SEXP makedf_xlpep(struct iobtd *iop){
SEXP df, df_names, idvec, protidvec, pepflagvec, pepmassvec, pepsitevec;
yamldom_node_t *xlseq, *tmp, *seq, *prottmp, *peptmp;
int i, count;
int id;
const int ncols=5;
if(!(xlseq=yamldom_find_map_val(iop->root,"xlink"))){
goto err;
}
count = 0;
for(seq=YAMLDOM_SEQ_NODES(xlseq);seq;seq=seq->next)
count += count_seq_elem(yamldom_find_map_val(seq,"peps"));
hidefromGC(idvec = allocVector(INTSXP,count));
hidefromGC(protidvec = allocVector(INTSXP,count));
hidefromGC(pepflagvec = allocVector(INTSXP,count));
hidefromGC(pepmassvec = allocVector(REALSXP,count));
hidefromGC(pepsitevec = allocVector(INTSXP,count));
i=0;
for(seq=YAMLDOM_SEQ_NODES(xlseq);seq;seq=seq->next){
if(!(peptmp=yamldom_find_map_val(seq,"peps")))
goto err;
peptmp = YAMLDOM_SEQ_NODES(peptmp);
push_elem(&id,0,seq,"id",strtoint);
while(peptmp){
INTEGER(idvec)[i] = id;
/* prot id/rank (via prot) */
if(!(prottmp=yamldom_find_map_val(peptmp,"prot")))
goto err;
tmp = YAMLDOM_DEREF(prottmp);
push_elem(INTEGER(protidvec),i,tmp,"id",strtoint);
push_elem(INTEGER(pepflagvec),i,peptmp,"flags",strtoint);
push_elem(REAL(pepmassvec),i,peptmp,"mass",strtodouble);
push_elem(INTEGER(pepsitevec),i,peptmp,"linksite",strtoint);
i++;
peptmp = peptmp->next;
}
}
make_list_names(df_names, ncols, "xlid", "protid", "pep.flag", "pep.mass", "pep.xlsite");
make_dataframe(df, RNULL, df_names, ncols, idvec, protidvec, pepflagvec, pepmassvec, pepsitevec);
unhideGC();
return df;
err:
unhideGC();
return RNULL;
}
SEXP makedf_scan(struct iobtd *iop){
SEXP df, df_names, plidvec, paridvec, sidvec, mzvec, zvec, intvec, rtvec;
yamldom_node_t *peakseq, *scanseq, *tmp, *seq, *scan;
int i, count;
int parid, id;
const int ncols=7;
if(!(scanseq=yamldom_find_map_val(iop->root,"scan"))){
goto err;
}
if(!(peakseq=yamldom_find_map_val(iop->root,"peaks"))){
goto err;
}
count=0;
for(seq=YAMLDOM_SEQ_NODES(peakseq);seq;seq=seq->next){
if(!(tmp=yamldom_find_map_val(seq,"scans")))
goto err;
count += count_seq_elem(tmp);
}
hidefromGC(sidvec = allocVector(INTSXP,count));
hidefromGC(plidvec = allocVector(INTSXP,count));
hidefromGC(paridvec = allocVector(INTSXP,count));
hidefromGC(mzvec = allocVector(REALSXP,count));
hidefromGC(zvec = allocVector(INTSXP,count));
hidefromGC(rtvec = allocVector(REALSXP,count));
hidefromGC(intvec = allocVector(REALSXP,count));
i=0;
for(seq=YAMLDOM_SEQ_NODES(peakseq);seq;seq=seq->next){
if(!(tmp=yamldom_find_map_val(seq,"id")))
goto err;
id=strtol(((yamldom_scalar_t*)tmp->data)->val,NULL,10);
if(!(tmp=yamldom_find_map_val(seq,"param")))
goto err;
tmp = YAMLDOM_DEREF(tmp);
if(!(tmp=yamldom_find_map_val(tmp,"id")))
goto err;
parid = strtol(((yamldom_scalar_t*)tmp->data)->val,NULL,10);
if(!(scanseq=yamldom_find_map_val(seq,"scans")))
goto err;
for(tmp=YAMLDOM_SEQ_NODES(scanseq);tmp;tmp=tmp->next){
scan=YAMLDOM_DEREF(tmp);
INTEGER(plidvec)[i]=id;
INTEGER(paridvec)[i]=parid;
push_elem(INTEGER(sidvec),i,scan,"id",strtoint);
push_elem(INTEGER(zvec),i,scan,"z",strtoint);
push_elem(REAL(mzvec),i,scan,"mz",strtodouble);
push_elem(REAL(intvec),i,scan,"preint",strtodouble);
push_elem(REAL(rtvec),i,scan,"rt",strtodouble);
if(REAL(rtvec)[i]<0.)
