/*}}}*/
int main(int argc, char** argv)/*{{{*/
{
if (argc < 2)
{
PrintHelp();
return -1;
}
int i = 0;
int j = 0;
char outpath[MAX_PATH+1] = "./";
char listfile[MAX_PATH+1] = "";
char outAlphabet[NUM_BLOSUM+1] = ""; //if outAlphabet not set, using the default BLOSUM alphabet
double scale = 100.0;
//char **filenamelist = NULL;
bool isOutputLast2Col = false;
bool isQuietMode = false;
set <string> filenamelist_set;
set <string> ::iterator iss;
int numfile = 0;
int errmsg = 0;
i = 1;
while(i < argc)/*{{{*/
{
if(strcmp(argv[i], "-h") == 0|| strcmp(argv[i], "--help") == 0)
{
PrintHelp();
errmsg = 1;
break;
}
else if (strcmp(argv[i], "-d") == 0)
{
my_strcpy(outpath,argv[i+1], MAX_PATH);
i += 2;
}
else if (strcmp(argv[i], "-s") == 0)
{
scale = atof(argv[i+1]);
i += 2;
}
else if (strcmp(argv[i], "-i") == 0)
{
isOutputInteger = true;
i ++;
}
else if (strcmp(argv[i], "-l") == 0 || strcmp(argv[i], "--list") == 0)
{
my_strcpy(listfile,argv[i+1], MAX_PATH);
i += 2;
}
else if (strcmp(argv[i], "--alphabet") == 0 || strcmp(argv[i], "-a") == 0)
{
my_strcpy(outAlphabet,argv[i+1], NUM_BLOSUM);
if(!IsValidAlphabet(outAlphabet))
{
errmsg = -1;
break;
}
i += 2;
}
else if (strcmp(argv[i], "-q") == 0)
{
isQuietMode = true;
i ++;
}
else if (strcmp(argv[i], "--pssm") == 0)
{
isOutputLast2Col = true;
i ++;
}
else
{
filenamelist_set.insert(argv[i]);
i ++;
}
}/*}}}*/
numfile = filenamelist_set.size();
if(errmsg != 0)
{
return errmsg;
}
if(strcmp(listfile,"") == 0 && filenamelist_set.size() == 0)
{
fprintf(stderr,"Error! neither listfile nor mtx file in the argument list are set\n");
return -1;
}
else if(strcmp(listfile,"") != 0)
{
FILE *fpin;
fpin = fopen(listfile,"r");
checkfilestream(fpin,listfile,"r");
int linesize;
int maxline = 300;
Array1D <char> line_1darray(maxline+1);
char *line = line_1darray.array1D;
while((linesize = fgetline(fpin, line , maxline)) != EOF)
{
if(linesize > 0) filenamelist_set.insert(line);
}
fclose(fpin);
}
VerifyFolder(outpath);
Array1D <char> aaSeq_1darray(LONGEST_SEQ+1);
Array2D <double> profile_2darray(LONGEST_SEQ, NUM_BLOSUM);
Array1D <double> parameter_1darray(NUM_PARAMETER);
char *aaSeq = aaSeq_1darray.array1D;
double **profile = profile_2darray.array2D;
double *parameter = parameter_1darray.array1D;
double *score1 = NULL;
double *score2 = NULL;
char modmfile[MAX_PATH+1] = "";
char pssmfile[MAX_PATH+1] = "";
char mtxfile[MAX_PATH+1] = "";
char rtname[MAX_PATH+1] = "";
char filepath[MAX_PATH+1] = "";
int length;
int lengthpssm;
int cntfile = 0;
for(iss = filenamelist_set.begin() ; iss != filenamelist_set.end(); iss ++)
{
score1 = NULL;
score2 = NULL;
my_strcpy(mtxfile, (*iss).c_str(), MAX_PATH);
rootname(mtxfile, rtname);
getfilepath(mtxfile, filepath);
if(getmtx(mtxfile, length, aaSeq, parameter, profile, scale) <= 0)
{
fprintf(stderr, "%d \t %s getting mtx file error!",cntfile+1, mtxfile);
continue;
}
lengthpssm = length ;
int profileIndex[NUM_BLOSUM]; //order the profile according to the outAlphabet
for(j = 0; j < NUM_BLOSUM; j ++) profileIndex[j] = j;
if(strcmp(outAlphabet,"") != 0)
{
for(i = 0 ; i < NUM_AA; i++)
{
