U_CAPI UBool U_EXPORT2
ucm_addMappingAuto(UCMFile *ucm, UBool forBase, UCMStates *baseStates,
UCMapping *m,
UChar32 codePoints[UCNV_EXT_MAX_UCHARS],
uint8_t bytes[UCNV_EXT_MAX_BYTES]) {
int32_t type;
if(m->f==2 && m->uLen>1) {
fprintf(stderr, "ucm error: illegal <subchar1> |2 mapping from multiple code points\n");
printMapping(m, codePoints, bytes, stderr);
return FALSE;
}
if(baseStates!=NULL) {
/* check validity of the bytes and count the characters in them */
type=ucm_mappingType(baseStates, m, codePoints, bytes);
if(type<0) {
/* illegal byte sequence */
printMapping(m, codePoints, bytes, stderr);
return FALSE;
}
} else {
/* not used - adding a mapping for an extension-only table before its base table is read */
type=1;
}
/*
* Add the mapping to the base table if this is requested and suitable.
* Otherwise, add it to the extension table.
*/
if(forBase && type==0) {
ucm_addMapping(ucm->base, m, codePoints, bytes);
} else {
ucm_addMapping(ucm->ext, m, codePoints, bytes);
}
return TRUE;
}
U_CAPI UBool U_EXPORT2
ucm_separateMappings(UCMFile *ucm, UBool isSISO) {
UCMTable *table;
UCMapping *m, *mLimit;
int32_t type;
UBool needsMove, isOK;
table=ucm->base;
m=table->mappings;
mLimit=m+table->mappingsLength;
needsMove=FALSE;
isOK=TRUE;
for(; m<mLimit; ++m) {
if(isSISO && m->bLen==1 && (m->b.bytes[0]==0xe || m->b.bytes[0]==0xf)) {
fprintf(stderr, "warning: removing illegal mapping from an SI/SO-stateful table\n");
ucm_printMapping(table, m, stderr);
m->moveFlag|=UCM_REMOVE_MAPPING;
needsMove=TRUE;
continue;
}
type=ucm_mappingType(
&ucm->states, m,
UCM_GET_CODE_POINTS(table, m), UCM_GET_BYTES(table, m));
if(type<0) {
/* illegal byte sequence */
printMapping(m, UCM_GET_CODE_POINTS(table, m), UCM_GET_BYTES(table, m), stderr);
isOK=FALSE;
} else if(type>0) {
m->moveFlag|=UCM_MOVE_TO_EXT;
needsMove=TRUE;
}
}
if(!isOK) {
return FALSE;
}
if(needsMove) {
ucm_moveMappings(ucm->base, ucm->ext);
return ucm_checkBaseExt(&ucm->states, ucm->base, ucm->ext, ucm->ext, FALSE);
} else {
ucm_sortTable(ucm->base);
return TRUE;
}
}
U_CAPI void U_EXPORT2
ucm_printMapping(UCMTable *table, UCMapping *m, FILE *f) {
printMapping(m, UCM_GET_CODE_POINTS(table, m), UCM_GET_BYTES(table, m), f);
}
void RNAFuncs::printMAliXML(deque<pair<double,RNAProfileAlignment*> > &resultList,const RNAforesterOptions &options, double &minPairProb,AddXmlInfos &xmlInfos,const string &outputFile)
{
string xsdurl = getXSDURL();
int j;
// get RNAforester call
const char** args;
int nrOptions;
string command;
args = options.getArgs();
nrOptions = options.getNrOfOptions();
for(int i=0;i<nrOptions;i++)
{
command.append(args[i]);
command.append(" ");
}
try
{
xmlpp::Document document;
deque<pair<string,string> > seqAli;
deque<string> strAli;
string consSeq, consStr;
deque<double> baseprobs;
deque<pair<pair<int,int>,double> > pairprobs;
stringstream tmpBase;
//create root node
xmlpp::Element* nodeRoot = document.create_root_node("rnastructAlignmentML", "", "");
//set namespace declarations to root element
nodeRoot->set_namespace_declaration(xsdurl, "");
