plt22gif.doc

mfold

Documentation for plt22gif.c

plt22gif.c


Darrin Stewart  and Michael Zuker
June 10, 1998 

The program is similar to plt22ps.c
The documentation is similar to plt22ps.doc

execute with plt22gif 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.
 
 -b   enables transparent background for GIF files                             
 -c           Use colored bases for annotation               
 -d           Use colored dots for annotation                
 -n           read ss-count file, default is                 
                   .ann for -c or -d option above        

 -o name.out                  
     gif file named name.out.gif 
     Default is name.gif 
     The default name is produced from name.plt2 by removing the .plt2 

 -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 


 -r resolution 
    resolution is an integer value between 20 and 400 
    Small values do not look as good, but large ones can produce files 
    that are too big. 
    The default value is 72 
    Multiply resolution by 8.5 for width, by 11 for height of gif */
     or vice versa if in landscape mode */
       72  for    612 x  792 GIF */
      110  for    935 x 1210 GIF */
      200  for   1700 x 2200 GIF */
      300  for   2550 x 3300 GIF */
 
 -s  
    Saves the tgd file. 
    To customize a gif slightly.
    Edit this file, run tgd on it.  Then delete it.


 -t h
 -t g
      For annotation,
      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)
      (This option does not work with -q, try the program color_table.)
      The file will not be created if it already exists.
 -x 
    create a file named name.gif2bp or name_out.gif2bp
    This lists the locations of the basepairs, (dots, midpoint of line),
    within the gif image.
    The origin is upper left, with x across and y down.
    record consists of:
    x_location y_location base_1 base_2
    All are integers.
    gif2bp.pl can use this program. See gif2bp.doc
    See below for more information.    
                                      
 -z s x y   zoom with scale s > 0.0 and                    ]
[              integers x,y at the center 

The program assumes naview is run with 21.59 27.94 as input for size of page.

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 
 ----------------------------------------------------------- 

 For GIF files, this program creates a temporary file name.temp.tgd 
 The program runs tgd name.temp.tgd to convert name.temp.tgd 
 into a gif file */
 If there is an error, name.temp.tgd may need to be deleted. */

 To compile cc -o plt22gif plt22gif.c -lm 



For the -x option to work:
The plt2 file must contain:
  1.  a)    CM BASE PAIRING LINES WITH BASE PAIRS (occurs exactly once)
      c)     MOV  real_number real_number i j ( occurs multiple times)
      d)     CIA  0.0                     ( as a pair)
        or 
             LI real_number real_number i j (occurs multiple times )
      h)  Some comment CM indicating the end of the basepairs.


The CM comments are essential.  When 1.a) is encountered, each circle or
line will be plotted and the .gif2bp file will be appended with x y i j
where x y are the location in pixels of the center of the segment or circle
representing basepair i j.


The name.gif2bp file contains:
max_dis
x y base_i base_j (occurs number_basepairs times)

where max_dis is the maximum distance in pixels from the center x,y
of a basepair that a user can click and expect to be told that
base i pairs with base j when viewing the gif file name.gif
max_dis has been multiplied by -1
The rest of the file has been sorted.




____________________________________________________________________


-z   s  x  y
      Given a location (x,y) in the original image, create
      a new image with data from location (x,y) in the center
      scaled by s.  (s=1 can be used to shift the image)
      ( s=2 will double the size of the basepair dots in the region)
      ( s=.5 will make the dots half as big).
      (using -z 1 hor_size/2 vert_size/2 will produce the original image.)
      The original image has 0,0 as the upper left
      with x increasing across and y increasing down.
      The image is then scaled by s.  
      It is intended that an image is produced without the -z
      The program is then run again based on a (x,y) pixel point specified
      The -r value should be the same on both runs.
      s should be a floating point value greater than zero and less
      than 100.  
      The image size will be the same in both instances.
      x and y are integers >=0 and < image size in the appropriate
      directions.

Sample Run:

plt22gif -z 2.0 319 514 trna_2







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Files used:
plt22gif.c        Main source code.
color_ann.h        Defines annotation colors.
plt22gif_or_ps.h  More color setup and opening of files.
copyright_gif.h   For copyright in corner
Makefile          The makefile