void Skin::save (const gdx_cpp::files::FileHandle& skinFile) {
String text = getJsonLoader(null).prettyPrint(this, true);
Writer writer = skinFile.writer(false);
try {
writer.write(text);
writer.close();
} catch (IOException ex) {
}
}
void Partition::write(const char* output_file_name) throw (Exception) {
Writer* writer = NULL;
block block;
const char* first_marker = NULL;
const char* last_marker = NULL;
unsigned int start_bp = 0u;
unsigned int end_bp = 0u;
unsigned int n_markers = 0u;
unsigned int n_haps = 0u;
unsigned int n_unique_haps = 0u;
unsigned int n_common_haps = 0u;
double haps_diversity = 0.0;
try {
writer = WriterFactory::create(Writer::TEXT);
writer->set_file_name(output_file_name);
writer->open(false);
writer->write("# VERSION: %s\n", LDEXPLORER_VERSION);
writer->write("# PHASE FILE: %s\n", db->hap_file_name);
writer->write("# MAP FILE: %s\n", db->map_file_name == NULL ? "NA" : db->map_file_name);
if ((db->start_position > 0u) || (db->end_position != numeric_limits<unsigned long int>::max())) {
writer->write("# REGION: [%u, %u]\n", db->start_position, db->end_position);
} else {
writer->write("# REGION: NA\n");
}
writer->write("# MAF FILTER: > %g\n", db->maf_threshold);
writer->write("# ALL SNPs: %u\n", db->n_unfiltered_markers);
writer->write("# FILTERED SNPs: %u\n",db->n_markers);
writer->write("# HAPLOTYPES: %u\n", db->n_haplotypes);
if (!rsq_blocks) {
writer->write("# D' CI COMPUTATION METHOD: %s\n", ci_method);
if (likelihood_density > 0u) {
writer->write("# D' LIKELIHOOD DENSITY: %u\n", likelihood_density);
} else {
writer->write("# D' LIKELIHOOD DENSITY: NA\n");
}
writer->write("# D' CI LOWER BOUND FOR STRONG LD: >= %g\n", strong_pair_cl);
writer->write("# D' CI UPPER BOUND FOR STRONG LD: >= %g\n", strong_pair_cu);
writer->write("# D' CI UPPER BOUND FOR RECOMBINATION: <= %g\n", recomb_pair_cu);
} else {
writer->write("# WEAK LD r^2: < %g\n", weak_pair_rsq);
writer->write("# STRONG LD r^2: >= %g\n", strong_pair_rsq);
}
writer->write("# FRACTION OF STRONG LD SNP PAIRS: >= %g\n", strong_pairs_fraction);
writer->write("# PRUNING METHOD: %s\n", pruning_method);
if (window > 0u) {
writer->write("# WINDOW: %ld\n", window);
} else {
writer->write("# WINDOW: NA\n", window);
}
writer->write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
"BLOCK_NAME", "FIRST_SNP", "LAST_SNP", "FIRST_SNP_ID", "LAST_SNP_ID", "START_BP", "END_BP", "N_SNPS", "N_HAPS", "N_UNIQUE_HAPS", "N_COMMON_HAPS", "HAPS_DIVERSITY");
for (unsigned int b = 0u; b < n_blocks; ++b) {
block = blocks[b];
first_marker = db->markers[block.start];
last_marker = db->markers[block.end];
start_bp = db->positions[block.start];
end_bp = db->positions[block.end];
n_markers = block.end - block.start + 1u;
get_block_diversity(b, &n_haps, &n_unique_haps, &n_common_haps, &haps_diversity);
writer->write("BLOCK%07u\t%s\t%s\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%u\t%g\n",
b + 1u, first_marker, last_marker, block.start, block.end, start_bp, end_bp, n_markers, n_haps, n_unique_haps, n_common_haps, haps_diversity);
}
writer->close();
delete writer;
} catch (Exception &e) {
if (writer != NULL) {
delete writer;
}
throw;
}
}
String AbstractContextI::loadValueFromURL(const String& urlstring) const throw (Exception)
{
String result;
StringBuffer buf;
buf->append(urlstring);
if (0 == buf->indexOf(L"http://"))
{
URL url = new URLI(urlstring);
HttpURLConnection httpurlconnection;
url->openConnection()->downcast(httpurlconnection);
if (verboseOutput()) cout << "JNDI context : Get response from url : " << urlstring << endl;
int rc = httpurlconnection->getResponseCode();
UTF8StringBuffer cbuf;
#if defined (_WINDOWS_SOURCE)
cbuf->append(getenv("TEMP"));
cbuf->append("\\");
cbuf->append(getenv("USERNAME"));
cbuf->append(".");
#else
cbuf->append(getenv("USER_HOME"));
cbuf->append("/.");
#endif
cbuf->append(urlstring->toMD5());
cbuf->append(".properties");
String cachefilepath = cbuf->toString()->toLowerCase();
if (200 != rc)
{
if (verboseOutput()) cout << "JNDI context : HTTP status = " << rc << endl;
if (verboseOutput()) cout << "JNDI context : Trying to load from cached file : " << cachefilepath << endl;
InputStream file = new FileInputStreamI(cachefilepath);
UTF8String content;
file->read(content, 0);
file->close();
result = content->toString();
}
else
{
String response = httpurlconnection->getResponseMessage();
Writer file = new FileWriterI(cachefilepath);
file->write(response);
file->close();
if (verboseOutput()) cout << "JNDI context : Caching to file : " << cachefilepath << endl;
result = response;
}
}
else if (0 == buf->indexOf(L"file://"))
{
result = loadValueFromFile(urlstring);
}
else
{
throw NamingException(WITHDETAILS(L"Unsupported URI format: " + urlstring));
}
StringBuffer b = result;
while (-1 < b->indexOf(L"${"))
{
InitialContext initialcontext = InitialContext::newInstance();
int bpos = 0;
int epos = 0;
while (bpos < b->length())
{
bpos = b->indexOf(L"${", bpos);
if (-1 == bpos) break;
epos = b->indexOf(L"}", bpos);
String variablename = b->substring(bpos + 2, epos);
StringAnything variablevalue ;
initialcontext->lookup(L"/" + variablename, variablevalue);
StringBuffer value = variablevalue->toString();
if (-1 < value->indexOf(L"${" + variablename + L"}") )
throw Exception(WITHDETAILS(L"Recursive reference found : ${" + variablename + L"}"));
b->replace(bpos, epos + 1, value->toString());
bpos = epos + 1;
}
}
return b->toString();
}
