errata-2.3

mfold

1. 12/10/96

Error: Used "-f" instead of "-s" in testing for files in the scripts
'mfold' and 'mfold-html'. The former tests for file existence and
rules out directories. The latter tests for non-empty files. Note also
the 'REUSE' error.

In mfold:  
if [ ! -f $SEQ ]; then   
  should be    
if [ ! -s $SEQ ]; then

if [ ! -f $FILE_PREFIX.sav ]; then  
  should be 
if [ ! -s $FILE_PREFIX.sav ]; then

if [ ! -f $FILE_PREFIX.sav -o REUSE = NO ]; then
  should be
if [ ! -s $FILE_PREFIX.sav -o $REUSE = NO ]; then

The same lines occur in pre-mfold and should be changed.

2. 12/17/96

In mfold, the first test for the existence of $SEQ.sav should be
eliminated. This means striking out 2 lines:

line 89 : if [ ! -s $SEQ.sav ]; then
line 115: fi

The same lines in pre-mfold-html must also be excised.

3. 12/20/96

In rna.f (and hence rna-nodot.f, rna-html.f), a new computed
structure must contain more than 'window' base pairs that were not in
previously computed foldings. 'window' is stored in cntrl(9). 'numbp'
is the number of new base pairs in a structure. If the number of base
pairs in the first folding is less than 'window', then no structure
will be found. This is undesirable. Hence, the test will be dropped
for the first structure, which will always be accepted.

In rna.f, rna-nodot.f and rna-html.f:
      if(numbp.le.cntrl(9)) then
becomes
      if(numbp.le.cntrl(9).and.rep.gt.1) then

4. 9/22/97

dot2ps.c and dot2ps.h are changed so that squares are plotted instead
of circles. They base pairs are still called 'dots'. Difference files:

dot2ps.c: (old vs. new)

19c19,31
< /dot  {rad  0.0  360.0  arc  fill} def\n\n";
---
> /dot {\n\
>    newpath\n\
>    moveto\n\
>    0.5 s mul   0 rlineto\n\
>    0   0.5 s mul rlineto\n\
>   -1 s mul     0 rlineto\n\
>    0    -1 s mul rlineto\n\
>    1 s mul     0 rlineto\n\
>    0   0.5 s mul rlineto\n\
>    closepath\n\
>    fill\n\
>    stroke\n\
> } def\n\n";
20a33
> 
221c234
<     float rad = RADIUS, big1;
---
>     float s = SIZE, big1;
235c248
<     rad *= size*size; 
---
>     s *= size*size; 
252c265
<                 fprintf (psf, "/rad %.3f scf div def\n", rad*big1);
---
>                 fprintf (psf, "/s %.3f scf div def\n", s*big1);
254c267
<                 fprintf (psf, "/rad %.3f scf div def\n", rad);
---
>                 fprintf (psf, "/s %.3f scf div def\n", s);

dot2ps.h: (old vs. new)

17c17
< #define RADIUS     0.004       /* base radius measure for setting dot size */
---
> #define SIZE       0.0057      /* base size measure for setting dot size */

5. 10/13/97  pre-auto_ct2ps altered to use more appropriate character
   size for plotting larger sequences. Also, TEST was removed.

< new                > old
67a68
>           TEST=`expr \( 600 / \( 88 \+ $LENGTH \) \)` 
70c71
<              CHAR_SIZE=0.0`echo $CHAR_SIZE | cut -c3-5`
---
>              CHAR_SIZE=0.1