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/* suitenout.c */
#include "suitename.h"
#define SUITENOUT
#include "suitenout.h"
#include "suitenhead.h" /* kinemageframe[] 070414*/
#undef SUITENOUT
#include "suitenscrt.h"
#include "suiteninit.h"
/****writesuite()*************************************************************/
void writesuite(int ibin,int jclst,char* sour, float distance, float suiteness,char* ptmaster,char* ptcolor)
{
int j=0,n=0;
/*static int nout=1; Lstringout residue/suite counter, suitenout.h 070421*/
char resstr[32];
char basestr[2]={'\0','\0'};
char clststr[4]={'\0','\0','\0','\0'};
static char lappedstr[256]={'\0'};
char reason[16]; /*used in report: reason for triage*/
char stray[16]; /*used in report: stray wannabe*/
char sourpuss[1]; /*070524*/
char* sourptr; /*070524*/
sourpuss[0] = '\0'; /*070524*/
if(Lkinemageout)
{/*kinemage showing clusters*/
if(Lsourout) {sourptr = sour;} /*070524*/
else {sourptr = sourpuss;}
sprintf(temps,"{%s %s %s:D==%5.3f:S==%5.3f: %s} %s%s ,%7.2f,%7.2f,%7.2f,%7.2f,%7.2f,%7.2f,%7.2f,%7.2f,%7.2f",
bin[ibin].binname,
bin[ibin].clst[jclst].clustername,
sourptr,
distance,
suiteness,
suiteptr->ptID,
ptmaster,
ptcolor,
suiteptr->chim,
suiteptr->deltam,
suiteptr->epsilon,
suiteptr->zeta,
suiteptr->alpha,
suiteptr->beta,
suiteptr->gamma,
suiteptr->delta,
suiteptr->chi );
if(ibin > 12 || ibin < 0)
{
fprintf(stderr,"%s\n",temps); /*e.g. 13: angles not fully specified*/
}
else
{
if(Ltest){fprintf(stderr,"PUT %s\n",temps);}
putonetextblockline(&mainscratch,temps);
}
}
else if(Lstringout)
{/*3char string in order of input for all entries*/
if(Lsequence)
{
basestr[0] = suiteptr->basechr[0]; /*070412 found previously*/
}
else /*colon instead of single-character Base code 070409*/
{
basestr[0] = ':';
}
fprintf(fpout,"%s%s",bin[ibin].clst[jclst].clustername,basestr);
if(!Loneline) /*070409*/
{
if(Loverlap && nout >= 11)
{
sprintf(clststr,"%s%s",bin[ibin].clst[jclst].clustername,basestr);
j = n = 0;
while(lappedstr[j] != '\0') {j++;} /*find end of lappedstr*/
while((lappedstr[j++] = clststr[n++]) != '\0') ; /*copy on end*/
}
if(nout == 20)
{
fprintf(fpout," {%s}\n",suiteptr->ptID);
if(Loverlap)
{
fprintf(fpout,"%s",lappedstr);
lappedstr[0] = '\0';
nout = 11;
}
else
{
nout = 1;
}
}
else {nout++;}
}
}
else if(Lreportout)
{
/*report on all entries, even if suite is incomplete*/
reason[0] = '\0'; /*default to none*/
stray[0] = '\0'; /*default to none*/
if(Ltriage==EPSILONM) {sprintf(reason," epsilon-1");} /*070628*/
else if(Ltriage==DELTAM){sprintf(reason," delta-1");} /*070628*/
else if(Ltriage==DELTA) {sprintf(reason," delta");} /*070628*/
else if(Ltriage==GAMMA) {sprintf(reason," gamma");} /*070521*/
else if(Ltriage==BETA) {sprintf(reason," beta");} /*070521*/
else if(Ltriage==ALPHA) {sprintf(reason," alpha");} /*070521*/
else if(Ltriage==ZETAM) {sprintf(reason," zeta-1");} /*070628*/
else if(Lcomment){sprintf(reason,"%s",commentstr);} /*070628*/
if(Liswannabe){sprintf(stray," wannabe");} /*070525*/
fprintf(fpout,"%s %s %s %5.3f%s%s\n",
suiteptr->ptID,
bin[ibin].binname,
bin[ibin].clst[jclst].clustername,
suiteness,
reason,
stray /*070628*/
);
reportcountall++; /*everything that suitename brought in */
/*now accummulate sum and count for complete suites*/
if(ibin == 0)
{
triagecountall++; /*070328*/
}
