int network_information_table_section::subtable::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for records**/ /* This line is probably buggy size needs to be adjusted */
numberOfRecords=((short)records.getCount() -(0));
}
{ /** fix dependent sizes for descriptor **/
}
int retVal= 0;
// write firstIndex
ostream.writeUI8(firstIndex);
retVal +=1;
// write numberOfRecords
ostream.writeUI8(numberOfRecords);
retVal +=1;
// write bf3
ostream.writeUI8(bf3);
retVal +=1;
// write records
{ for (ArrayList_iterator(network_information_table_section::subtable::Record) it= records.getIterator() ; it.hasNext();) {
{
retVal +=it.get()->write(ostream);
}
}
}
// write descriptor
if ( descriptor != NULL ) {
retVal +=descriptor->write(ostream);
}
return retVal;
}
int network_information_table_section::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for tableHeader **/
}
{ /** fix dependent sizes for subtableInstance **/ if ( subtableInstance != NULL ) {
tableHeader->setSection_length((short)subtableInstance->getSize());
}
}
int retVal= 0;
// write tableHeader
if ( tableHeader != NULL ) {
retVal +=tableHeader->write(ostream);
}
// write bf2
ostream.writeUI8(bf2);
retVal +=1;
// write subtableInstance
if ( subtableInstance != NULL ) {
retVal +=subtableInstance->write(ostream);
}
// write CRC
ostream.writeUI32(CRC);
retVal +=4;
return retVal;
}
void
TexturePaletteManager::write( DataOutputStream& dos ) const
{
int x( 0 ), y( 0 ), height( 0 );
TextureIndexMap::const_iterator it = _indexMap.begin();
while (it != _indexMap.end())
{
const osg::Texture2D* texture = it->first;
int index = it->second;
std::string fileName;
if ( _fltOpt.getStripTextureFilePath() )
fileName = osgDB::getSimpleFileName( texture->getImage()->getFileName() );
else
fileName = texture->getImage()->getFileName();
dos.writeInt16( (int16) TEXTURE_PALETTE_OP );
dos.writeUInt16( 216 );
dos.writeString( fileName, 200 );
dos.writeInt32( index );
dos.writeInt32( x );
dos.writeInt32( y );
it++;
x += texture->getImage()->s();
if (texture->getImage()->t() > height)
height = texture->getImage()->t();
if (x > 1024)
{
x = 0;
y += height;
height = 0;
}
}
}
int softwareVerMMsg::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for applicationNameByte**/
}
{ /** fix dependent sizes for applicationSignbyte**/
}
{ /** fix dependent sizes for applicationVersionbyte**/
}
int retVal= 0;
// write ApplicationStatusflag
ostream.writeUI8(ApplicationStatusflag);
retVal +=1;
// write applicationNameByte
{
retVal += applicationNameByte->write(ostream);
}
// write applicationSignbyte
{
retVal += applicationSignbyte->write(ostream);
}
// write applicationVersionbyte
{
retVal += applicationVersionbyte->write(ostream);
}
return retVal;
}
int codeVersionTable1_3::statusfld2::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for mcAddress **/
}
{ /** fix dependent sizes for sourceIpAddress **/
}
{ /** fix dependent sizes for destinationIpAddress **/
}
int retVal= 0;
// write mcAddress
if ( mcAddress != NULL ) {
retVal +=mcAddress->write(ostream);
}
// write sourceIpAddress
if ( sourceIpAddress != NULL ) {
retVal +=sourceIpAddress->write(ostream);
}
// write destinationIpAddress
if ( destinationIpAddress != NULL ) {
retVal +=destinationIpAddress->write(ostream);
}
// write sourcePortNumber
ostream.writeUI16(sourcePortNumber);
retVal +=2;
// write destinatioPortNumber
ostream.writeUI16(destinatioPortNumber);
retVal +=2;
// write applicationId
ostream.writeUI16(applicationId);
retVal +=2;
// write modulationType
ostream.writeUI8(modulationType);
retVal +=1;
// write bf2
ostream.writeUI16(bf2);
retVal +=2;
return retVal;
}
int DSG_packetError::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for header **/
}
int retVal= 0;
// write header
if ( header != NULL ) {
retVal +=header->write(ostream);
}
// write length
ostream.writeUI8(length);
retVal +=1;
// write transaction_id
ostream.writeUI8(transaction_id);
retVal +=1;
return retVal;
}
int CloseMmiCnf::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for header **/
