//**********************************************************************************************************************
int SharedCommand::createSharedFromListGroup() {
try {
GroupMap* groupMap = NULL;
CountTable* countTable = NULL;
pickedGroups = false;
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
int groupError = groupMap->readMap();
if (groupError == 1) { delete groupMap; return 0; }
vector<string> allGroups = groupMap->getNamesOfGroups();
if (Groups.size() == 0) { Groups = allGroups; }
else { pickedGroups = true; }
}else{
countTable = new CountTable();
countTable->readTable(countfile, true, false);
vector<string> allGroups = countTable->getNamesOfGroups();
if (Groups.size() == 0) { Groups = allGroups; }
else { pickedGroups = true; }
}
int numGroups = Groups.size();
if (m->getControl_pressed()) { return 0; }
ofstream out;
string filename = "";
if (!pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
util.openOutputFile(filename, out);
}
//set fileroot
fileroot = outputDir + util.getRootName(util.getSimpleName(listfile));
map<string, string> variables;
variables["[filename]"] = fileroot;
string errorOff = "no error";
InputData input(listfile, "shared", Groups);
SharedListVector* SharedList = input.getSharedListVector();
string lastLabel = SharedList->getLabel();
SharedRAbundVectors* lookup;
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
out.close(); if (!pickedGroups) { util.mothurRemove(filename); }
return 0;
}
//sanity check
vector<string> namesSeqs;
int numGroupNames = 0;
if (current->getGroupMode() == "group") { namesSeqs = groupMap->getNamesSeqs(); numGroupNames = groupMap->getNumSeqs(); }
else { namesSeqs = countTable->getNamesOfSeqs(); numGroupNames = countTable->getNumUniqueSeqs(); }
int error = ListGroupSameSeqs(namesSeqs, SharedList);
if ((!pickedGroups) && (SharedList->getNumSeqs() != numGroupNames)) { //if the user has not specified any groups and their files don't match exit with error
m->mothurOut("Your group file contains " + toString(numGroupNames) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct.\n"); m->setControl_pressed(true);
out.close(); if (!pickedGroups) { util.mothurRemove(filename); } //remove blank shared file you made
//delete memory
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
return 0;
}
if (error == 1) { m->setControl_pressed(true); }
//if user has specified groups make new groupfile for them
if ((pickedGroups) && (current->getGroupMode() == "group")) { //make new group file
string groups = "";
if (numGroups < 4) {
for (int i = 0; i < numGroups-1; i++) {
groups += Groups[i] + ".";
}
groups+=Groups[numGroups-1];
}else { groups = "merge"; }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(listfile));
variables["[group]"] = groups;
string newGroupFile = getOutputFileName("group",variables);
outputTypes["group"].push_back(newGroupFile);
outputNames.push_back(newGroupFile);
ofstream outGroups;
util.openOutputFile(newGroupFile, outGroups);
vector<string> names = groupMap->getNamesSeqs();
string groupName;
for (int i = 0; i < names.size(); i++) {
groupName = groupMap->getGroup(names[i]);
if (isValidGroup(groupName, Groups)) {
outGroups << names[i] << '\t' << groupName << endl;
}
}
outGroups.close();
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
bool printHeaders = true;
while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
delete lookup;
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
}
if ((util.anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) ) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = SharedList->getLabel();
delete SharedList;
SharedList = input.getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
delete SharedList; if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
delete lookup;
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
//restore real lastlabel to save below
SharedList->setLabel(saveLabel);
}
lastLabel = SharedList->getLabel();
delete SharedList;
SharedList = input.getSharedListVector(); //get new list vector to process
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
if (processedLabels.count(lastLabel) != 1) {
needToRun = true;
}
}
//run last label if you need to
if (needToRun ) {
if (SharedList != NULL) { delete SharedList; }
SharedList = input.getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup->getLabel()+"\n");
if (m->getControl_pressed()) {
if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (!pickedGroups) { out.close(); util.mothurRemove(filename); }
return 0;
}
//if picked groups must split the shared file by label
if (pickedGroups) {
string filename = listfile;
if (outputDir == "") { outputDir += util.hasPath(filename); }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(filename));
variables["[distance]"] = lookup->getLabel();
filename = getOutputFileName("shared",variables);
outputNames.push_back(filename); outputTypes["shared"].push_back(filename);
ofstream out2;
util.openOutputFile(filename, out2);
lookup->eliminateZeroOTUS();
printSharedData(lookup, out2, printHeaders);
out2.close();
}else {
printSharedData(lookup, out, printHeaders); //prints info to the .shared file
}
delete lookup;
delete SharedList;
}
if (!pickedGroups) { out.close(); }
if (groupMap != NULL) { delete groupMap; } if (countTable != NULL) { delete countTable; }
if (m->getControl_pressed()) {
if (!pickedGroups) { util.mothurRemove(filename); }
return 0;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "createSharedFromListGroup");
exit(1);
}
}
bool FILE_DATASET_CLASS::deduceTransferSyntax(FILE_TF_CLASS *fileTf_ptr, string &transferSyntax)
// DESCRIPTION : Try to deduce the transfer syntax by interpretating the first
// data element found.
