bio-incanter 0.1.0

data/lib/scatter_plot/scatter_plot.rb

@@ -0,0 +1,162 @@
+class ScatterPlot
+# ==== Attributes  
+    #  
+    # * +valuex+ - a vector of Float numeric value
+    # * +valuey+ - 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. 
+    # * +:density+ - (default false) Chart will represent density instead of frequency 
+    # * +:nbins+ - (default 10) Number of bins
+    # * +:gradient+ - (default false) Use gradient on bars
+    # * +:height+ - (default 1500)  Chart height
+    # * +:width+ -  (default 800)   Chart width
+    # * +:file_name+ - (default sample.jpg) Chart File Name/Path to save plot. You can chose jpg or pdf   
+    #
+    # ==== Examples  
+    #   
+    # Class Usage:  
+    # 
+    #    valuesx = [1.0,2.0,3.0]
+    #    valuesy = [1.0,2.0,3.0]
+    #    params = {}
+    #    plot = ScatterPlot.new(valuesx,valuesy,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+    #    plot.save
+
+
+	def initialize(valuex,valuey,params)
+		@value_x=check_val(valuex)
+		@value_y=check_val(valuey)
+		@params=self.check_par(params)
+	end
+
+	def check_par(params)
+        	hash = Hash.new
+		permitted = ["title","x_label","y_label","vertical","n_bins","density","gruop_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,n_bins,density,group_by,gardient,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["group_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 getValuex
+		@value_x 
+	end
+
+	 def getValuey
+                @value_y
+        end
+	
+
+	 def getParams
+                @params
+        end
+
+
+	def save
+		begin
+        		a = Java::ComDomain::clocomics
+       			a.save_scatter(self.getValuex,self.getValuey,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_scatter(self.getValuex,self.getValuey,self.getParams)
+                rescue Exception => ex
+                end
+	end
+
+end

data/lib/time_chart/time_chart.rb

@@ -0,0 +1,142 @@
+class TimeChart
+# ==== Attributes  
+    #  
+    # * +x+ - a vector of Int Sequence passed in for the x axis should be number of milliseconds from the epoch (1 Janurary 1970).
+    # * +y+ - 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:  
+    # 
+    #    time = [1200,23330]
+    #    values = [1.0,2.0]
+    #    params = {"title" => "Time Go On"}
+    #    plot = TimeChart.new(time,values,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+    #    plot.save
+
+	def initialize(x,y,params)
+		@y=check_val(y)
+		@x=check_val_int(x)
+		@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 getX
+		@x
+	end
+
+	def getY
+		@y
+	end
+
+	 def getParams
+                @params
+        end
+
+
+	def save
+		begin
+        		a = Java::ComDomain::clocomics
+       			a.save_time(self.getX,self.getY,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_time(self.getX,self.getY,self.getParams)
+                rescue Exception => ex
+                end
+
+
+	end
+
+end

data/lib/trace_plot/trace_plot.rb

@@ -0,0 +1,108 @@
+class TracePlot
+# ==== 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 = {}
+    #    plot = TracePlot.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","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_trace(self.getValue,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_trace(self.getValue,self.getParams)
+                rescue Exception => ex
+                end
+
+
+	end
+
+end

data/lib/xy_plot/xy_plot.rb

@@ -0,0 +1,149 @@
+class XyPlot
+# ==== Attributes  
+    #  
+    # * +valuex+ - a vector of Float numeric value   
+    # * +valuey+ - 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.
+    # * +:points+ - (default false) includes point-markers
+    # * +: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:  
+    # 
+    #    x = [1.0,2.0,3.0]
+    #    y = [1.0,2.0,3.0]
+    #    params = {"title" => "XY Plot","points"=>"true"}
+    #    plot = XyPlot.new(x,y,params)
+    #    #To view
+    #    plot.view 
+    #    #to save
+    #    plot.save
+
+
+	def initialize(valuex,valuey,params)
+		@value_x=check_val(valuex)
+		@value_y=check_val(valuey)
+		@params=self.check_par(params)
+	end
+
+	def check_par(params)
+        	hash = Hash.new
+		permitted = ["title","x_label","y_label","vertical","points","gruop_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,n_bins,density,group_by,gardient,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["points"]==nil
+                        hash["points"]=false
+                else
+                        hash["points"]=params["points"]
+                end
+		
+		if params["group_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 getValuex
+		@value_x 
+	end
+
+	 def getValuey
+                @value_y
+        end
+	
+
+	 def getParams
+                @params
+        end
+
+
+	def save
+		begin
+        		a = Java::ComDomain::clocomics
+       			a.save_xy(self.getValuex,self.getValuey,self.getParams)
+		rescue Exception => ex
+		end
+	end
+	def view
+		 begin
+                        a = Java::ComDomain::clocomics
+                        a.view_xy(self.getValuex,self.getValuey,self.getParams)
+                rescue Exception => ex
+                end
+	end
+
+end