}
int retVal= 0;
// write header
if ( header != NULL ) {
retVal +=header->write(ostream);
}
// write length
ostream.writeUI8(length);
retVal +=1;
// write dialogNumber
ostream.writeUI8(dialogNumber);
retVal +=1;
return retVal;
}
void SaveHandler::func_22154_d()
{
try
{
File file = new File(saveDirectory, "session.lock");
DataOutputStream dataoutputstream = new DataOutputStream(new FileOutputStream(file));
try
{
dataoutputstream.writeLong(now);
}
ly
{
dataoutputstream.close();
}
}
catch(IOException ioexception)
{
ioexception.printStackTrace();
throw new RuntimeException("Failed to check session lock, aborting");
}
}
int OpenSessionResponse::write(DataOutputStream& ostream) { // throws IOException
int retVal= 0;
// write length
ostream.writeUI8(length);
retVal +=1;
// write resourceIdentifier
ostream.writeUI32(resourceIdentifier);
retVal +=4;
// write sessionStatus
ostream.writeUI8(sessionStatus);
retVal +=1;
// write sessionNb
ostream.writeUI16(sessionNb);
retVal +=2;
return retVal;
}
int HomingCancelled::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for header **/
}
int retVal= 0;
// write header
if ( header != NULL ) {
retVal +=header->write(ostream);
}
// write length
ostream.writeUI8(length);
retVal +=1;
return retVal;
}
int diagnosticReq_2_Smode::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for selfDiagnostics**/
}
int retVal= 0;
// write length
ostream.writeUI8(length);
retVal +=1;
// write selfDiagnostics
{
retVal += selfDiagnostics->write(ostream);
}
return retVal;
}
void Engine::write_socket(DataOutputStream & network_out)
{
while(true)
{
if( waiting_to_socket_data.empty() )
{
int cbPending = int(BIO_ctrl_pending(bioOut));
if( cbPending == 0 )
break;
waiting_to_socket_data = Data(cbPending);
int len = BIO_read(bioOut, waiting_to_socket_data.lock(), waiting_to_socket_data.getSize());
wLog("BIO_read: %d", len);
waiting_to_socket_data = Data(waiting_to_socket_data, 0, len);
}
int slen = network_out.write(waiting_to_socket_data);
wLog("sock.write: %d", slen);
if( !waiting_to_socket_data.empty() )
break;
}
}
int DescriptorCollection::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for descriptors**/ /* This line is probably buggy size needs to be adjusted */
descriptor_count=((short)descriptors.getCount() -(0));
}
int retVal= 0;
// write descriptor_count
ostream.writeUI8(descriptor_count);
retVal +=1;
// write descriptors
{ for (ArrayList_iterator(SCTE65DescriptorFactory::SCTE65Descriptor) it= descriptors.getIterator() ; it.hasNext();) {
{
retVal +=it.get()->write(ostream);
}
}
}
return retVal;
}
int HistoryReq::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for header **/
}
{ /** fix dependent sizes for pincodeLength**/
}
int retVal= 0;
// write header
if ( header != NULL ) {
retVal +=header->write(ostream);
}
// write length
ostream.writeUI8(length);
retVal +=1;
// write pincodeLength
{
retVal += pincodeLength->write(ostream);
}
return retVal;
}
int main (int argc, char **argv) {
if(isatty(STDIN_FILENO) && argc==1) {
cout<<"No input data or parameters. Use -h,--help for more information"<<endl;
exit(EXIT_FAILURE);
}
gengetopt_args_info args_info;
TRY_EXCEPTION();
if (cmdline_parser (argc, argv, &args_info) != 0)
exit(EXIT_FAILURE);
#ifndef WITH_LIBXML
if ( args_info.input_format_arg == input_format_arg_xml ) {
cerr << "The software was built with WITH_LIBXML=OFF. Please rebuild it if you want XML functionality." << endl;
exit(EXIT_FAILURE);
}
#endif // WITH_LIBXML
if ( args_info.print_relaxng_input_given && args_info.print_relaxng_output_given ) {
cerr << "error: --print-relaxng-input and --print-relaxng-output can not be used at the same time" << endl;
exit(EXIT_FAILURE);
}
if ( args_info.print_relaxng_input_given ) {
cout << fastphylo_distance_matrix_xml_relaxngstr << std::endl;
exit(EXIT_SUCCESS);
};
if ( args_info.print_relaxng_output_given ) {
cout << fastphylo_tree_count_xml_relaxngstr << std::endl;
exit(EXIT_SUCCESS);
};
//----------------------------------------------
