bio-incanter 0.1.0

data/lib/histogram/histogram.rb

@@ -0,0 +1,139 @@
+class Histogram
+# ==== 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   
+    # * +:n_bins+ -  (default 10)   number of bins 
+    # * +: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 = {}
+    #    plot = BarChart.new(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","n_bins","density","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,n_bins,density,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["n_bins"]==nil
+                        hash["n_bins"]=10
+                else
+                        hash["n_bins"]=params["n_bins"]
+                end
+		
+		if params["density"]==nil
+                        hash["density"]=false
+                else
+                        hash["density"]=params["density"]
+                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_histo(self.getValue,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_histo(self.getValue,self.getParams)
+                rescue Exception => ex
+                end
+	end
+
+end

data/lib/line_chart/line_chart.rb

@@ -0,0 +1,148 @@
+class LineChart
+# ==== Attributes  
+    #  
+    # * +group+ - a vector of String categories  
+    # * +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. 
+    # * +:gradient + - (default false)  Use gradient on bars
+    # * +: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:  
+    # 
+    #    categories = ["uman","elf","dwarfs"]
+    #    values = [1.0,2.0,3.0]
+    #    params = {"title" => "Popolation of middle heart","x_label"=>"Popolation","y_label"=>"greed"}
+    #    plot = LineChart.new(categories,values,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+    #    plot.save
+	def initialize(group,value,params)
+		@group=check_grp(group)
+		@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","gradient","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,gradient,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["gradient"]==nil
+                        hash["gradient"]=false
+                else
+                        hash["gradient"]=params["gradient"]
+                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_area(self.getGroup,self.getValue,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_area(self.getGroup,self.getValue,self.getParams)
+                rescue Exception => ex
+                end
+
+
+	end
+
+end

data/lib/pie_chart/pie_chart.rb

@@ -0,0 +1,121 @@
+class PieChart
+# ==== Attributes  
+    #  
+    # * +group+ - a vector of String categories  
+    # * +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  
+    # * +: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:  
+    # 
+    #    categories = ["uman","elf","dwarfs"]
+    #    values = [1.0,2.0,3.0]
+    #    params = {"title" => "Popolation of middle heart","x_label"=>"Popolation","y_label"=>"greed"}
+    #    plot = PieChart.new(categories,values,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+    #    plot.save
+
+	def initialize(group,value,params)
+		@group=check_grp(group)
+		@value=check_val(value)
+		@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_pie(self.getGroup,self.getValue,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_pie(self.getGroup,self.getValue,self.getParams)
+                rescue Exception => ex
+                end
+
+
+	end
+
+end

data/lib/qq_plot/qq_plot.rb

@@ -0,0 +1,105 @@
+class QqPlot
+# ==== 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  
+    # * +: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 = [1.0,2.0,3.0]
+    #    params = {"title" => "A QQ Plot"}
+    #    plot = QqPlot.new(values,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+
+	def initialize(value,params)
+		@value=check_val(value)
+		@params=self.check_par(params)
+	end
+
+	def check_par(params)
+        	hash = Hash.new
+		permitted = ["title","vertical","width","height","file_name"]
+        	keys = params.keys
+        	keys.each{ |key|
+                	 if permitted.include?(key)==false
+                        	raise "Error : Permitted key are title,vertical,width,height,file-name"
+                 	end
+        	}
+		
+		if params["title"]==nil
+                	hash["title"]="A sample Graph"
+        	else
+                	 hash["title"]=params["title"]
+        	end
+
+		if params["vertical"]==nil
+                	hash["vertical"]=true
+       		else
+                	hash["vertical"]=params["vertical"]
+        	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_qq(self.getValue,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_qq(self.getValue,self.getParams)
+                rescue Exception => ex
+                end
+
+
+	end
+
+end