nodeRoot->set_namespace_declaration("http://www.w3.org/2001/XMLSchema-instance","xsi");
nodeRoot->set_attribute("schemaLocation",xsdurl + " http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060515/rnastructAlignmentML.xsd","xsi");
// N VALues in the deque are n cluster
deque<pair<double,RNAProfileAlignment*> >::const_iterator it;
for(it=resultList.begin();it!=resultList.end();it++)
{
// create node rnastructalignment
xmlpp::Element* nodeRnaStructAlignment = nodeRoot->add_child("rnastructurealignment");
//print aligned sequences and structures
seqAli = it->second->getSeqAli();
strAli = it->second->getStrAli();
// j iterator to get structure alignment
j=0;
deque<pair<string,string> >::const_iterator it2;
for(it2=seqAli.begin();it2!=seqAli.end();it2++)
{
xmlpp::Element* nodeSequence = nodeRnaStructAlignment->add_child("sequence");
nodeSequence->set_attribute("seqID",xmlInfos.idmapping[atoi(it2->first.c_str())]);
if(xmlInfos.names.count(atoi(it2->first.c_str())) > 0){
nodeSequence->add_child("name")->set_child_text(xmlInfos.names[atoi(it2->first.c_str())]);
}
if(xmlInfos.synonyms.count(atoi(it2->first.c_str())) > 0){
nodeSequence->add_child("synonyms")->set_child_text(xmlInfos.synonyms[atoi(it2->first.c_str())]);
}
if(xmlInfos.descriptions.count(atoi(it2->first.c_str())) > 0){
nodeSequence->add_child("description")->set_child_text(xmlInfos.descriptions[atoi(it2->first.c_str())]);
}
xmlpp::Element* nodeAlignedFreeSequence = nodeSequence->add_child("alignedFreeSequence");
nodeAlignedFreeSequence->set_child_text(UpperCase(it2->second));
xmlpp::Element* nodeStructure = nodeSequence->add_child("structure");
nodeStructure->set_child_text(strAli[j]);
if(xmlInfos.comments.count(atoi(it2->first.c_str())) > 0){
nodeSequence->add_child("comment")->set_child_text(xmlInfos.comments[atoi(it2->first.c_str())]);
}
j++;
}
// insert consensus element
xmlpp::Element* nodeConsensus = nodeRnaStructAlignment->add_child("consensus");
// get and insert structure pairprobs
it->second->getPairProb(minPairProb, pairprobs);
xmlpp::Element* nodeStrProbs = nodeConsensus->add_child("structureprobabilities");
deque<pair<pair<int,int>,double> >::iterator it3;
for(it3=pairprobs.begin();it3!=pairprobs.end();it3++) {
xmlpp::Element* nodePt = nodeStrProbs->add_child("pt");
tmpBase << it3->first.first;
nodePt->set_attribute("a",tmpBase.str());
tmpBase.str("");
tmpBase << it3->first.second;
nodePt->set_attribute("b",tmpBase.str());
tmpBase.str("");
tmpBase << it3->second;
nodePt->set_attribute("probability",tmpBase.str());
tmpBase.str("");
}
// get and insert consensus sequence
consSeq = it->second->getConsSeq();
xmlpp::Element* nodeConsSeq = nodeConsensus->add_child("sequence");
nodeConsSeq->set_attribute("seqID","consensus");
xmlpp::Element* nodeAlignedFSCons = nodeConsSeq->add_child("alignedFreeSequence");
nodeAlignedFSCons->set_child_text(UpperCase(consSeq));
// get and insert consensus structure
consStr = it->second->getConsStr(minPairProb);
xmlpp::Element* nodeConsStr = nodeConsSeq->add_child("structure");