profileIndex[i] = Char2Digit(outAlphabet[i], BLOSUM1D_alphabet);
}
}
else
{
my_strcpy(outAlphabet, BLOSUM1D_alphabet, NUM_BLOSUM);
}
if(isOutputLast2Col)
{
score1 = new double [LONGEST_SEQ];
score2 = new double [LONGEST_SEQ];
sprintf(pssmfile, "%s/%s.pssm", filepath, rtname);
lengthpssm = GetPSSM(pssmfile, lengthpssm, NULL, NULL, NULL, score1, score2);
}
if ( length != lengthpssm)
{
fprintf(stderr,"Error! length of mtx file and pssm not the same for %s", rtname);
}
else
{
sprintf(modmfile, "%s/%s.modm", outpath, rtname);
WriteMODMFile(modmfile, aaSeq, length, profile, profileIndex, outAlphabet, score1, score2, parameter, isOutputInteger);
if(!isQuietMode) fprintf(stdout,"%d %s output\n", cntfile+1, modmfile);
}
if (score1 != NULL) delete [] score1;
if (score2 != NULL) delete [] score2;
}
//
return 0;
}
void FillTreeClass<T>::setTreeInternal2(T& _safelocker, Items& _items, ThreadedItems& _topLevelItems, const ::profiler::timestamp_t& _beginTime, const ::profiler_gui::TreeBlocks& _blocks, ::profiler::timestamp_t _left, ::profiler::timestamp_t _right, bool _strict, bool _colorizeRows)
{
//size_t blocksNumber = 0;
//for (const auto& block : _blocks)
// blocksNumber += calculateTotalChildrenNumber(*block.tree);
// //blocksNumber += block.tree->total_children_number;
//m_items.reserve(blocksNumber + _blocks.size()); // blocksNumber does not include root blocks
RootsMap threadsMap;
const auto u_thread = ::profiler_gui::toUnicode("thread");
int i = 0, total = static_cast<int>(_blocks.size());
//const QSignalBlocker b(this);
for (const auto& block : _blocks)
{
if (_safelocker.interrupted())
break;
auto& gui_block = easyBlock(block.tree);
const auto startTime = gui_block.tree.node->begin();
const auto endTime = gui_block.tree.node->end();
if (startTime > _right || endTime < _left)
{
_safelocker.setProgress((90 * ++i) / total);
continue;
}
::profiler::timestamp_t duration = 0;
EasyTreeWidgetItem* thread_item = nullptr;
auto thread_item_it = threadsMap.find(block.root->thread_id);
if (thread_item_it != threadsMap.end())
{
thread_item = thread_item_it->second;
}
else
{
thread_item = new EasyTreeWidgetItem();
QString threadName;
if (block.root->got_name())
{
QString rootname(::profiler_gui::toUnicode(block.root->name()));
if (rootname.contains(u_thread, Qt::CaseInsensitive))
threadName = ::std::move(QString("%1 %2").arg(rootname).arg(block.root->thread_id));
else
threadName = ::std::move(QString("%1 Thread %2").arg(rootname).arg(block.root->thread_id));
}
else
{
threadName = ::std::move(QString("Thread %1").arg(block.root->thread_id));
}
thread_item->setText(COL_NAME, threadName);
if (!block.root->children.empty())
duration = blocksTree(block.root->children.back()).node->end() - blocksTree(block.root->children.front()).node->begin();
thread_item->setTimeSmart(COL_DURATION, duration);
thread_item->setBackgroundColor(::profiler_gui::SELECTED_THREAD_BACKGROUND);
thread_item->setTextColor(::profiler_gui::SELECTED_THREAD_FOREGROUND);
// Sum of all children durations:
thread_item->setTimeSmart(COL_SELF_DURATION, block.root->active_time);
