int RemoveGroupsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get groups you want to remove
if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
groupMap->readMap();
//make sure groups are valid
//takes care of user setting groupNames that are invalid or setting groups=all
vector<string> namesGroups = groupMap->getNamesOfGroups();
vector<string> checkedGroups;
for (int i = 0; i < Groups.size(); i++) {
if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
else { m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
}
if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
else {
Groups = checkedGroups;
m->setGroups(Groups);
}
//fill names with names of sequences that are from the groups we want to remove
fillNames();
delete groupMap;
}else if (countfile != ""){
if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
}
CountTable ct;
ct.readTable(countfile, true);
if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
vector<string> gNamesOfGroups = ct.getNamesOfGroups();
SharedUtil util;
util.setGroups(Groups, gNamesOfGroups);
vector<string> namesOfSeqs = ct.getNamesOfSeqs();
sort(Groups.begin(), Groups.end());
for (int i = 0; i < namesOfSeqs.size(); i++) {
vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
names.insert(namesOfSeqs[i]);
}
}
}
if (m->control_pressed) { return 0; }
//read through the correct file and output lines you want to keep
if (namefile != "") { readName(); }
if (fastafile != "") { readFasta(); }
if (groupfile != "") { readGroup(); }
if (countfile != "") { readCount(); }
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (sharedfile != "") { readShared(); }
if (designfile != "") { readDesign(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
m->mothurOutEndLine();
m->mothurOut("Output File names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
itTypes = outputTypes.find("list");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
}
itTypes = outputTypes.find("taxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
}
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
itTypes = outputTypes.find("design");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "execute");
exit(1);
}
}
int GetSeqsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get names you want to keep
readAccnos();
if (m->control_pressed) { return 0; }
//read through the correct file and output lines you want to keep
if (namefile != "") { readName(); }
if (fastafile != "") { readFasta(); }
if (groupfile != "") { readGroup(); }
if (alignfile != "") { readAlign(); }
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (qualfile != "") { readQual(); }
if (accnosfile2 != "") { compareAccnos(); }
if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
itTypes = outputTypes.find("list");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
}
itTypes = outputTypes.find("taxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
}
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "execute");
exit(1);
}
}
// 解析出刀塔骨架数据
Dota_Skeleton_Data* DotaAnimParser::parseDotaSkeletonData(
const std::string &fcaFile)
{
const float PI = 3.14159265358979323846f;
ByteArray byteArray;
bool bRet = byteArray.loadFromZipFile(fcaFile.c_str(), "cha");
if (!bRet)
return nullptr;
Dota_Skeleton_Data * skeletonData = new Dota_Skeleton_Data();
if (skeletonData == nullptr)
{
byteArray.close();
return nullptr;
}
skeletonData->name = readName(byteArray);
CCLOG("RoleName:%s\n", skeletonData->name.c_str());
float factor = 0.1f;
if (skeletonData->name.substr(0, 14) == "effect/eff_UI_")
factor = 0.5f;
int boneCount = byteArray.readInt();
CCLOG("BoneCnt:%d\n", boneCount);
for (int i = 0; i < boneCount; i++)
{
Dota_Bone_Data * boneData = new Dota_Bone_Data();
boneData->name = readName(byteArray);
boneData->textureName = readName(byteArray);
boneData->index = byteArray.readInt();
skeletonData->boneDataList.push_back(boneData);
CCLOG("BoneData:\nName:%s\nTextureName:%s\nIndex:%d\n\n",
boneData->name.c_str(), boneData->textureName.c_str(), boneData->index);
}
CCLOG("BoneCnt:%d\n", (int)skeletonData->boneDataList.size());
int animCount = byteArray.readInt();
CCLOG("AnimCnt:%d\n", animCount);
for (int i = 0; i < animCount; i++)
{
Dota_Anim_Data * animData = new Dota_Anim_Data();
animData->name = readName(byteArray);
CCLOG("AnimName:%s\n", animData->name.c_str());
byteArray.readBytes(animData->unknownData, sizeof(animData->unknownData));
int frameCount = byteArray.readInt();
CCLOG("FrameCnt:%d\n", frameCount);
for (int j = 0; j < frameCount; j++)
{
Dota_Frame_Data * frameData = new Dota_Frame_Data();
frameData->type = byteArray.readInt();
if (frameData->type == 1)
{
frameData->unknownData1 = byteArray.readInt();