else if(ibin >= 0 && ibin < 13) /*ibin==13 when angles not all defined*/
{
/*defineable suites, including triaged and outliers */
suitenesssumall = suitenesssumall + suiteness;
/*adding (float)zero won't hurt this sum*/
binnedsuitecountall++;
}
/*distribution of suiteness values...*/
/*j==0 pseudo clusters always have a suiteness == 0, so sum not changed*/
if(jclst == 0) /*augment the k==11 outlier place for this cluster*/
{ /*outliers in bins 1 to 12, triages in bin 0, not defined in bin 13*/
/*jclst membership 4D distance < 1, suiteness > 0 if 7D distance > 1*/
/*outliers in jclst 0, suiteness can be == 0 for others if 7D dist>1 */
suitenesscnt[ibin][jclst][11]++;
}
else
{
suitenesssum[ibin][jclst] = suitenesssum[ibin][jclst] + suiteness;
/*3rd index for suiteness intervals: 10 at 10ths + extra at zero*/
if(suiteness == 0 ) {suitenesscnt[ibin][jclst][0]++;}
if(suiteness > 0 && suiteness < .1) {suitenesscnt[ibin][jclst][1]++;}
if(suiteness >= .1 && suiteness < .2) {suitenesscnt[ibin][jclst][2]++;}
if(suiteness >= .2 && suiteness < .3) {suitenesscnt[ibin][jclst][3]++;}
if(suiteness >= .3 && suiteness < .4) {suitenesscnt[ibin][jclst][4]++;}
if(suiteness >= .4 && suiteness < .5) {suitenesscnt[ibin][jclst][5]++;}
if(suiteness >= .5 && suiteness < .6) {suitenesscnt[ibin][jclst][6]++;}
if(suiteness >= .6 && suiteness < .7) {suitenesscnt[ibin][jclst][7]++;}
if(suiteness >= .7 && suiteness < .8) {suitenesscnt[ibin][jclst][8]++;}
if(suiteness >= .8 && suiteness < .9) {suitenesscnt[ibin][jclst][9]++;}
if(suiteness >= .9) {suitenesscnt[ibin][jclst][10]++;}
}
}
}
/*___writesuite()____________________________________________________________*/
/****suitenessaverage()******************************************************/
void suitenessaverage(int mode) /*mode for all, just Aform, etc. */
{
int i=0,j=0,k=0;
int ibin=0,nbin=0,jclst=0,nclst=0,xbin = -1,xclst = -1;
double sum = 0;
int num[12] = {0,0,0,0,0,0,0,0,0,0,0,0};
float average = 0;
int number = 0;
char comment[256];
int Ntriaged = 0; /*070328*/
if(mode == 0) /*all complete suites, all ways*/
{ /*bin==13 has the incomplete pseudo-suites with incomplete angles*/
ibin = 1; nbin = 12; jclst = 0; nclst = 11;
xbin = -1; xclst = -1; /*exception when >= 0*/
/*ibin 0 contains triaged clusters, never use these*/
fprintf(fpout,"Found %d complete suites derived from %d entries\n"
,binnedsuitecountall+triagecountall,reportcountall);
fprintf(fpout,"%d suites were triaged, leaving %d assigned to bins\n"
,triagecountall,binnedsuitecountall); /*070328*/
sprintf(comment,"For all");
}
else if(mode == 1) /* A form 1,1*/
{ /*bin==13 has the incomplete, pseudo-suites with incomplete angles*/
ibin = 1; nbin = 1; jclst = 1; nclst = 1;
/*no outliers (j==0)*/
xbin = -1; xclst = -1; /*exception for this clst in this bin when >= 0*/
sprintf(comment," A form (1a)");
}
else if(mode == 2) /* everything except A form, i.e. except 1,1*/
{ /*bin==13 has the incomplete pseudo-suites with incomplete angles*/
ibin = 1; nbin = 12; jclst = 1; nclst = 11; /*only complete suite pts*/
/*no outliers (j==0)*/
xbin = 1; xclst = 1; /*exception when >= 0*/
sprintf(comment," non-1a has");
}
for(i=ibin; i<=nbin; i++)
{
for(j=jclst; j<=nclst; j++) /*some clusters not defined in some bins*/
{
if(i != xbin || (i == xbin && j != xclst))
{
sum = sum + suitenesssum[i][j];
for(k=0; k<12; k++)
{
num[k] = num[k] + suitenesscnt[i][j][k];