REAL(rtvec)[i]=0.;
i++;
}
}
make_list_names(df_names, ncols, "plid", "parid", "scanid", "mz", "z", "rt", "pre.int");
make_dataframe(df, RNULL, df_names, ncols, plidvec, paridvec, sidvec, mzvec, zvec, rtvec, intvec);
unhideGC();
return df;
err:
unhideGC();
return RNULL;
}
SEXP makedf_xlink(struct iobtd *iop){
SEXP df, df_names, idvec, peakidvec, errvec, covvec, modsv;
yamldom_node_t *xlseq, *tmp, *seq, *prottmp, *peptmp;
int i, count, modstrlen;
const int ncols=5;
char *mods;
if(!(xlseq=yamldom_find_map_val(iop->root,"xlink"))){
goto err;
}
count = count_seq_elem(xlseq);
hidefromGC(idvec = allocVector(INTSXP,count));
hidefromGC(peakidvec = allocVector(INTSXP,count));
hidefromGC(errvec = allocVector(REALSXP,count));
hidefromGC(covvec = allocVector(REALSXP,count));
hidefromGC(modsv = allocVector(STRSXP,count));
i=0;
for(seq=YAMLDOM_SEQ_NODES(xlseq);seq;seq=seq->next){
if(!(peptmp=yamldom_find_map_val(seq,"peps")))
goto err;
peptmp = YAMLDOM_SEQ_NODES(peptmp);
push_elem(INTEGER(idvec),i,seq,"id",strtoint);
push_elem(REAL(errvec),i,seq,"error",strtodouble);
push_elem(REAL(covvec),i,seq,"fragcov",strtodouble);
/* peaklist id (via prot -> param) */
if(!(prottmp=yamldom_find_map_val(peptmp,"prot")))
goto err;
tmp = YAMLDOM_DEREF(prottmp);
if(!(tmp=yamldom_find_map_val(tmp,"peaks")))
goto err;
tmp = YAMLDOM_DEREF(tmp);
push_elem(INTEGER(peakidvec),i,tmp,"id",strtoint);
if(!(tmp=yamldom_find_map_val(tmp,"param")))
goto err;
tmp = YAMLDOM_DEREF(tmp);
modstrlen = getmodstrlen(yamldom_find_map_val(tmp,"vmod"));
if(!(mods=malloc(modstrlen)))
goto err;
modstr(yamldom_find_map_val(seq,"mods"),mods);
if(mods && *mods)
SET_STRING_ELT(modsv, i, mkChar(mods));
else
SET_STRING_ELT(modsv, i, mkChar(""));
free(mods);
i++;
}
make_list_names(df_names, ncols, "xlid", "peakid", "error", "frag.cov", "mods");
make_dataframe(df, RNULL, df_names, ncols, idvec, peakidvec, errvec, covvec, modsv);
unhideGC();
return df;
err:
unhideGC();
return RNULL;
}
int run_shell() {
Value tmp_value;
int ascii_code = -1;
int cmd_code = -1;
wprintf(L"");
for (;;) {
tmp_value = get_char();
ascii_code = tmp_value.integer;
// EXPECTATIONS
cmd_code = analyse_expectations(ascii_code);
//wprintf(L"%d %d %lc\n",ascii_code, cmd_code, tmp_value.character);
switch(cmd_code) {
case EOT_CMD:
quit_shell();
break;
case DEL_L:
delete_from_buffer(false);
break;
case DEL_R:
delete_from_buffer(true);
break;
case UP_A_K:
wprintf(L"UP");
break;
case DOWN_A_K:
wprintf(L"DOWN");
break;
case RIGHT_A_K:
move_cusor(CURSOR_DIR_RIGHT);
break;
case LEFT_A_K:
move_cusor(CURSOR_DIR_LEFT);
break;
case BEGIN:
move_cusor(CURSOR_DIR_BEGIN);
break;
case END:
move_cusor(CURSOR_DIR_END);
break;
case ENTER_CMD:
if(handle_cmd() == RET_ERROR) {
print_error("Error while executing command!");
}
break;
case NO_CMD:
push_elem(buffer, tmp_value);
print_buffer(true);
break;
default:
//printf("%d => %c\n", ascii_code, tmp_value.character);
break;
}
}
return RET_OK;
}