threadsMap.insert(::std::make_pair(block.root->thread_id, thread_item));
}
auto item = new EasyTreeWidgetItem(block.tree, thread_item);
duration = endTime - startTime;
auto name = *gui_block.tree.node->name() != 0 ? gui_block.tree.node->name() : easyDescriptor(gui_block.tree.node->id()).name();
item->setText(COL_NAME, ::profiler_gui::toUnicode(name));
item->setTimeSmart(COL_DURATION, duration);
item->setTimeMs(COL_BEGIN, startTime - _beginTime);
item->setTimeMs(COL_END, endTime - _beginTime);
item->setData(COL_PERCENT_PER_FRAME, Qt::UserRole, 0);
auto percentage_per_thread = ::profiler_gui::percent(duration, block.root->active_time);
item->setData(COL_PERCENT_PER_PARENT, Qt::UserRole, percentage_per_thread);
item->setText(COL_PERCENT_PER_PARENT, QString::number(percentage_per_thread));
if (gui_block.tree.per_thread_stats != nullptr) // if there is per_thread_stats then there are other stats also
{
const auto& per_thread_stats = gui_block.tree.per_thread_stats;
const auto& per_parent_stats = gui_block.tree.per_parent_stats;
const auto& per_frame_stats = gui_block.tree.per_frame_stats;
if (per_thread_stats->calls_number > 1 || !EASY_GLOBALS.display_only_relevant_stats)
{
item->setTimeSmart(COL_MIN_PER_THREAD, per_thread_stats->min_duration, "min ");
item->setTimeSmart(COL_MAX_PER_THREAD, per_thread_stats->max_duration, "max ");
item->setTimeSmart(COL_AVERAGE_PER_THREAD, per_thread_stats->average_duration());
item->setTimeSmart(COL_DURATION_SUM_PER_THREAD, per_thread_stats->total_duration);
}
item->setData(COL_NCALLS_PER_THREAD, Qt::UserRole, per_thread_stats->calls_number);
item->setText(COL_NCALLS_PER_THREAD, QString::number(per_thread_stats->calls_number));
percentage_per_thread = ::profiler_gui::percent(per_thread_stats->total_duration, block.root->active_time);
item->setData(COL_PERCENT_SUM_PER_THREAD, Qt::UserRole, percentage_per_thread);
item->setText(COL_PERCENT_SUM_PER_THREAD, QString::number(percentage_per_thread));
if (per_parent_stats->calls_number > 1 || !EASY_GLOBALS.display_only_relevant_stats)
{
item->setTimeSmart(COL_MIN_PER_PARENT, per_parent_stats->min_duration, "min ");
item->setTimeSmart(COL_MAX_PER_PARENT, per_parent_stats->max_duration, "max ");
item->setTimeSmart(COL_AVERAGE_PER_PARENT, per_parent_stats->average_duration());
item->setTimeSmart(COL_DURATION_SUM_PER_PARENT, per_parent_stats->total_duration);
}
item->setData(COL_NCALLS_PER_PARENT, Qt::UserRole, per_parent_stats->calls_number);
item->setText(COL_NCALLS_PER_PARENT, QString::number(per_parent_stats->calls_number));
if (per_frame_stats->calls_number > 1 || !EASY_GLOBALS.display_only_relevant_stats)
{
item->setTimeSmart(COL_MIN_PER_FRAME, per_frame_stats->min_duration, "min ");
item->setTimeSmart(COL_MAX_PER_FRAME, per_frame_stats->max_duration, "max ");
item->setTimeSmart(COL_AVERAGE_PER_FRAME, per_frame_stats->average_duration());
item->setTimeSmart(COL_DURATION_SUM_PER_FRAME, per_frame_stats->total_duration);
}
item->setData(COL_NCALLS_PER_FRAME, Qt::UserRole, per_frame_stats->calls_number);
item->setText(COL_NCALLS_PER_FRAME, QString::number(per_frame_stats->calls_number));
}
else
{