}
}
}
}
for(k=0; k<12; k++) { number = number + num[k]; }
if(number > 1){average = sum/number;}
else {average = 0;}
fprintf(fpout,"%s %d suites: average suiteness== %5.3f (power==%4.2f)\n"
,comment,number,average,power);
if(mode == 0) {fprintf(fpout,"%6d suites are outliers\n",num[11]);}
fprintf(fpout,"%6d suites have suiteness == 0 \n",num[0]);
fprintf(fpout,"%6d suites have suiteness > 0 <.1\n",num[1]);
fprintf(fpout,"%6d suites have suiteness >=.1 <.2\n",num[2]);
fprintf(fpout,"%6d suites have suiteness >=.2 <.3\n",num[3]);
fprintf(fpout,"%6d suites have suiteness >=.3 <.4\n",num[4]);
fprintf(fpout,"%6d suites have suiteness >=.4 <.5\n",num[5]);
fprintf(fpout,"%6d suites have suiteness >=.5 <.6\n",num[6]);
fprintf(fpout,"%6d suites have suiteness >=.6 <.7\n",num[7]);
fprintf(fpout,"%6d suites have suiteness >=.7 <.8\n",num[8]);
fprintf(fpout,"%6d suites have suiteness >=.8 <.9\n",num[9]);
fprintf(fpout,"%6d suites have suiteness >=.9 \n",num[10]);
}
/*___suitenessaverage()______________________________________________________*/
/****writeoutput()************************************************************/
void writeoutput(void)
{
char commentstr[128];
if(Lgeneralsatw)
{
sprintf(commentstr,
" special general case satellite widths, power = %4.2f",power);
}
else
{
sprintf(commentstr,
" all general case widths, power = %4.2f",power);
}
if(Lreportout && !Lchart)
{
fprintf(fpout,"%s\n",commentstr);
suitenessaverage(0); /* 0 mode reports on all suites */
if(clusterout[1][1] > 0) /*Aform 1a 070325*/
{
suitenessaverage(1); /* 1 mode reports on A form suites */
suitenessaverage(2); /* 2 mode reports on non-A suites */
}
}
if(Lkinemageout &&(L33out || L32out || L23out || L22out || Ltriageout))
{/*stuff for a kinemage*/
/*Ltriageout for intact suites that fail individual angle test(s) */
/*each populated bin gets a subgroup*/
kinemageheader(commentstr);
kinemagestuffer(janesviews); /*070421*/
kinemagestuffer(kinemageframe); /*070414, 070421*/
/*work through all possible bins and their suites in standard order*/
if(L33out)
{
fprintf(fpout,"@group {33} recessiveon dimension=9 wrap=360 select animate off\n");
binstuffout(1,3); /*bins in this group*/
}
if(L32out)
{
fprintf(fpout,"@group {32} recessiveon dimension=9 wrap=360 select animate off\n");
binstuffout(4,6); /*bins in this group*/
}
if(L23out)
{
fprintf(fpout,"@group {23} recessiveon dimension=9 wrap=360 select animate off\n");
binstuffout(7,9); /*bins in this group*/
}
if(L22out)
{
fprintf(fpout,"@group {22} recessiveon dimension=9 wrap=360 select animate off\n");
binstuffout(10,12); /*bins in this group*/
}
if(Ltriageout)
{
fprintf(fpout,"@group {triaged} dominant dimension=9 wrap=360 select off\n");
binstuffout(0,0); /*one bin (0th) in this group*/
}
}/*stuff for a kinemage*/
if(Lstringout)
{
if(nout != 1) {fprintf(fpout," {%s}\n",suiteptr->ptID);}
else {fprintf(fpout,"\n");} /*just final EOL*/
}
}
/*___writeoutput()___________________________________________________________*/
/****binstuffout()************************************************************/
void binstuffout(int nbin, int mbin)
{
int i=0,j=0,ncnt=0;
char ctrl[10]; /* 7 actual characters in curly braces*/
char extras[32];
for(i=nbin; i<=mbin; i++)
{/*loop over the three bins in this delta delta group*/
if(binout[i])
{/*ith bin has points*/
