/scatter_plot.rb'
+require 'time_chart/time_chart.rb'
+require 'xy_plot/xy_plot.rb'
+require 'trace_plot/trace_plot.rb'
+
+java_import "java.util.HashMap"
+
+
+def check_grp(grp)
+	grp.each{ |item|
+		if item.class!= String 
+			raise "Error : Vector of class must be String"
+		end
+	}
+	return grp
+end
+
+def check_val(value)
+	value.each {|item|
+                if item.class!= Float
+                        raise "Error : Vector of point  must be Double"
+                end     
+        }
+	return value
+end
+
+
+def check_val_int(value)
+        value.each {|item|
+                if item.class!= Fixnum
+                        raise "Error : Vector of point  must be Integer"
+                end     
+        }
+        return value
+end
+
+
+
+=begin
+def check_par(params)
+	hash = Hash.new
+	permitted = ["title","vertical","legend","width","height","file_name"]
+	keys = params.keys
+	keys.each{ |key|
+		 if permitted.include?(key)==false
+			raise "Error : Permitted key are title,vertical,legend,width,height"
+		 end
+	}
+	if params["title"]==nil
+		hash["title"]="A sample Graph"
+	else
+		 hash["title"]=params["title"]
+	end
+
+	if params["vertical"]==nil
+                hash["vertical"]=false
+        else
+                hash["vertical"]=params["vertical"]
+        end
+
+	if params["legend"]==nil
+                hash["legend"]=false
+        else
+                hash["legend"]=params["legend"]
+        end
+
+	if params["width"]==nil
+                hash["width"]=1500
+        else
+                 hash["width"]=params["width"]
+        end
+
+	if params["height"]==nil
+                hash["height"]=800
+        else
+                hash["height"]=params["height"]
+        end
+	
+	if params["file_name"]==nil
+                hash["file_name"]="sample.jpg"
+        else
+                hash["file_name"]=params["file_name"]
+        end
+
+
+	
+	params_map = HashMap.new(hash)
+	return params_map
+	
+end
+=end

data/lib/bland_altman/bland_altman.rb

@@ -0,0 +1,120 @@
+class BlandAltman
+# ==== Attributes  
+    #  
+    # * +x_1+ - a vector of Float numeric value  
+    # * +x_2+ - a vector of Float numeric value   
+    # * +parms+ - an Hash whit parametrs value  
+    #  
+    # ==== Parms  
+    #  
+    # This Hash contain parmas . 
+    # List of key permitted .   
+    # 
+    # 
+    #  
+    # * +:title+ - (default "A sample Graph") Graph main title  
+    # * +:legend+ - (default false) Prints legend   
+    # * +:vertical+ -  (default true) The orientation of the plot   
+    # * +:height+ - (default 1500)  Graph height
+    # * +:width+ -  (default 800)   Graph width
+    # * +:file_name+ - (default sample.jpg) Graph File Name/Path to save plot. You can chose jpg or pdf   
+    #
+    # ==== Examples  
+    #   
+    # Class Usage:  
+    # 
+    #    values_1= [6.0,2.0,8.4]
+    #    values_2 = [1.0,2.0,3.0]
+    #    params = {"title" => "My_PLot"}
+    #    plot = BlandAltman.new(values_1,values_2,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+    #    plot.save
+
+	def initialize(x_1,x_2,params)
+		@group=check_val(x_1)
+		@value=check_val(x_2)
+		@params=self.check_par(params)
+	end
+
+	def check_par(params)
+        	hash = Hash.new
+		permitted = ["title","vertical","legend","width","height","file_name"]
+        	keys = params.keys
+        	keys.each{ |key|
+                	 if permitted.include?(key)==false
+                        	raise "Error : Permitted key are title,vertical,legend,width,height"
+                 	end
+        	}
+		
+		if params["title"]==nil
+                	hash["title"]="A sample Graph"
+        	else
+                	 hash["title"]=params["title"]
+        	end
+
+		if params["vertical"]==nil
+                	hash["vertical"]=false
+       		else
+                	hash["vertical"]=params["vertical"]
+        	end
+
+	 	if params["legend"]==nil
+        	        hash["legend"]=false
+      		else
+                	hash["legend"]=params["legend"]
+        	end
+
+		if params["width"]==nil
+                	hash["width"]=1500
+        	else
+                	hash["width"]=params["width"]
+        	end
+
+		if params["height"]==nil
+                	hash["height"]=800
+        	else
+                	hash["height"]=params["height"]
+        	end
+
+        	if params["file_name"]==nil
+                	hash["file_name"]="sample.jpg"
+        	else
+                	hash["file_name"]=params["file_name"]
+       		end
+
+		params_map = HashMap.new(hash)
+        	return params_map
+	end
+
+	def getGroup
+		@group
+	end
+
+	def getValue
+		@value 
+	end
+
+	 def getParams
+                @params
+        end
+
+
+	def save
+		begin
+        		a = Java::ComDomain::clocomics
+       			a.save_altman(self.getGroup,self.getValue,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_altman(self.getGroup,self.getValue,self.getParams)
+                rescue Exception => ex
+                end
+	end
+
+
+end