// PRECONDITIONS :
// POSTCONDITIONS :
// EXCEPTIONS :
// NOTES :
//<<===========================================================================
{
BYTE buffer[8];
TS_CODE tsCode;
if (loggerM_ptr)
{
loggerM_ptr->text(LOG_DEBUG, 1, "Trying to deduce Transfer Syntax directly from first few bytes of stored Dataset...");
}
// check file is open
if (!fileTf_ptr->isOpen())
{
// can't determine anything
return false;
}
// rewind the file buffer
fileTf_ptr->rewind(0);
// read the first few bytes of data from the beginning of the file
if (fileTf_ptr->readBinary(buffer, 8) != 8)
{
// rewind the file buffer
fileTf_ptr->rewind(0);
// can't find the preamble
return false;
}
// rewind the file buffer
fileTf_ptr->rewind(0);
// check if we can make any sense of the first few bytes - they should represent the tag [VR] and length
// - get big endian values
UINT16 bigGroup = (buffer[0] * 256) + buffer[1];
UINT16 bigElement = (buffer[2] * 256) + buffer[3];
// - get little endian values
UINT16 littleGroup = (buffer[1] * 256) + buffer[0];
UINT16 littleElement = (buffer[3] * 256) + buffer[2];
// debug log the values read
if (loggerM_ptr)
{
loggerM_ptr->text(LOG_DEBUG, 1, "Big endian tag read (%04X,%04X)", bigGroup, bigElement);
loggerM_ptr->text(LOG_DEBUG, 1, "Little endian tag read (%04X,%04X)", littleGroup, littleElement);
}
// try to get a known VR using the endian representations
ATTR_VR_ENUM vrBig = DEFINITION->GetAttributeVr(bigGroup, bigElement);
ATTR_VR_ENUM vrLittle = DEFINITION->GetAttributeVr(littleGroup, littleElement);
// check if we have big endian
if ((vrBig != ATTR_VR_UN) &&
(vrLittle == ATTR_VR_UN))
{
// byte ordering is big endian
tsCode = TS_BIG_ENDIAN;
}
else if ((vrBig == ATTR_VR_UN) &&
(vrLittle != ATTR_VR_UN))
{
// byte ordering is little endian
tsCode = TS_LITTLE_ENDIAN;
}
else if (isValidGroup(littleGroup) &&
(littleElement == LENGTH_ELEMENT))
{
// special check for a Group Length - not available in definition files
// byte ordering is little endian
tsCode = TS_LITTLE_ENDIAN;
vrLittle = ATTR_VR_UL;
}
else if (isValidGroup(bigGroup) &&
(bigElement == LENGTH_ELEMENT))
{
// special check for a Group Length - not available in definition files
// byte ordering is big endian
tsCode = TS_BIG_ENDIAN;
vrBig = ATTR_VR_UL;
}
else if (((bigGroup & 0x0001) != 0) &&
(bigElement >= 0x0010) &&
(bigElement <= 0x00FF))
{
// special check for a Private Recognition Code - not available in definition files
// byte ordering is big endian
tsCode = TS_BIG_ENDIAN;
vrBig = ATTR_VR_LO;
}
else if (((littleGroup & 0x0001) != 0) &&
(littleElement >= 0x0010) &&
(littleElement <= 0x00FF))
{
// special check for a Private Recognition Code - not available in definition files
// byte ordering is little endian
tsCode = TS_LITTLE_ENDIAN;
vrLittle = ATTR_VR_LO;
}
else
{
// cannot determine endianess from VR - must stop
return false;
}
// get VR from definition
ATTR_VR_ENUM vr = vrLittle;
if (tsCode == TS_BIG_ENDIAN)
{
vr = vrBig;
}
// now try to determine if we have an implicit or explicit VR
// - get the VR of the attribute in 16 bit format
UINT16 vr16 = (buffer[4] * 256) + buffer[5];
// check if VR's match
if (fileTf_ptr->vrToVr16(vr) == vr16)
{
// VR is explicit
tsCode |= TS_EXPLICIT_VR;
}
else
{
// VR is implicit
tsCode |= TS_IMPLICIT_VR;
}
switch(tsCode)
{
case TS_IMPLICIT_VR | TS_LITTLE_ENDIAN:
transferSyntax = IMPLICIT_VR_LITTLE_ENDIAN;
if (loggerM_ptr)
{
loggerM_ptr->text(LOG_INFO, 1, "Detected Implicit VR Little Endian Transfer Syntax for File Dataset");
}
break;
case TS_EXPLICIT_VR | TS_LITTLE_ENDIAN:
transferSyntax = EXPLICIT_VR_LITTLE_ENDIAN;
if (loggerM_ptr)
{
loggerM_ptr->text(LOG_INFO, 1, "Detected Explicit VR Little Endian Transfer Syntax for File Dataset");
}
break;
case TS_EXPLICIT_VR | TS_BIG_ENDIAN:
transferSyntax = EXPLICIT_VR_BIG_ENDIAN;
if (loggerM_ptr)
{
loggerM_ptr->text(LOG_INFO, 1, "Detected Explicit VR Big Endian Transfer Syntax for File Dataset");
}
break;
default:
break;
}
// return result
return true;
}
int SharedCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//getting output filename
filename = listfile;
if (outputDir == "") { outputDir += m->hasPath(filename); }
filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