fprintf(fpout,"@subgroup {%s} recessiveon \n",bin[i].binname);
j=1; /*zeroth cluster is for bin outliers, if any, do them later */
while(bin[i].clst[j].LOK) /*named clusters j>0 ... 070429*/
{/*loop over named clusters in this ith bin, NOT including outliers*/
if(clusterout[i][j])
{
if(strcmp(bin[i].clst[j].status,"wannabe")==0) /*070429*/
{
sprintf(extras," master= {wannabees}");
Lwannabeout = 1; /*redundant, already been set*/
}
else {extras[0] = '\0';}
fprintf(fpout,
"@balllist {%s %s} color= %s radius= 1 nohilite master= {data}%s\n"
,bin[i].binname,bin[i].clst[j].clustername,bin[i].clst[j].clustercolor,extras);
sprintf(ctrl,"{%s %s}"
,bin[i].binname,bin[i].clst[j].clustername);
ncnt = transferout(ctrl); /*gets just pts starting with ctrl*/
if(j>0) /*obselete, but is a safety*/
{/*belong to a named cluster (av & labels initially on 070414)*/
fprintf(fpout,
"@ringlist {%s %s} color= %s radius= 10 width= 1 nobutton master= {avsigma}%s\n"
,bin[i].binname,bin[i].clst[j].clustername,bin[i].clst[j].clustercolor,extras);
fprintf(fpout,
"{%s %s} 180 %7.2f %7.2f %7.2f %7.2f %7.2f %7.2f %7.2f 180\n"
,bin[i].binname,bin[i].clst[j].clustername
,bin[i].clst[j].ang[1]
,bin[i].clst[j].ang[2]
,bin[i].clst[j].ang[3]
,bin[i].clst[j].ang[4]
,bin[i].clst[j].ang[5]
,bin[i].clst[j].ang[6]
,bin[i].clst[j].ang[7]);
fprintf(fpout,
"@labellist {%s %s} color= %s nobutton master= {labels}%s\n"
,bin[i].binname,bin[i].clst[j].clustername,bin[i].clst[j].clustercolor,extras);
fprintf(fpout,
"{%s %s} 180 %7.2f %7.2f %7.2f %7.2f %7.2f %7.2f %7.2f 180\n"
,bin[i].binname,bin[i].clst[j].clustername
,bin[i].clst[j].ang[1]
,bin[i].clst[j].ang[2]
,bin[i].clst[j].ang[3]
,bin[i].clst[j].ang[4]
,bin[i].clst[j].ang[5]
,bin[i].clst[j].ang[6]
,bin[i].clst[j].ang[7]);
}/*belong to a named cluster*/
}/*members in i,j cluster*/
j++; /*increment cluster index for the while condition 070429*/
}/*loop over named clusters in this ith bin*/
j = 0; /*look for outliers... (set j==0 to reuse code from above)*/
if(clusterout[i][j]) /*outliers in this bin*/
{
extras[0] = '\0';
fprintf(fpout,
"@balllist {%s %s} color= %s radius= 1 nohilite master= {data}%s\n"
,bin[i].binname,bin[i].clst[j].clustername,bin[i].clst[j].clustercolor,extras);
sprintf(ctrl,"{%s %s}"
,bin[i].binname,bin[i].clst[j].clustername);
ncnt = transferout(ctrl); /*gets just pts starting with ctrl*/
}/*outliers in this bin*/
}/*ith bin has points*/
}/*loop over bins*/
}
/*___binstuffout()___________________________________________________________*/
/****transferout()************************************************************/
int transferout(char* ctrl)
{
/*cribbed from PKINCOUT/transferout() 070210 */
/* for later flexibility, include some controls not now needed 070210 */
int LatEOF=0, LOK=0;
int j=0, iscrt=0, iexist=0;
char scrts[256];
rewindtextblock(&mainscratch);
LatEOF = 0;
while(!LatEOF)
{/*scan through scratch block*/
getonetextblockline(&mainscratch,temps);
if(temps[0] != '\0')
{/*entries still in scratch block*/
if( (temps[0]==ctrl[0]) /*check chars at beginning of ptID*/
&&(temps[1]==ctrl[1])
&&(temps[2]==ctrl[2])
&&(temps[3]==ctrl[3])
&&(temps[4]==ctrl[4])
&&(temps[5]==ctrl[5])
&&(temps[6]==ctrl[6])
&&(temps[7]==ctrl[7]) )
{
LOK = 1; /*this point belongs in this list*/
iscrt = 0;
if(Ltest){fprintf(stderr,"GOT %s\n",temps);}
}
else