data/lib/box_plot/box_plot.rb

@@ -0,0 +1,136 @@
+class BoxPlot
+# ==== Attributes  
+    #  
+    # * +value+ - a vector of Float numeric value   
+    # * +parms+ - an Hash whit parametrs value  
+    #  
+    # ==== Parms  
+    #  
+    # This Hash contain parmas . 
+    # List of key permitted .   
+    # 
+    # 
+    # * +:title+ - (default "A sample Graph") Graph main title  
+    # * +:x_label+ - (default 'Categories') Label of x ass   
+    # * +:y_label+ -  (default 'Value') Label of y ass
+    # * +:legend+ - (default false) Prints legend   
+    # * +:vertical+ -  (default true) The orientation of the plot   
+    # * +:group_by+ -  (default nil) A vector of values used to group the values into series within each category. 
+    # * +:height+ - (default 1500)  Graph height
+    # * +:width+ -  (default 800)   Graph width
+    # * +:file_name+ - (default sample.jpg) Graph File Name/Path to save plot. You can chose jpg or pdf   
+    #
+    # ==== Examples  
+    #   
+    # Class Usage:  
+    # 
+    #    values = [1.0,2.0,3.0]
+    #    params = {"title" => "Popolation of middle heart","x_label"=>"Popolation","y_label"=>"greed"}
+    #    plot = BoxPlot.new(categories,values,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+    #    plot.save
+
+
+	def initialize(value,params)
+		@value=check_val(value)
+		@params=self.check_par(params)
+	end
+
+	def check_par(params)
+        	hash = Hash.new
+		permitted = ["title","x_label","y_label","vertical","group_by","legend","width","height","file_name"]
+        	keys = params.keys
+        	keys.each{ |key|
+                	 if permitted.include?(key)==false
+                        	raise "Error : Permitted key are title,x_label,y_label,vertical,group_by,legend,width,height"
+                 	end
+        	}
+		
+		if params["title"]==nil
+                	hash["title"]="A sample Graph"
+        	else
+                	 hash["title"]=params["title"]
+        	end
+
+		if params["x_label"]==nil
+                        hash["x_label"]="Categories"
+                else
+                         hash["x_label"]=params["x_label"]
+                end
+
+		if params["y_label"]==nil
+                        hash["y_label"]="Values"
+                else
+                        hash["y_label"]=params["y_label"]
+                end
+
+		if params["vertical"]==nil
+                	hash["vertical"]=true
+       		else
+                	hash["vertical"]=params["vertical"]
+        	end
+
+	 	if params["legend"]==nil
+        	        hash["legend"]=false
+      		else
+                	hash["legend"]=params["legend"]
+        	end
+		
+		if params["gruop_by"]==nil
+                        hash["group_by"]=nil
+                else
+                        hash["group_by"]=params["group_by"]
+                end
+
+		if params["width"]==nil
+                	hash["width"]=1500
+        	else
+                	hash["width"]=params["width"]
+        	end
+
+		if params["height"]==nil
+                	hash["height"]=800
+        	else
+                	hash["height"]=params["height"]
+        	end
+
+        	if params["file_name"]==nil
+                	hash["file_name"]="sample.jpg"
+        	else
+                	hash["file_name"]=params["file_name"]
+       		end
+
+		params_map = HashMap.new(hash)
+        	return params_map
+	end
+
+
+	def getValue
+		@value 
+	end
+
+	 def getParams
+                @params
+        end
+
+
+	def save
+		begin
+        		a = Java::ComDomain::clocomics
+       			a.save_box(self.getValue,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_box(self.getValue,self.getParams)
+                rescue Exception => ex
+                end
+
+
+	end
+
+end

