plt22ps.doc

mfold

Documentation for plt22ps.c


Darrin Stewart and Michael Zuker 
June 10, 1998 

This program is similar to plt22gif.c
Some information in plt22gif.doc is similar and more detailed.

execute with plt22ps name 
                                      
  name is a plt2 file that already exists
  The program will add .plt2 if necessary

For annotating the dots or characters based on the files
name.ann or name.ss-count,

Use:       plt22gif 'name'.plt2                               ]
[        Where 'name'.plt2 is a plt2 file                     ]
[        and 'name'.ann exists for -c or -d and is a p-num    ]
[        (default) or a probability annotation file (see -q   ]
[        flag below).                                         ]
[        If -n flag is used, the file 'name'.ss-count is used ]
[        instead of 'name'.ann                     



  Valid lower case parameters  

 -a name2      Specify alternate name for annotation file with -c or -d,
         .ann or .ss-count extensions will be appended.
                             
 -c           Use colored bases for annotation               
 -d           Use colored dots for annotation                
 -n           read ss-count file, default is  ann for -c or -d above      
  
 -o name_out                  
     ps file named name_out.ps 
     Default is name.ps 
     The default name is produced from name.plt2 by removing the .plt2
     and adding .ps 

-p forces portrait mode 
     The default is to guess between portrait and landscape  by reading 
     the file and determining which direction works better.

-q   read probability annotation file,              
     default is 'name'_k.ann, then name.ann     
     for -c -d option above 


 -s real_number
     Scales the size of the postscript file by real number.
     1.0 is the default.
     0.25 produces an image .25 * 8.5 inches wide and .25 *11 inches tall
     real_number must be between .05 and 1.00
      
     If it is preferred to make a size change after the .ps file is
     generated, two lines within the file need to be edited.


 -t h
 -t g
      Create html or gif color table with -c or -d option.
      The color table is specific to the given .ann or .ss-count file.
      Name is name.ann.col.html or name.ss-count.col.html or
              name.ss-count.col.gif or name.ss-count.col.gif
      (gif option of .ann not created yet)
      The file will not be created if it already exists.
          
-y real_number ix,iy
     zoom about the pixel (ix,iy) as gif coordinates with
     magnification, real_number,  upper left is 0,0,
     lower right is 612,792 or 792,612 depending on 
     portrait or landscape mode.  The programs determines
     whether portrait or landscape is best and treats
     the coordinates that way.  Create the same image
     with plt22gif and resolution 72 and enter
     coordinates from the image.

-z real_number ix iy
     zoom about the point ix,iy with magnification real_number
     lower left is 0,0 upper right is 612,792.

The program assumes naview is run with 21.59 27.94 as input for size of page.
The character size is expected to be 
         60000/(100 +length of sequence).
See auto_ct2ps of mfold-3.0 for the usual execution.
 

                                      
 Note:  The file name must be the last parameter 
 Other parameters will be searched for and processed whenever found 
 Invalid parameters will probably be ignored and default values used 
 ----------------------------------------------------------- 

 To compile cc -o plt22ps plt22ps.c -lm 
 or use the make file


__________________________________________________________________________

Files used:
plt22ps.c        Main source code.
color_ann.h        Defines annotation colors.
plt22gif_or_ps.h  More color setup and opening of files.
copyright_ps.h    For the copyright in the corner
Makefile          The makefile