{/*unrecognized, can't use this point in this list*/
LOK = 0;
}
if(LOK)
{/*this point belongs in this list*/
for( j=iscrt ; j<=255 ; j++) /*extract content from temps[] */
{
scrts[j-iscrt] = temps[j];
if(temps[j] == '\0') break;
}
iexist++; /*increase counter*/
/*suitename writeoutput has already written list header*/
/* so do not write this here when iexist==1 */
fprintf(fpout,"%s\n",scrts);
/*this point belongs in this list*/}
}/*entries still in scratch block*/
else
{/*reached end of scratch block*/
LatEOF = 1;
}
}
return(iexist);
}
/*___transferout()___________________________________________________________*/
/****kinemageheader()*********************************************************/
void kinemageheader(char* textstr)
{
fprintf(fpout,"@text\n %s\n %s\n",version,textstr);
fprintf(fpout,"@kinemage 1\n");
fprintf(fpout,"@onewidth\n");
if(Letatheta) /*070524*/
{fprintf(fpout,"@dimension {theta} {delta-1} {epsilon-1} {zeta-1} {alpha} {beta} {gamma} {delta} {eta}\n");}
else
{fprintf(fpout,"@dimension {chi-1} {delta-1} {epsilon-1} {zeta-1} {alpha} {beta} {gamma} {delta} {chi}\n");}
fprintf(fpout,"@dimminmax 0.000 360.000 0.000 360.000 0.000 360.000 0.000 360.000 0.000 360.000 0.000 360.000 0.000 360.000 0.000 360.000 0.000 360.000\n");
if(LTepsilon) {fprintf(fpout,"@pointmaster 'E' {epsilon bad}\n");}
else if(LTdelta || LTdeltam)
{fprintf(fpout,"@pointmaster 'D' {delta bad}\n");}
else if(LTzeta || LTalpha || LTbeta || LTgamma)
{fprintf(fpout,"@pointmaster 'T' {various bad}\n");}
if(Loutlier) {fprintf(fpout,"@pointmaster 'O' {outliers}\n");}
if(Lwannabeout) {fprintf(fpout,"@master {wannabees}\n");}
}
/*___kinemageheader()________________________________________________________*/
/****kinemagestuffer()********************************************************/
void kinemagestuffer(char* kinemagestuff[])
{
int more = 1, j=0, Nth=0;
char temps[256];
while(more)
{/*loop over all text for this call*/
for(j=0; j<255; j++) /*save a space for safety '\0' */
{/*load transfer string*/
temps[j] = kinemagestuff[Nth][j];
if(temps[j] == '\r')
{/*ASCII Carraige Return*/
temps[j] = EOL; /*platform specific End-Of-Line character*/
}
if(temps[j] == '\0'){ break;} /*separate end of text piece*/
}/*load transfer string*/
/*check for END before writing to stdout*/
if(temps[0] =='E' && temps[1] =='N' && temps[2] =='D'){more = 0;}
temps[j+1] = '\0'; /*safety if runs off end of temps str*/
if(more != 0) {fprintf(fpout,"%s",temps);}
Nth++; /*local, not static, so will get reset ==0 on new call*/
}/*loop over all text for this call*/
}
/*___kinemagestuffer()_______________________________________________________*/
/****clearbinout()************************************************************/
void clearbinout(void)
{
int i=0,j=0;
for(i=1; i<MAXBINS; i++)
{
binout[i] = 0; /*set 1 if an entry is encountered*/
}
}
/*___clearbinout()___________________________________________________________*/
/****clearclusterout()********************************************************/
void clearclusterout(void)
{ /* clear storage arrays, re suitenout.h */
int i=0,j=0,k=0;
for(i=0; i<MAXBINS; i++)
{
for(j=0; j<MAXCLST; j++)
{
clusterout[i][j] = 0; /*set 1 if an entry is encountered*/
suitenesssum[i][j] = 0;
for(k=0; k<12; k++) /*intervals: 10 10ths + extras at zero & 12*/
{
suitenesscnt[i][j][k] = 0;
}
}
}
suitenesssumall = 0;
