bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
return true;
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (_program != GROUP_BY &&
_files[0]->getRecordType() == FileRecordTypeChecker::NO_POS_PLUS_RECORD_TYPE)
{
_errorMsg = "ERROR: file ";
_errorMsg.append(_files[0]->getFileName());
_errorMsg.append(" has non positional records, which are only valid for \n");
_errorMsg.append(" the groupBy tool. Perhaps you are using a header");
_errorMsg.append(" line(s) that starts with \n");
_errorMsg.append(" something other than \"#\", \"chrom\", or \"chr\" (any case)?");
return false;
}
if (getObeySplits()) {
_splitBlockInfo = new BlockMgr(_overlapFractionA, _reciprocalFraction);
}
if (hasColumnOpsMethods()) {
if (hasIntersectMethods()) {
for (int i=0; i < (int)_dbFileIdxs.size(); i++) {
FileRecordMgr *dbFile = getFile(_dbFileIdxs[i]);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
} else {
FileRecordMgr *dbFile = getFile(0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
//if user specified a precision, pass it to
//keyList ops
if (_reportPrecision != -1) {
_keyListOps->setPrecision(_reportPrecision);
}
}
return true;
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (hasColumnOpsMethods()) {
FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
return true;
}
bool ContextBase::isValidState()
{
if (!openFiles()) {
return false;
}
if (!cmdArgsValid()) {
return false;
}
if (!determineOutputType()) {
return false;
}
if (getObeySplits()) {
_splitBlockInfo = new BlockMgr(_overlapFraction, _reciprocal);
}
if (hasColumnOpsMethods()) {
if (hasIntersectMethods()) {
for (int i=0; i < (int)_dbFileIdxs.size(); i++) {
FileRecordMgr *dbFile = getFile(_dbFileIdxs[i]);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
} else {
FileRecordMgr *dbFile = getFile(0);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
}
}
//if user specified a precision, pass it to
//keyList ops
if (_reportPrecision != -1) {
_keyListOps->setPrecision(_reportPrecision);
}
}
return true;
}
int
main(int argc, const char *argv[]) {
struct cmdlineInfo cmdline;
FILE * underlayFileP;
FILE * overlayFileP;
FILE * alphaFileP;
struct pam underlayPam;
struct pam overlayPam;
struct pam alphaPam;
struct pam composedPam;
int originLeft, originTop;
pm_proginit(&argc, argv);
parseCommandLine(argc, argv, &cmdline);
overlayFileP = pm_openr(cmdline.overlayFilespec);
overlayPam.comment_p = NULL;
pnm_readpaminit(overlayFileP, &overlayPam,
PAM_STRUCT_SIZE(opacity_plane));
if (overlayPam.len < PAM_STRUCT_SIZE(opacity_plane))
pm_error("Libnetpbm is too old. This program requires libnetpbm from "
"Netpbm 10.56 (September 2011) or newer");
if (!overlayPam.visual)
pm_error("Overlay image has tuple type '%s', which is not a "
"standard visual type. We don't know how to compose.",
overlayPam.tuple_type);
initAlphaFile(cmdline, &overlayPam, &alphaFileP, &alphaPam);
underlayFileP = pm_openr(cmdline.underlyingFilespec);
underlayPam.comment_p = NULL;
pnm_readpaminit(underlayFileP, &underlayPam,
PAM_STRUCT_SIZE(opacity_plane));
assert(underlayPam.len >= PAM_STRUCT_SIZE(opacity_plane));
if (!overlayPam.visual)
pm_error("Overlay image has tuple type '%s', which is not a "
"standard visual type. We don't know how to compose.",
overlayPam.tuple_type);
computeOverlayPosition(underlayPam.width, underlayPam.height,
overlayPam.width, overlayPam.height,
cmdline, &originLeft, &originTop);
composedPam.size = PAM_STRUCT_SIZE(opacity_plane);
composedPam.len = PAM_STRUCT_SIZE(allocation_depth);
composedPam.allocation_depth = 0;
composedPam.file = pm_openw(cmdline.outputFilespec);
composedPam.comment_p = NULL;
determineOutputType(&underlayPam, &overlayPam, &composedPam);
pnm_setminallocationdepth(&underlayPam, composedPam.depth);
pnm_setminallocationdepth(&overlayPam, composedPam.depth);
composite(originLeft, originTop,
&underlayPam, &overlayPam, alphaFileP ? &alphaPam : NULL,
cmdline.alphaInvert, cmdline.opacity,
&composedPam, cmdline.linear, cmdline.mixtransparency);
if (alphaFileP)
pm_close(alphaFileP);
pm_close(overlayFileP);
pm_close(underlayFileP);
pm_close(composedPam.file);
/* If the program failed, it previously aborted with nonzero completion
code, via various function calls.
*/
return 0;
}
int
main(int argc, char *argv[]) {
struct cmdlineInfo cmdline;
FILE * underlayFileP;
FILE * overlayFileP;
FILE * alphaFileP;
struct pam underlayPam;
struct pam overlayPam;
struct pam alphaPam;
struct pam composedPam;
int originLeft, originTop;
pnm_init(&argc, argv);
parseCommandLine(argc, argv, &cmdline);
overlayFileP = pm_openr(cmdline.overlayFilespec);
pnm_readpaminit(overlayFileP, &overlayPam,
PAM_STRUCT_SIZE(allocation_depth));
if (cmdline.alphaFilespec) {
alphaFileP = pm_openr(cmdline.alphaFilespec);
pnm_readpaminit(alphaFileP, &alphaPam,
PAM_STRUCT_SIZE(allocation_depth));
if (overlayPam.width != alphaPam.width ||
overlayPam.height != alphaPam.height)
pm_error("Opacity map and overlay image are not the same size");
} else
alphaFileP = NULL;
underlayFileP = pm_openr(cmdline.underlyingFilespec);
pnm_readpaminit(underlayFileP, &underlayPam,
PAM_STRUCT_SIZE(allocation_depth));
computeOverlayPosition(underlayPam.width, underlayPam.height,
overlayPam.width, overlayPam.height,
cmdline, &originLeft, &originTop);
composedPam.size = sizeof(composedPam);
composedPam.len = PAM_STRUCT_SIZE(allocation_depth);
composedPam.allocation_depth = 0;
composedPam.file = pm_openw(cmdline.outputFilespec);
determineOutputType(&composedPam, &underlayPam, &overlayPam);
pnm_setminallocationdepth(&underlayPam, composedPam.depth);
pnm_setminallocationdepth(&overlayPam, composedPam.depth);
composite(originLeft, originTop,
&underlayPam, &overlayPam, alphaFileP ? &alphaPam : NULL,
cmdline.alphaInvert, cmdline.opacity,
&composedPam, cmdline.linear);
if (alphaFileP)
pm_close(alphaFileP);
pm_close(overlayFileP);
pm_close(underlayFileP);
pm_close(composedPam.file);
/* If the program failed, it previously aborted with nonzero completion
code, via various function calls.
*/
return 0;
}
