seqtrimnext 2.0.29

data/lib/seqtrimnext/actions/action_indetermination.rb

@@ -0,0 +1,30 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionIndetermination < SeqtrimAction
+      
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)
+     @cut =true     
+   end
+
+  # def apply_to(seq)
+  #  
+  #    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+  #    $LOG.debug " Applying #{self.class} to seq #{seq.seq_name} . BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+  #  
+  #  end    
+
+def apply_decoration(char) 
+  return char.on_red
+  
+end       
+
+
+end

data/lib/seqtrimnext/actions/action_induced_low_complexity.rb

@@ -0,0 +1,29 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionInducedLowComplexity < SeqtrimAction
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)
+    @cut =true
+  end
+
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class} " 
+#   
+# end  
+
+
+def apply_decoration(char)
+  return char.red.bold
+end  
+
+
+end

data/lib/seqtrimnext/actions/action_insert.rb

@@ -0,0 +1,32 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute ActionInserted                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionInsert < SeqtrimAction
+       
+  def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =false
+     @informative = true
+  end
+
+# #this method is launched when the size of inserted is enough   
+# def apply_to(seq)
+#    
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class}. ------Inserted has enough size ------ . BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+#  
+#   
+# end 
+
+def apply_decoration(char)
+  return char
+end      
+   
+
+end

data/lib/seqtrimnext/actions/action_is_contaminated.rb

@@ -0,0 +1,30 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionIsContaminated < SeqtrimAction
+      
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+   end
+
+  # def apply_to(seq)
+  #  
+  #    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+  #    $LOG.debug " Applying #{self.class} to seq #{seq.seq_name} . BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+  #  
+  #  end    
+
+def apply_decoration(char)
+  return char.red
+  
+end       
+
+
+end

data/lib/seqtrimnext/actions/action_key.rb

@@ -0,0 +1,30 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionKey < SeqtrimAction
+      
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true 
+   end
+
+  # def apply_to(seq)
+  #  
+  #    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+  #    $LOG.debug " Applying #{self.class} to seq #{seq.seq_name} . BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+  #  
+  #  end    
+
+def apply_decoration(char) 
+  return char.on_yellow
+  
+end       
+
+
+end

data/lib/seqtrimnext/actions/action_left_adapter.rb

@@ -0,0 +1,32 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionLeftAdapter < SeqtrimAction
+      
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+
+   end
+#    
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class} . BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+#   
+# end   
+
+def apply_decoration(char) 
+  return char.magenta
+  
+  #  return char.magenta.negative
+end  
+
+
+end

data/lib/seqtrimnext/actions/action_left_primer.rb

@@ -0,0 +1,17 @@
+require "seqtrim_action"
+
+
+class ActionLeftPrimer < SeqtrimAction
+
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)
+    @cut =true
+
+  end
+
+  def apply_decoration(char)
+    return char.blue.underline
+  end
+
+
+end

data/lib/seqtrimnext/actions/action_linker.rb

@@ -0,0 +1,30 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionLinker < SeqtrimAction
+      
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =false
+   end
+
+  # def apply_to(seq)
+  #  
+  #    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+  #    $LOG.debug " Applying #{self.class} to seq #{seq.seq_name} . BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+  #  
+  #  end    
+
+def apply_decoration(char)
+  return char.underline
+  
+end       
+
+
+end

data/lib/seqtrimnext/actions/action_low_complexity.rb

@@ -0,0 +1,30 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionLowComplexity < SeqtrimAction
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)
+    @cut = false
+    @informative = true
+  end
+
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class} " 
+#   
+# end  
+
+
+def apply_decoration(char)
+  return char.red.bold
+end  
+
+
+end

data/lib/seqtrimnext/actions/action_low_high_size.rb

@@ -0,0 +1,31 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute PluginActionLowHighSize                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionLowHighSize < SeqtrimAction   
+  
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)    
+    @cut =false
+
+  end
+   
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class}  to #{seq.seq_name}. This sequence will be ignored due to low or high size " 
+#    #delete sequence if it was created
+#    
+#   
+# end  
+
+def apply_decoration(char)
+  return char.on_magenta
+end         
+
+end

data/lib/seqtrimnext/actions/action_low_quality.rb

@@ -0,0 +1,33 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute PluginActionLowHighSize                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionLowQuality < SeqtrimAction    
+  
+  def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =false
+
+   end
+   
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class}  to #{seq.seq_name} . This sequence will be ignored due to low quality " 
+#    #delete sequence if it was created
+#    
+#   
+# end   
+
+
+  def apply_decoration(char)
+    return char.downcase.on_white
+  end 
+
+
+end

data/lib/seqtrimnext/actions/action_mid.rb

@@ -0,0 +1,30 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionMid < SeqtrimAction
+      
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+   end
+
+  # def apply_to(seq)
+  #  
+  #    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+  #    $LOG.debug " Applying #{self.class} to seq #{seq.seq_name} . BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+  #  
+  #  end    
+
+def apply_decoration(char)
+  return char.yellow.bold
+  
+end       
+
+
+end

