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; }