nodeConsStr->set_child_text(consStr);
//xmlpp::Element* nodeConsStr = nodeConsensus->add_child("structure");
//nodeConsStr->set_child_text(consStr);
// insert nodes program and attribute command
xmlpp::Element* nodeProgram = nodeRnaStructAlignment->add_child("program");
nodeProgram->set_attribute("command",command);
} // end for
document.write_to_file("./" + outputFile,"UTF-8");
// display the mapping from the internal id to the name of the sequence / structure qualified in the name element in the rnastructML
if(xmlInfos.xmlInput){
printMapping(xmlInfos.idmapping);
}
} catch(const std::exception& ex)
{
cout << "xml exception: " << ex.what() << std::endl;
}
}
void RNAFuncs::printPAliXML(const string &id1, const string &id2, const string &seq1, const string &seq2, const string &str1, const string &str2, double &score, const RNAforesterOptions &options,AddXmlInfos &xmlInfos,const string &outputFile)
{
char arr_Score[20];
const char** args;
int nrOptions;
string command;
bool xmlInput;
string comment1;
string comment2;
string description1;
string description2;
xmlpp::Document* xmlDocOrig;
xmlpp::DomParser domParser;
xmlpp::Element* elemRootOrig;
xmlpp::NodeSet nodeSetOrig;
args = options.getArgs();
nrOptions = options.getNrOfOptions();
for(int i=0;i<nrOptions;i++){
command.append(args[i]);
command.append(" ");
}
try
{
xmlpp::Document document;
xmlpp::Element* nodeSequences[2];
xmlpp::Element* nodeProgram;
string xsdurl;
xsdurl = getXSDURL();
//create root node
xmlpp::Element* nodeRoot = document.create_root_node("rnastructAlignmentML", "", "");
//set namespace declarations to root element
nodeRoot->set_namespace_declaration(xsdurl, "");
nodeRoot->set_namespace_declaration("http://www.w3.org/2001/XMLSchema-instance","xsi");
nodeRoot->set_attribute("schemaLocation",xsdurl + " http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060515/rnastructAlignmentML.xsd","xsi");
xmlpp::Element* nodeRnaStructAlignment = nodeRoot->add_child("rnastructurealignment");
//convert double to char array to use in set_attribute
sprintf(arr_Score,"%.0f",score);
nodeRnaStructAlignment->set_attribute("score",arr_Score);
nodeSequences[1] = nodeRnaStructAlignment->add_child("sequence");
nodeSequences[1]->set_attribute("seqID",xmlInfos.idmapping[atoi(id1.c_str())]);
if(options.has(RNAforesterOptions::LocalSimilarity)){
stringstream ss;
ss << xmlInfos.xbasepos;
nodeSequences[1]->set_attribute("startingposition",ss.str());
}
if(xmlInfos.names.count(atoi(id1.c_str())) > 0){
nodeSequences[1]->add_child("name")->set_child_text(xmlInfos.names[atoi(id1.c_str())]);
}
if(xmlInfos.synonyms.count(atoi(id1.c_str())) > 0){
nodeSequences[1]->add_child("synonyms")->set_child_text(xmlInfos.synonyms[atoi(id1.c_str())]);
}
if(xmlInfos.descriptions.count(atoi(id1.c_str())) > 0){
nodeSequences[1]->add_child("description")->set_child_text(xmlInfos.descriptions[atoi(id1.c_str())]);
}
nodeSequences[1]->add_child("alignedFreeSequence")->set_child_text(UpperCase(seq1));
nodeSequences[1]->add_child("structure")->set_child_text(str1);
