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revision 1.13, Tue Aug 1 17:57:15 2006 UTC revision 1.14, Tue Feb 5 02:05:06 2008 UTC
# Line 20  Line 20 
20    
21  =pod  =pod
22    
23  =head1 raedraw.pm  =head3 raedraw.pm
24    
25   A bunch of modules written by Rob to draw different things. Most of these are going to draw images   A bunch of modules written by Rob to draw different things. Most of these are going to draw images
26   using SVG that has many advantages over png/gif images.   using SVG that has many advantages over png/gif images.
# Line 39  Line 39 
39  my $fig=new FIG;  my $fig=new FIG;
40    
41    
42  =head1 new  =head2 Methods
43    
44    =head3 new
45    
46   Instantiate the script and figure out what we are looking for. These are the options.   Instantiate the script and figure out what we are looking for. These are the options.
47   Remeber, this was originally taken from a standalone script I wrote, and then cgi-iffied.   Remeber, this was originally taken from a standalone script I wrote, and then cgi-iffied.
# Line 135  Line 137 
137  }  }
138    
139    
140  =head2 compareto  =head3 compareto
141    
142   Get or set the list of genomes or other things that we will compare this to.   Get or set the list of genomes or other things that we will compare this to.
143   args:          A reference to an array of things to add to the comparisons   args:          A reference to an array of things to add to the comparisons
# Line 156  Line 158 
158   return $self->{'compareto'};   return $self->{'compareto'};
159  }  }
160    
161  =head2 show_function  =head3 show_function
162    
163   Set a boolean to show the function   Set a boolean to show the function
164   args:          boolean whether to set the function   args:          boolean whether to set the function
# Line 171  Line 173 
173  }  }
174    
175    
176  =head2 write_image  =head3 write_image
177    
178   Write out the image to a file   Write out the image to a file
179   Args: A file name to write to   Args: A file name to write to
# Line 222  Line 224 
224  }  }
225    
226    
227  =head2 _define_tracks  =head3 _define_tracks
228    
229   Each genome has a track that contains all the information about the genome, including the boxes, names, and drawings. This is an internal method to define those tracks   Each genome has a track that contains all the information about the genome, including the boxes, names, and drawings. This is an internal method to define those tracks
230    
# Line 263  Line 265 
265    
266    
267    
268  =head1 _scale_image  =head3 _scale_image
269    
270   An internal method to figure out how long the whole genome is and use this as the baseline for the image   An internal method to figure out how long the whole genome is and use this as the baseline for the image
271    
# Line 352  Line 354 
354   }   }
355  } # end _scale_image  } # end _scale_image
356    
357  =head1 _draw_genome  =head3 _draw_genome
358    
359   An internal method to draw the genome that we are comparing to, and to define the locations of the pegs (perhaps)   An internal method to draw the genome that we are comparing to, and to define the locations of the pegs (perhaps)
360    
# Line 444  Line 446 
446  }  }
447    
448    
449  =head2 _add_functions  =head3 _add_functions
450    
451   An internal method to add the functions to the image.   An internal method to add the functions to the image.
452   Args:          definitions (defs), peg, position (x) where to add the text, box width, row (y group) to add the text   Args:          definitions (defs), peg, position (x) where to add the text, box width, row (y group) to add the text
# Line 472  Line 474 
474  }  }
475    
476    
477  =head2 _plot_subsystems  =head3 _plot_subsystems
478    
479   An internal method to plot a box if the peg is in a subsystem   An internal method to plot a box if the peg is in a subsystem
480   Takes the following as arguments:   Takes the following as arguments:
# Line 515  Line 517 
517   }   }
518  }  }
519    
520  =head2 _plot_tag_value  =head3 _plot_tag_value
521    
522   An internal method to plot tag value pairs.   An internal method to plot tag value pairs.
523   Takes the following as arguments:   Takes the following as arguments:
# Line 576  Line 578 
578    
579    
580    
581  =head2 _plot_sims  =head3 _plot_sims
582    
583   An internal method to add the similarities to the image   An internal method to add the similarities to the image
584   Args:          peg, position (x) where to add the text, width of the box to draw, row (y group) to add the text,   Args:          peg, position (x) where to add the text, width of the box to draw, row (y group) to add the text,
# Line 620  Line 622 
622    
623    
624    
625  =head2 _hz_lines  =head3 _hz_lines
626    
627   An internal method to add horizontal lines to an image where the genomes are   An internal method to add horizontal lines to an image where the genomes are
628   Args:          None   Args:          None

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