data/lib/function_plot/function_plot.rb

@@ -0,0 +1,137 @@
+class FunctionPlot
+# ==== Attributes  
+    #  
+    # * +function+ - a String function in Clojure Style
+    # * +min+ - Lower Bound   
+    # * +max+ - Upper Bound
+    # * +parms+ - an Hash whit parametrs value  
+    #  
+    # ==== Parms  
+    #  
+    # This Hash contain parmas . 
+    # List of key permitted .   
+    # 
+    # 
+    #  
+    # * +:title+ - (default "A sample Graph") Graph main title  
+    # * +:x_label+ - (default 'Categories') Label of x ass   
+    # * +:y_label+ -  (default 'Value') Label of y ass
+    # * +:legend+ - (default false) Prints legend   
+    # * +:height+ - (default 1500)  Graph height
+    # * +:width+ -  (default 800)   Graph width
+    # * +:file_name+ - (default sample.jpg) Graph File Name/Path to save plot. You can chose jpg or pdf   
+    #
+    # ==== Examples  
+    #   
+    # Class Usage:  
+    #
+    #    function = "(defn cubic [x] (+ (* x x x) (* 2 x x) (* 2 x) 3))" 
+    #    min = 0
+    #    max = 50
+    #    params = {"title" => "Plot my Function"}
+    #    plot = FunctionPlot.new(function,min,max,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+    #    plot.save
+ 
+	def initialize(function,min,max,params)
+		@params=self.check_par(params)
+		@function=function
+		@min=min
+		@max=max
+	end
+
+	def check_par(params)
+        	hash = Hash.new
+		permitted = ["title","x_label","y_label","legend","width","height","file_name"]
+        	keys = params.keys
+        	keys.each{ |key|
+                	 if permitted.include?(key)==false
+                        	raise "Error : Permitted key are title,x_label,y_label,legend,width,height,file_name"
+                 	end
+        	}
+		
+		if params["title"]==nil
+                	hash["title"]="A sample Graph"
+        	else
+                	 hash["title"]=params["title"]
+        	end
+
+		if params["x_label"]==nil
+                        hash["x_label"]="Categories"
+                else
+                         hash["x_label"]=params["x_label"]
+                end
+
+		if params["y_label"]==nil
+                        hash["y_label"]="Values"
+                else
+                        hash["y_label"]=params["y_label"]
+                end
+
+
+	 	if params["legend"]==nil
+        	        hash["legend"]=false
+      		else
+                	hash["legend"]=params["legend"]
+        	end
+		
+
+		if params["width"]==nil
+                	hash["width"]=1500
+        	else
+                	hash["width"]=params["width"]
+        	end
+
+		if params["height"]==nil
+                	hash["height"]=800
+        	else
+                	hash["height"]=params["height"]
+        	end
+
+        	if params["file_name"]==nil
+                	hash["file_name"]="sample.jpg"
+        	else
+                	hash["file_name"]=params["file_name"]
+       		end
+
+		params_map = HashMap.new(hash)
+        	return params_map
+	end
+
+	def getFunction
+		@function
+	end
+
+	def getMin
+		@min 
+	end
+
+	def getMax
+		@max
+	end
+	
+	def getParams
+                @params
+        end
+
+
+	def save
+		begin
+        		a = Java::ComDomain::clocomics
+       			a.save_function(self.getFunction,self.getMin,self.getMax,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_function(self.getFunction,self.getMin,self.getMax,self.getParams)
+                rescue Exception => ex
+                end
+
+
+	end
+
+end