// DISTANCE METHODS
std::vector<NJ_method> methods;
if( args_info.number_of_runs_given && args_info.input_format_arg == input_format_arg_xml ) {
cerr << "error: --number-of-runs can not be used together with input format xml." << endl;
exit(EXIT_FAILURE);
}
switch ( args_info.method_arg ) {
case method_arg_NJ:
methods.push_back(NJ);
break;
case method_arg_FNJ:
methods.push_back(FNJ);
break;
case method_arg_BIONJ:
methods.push_back(BIONJ);
break;
default:
cerr << "error: method chosen not available" << endl;
exit(EXIT_FAILURE);
}
bool printCounts = args_info.print_counts_flag;
try {
char * inputfilename = NULL;
char * outputfilename = NULL;
DataInputStream *istream;
DataOutputStream *ostream;
switch( args_info.inputs_num ) {
case 0:
break; /* inputfilename will be null and indicate stdin as input */
case 1:
inputfilename = args_info.inputs[0];
break;
default: cerr << "Error: you can at most specify one input filename" << endl;
exit(EXIT_FAILURE);
}
if( args_info.outfile_given )
outputfilename = args_info.outfile_arg;
switch ( args_info.input_format_arg ) {
case input_format_arg_phylip:
istream = new PhylipDmInputStream(inputfilename);
break;
case input_format_arg_binary: istream = new BinaryInputStream(inputfilename);
break;
#ifdef WITH_LIBXML
case input_format_arg_xml: istream = new XmlInputStream(inputfilename);
break;
#endif // WITH_LIBXML
default:
exit(EXIT_FAILURE);
}
switch (args_info.output_format_arg) {
case output_format_arg_newick:
ostream = new TreeTextOutputStream(outputfilename);
break;
case output_format_arg_xml:
ostream = new XmlOutputStream(outputfilename);
break;
default:
exit(EXIT_FAILURE);
}
//printf("%d\n", args_info.input_format_arg);
// THE DATA WE WILL PROCESS
vector<Sequence> seqs;
vector<std::string> names;
vector<DNA_b128_String> b128seqs;
Extrainfos extrainfos;
bool latestReadSuccessful = true;
vector<string> speciesnames;
readstatus status;
int run = 0;
status = END_OF_RUN;
while (status == END_OF_RUN && (args_info.input_format_arg == input_format_arg_xml || run<args_info.number_of_runs_arg)) {
string runId("");
run++;
tree2int_map tree2count((size_t)(args_info.bootstraps_arg * 1.3));
str2int_hashmap name2id;
if (args_info.input_format_arg==input_format_arg_binary) {
StrFloMatrix dm;
for (int runNo=1; (status = istream->readDM(dm, names, runId, extrainfos))==DM_READ; runNo++) {
if (args_info.analyze_run_number_given) {
if (runNo<args_info.analyze_run_number_arg)
continue;
if (runNo>args_info.analyze_run_number_arg) {
status=END_OF_RUN;
break;
}
}
for(size_t namei=0; namei<dm.getSize(); namei++)
name2id[dm.getIdentifier(namei)] = namei;
buildTrees(dm, tree2count, methods,name2id);
}
}
else {
StrDblMatrix dm;
for (int runNo=1; (status = istream->readDM(dm, names, runId, extrainfos))==DM_READ; runNo++) {
if (args_info.analyze_run_number_given) {
if (runNo<args_info.analyze_run_number_arg)
continue;
if (runNo>args_info.analyze_run_number_arg) {
status=END_OF_RUN;
break;
}
}
for(size_t namei=0; namei<dm.getSize(); namei++) {
name2id[dm.getIdentifier(namei)] = namei;
}
buildTrees(dm, tree2count, methods,name2id);
}
}
if (status==END_OF_RUN)
ostream->print(tree2count,printCounts, runId, names, extrainfos);
if (args_info.analyze_run_number_given)
break;
}//end run loop
delete ostream;
delete istream;
}
catch(...){
throw;
}
CATCH_EXCEPTION();
cmdline_parser_free(&args_info);
return 0;
}
int codeVersionTable1_3::write(DataOutputStream& ostream) { // throws IOException
{ /** fix dependent sizes for header **/
}
{ /** fix dependent sizes for pgmmsg**/
}
{ /** fix dependent sizes for statusfldInstance **/
}
{ /** fix dependent sizes for statusfld2Instance **/
}
{ /** fix dependent sizes for statusfld3Instance **/
}
{ /** fix dependent sizes for codeFileByte**/
}
{ /** fix dependent sizes for codeVeriFicationCertiFication **/
}
int retVal= 0;
// write header
if ( header != NULL ) {
retVal +=header->write(ostream);
}
// write length
ostream.writeUI8(length);
retVal +=1;
// write configurationCountChange
