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)

return

;

1431

nextseg = seg->

;

1451

seqmax = seq + win->

;

1453 while

(seq < seqmax) {

1471 return

(*np2 - *np1);

1485 char

* seq,* seqmax;

1487 unsigned char

* alphaflag;

1497

seqmax = seq + win->

;

1499 while

(seq < seqmax) {

1501 if

(!alphaflag[

letter

])

1502

comp[alphaindex[

letter

]]++;

1532

win->

state

[nel++] = c;

1556 if

(start<0 || length<0 || start+length>parent->

)

1570

win->

start

= start;

1572

win->

seq

= parent->

seq

+ start;

1599 for

(

=0; sv[

]!=0;

++)

1603 if

(total==0)

return

(0.);

1608 for

(

=0; sv[

]!=0;

++)

1616 for

(

=0; sv[

]!=0;

++)

1618

ent += ((double)sv[

])*

log

(((

double

)sv[

])/(

double

)total)/

NCBIMATH_LN2

;

1621

ent =

fabs

(ent/(

double

)total);

1642 while

((svi = *sv++) != 0) {

1643 if

(svi ==

class

&& *sv <

class

) {

1659 if

(*sv++ ==

class

) {

1678 unsigned char

* alphaflag;

1697 else

win->

bogus

--;

1704 else

win->

bogus

++;

1721 if

(win==

)

return

;

1760

downset = (window+1)/2 - 1;

1761

upset = window - downset;

1763 if

(window>seq->

)

1765 return

((

double

);

1789 if

(win->

bogus

> maxbogus)

1818 for

(j=

; j>=limit; j--)

1820 if

(

[j]==-1.0)

break

;

1821 if

(

[j]>hicut)

break

;

1841 for

(j=

; j<=limit; j++)

1843 if

(

[j]==-1.0)

break

;

1844 if

(

[j]>hicut)

break

;

1858 else return

((

+0.5)*

log

(

) -

+ 0.9189385332);

1876 for

(

=0; sv[

]!=0;

++)

1901

ans =

lnfact

[alphasize];

1909 for

(

=0;; svim1 = svi) {

1910 if

(++

==alphasize) {

1914 else if

((svi = *++sv) == svim1) {

1947 double

ans, ans1, ans2 = 0, totseq;

1949

totseq = ((double) total) * palpha->

lnalphasize

;

1952 if

(ans1 > -100000.0 && sv[0] !=

INT4_MIN

)

1958 #ifdef ERR_POST_EX_DEFINED 1962

ans = ans1 + ans2 - totseq;

1977 double prob

, minprob;

1987

maxtrim = sparamsp->

maxtrim

;

1988 if

((seq->

-maxtrim)>minlen)

1989

minlen = seq->

-maxtrim;

2013

*leftend = *leftend + lend;

2014

*rightend = *rightend - (seq->

- rend - 1);

2035 double

locut, hicut;

2036 Int4

downset, upset;

2039 Int4

leftend, rightend;

2043 if

(sparamsp->

window

<=0)

return

status;

2044 if

(sparamsp->

<=0.) sparamsp->

= 0.;

2045 if

(sparamsp->

<=0.) sparamsp->

= 0.;

2047

window = sparamsp->

window

;

2048

locut = sparamsp->

;

2049

hicut = sparamsp->

;

2050

downset = (window+1)/2 - 1;

2051

upset = window - downset;

2064 if

(

[

] <= locut &&

[

] != -1.0)

2070

leftend = loi - downset;

2071

rightend = hii + upset - 1;

2073

temp_seq =

s_OpenWin

(seq, leftend, rightend-leftend+1);

2074

status =

s_Trim

(temp_seq, &leftend, &rightend, sparamsp);

2081 if

(

+upset-1<leftend)

2083 Int4

lend = loi - downset;

2084 Int4

rend = leftend - 1;

2096 if

(leftsegs!=

)

2098

leftsegs->

= *segs;

2110 i

MIN

(hii, rightend+downset);

2127 SSeg

* seg,* nextseg;

2132 if

(segs==

)

return

;

2134 if

(seq->

-1 - segs->

< hilenmin)

2138

nextseg = seg->

;

2140 while

(nextseg!=

) {

2141 if

(seg->

begin

- nextseg->

- 1 < hilenmin) {

2142 if

(seg->

< nextseg->

) seg->

= nextseg->

;

2149

nextseg = seg->

;

2167 for

( ; segs; segs = segs->

) {

2172

loc->

= *seg_locs;

2193 unsigned char

* alphaflag;

2195 const int

kCharSet = 128;

2196 const double

kLn20 = 2.9957322735539909;

2205

alphaflag = (

unsigned char

calloc

(kCharSet ,

sizeof

(

unsigned char

));

2207 for

(c=0,

=0; c<kCharSet; c++)

2209 if

(c == 1 || (c >= 3 && c <= 20) || c == 22) {

2210

alphaflag[c] =

FALSE

;

2214

alphaflag[c] =

TRUE

; alphaindex[c] = 20;

2249 if

(!sparamsp)

return

;

2253 if

(sparamsp->

< 0.0) sparamsp->

= 0.0;

2255 if

(sparamsp->

< 0.0) sparamsp->

= 0.0;

2293

params_allocated =

TRUE

;

2303

seqwin->

seq

= (

char

*) sequence;

2304

seqwin->