data/lib/seqtrimnext/actions/action_multiple_linker.rb

@@ -0,0 +1,29 @@
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+########################################################
+
+require "seqtrim_action"
+
+
+class ActionMultipleLinker < SeqtrimAction
+      
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+   end
+
+  # def apply_to(seq)
+  #  
+  #    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+  #    $LOG.debug " Applying #{self.class} to seq #{seq.seq_name} . BEGIN: #{@start_pos}   END: #{@end_pos}  "
+  #  
+  #  end    
+
+def apply_decoration(char)
+  return char.underline
+  
+end       
+
+
+end

data/lib/seqtrimnext/actions/action_paired_reads.rb

@@ -0,0 +1,28 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute PluginPairedReads                                                     
+# Inherit: Plugin
+########################################################
+class ActionPairedReads < SeqtrimAction    
+  def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+
+   end
+ 
+  
+   def apply_to(seq)
+     $LOG.debug "Applying #{self.class}"
+     
+     #Storage the first and second subsequences
+     subseq1 = seq.seq_fasta[0,@start_pos-1]        
+     subseq2 = seq.seq_fasta[@end_pos+1,seq.seq_fasta.length-1]
+     #$LOG.debug "\nSubsequence left: #{subseq1} \n Subsequence right: #{subseq2}}"
+
+   end
+  
+  
+end

data/lib/seqtrimnext/actions/action_poly_a.rb

@@ -0,0 +1,29 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionPolyA < SeqtrimAction
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)    
+    @cut =true
+  end
+  
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class} " 
+#       
+# end  
+
+
+def apply_decoration(char)
+  return char.bold
+end
+
+
+end

data/lib/seqtrimnext/actions/action_poly_t.rb

@@ -0,0 +1,29 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionPolyT < SeqtrimAction
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)    
+    @cut =true
+  end
+
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class} " 
+#   
+# end  
+
+
+def apply_decoration(char)
+  return char.bold
+end  
+
+
+end

data/lib/seqtrimnext/actions/action_rem_adit_artifacts.rb

@@ -0,0 +1,32 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute PluginActionLowHighSize                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionRemAditArtifacts < SeqtrimAction      
+  
+  def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+
+   end
+   
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class}  to #{seq.seq_name}  " 
+#    #delete sequence if it was created
+#    
+#   
+# end 
+
+def apply_decoration(char)
+  return char.yellow.negative
+end    
+
+
+end

data/lib/seqtrimnext/actions/action_right_adapter.rb

@@ -0,0 +1,29 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionRightAdapter < SeqtrimAction       
+  
+  def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+
+   end
+   
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class}. BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+#   
+# end  
+
+def apply_decoration(char)
+  return char.magenta
+end 
+
+end

data/lib/seqtrimnext/actions/action_right_primer.rb

@@ -0,0 +1,25 @@
+require "seqtrim_action"
+
+class ActionRightPrimer < SeqtrimAction
+
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)
+    @cut =true
+
+  end
+  #
+  # def apply_to(seq)
+  #
+  #    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+  #    $LOG.debug " Applying #{self.class} . BEGIN: #{@start_pos}   END: #{@end_pos}  "
+  #
+  # end
+
+  def apply_decoration(char)
+    return char.blue.underline
+
+    #  return char.magenta.negative
+  end
+
+
+end

data/lib/seqtrimnext/actions/action_short_insert.rb

@@ -0,0 +1,32 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute ActionShortInserted                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionShortInsert < SeqtrimAction
+
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)    
+    # @cut =true  
+    @cut = false
+    @informative = true
+  end
+     
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class}. ------ Error.Sequence is not good ------ . BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+#  
+#   
+# end 
+
+def apply_decoration(char)
+  return char.on_red
+end             
+
+
+end

data/lib/seqtrimnext/actions/action_unexpected_poly_t.rb

@@ -0,0 +1,29 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionUnexpectedPolyT < SeqtrimAction
+  def initialize(start_pos,end_pos)
+    super(start_pos,end_pos)    
+    @cut =true
+  end
+
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class} " 
+#   
+# end  
+
+
+def apply_decoration(char)
+  return char.bold
+end  
+
+
+end

data/lib/seqtrimnext/actions/action_unexpected_vector.rb

@@ -0,0 +1,31 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionUnexpectedVector < SeqtrimAction
+    
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =true
+
+   end
+   
+# def apply_to(seq)
+#   
+#    # seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
+#    $LOG.debug " Applying #{self.class} to seq #{seq.seq_name}. BEGIN: #{@start_pos}   END: #{@end_pos}  " 
+#   
+# end  
+
+  def apply_decoration(char)
+    return char.on_green
+  end      
+
+
+
+end