ostream.writeUI8(configurationCountChange);
retVal +=1;
// write statusField
ostream.writeUI8(statusField);
retVal +=1;
// write pgmmsg
{ for (ArrayList_iterator(codeVersionTableMsg) it= pgmmsg.getIterator() ; it.hasNext();) {
{
retVal +=it.get()->write(ostream);
}
}
}
// write bf1
ostream.writeUI8(bf1);
retVal +=1;
// write statusfldInstance
if ( statusfldInstance != NULL ) {
retVal +=statusfldInstance->write(ostream);
}
// write statusfld2Instance
if ( statusfld2Instance != NULL ) {
retVal +=statusfld2Instance->write(ostream);
}
// write statusfld3Instance
if ( statusfld3Instance != NULL ) {
retVal +=statusfld3Instance->write(ostream);
}
// write codeFileByte
{
retVal += codeFileByte->write(ostream);
}
// write codeVeriFicationCertiFication
if ( codeVeriFicationCertiFication != NULL ) {
retVal +=codeVeriFicationCertiFication->write(ostream);
}
return retVal;
}
void
LightSourcePaletteManager::write( DataOutputStream& dos ) const
{
using osg::Vec4f;
static int const INFINITE_LIGHT = 0;
static int const LOCAL_LIGHT = 1;
static int const SPOT_LIGHT = 2;
LightPalette::const_iterator it = _lightPalette.begin();
for ( ; it != _lightPalette.end(); ++it)
{
LightRecord m = it->second;
static char lightName[64];
sprintf(lightName, "Light%02d", m.Light->getLightNum() );
int lightType = INFINITE_LIGHT;
Vec4f const& lightPos = m.Light->getPosition();
if (lightPos.w() != 0)
{
if (m.Light->getSpotCutoff() < 180)
lightType = SPOT_LIGHT;
else
lightType = LOCAL_LIGHT;
}
dos.writeInt16( (int16) LIGHT_SOURCE_PALETTE_OP );
dos.writeInt16( 240 );
dos.writeInt32( m.Index );
dos.writeFill(2*4, '\0'); // Reserved
dos.writeString( lightName, 20 );
dos.writeFill(4, '\0'); // Reserved
dos.writeVec4f(m.Light->getAmbient() );
dos.writeVec4f(m.Light->getDiffuse() );
dos.writeVec4f(m.Light->getSpecular() );
dos.writeInt32(lightType);
dos.writeFill(4*10, '\0'); // Reserved
dos.writeFloat32(m.Light->getSpotExponent() );
dos.writeFloat32(m.Light->getSpotCutoff() );
dos.writeFloat32(0); // Yaw (N/A)
dos.writeFloat32(0); // Pitch (N/A)
dos.writeFloat32(m.Light->getConstantAttenuation() );
dos.writeFloat32(m.Light->getLinearAttenuation() );
dos.writeFloat32(m.Light->getQuadraticAttenuation() );
dos.writeInt32(0); // Modeling flag (N/A)
dos.writeFill(4*19, '\0'); // Reserved
}
}
void
MaterialPaletteManager::write( DataOutputStream& dos ) const
{
using osg::Vec4f;
MaterialPalette::const_iterator it = _materialPalette.begin();
for ( ; it != _materialPalette.end(); ++it)
{
MaterialRecord m = it->second;
Vec4f const& ambient = m.Material->getAmbient(osg::Material::FRONT);
Vec4f const& diffuse = m.Material->getDiffuse(osg::Material::FRONT);
Vec4f const& specular = m.Material->getSpecular(osg::Material::FRONT);
Vec4f const& emissive = m.Material->getEmission(osg::Material::FRONT);
float shininess = m.Material->getShininess(osg::Material::FRONT);
dos.writeInt16( (int16) MATERIAL_PALETTE_OP );
dos.writeInt16( 84 ); // Length - FIXME: hard-code/FLT version?
dos.writeInt32( m.Index );
dos.writeString( m.Material->getName(), 12 );
dos.writeInt32( 0 ); // Flags
dos.writeFloat32(ambient.r() );
dos.writeFloat32(ambient.g() );
dos.writeFloat32(ambient.b() );
dos.writeFloat32(diffuse.r() );
dos.writeFloat32(diffuse.g() );
dos.writeFloat32(diffuse.b() );
dos.writeFloat32(specular.r() );
dos.writeFloat32(specular.g() );
dos.writeFloat32(specular.b() );
dos.writeFloat32(emissive.r() );
dos.writeFloat32(emissive.g() );
dos.writeFloat32(emissive.b() );
dos.writeFloat32(shininess);
dos.writeFloat32( diffuse.a() ); // alpha
dos.writeFloat32(1.0f); // 'Reserved' - unused
if (m.Material->getAmbientFrontAndBack() == false ||
m.Material->getDiffuseFrontAndBack() == false ||
m.Material->getSpecularFrontAndBack() == false ||
m.Material->getEmissionFrontAndBack() == false ||
m.Material->getShininessFrontAndBack() == false )
{
std::string warning( "fltexp: No support for different front and back material properties." );
osg::notify( osg::WARN ) << warning << std::endl;
_fltOpt.getWriteResult().warn( warning );
}
}
}