item->setData(COL_PERCENT_SUM_PER_THREAD, Qt::UserRole, 0);
item->setText(COL_PERCENT_SUM_PER_THREAD, "");
}
const auto color = easyDescriptor(gui_block.tree.node->id()).color();
//const auto bgColor = ::profiler_gui::fromProfilerRgb(::profiler::colors::get_red(color), ::profiler::colors::get_green(color), ::profiler::colors::get_blue(color));
const auto fgColor = ::profiler_gui::textColorForRgb(color);//0x00ffffff - bgColor;
item->setBackgroundColor(color);
item->setTextColor(fgColor);
auto item_index = static_cast<unsigned int>(_items.size());
_items.push_back(item);
size_t children_items_number = 0;
::profiler::timestamp_t children_duration = 0;
if (!gui_block.tree.children.empty())
{
children_items_number = FillTreeClass<T>::setTreeInternal(_safelocker, _items, _beginTime, gui_block.tree.children, item, item, thread_item, _left, _right, _strict, children_duration, _colorizeRows);
if (_safelocker.interrupted())
break;
}
int percentage = 100;
auto self_duration = duration - children_duration;
if (children_duration > 0 && duration > 0)
{
percentage = static_cast<int>(0.5 + 100. * static_cast<double>(self_duration) / static_cast<double>(duration));
}
item->setTimeSmart(COL_SELF_DURATION, self_duration);
item->setData(COL_SELF_DURATION_PERCENT, Qt::UserRole, percentage);
item->setText(COL_SELF_DURATION_PERCENT, QString::number(percentage));
if (children_items_number > 0 || !_strict || (startTime >= _left && endTime <= _right))
{
//total_items += children_items_number + 1;
gui_block.tree_item = item_index;
if (_colorizeRows)
item->colorize(_colorizeRows);
if (gui_block.expanded)
item->setExpanded(true);
}
else
{
_items.pop_back();
delete item;
}
_safelocker.setProgress((90 * ++i) / total);
}
i = 0;
total = static_cast<int>(threadsMap.size());
for (auto& it : threadsMap)
{
auto item = it.second;
if (item->childCount() > 0)
{
//addTopLevelItem(item);
//m_roots[it.first] = item;
//_items.push_back(item);
_topLevelItems.emplace_back(it.first, item);
//++total_items;
}
else
{
delete item;
}
_safelocker.setProgress(90 + (10 * ++i) / total);
}
_safelocker.setDone();
//return total_items;
}
void SplitFasta(const char* seqDataFile, const char *outpath, const char *ext)/*{{{*/
{
char seqFile[MAX_PATH+1] = "";
//char command[MAX_COMMAND_LINE+1] = "";
FILE *fpSeqData;
FILE *fpSeq;
fpSeqData = fopen(seqDataFile,"r");
checkfilestream(fpSeqData, seqDataFile, "r");
char id[SIZE_ID+1] = "";
char str[SIZE_ID+10+1] = "";
char rtname[MAX_PATH+1] = "";
rootname(seqDataFile,rtname);
int linesize;
Array1D <char> line_1darray(maxline+1);
char *line = line_1darray.array1D;
char delim[] = " \t\r\n>";
char *pch = NULL;
fpos_t pos;
//int i;
int cnt = 0 ;
while((linesize = fgetline(fpSeqData,line,maxline)) != EOF)
{
if(linesize == 0 || IsBlankLine(line)) continue;
if(line[0] == '>')//beginning of a record
{
cnt ++ ;
my_strcpy(str, line, SIZE_ID+10);
pch = strtok(str,delim);
while(pch != NULL) //take the first word following '>' as id
{
my_strcpy(id, pch, SIZE_ID);
break;
}
if(strcmp(id,"") == 0)// if no word following '>', set the id as rootname(seq-file)_cnt
{
