MANUAL

LogoDrawer Help.
LogoDrawer is a simple utility to draw Sequences Logos as decribes in :
Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100 

Usage: 
       java -jar logoDrawercli.jar
         Goes to Graphic User Interface

       java -jar logoDrawercli.jar options
         Runs command line interpreter
         
Options:
       --infile filepath 
         Reads sequences from the specified filepath. Data is expected to be in fasta format.
         if --infile is not present then the data is readed from standard input.

       --outfile filepath 
         Specifies the destination jpg file with the image.

       --type moltype
         Specifies if sequences are from DNA or Proteins, moltype can be (without the quotes):
         \"d\" or \"DNA\"         for DNA sequences.
         \"p\" or \"Protein\"     for Protein Sequences.
         If --type is not present, then the type is autodetected.
       
       --NoCountGaps
         If --NoCountGaps options is present, then the gaps are ignored to estimate frequencies. This result in a higher logo in the positions with gaps.
         By default gaps are taken into account to estimate frequencies.
         
       --font [font name, font style]
         By default, verdana plain font is used to draw the logos.
         The font name can be any font installed in your system.
         The font style is a number that specifies the style:
           Plain        : 0.
           Bold         : 1.
           Italics      : 2.
           Bold+Italics : 3.
         The \"[\" and \"]\" symbols must be present.

       --layout LogoHeader, LogoHeight, PositionsPerLine, PosWidth, RowHeight, RulerColumn 
         Are integers that define the layout drawing of the Sequence Logo.
         Where:
           LogoHeader: is the number of pixels from the top of the row to the beginning of the Logo.
           LogoHeight: is the number of pixels from of the Logo.
           PositionsPerLine: is the number of positions of the sequence Logo that are shown in a single line.
           PosWidth: is the number os pixels of the width of each character in the logo.
           RowHeight: is the number of pixels of the entire row. It includes the Logo Header, the Sequence Logo itself and the horizontal Ruler.
           RulerColumn: is the number of pixels from the left to the beginning of the Sequence Logo. This part is used to draw the Vertical Ruler.
         The default values are 8, 300, 20, 45, 320, 15.

       --help
         Shows this help.

Example:
       java -jar logoDrawerCli.jar --outfile image.jpg --infile Nuc.fas
       cat nuc.fas | java -jar logoDrawerCli.jar --outfile image.jpg 
       java -jar logoDrawerCli.jar --outfile image.jpg --infile Nuc.fas --type protein
       java -jar logoDrawerCli.jar --outfile image.jpg --infile Nuc.fas --font [times new roman,3]
       java -jar logoDrawerCli.jar --outfile image.jpg --infile Nuc.fas --NoCountGaps
       java -jar logoDrawerCli.jar --outfile image.jpg --infile Nuc.fas --NoCountGaps -- layout 8, 300, 20, 45, 350, 45