// id is of type string index of map is of size int => convert
if(xmlInfos.comments.count(atoi(id1.c_str())) > 0){
nodeSequences[1]->add_child("comment")->set_child_text(xmlInfos.comments[atoi(id1.c_str())]);
}
nodeSequences[2] = nodeRnaStructAlignment->add_child("sequence");
nodeSequences[2]->set_attribute("seqID",xmlInfos.idmapping[atoi(id2.c_str())]);
if(options.has(RNAforesterOptions::LocalSimilarity)){
stringstream ss;
ss << xmlInfos.ybasepos;
nodeSequences[2]->set_attribute("startingposition",ss.str());
}
if(xmlInfos.names.count(atoi(id2.c_str())) > 0){
nodeSequences[2]->add_child("name")->set_child_text(xmlInfos.names[atoi(id2.c_str())]);
}
if(xmlInfos.synonyms.count(atoi(id2.c_str())) > 0){
nodeSequences[2]->add_child("synonyms")->set_child_text(xmlInfos.synonyms[atoi(id2.c_str())]);
}
if(xmlInfos.descriptions.count(atoi(id2.c_str())) > 0){
nodeSequences[2]->add_child("description")->set_child_text(xmlInfos.descriptions[atoi(id2.c_str())]);
}
nodeSequences[2]->add_child("alignedFreeSequence")->set_child_text(UpperCase(seq2));
nodeSequences[2]->add_child("structure")->set_child_text(str2);
// id is of type string index of map is of size int => convert
if(xmlInfos.comments.count(atoi(id2.c_str())) > 0){
nodeSequences[2]->add_child("comment")->set_child_text(xmlInfos.comments[atoi(id2.c_str())]);
}
nodeRnaStructAlignment->add_child("program")->set_attribute("command",command);
document.write_to_file("./" + outputFile,"UTF-8");
// display the mapping from the internal id to the name of the sequence / structure qualified in the name element in the rnastructML
if(xmlInfos.xmlInput){
printMapping(xmlInfos.idmapping);
}
} catch(const std::exception& ex) {
cout << "xml exception: " << ex.what() << std::endl;
}
}
int
main(int argc, char **argv)
{
extern int optind;
char *database = NULL;
char *ldapfilter = NULL;
char *attribute = "dn";
char **key = NULL;
char **ldapattribute = NULL;
char *buffer[100];
char *err = NULL;
char *p;
int index = 1;
int c;
int rc;
int verbose = 0;
char *udata = NULL;
ns_standalone_conf_t standalone_cfg = standaloneDefaults;
ns_ldap_error_t *errorp = NULL;
char *authmech = NULL;
ns_auth_t auth = {NS_LDAP_AUTH_NONE,
NS_LDAP_TLS_NONE,
NS_LDAP_SASL_NONE,
NS_LDAP_SASLOPT_NONE};
(void) setlocale(LC_ALL, "");
(void) textdomain(TEXT_DOMAIN);
openlog("ldaplist", LOG_PID, LOG_USER);
if (argc == 2 &&
strlen(argv[1]) == 2 && strncmp(argv[1], "-h", 2) == 0) {
/* preserve backwards compatability, support old -h option */
(void) printMapping();
exit(0);
}
while ((c = getopt(argc, argv, "h:M:N:P:r:a:D:w:j:dgvl")) != EOF) {
switch (c) {
case 'd':
listflag |= NS_LDAP_SCOPE_BASE;
break;
case 'g':
(void) printMapping();
exit(0);
break; /* Never reached */
case 'l':
attribute = "NULL";
break;
case 'v':
verbose = 1;
break;
case 'M':
standalone_cfg.type = NS_LDAP_SERVER;
standalone_cfg.SA_DOMAIN = optarg;
break;
case 'h':
standalone_cfg.type = NS_LDAP_SERVER;
if (separatePort(optarg,
&standalone_cfg.SA_SERVER,
&standalone_cfg.SA_PORT) > 0) {