CCLOG("UnknownData1:%d\n", frameData->unknownData1);
frameData->soundName = readName(byteArray);
byteArray.readBytes(frameData->soundData, sizeof(frameData->soundData));
frameData->unknownData2 = byteArray.readInt();
CCLOG("UnknownData2:%d\n", frameData->unknownData2);
}
int slotCount = byteArray.readInt();
for (int k = 0; k < slotCount; k++)
{
Dota_Slot_Data * slotData = new Dota_Slot_Data();
slotData->boneIndex = byteArray.readShort();
slotData->opacity = byteArray.readByte();
float a = byteArray.readFloat();
float b = byteArray.readFloat();
float c = byteArray.readFloat();
float d = byteArray.readFloat();
float tx = byteArray.readFloat();
float ty = byteArray.readFloat();
slotData->x = tx * factor;
slotData->y = ty * factor;
slotData->skX = atan2(-c, d) * (180/PI);
slotData->skY = atan2(b, a) * (180/PI);
slotData->scX = sqrt(a*a + b*b);
slotData->scY = sqrt(c*c + d*d);
frameData->slotDataList.push_back(slotData);
}
animData->frameDataList.push_back(frameData);
}
CCLOG("FrameCnt:%d\n", animData->frameDataList.size());
skeletonData->animDataList.push_back(animData);
}
byteArray.close();
for (int i = 0; i < (int)skeletonData->animDataList.size(); i++)
{
Dota_Anim_Data * animData = skeletonData->animDataList[i];
Dota_Anim_Data2 * animData2 = new Dota_Anim_Data2();
for (int j = 0; j < (int)animData->frameDataList.size(); j++)
{
Dota_Frame_Data * frameData = animData->frameDataList[j];
for (int k = 0; k < (int)frameData->slotDataList.size(); k++)
{
Dota_Slot_Data * slotData = frameData->slotDataList[k];
if (frameData->type == 1 && 0 == k)
slotData->soundName = frameData->soundName;
slotData->zOrder = k; //slotData->boneIndex;
std::string boneName = getBone(skeletonData->boneDataList, slotData->boneIndex);
Dota_Anim_Data2::iterator iter = animData2->find(boneName);
if (iter == animData2->end())
{
Dota_Timeline_Data * timelineData = new Dota_Timeline_Data();
timelineData->insert(Dota_Timeline_Data::value_type(toString(j), slotData));
animData2->insert(Dota_Anim_Data2::value_type(boneName, timelineData));
skeletonData->firstFrameOfBoneMap.insert(Dota_First_Frame_Data::value_type(boneName, slotData));
}
else
{
Dota_Timeline_Data * timelineData = iter->second;
Dota_Timeline_Data::iterator iter2 = timelineData->find(toString(j));
if (iter2 == timelineData->end())
{
timelineData->insert(Dota_Timeline_Data::value_type(toString(j), slotData));
}
}
}
}
skeletonData->animDataMap.insert(std::map<std::string, Dota_Anim_Data2 *>::value_type(animData->name, animData2));
}
return skeletonData;
}
temp<Token> Lexer::readToken()
{
while (true)
{
if (isDone()) return Token::create(TOKEN_EOF, String::create(""));
start_ = pos_;
char c = advance();
switch (c)
{
case ' ':
case '\t':
case '\r':
// Skip whitespace.
while (isWhitespace(peek())) advance();
break;
case '(': return makeToken(TOKEN_LEFT_PAREN);
case ')': return makeToken(TOKEN_RIGHT_PAREN);
case '[': return makeToken(TOKEN_LEFT_BRACKET);
case ']': return makeToken(TOKEN_RIGHT_BRACKET);
case '{': return makeToken(TOKEN_LEFT_BRACE);
case '}': return makeToken(TOKEN_RIGHT_BRACE);
case '=': return makeToken(TOKEN_EQUALS);
case '+': return makeToken(TOKEN_PLUS);
case '-': return makeToken(TOKEN_MINUS);
case '*': return makeToken(TOKEN_STAR);
case '%': return makeToken(TOKEN_PERCENT);
case '<': return makeToken(TOKEN_LESS_THAN);
case '\n': return makeToken(TOKEN_LINE);
case '/':
if (peek() == '/')
{
skipLineComment();
/*}
else if (peek() == '*')
{
skipBlockComment();*/
}
else
{
return makeToken(TOKEN_SLASH);
}
break;
/*
case ',': return singleToken(TOKEN_LINE);
case '@': return singleToken(TOKEN_AT);
case '.': return singleToken(TOKEN_DOT);
case '#': return singleToken(TOKEN_HASH);
case ';': return singleToken(TOKEN_SEMICOLON);
case '\\': return singleToken(TOKEN_IGNORE_LINE);
case '|': return singleToken(TOKEN_PIPE);
case ':':
advance();
if (peek() == ':')
{
// "::".
advance();
return Ref<Token>(new Token(TOKEN_BIND));
}
// Just a ":" by itself.
return Ref<Token>(new Token(TOKEN_KEYWORD, ":"));
case '-':
advance();
if (isDigit(peek())) return readNumber();
return readOperator();
case '/':
advance();
if (peek() == '/')
{
// Line comment, so ignore the rest of the line and
// emit the line token.
mNeedsLine = true;
return Ref<Token>(new Token(TOKEN_LINE));
}
else if (peek() == '*')
{
skipBlockComment();
}
else
{
return readOperator();
}
break;
case '"': return readString();
default:
if (isDigit(c)) return readNumber();
if (isOperator(c)) return readOperator();
*/
default:
if (isNameStart(c)) return readName();
if (isDigit(c)) return readNumber();
// If we got here, we don't know what it is.
return makeToken(TOKEN_ERROR);
}
}
}