binnedsuitecountall = 0;
triagecountall = 0;
reportcountall = 0;
}
/*___clearclusterout()_______________________________________________________*/
/****usageout()***************************************************************/
void usageout(void) /* -h -help */
{
fprintf(stderr,"%s\n",version);
fprintf(stderr,"suitename -flags <stdin >stdout\n");
fprintf(stderr,"output flags: [ -report || -string || -kinemage ]\n");
fprintf(stderr,"default: -report -residuein \n");
fprintf(stderr,"input flags: [ -residuein || -suitein ]\n");
fprintf(stderr,"flags: [ -residuein [ -pointIDfields # ] ] default#==%d\n"
,NptIDfields);
fprintf(stderr," OR ");
fprintf(stderr,"flags: [ -suitein [ -anglefields # ] ] default#==%d\n"
,Nanglefields);
fprintf(stderr,"\n");
fprintf(stderr,"defaults: -residuein -pointIDfields %d\n",NptIDfields);
fprintf(stderr," as made by dangle \n");
fprintf(stderr,
"dangle \"alpha, beta, gamma, delta, epsilon, zeta\" in.pdb >out.dngl\n");
fprintf(stderr,
"label:model:chain:number:ins:type:alpha:beta:gamma:delta:epsilon:zeta\n");
fprintf(stderr,"-suitein presumes point records from a kinemage\n");
fprintf(stderr,"{pointID} 7 or 9 anglefields \n");
fprintf(stderr,
"{ptID} [chi] deltam epsilon zeta alpha beta gamma delta [chi] \n");
fprintf(stderr," Note that all other kinemage lines must be stripped off.\n");
fprintf(stderr,"-thetaeta kinemage labels theta,eta instead of chi-1,chi\n");
fprintf(stderr,"Note dangle trick to make theta,...,eta suites directly\n");
fprintf(stderr,"\n");
fprintf(stderr,"flag: -report [ -chart ]\n");
fprintf(stderr," suites in order of input, suiteness summary at end\n");
fprintf(stderr,"( -chart : NO summary at end, for MolProbity multichart\n");
fprintf(stderr,"\n");
fprintf(stderr,"flag: -string\n");
fprintf(stderr," 3 character per suite string in order of input\n");
fprintf(stderr," 20 per line, ptID of n*20th at end of line\n");
fprintf(stderr," flag: -nosequence\n");
fprintf(stderr," only suite names, no Base sequence character\n");
fprintf(stderr," flag: -oneline\n");
fprintf(stderr," string all one line, no point IDs\n");
fprintf(stderr," flag: -overlap\n");
fprintf(stderr," 20 per line: overlap 10 each line, 10 new per line\n");
fprintf(stderr,"\n");
fprintf(stderr,"flag: -kinemage\n");
fprintf(stderr," kinemage of clusters grouped by pucker,pucker ... \n");
fprintf(stderr," group {delta,delta},subgroup {gamma},list {cluster name}\n");
fprintf(stderr,"\n");
/*fprintf(stderr,"flag: -satellite\n"); DO NOT ADVERTISE THIS OPTION*/
/*fprintf(stderr," use special general case satellite widths\n");*/
fprintf(stderr," assigns to designated wannabe clusters, default: wannabe\n");
/*fprintf(stderr,"flag: -wannabe\n");*/
fprintf(stderr,"flag: -nowannabe to not assign them\n");
fprintf(stderr,"\n");
fprintf(stderr,"[ -power #.#] default# %4.2f multi-dimension distance calc\n"
,power);
fprintf(stderr,"[ -test ] dump cluster centers, halfwidths,... to stderr\n");
fprintf(stderr,"cluster averages version: %s\n",clusteraveragesversion);
fprintf(stderr,"cluster half-widths version: %s\n",clusterhalfwidthsversion);
fprintf(stderr,"axes limits version: %s\n",axeslimitsversion);
fprintf(stderr,"suitename is not paying attention to chains...\n");
fprintf(stderr,"%s\n",version);
}
/*___usageout()______________________________________________________________*/
|