exit(1);
}
break;
case 'P':
standalone_cfg.type = NS_LDAP_SERVER;
standalone_cfg.SA_CERT_PATH = optarg;
break;
case 'N':
standalone_cfg.type = NS_LDAP_SERVER;
standalone_cfg.SA_PROFILE_NAME = optarg;
break;
case 'D':
standalone_cfg.type = NS_LDAP_SERVER;
standalone_cfg.SA_BIND_DN = strdup(optarg);
break;
case 'w':
if (standalone_cfg.SA_BIND_PWD != NULL) {
(void) fprintf(stderr,
gettext("The -w option is mutually "
"exclusive of -j. -w is ignored.\n"));
break;
}
if (optarg != NULL &&
optarg[0] == '-' && optarg[1] == '\0') {
/* Ask for a password later */
break;
}
standalone_cfg.type = NS_LDAP_SERVER;
standalone_cfg.SA_BIND_PWD = strdup(optarg);
break;
case 'j':
if (standalone_cfg.SA_BIND_PWD != NULL) {
(void) fprintf(stderr,
gettext("The -w option is mutually "
"exclusive of -j. -w is ignored.\n"));
free(standalone_cfg.SA_BIND_PWD);
}
standalone_cfg.type = NS_LDAP_SERVER;
standalone_cfg.SA_BIND_PWD = readPwd(optarg);
if (standalone_cfg.SA_BIND_PWD == NULL) {
exit(1);
}
break;
case 'a':
authmech = optarg;
break;
default:
usage(gettext("Invalid option"));
}
}
if (standalone_cfg.type == NS_LDAP_SERVER &&
standalone_cfg.SA_SERVER == NULL) {
(void) fprintf(stderr,
gettext("Please specify an LDAP server you want "
"to connect to. \n"));
exit(1);
}
if ((c = argc - optind) > 0)
database = argv[optind++];
if ((--c) > 0)
key = &argv[optind];
if (authmech != NULL) {
if (__ns_ldap_initAuth(authmech,
&auth,
&errorp) != NS_LDAP_SUCCESS) {
if (errorp) {
(void) fprintf(stderr, "%s", errorp->message);
(void) __ns_ldap_freeError(&errorp);
}
exit(1);
}
}
if (auth.saslmech != NS_LDAP_SASL_GSSAPI &&
standalone_cfg.SA_BIND_DN != NULL &&
standalone_cfg.SA_BIND_PWD == NULL) {
/* If password is not specified, then prompt user for it. */
standalone_cfg.SA_BIND_PWD =
strdup(getpassphrase("Enter password:"******"%s\n", errorp->message);
(void) __ns_ldap_freeError(&errorp);
}
exit(1);
}
if (authmech != NULL) {
if (__ns_ldap_setParam(NS_LDAP_AUTH_P,
authmech, &errorp) != NS_LDAP_SUCCESS) {
__ns_ldap_cancelStandalone();
if (errorp != NULL) {
(void) fprintf(stderr, "%s", errorp->message);
(void) __ns_ldap_freeError(&errorp);
}
exit(1);
}
}
if (standalone_cfg.SA_CRED != NULL) {
if (__ns_ldap_setParam(NS_LDAP_CREDENTIAL_LEVEL_P,
standalone_cfg.SA_CRED, &errorp) != NS_LDAP_SUCCESS) {
__ns_ldap_cancelStandalone();
if (errorp != NULL) {
(void) fprintf(stderr, "%s", errorp->message);
(void) __ns_ldap_freeError(&errorp);
}
exit(1);
}
}
if (standalone_cfg.type != NS_CACHEMGR &&
standalone_cfg.SA_BIND_DN != NULL) {
ns_auth_t **authpp = NULL, **authp = NULL;
if (__ns_ldap_getParam(NS_LDAP_AUTH_P,
(void ***)&authpp,
&errorp) != NS_LDAP_SUCCESS || authpp == NULL) {
__ns_ldap_cancelStandalone();
(void) __ns_ldap_freeParam((void ***)&authpp);
if (errorp) {
(void) fprintf(stderr,
gettext(errorp->message));
(void) __ns_ldap_freeError(&errorp);
}
exit(1);
}
for (authp = authpp; *authp; authp++) {
if ((*authp)->saslmech == NS_LDAP_SASL_GSSAPI) {
/*
* For now we have no use for bindDN and
* bindPassword when using SASL/GSSAPI.