outputTypes["shared"].push_back(filename);
m->openOutputFile(filename, out);
pickedGroups = false;
//if hte user has not specified any groups then use them all
if (Groups.size() == 0) {
Groups = groupMap->getNamesOfGroups(); m->setGroups(Groups);
}else { pickedGroups = true; }
//fill filehandles with neccessary ofstreams
int i;
ofstream* temp;
for (i=0; i<Groups.size(); i++) {
temp = new ofstream;
filehandles[Groups[i]] = temp;
}
//set fileroot
fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
//clears file before we start to write to it below
for (int i=0; i<Groups.size(); i++) {
m->mothurRemove((fileroot + Groups[i] + ".rabund"));
outputNames.push_back((fileroot + Groups[i] + ".rabund"));
outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
}
//lookup.clear();
string errorOff = "no error";
//errorOff = "";
//if user provided an order file containing the order the shared file should be in read it
if (ordergroupfile != "") { readOrderFile(); }
input = new InputData(listfile, "shared");
SharedList = input->getSharedListVector();
string lastLabel = SharedList->getLabel();
vector<SharedRAbundVector*> lookup;
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
//sanity check
int error = ListGroupSameSeqs();
if ((!pickedGroups) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine();
out.close();
m->mothurRemove(filename); //remove blank shared file you made
createMisMatchFile();
//delete memory
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
delete input; delete SharedList; delete groupMap;
return 0;
}
if (error == 1) { m->control_pressed = true; }
//if user has specified groups make new groupfile for them
if (pickedGroups) { //make new group file
string groups = "";
if (m->getNumGroups() < 4) {
for (int i = 0; i < m->getNumGroups(); i++) {
groups += (m->getGroups())[i] + ".";
}
}else { groups = "merge"; }
string newGroupFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + groups + "groups";
outputTypes["group"].push_back(newGroupFile);
outputNames.push_back(newGroupFile);
ofstream outGroups;
m->openOutputFile(newGroupFile, outGroups);
vector<string> names = groupMap->getNamesSeqs();
string groupName;
for (int i = 0; i < names.size(); i++) {
groupName = groupMap->getGroup(names[i]);
if (isValidGroup(groupName, m->getGroups())) {
outGroups << names[i] << '\t' << groupName << endl;
}
}
outGroups.close();
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
while((SharedList != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if(allLines == 1 || labels.count(SharedList->getLabel()) == 1){
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
}
if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = SharedList->getLabel();
delete SharedList;
SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete SharedList; delete groupMap;
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
processedLabels.insert(SharedList->getLabel());
userLabels.erase(SharedList->getLabel());
//restore real lastlabel to save below
SharedList->setLabel(saveLabel);
}
lastLabel = SharedList->getLabel();
delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
if (processedLabels.count(lastLabel) != 1) {
needToRun = true;
}
}
//run last label if you need to
if (needToRun == true) {
if (SharedList != NULL) { delete SharedList; }
SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (pickedGroups) { //check for otus with no seqs in them
eliminateZeroOTUS(lookup);
}
if (m->control_pressed) {
delete input; delete groupMap;
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
out.close(); m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
delete SharedList;
}
out.close();
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
delete it3->second;
}
delete input; delete groupMap;
if (m->control_pressed) {
m->mothurRemove(filename);
for (int i=0; i<Groups.size(); i++) { m->mothurRemove((fileroot + Groups[i] + ".rabund")); }
return 0;
}
//set rabund file as new current rabundfile
string current = "";
itTypes = outputTypes.find("rabund");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
}
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOut(filename); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "execute");
exit(1);
}
}