*/
(void) fprintf(stderr,
gettext("Warning: SASL/GSSAPI will be "
"used as an authentication method"
"The bind DN and password will "
"be ignored.\n"));
break;
}
}
}
/*
* If dumpping a database,
* or all the containers,
* use page control just
* in case there are too many entries
*/
if (!key && !(listflag & NS_LDAP_SCOPE_BASE))
listflag |= NS_LDAP_PAGE_CTRL;
/* build the attribute array */
if (strncasecmp(attribute, "NULL", 4) == 0)
ldapattribute = NULL;
else {
buffer[0] = strdup(attribute);
while ((p = strchr(attribute, ',')) != NULL) {
buffer[index++] = attribute = p + 1;
*p = '\0';
}
buffer[index] = NULL;
ldapattribute = buffer;
}
/* build the filter */
if (database && (strcasecmp(database, "publickey") == NULL)) {
/* user publickey lookup */
char *err1 = NULL;
int rc1;
rc = rc1 = -1;
ldapfilter = set_filter_publickey(key, database, 0, &udata);
if (ldapfilter) {
if (verbose) {
(void) fprintf(stdout,
gettext("+++ database=%s\n"),
(database ? database : "NULL"));
(void) fprintf(stdout,
gettext("+++ filter=%s\n"),
(ldapfilter ? ldapfilter : "NULL"));
(void) fprintf(stdout,
gettext("+++ template for merging"
"SSD filter=%s\n"),
(udata ? udata : "NULL"));
}
rc = list("passwd", ldapfilter, ldapattribute,
&err, udata);
free(ldapfilter);
free(udata);
}
/* hosts publickey lookup */
ldapfilter = set_filter_publickey(key, database, 1, &udata);
if (ldapfilter) {
if (verbose) {
(void) fprintf(stdout,
gettext("+++ database=%s\n"),
(database ? database : "NULL"));
(void) fprintf(stdout,
gettext("+++ filter=%s\n"),
(ldapfilter ? ldapfilter : "NULL"));
(void) fprintf(stdout,
gettext("+++ template for merging"
"SSD filter=%s\n"),
(udata ? udata : "NULL"));
}
rc1 = list("hosts", ldapfilter, ldapattribute,
&err1, udata);
free(ldapfilter);
free(udata);
}
if (rc == -1 && rc1 == -1) {
/* this should never happen */
(void) fprintf(stderr,
gettext("ldaplist: invalid publickey lookup\n"));
rc = 2;
} else if (rc != 0 && rc1 != 0) {
(void) fprintf(stderr,
gettext("ldaplist: %s\n"), (err ? err : err1));
if (rc == -1)
rc = rc1;
} else
rc = 0;
exit(switch_err(rc));
}
/*
* we set the search filter to (objectclass=*) when we want
* to list the directory attribute instead of the entries
* (the -d option).
*/
if (((ldapfilter = set_filter(key, database, &udata)) == NULL) ||
(listflag == NS_LDAP_SCOPE_BASE)) {
ldapfilter = strdup("objectclass=*");
udata = strdup("%s");
}
if (verbose) {
(void) fprintf(stdout, gettext("+++ database=%s\n"),
(database ? database : "NULL"));
(void) fprintf(stdout, gettext("+++ filter=%s\n"),
(ldapfilter ? ldapfilter : "NULL"));
(void) fprintf(stdout,
gettext("+++ template for merging SSD filter=%s\n"),
(udata ? udata : "NULL"));
}
if (rc = list(database, ldapfilter, ldapattribute, &err, udata))
(void) fprintf(stderr, gettext("ldaplist: %s\n"), err);
__ns_ldap_cancelStandalone();
if (ldapfilter)
free(ldapfilter);
if (udata)
free(udata);
exit(switch_err(rc));
return (0); /* Never reached */
}