sprintf(id,"%s_%d", rtname, cnt);
}
printf("%d\t:%s exported\n",cnt,id);
sprintf(seqFile,"%s/%s.%s",outpath,id,ext);
fpSeq = fopen(seqFile,"w");
checkfilestream(fpSeq, seqFile, "r");
fprintf(fpSeq,"%s\n",line);
while(!feof(fpSeqData))
{
fgetpos(fpSeqData,&pos);
linesize = fgetline(fpSeqData,line,maxline);
if(linesize == 0 || IsBlankLine(line)) continue;
if(line[0] == '>')
{
fsetpos(fpSeqData,&pos);
break;
}
else
fprintf(fpSeq,"%s\n",line);
}
fclose(fpSeq);
}
}
fclose(fpSeqData);
printf("%d sequences exported!\n",cnt);
}
void FillTreeClass<T>::setTreeInternal1(T& _safelocker, Items& _items, ThreadedItems& _topLevelItems, ::profiler::timestamp_t& _beginTime, const unsigned int _blocksNumber, const ::profiler::thread_blocks_tree_t& _blocksTree, bool _colorizeRows)
{
_items.reserve(_blocksNumber + _blocksTree.size()); // _blocksNumber does not include Thread root blocks
::profiler::timestamp_t finishtime = 0;
for (const auto& threadTree : _blocksTree)
{
const auto node_block = blocksTree(threadTree.second.children.front()).node;
const auto startTime = node_block->begin();
const auto endTime = node_block->end();
if (_beginTime > startTime)
_beginTime = startTime;
if (finishtime < endTime)
finishtime = endTime;
}
//const QSignalBlocker b(this);
const auto u_thread = ::profiler_gui::toUnicode("thread");
int i = 0;
const int total = static_cast<int>(_blocksTree.size());
for (const auto& threadTree : _blocksTree)
{
if (_safelocker.interrupted())
break;
const auto& root = threadTree.second;
auto item = new EasyTreeWidgetItem();
QString threadName;
if (root.got_name())
{
QString rootname(::profiler_gui::toUnicode(root.name()));
if (rootname.contains(u_thread, Qt::CaseInsensitive))
threadName = ::std::move(QString("%1 %2").arg(rootname).arg(root.thread_id));
else
threadName = ::std::move(QString("%1 Thread %2").arg(rootname).arg(root.thread_id));
}
else
{
threadName = ::std::move(QString("Thread %1").arg(root.thread_id));
}
item->setText(COL_NAME, threadName);
::profiler::timestamp_t duration = 0;
if (!root.children.empty())
duration = blocksTree(root.children.back()).node->end() - blocksTree(root.children.front()).node->begin();
item->setTimeSmart(COL_DURATION, duration);
item->setBackgroundColor(::profiler_gui::SELECTED_THREAD_BACKGROUND);
item->setTextColor(::profiler_gui::SELECTED_THREAD_FOREGROUND);
//_items.push_back(item);
item->setTimeSmart(COL_SELF_DURATION, root.active_time);
::profiler::timestamp_t children_duration = 0;
const auto children_items_number = FillTreeClass<T>::setTreeInternal(_safelocker, _items, _beginTime, root.children, item, nullptr, item, _beginTime, finishtime + 1000000000ULL, false, children_duration, _colorizeRows);
if (children_items_number > 0)
{
//total_items += children_items_number + 1;
//addTopLevelItem(item);
//m_roots[threadTree.first] = item;
_topLevelItems.emplace_back(root.thread_id, item);
}
else
{
//_items.pop_back();
delete item;
}
_safelocker.setProgress((100 * ++i) / total);
}
_safelocker.setDone();
//return total_items;
}
int main(int argc, char** argv)/*{{{*/
{
bool isNonOptionArg = false;
if(argc < 2)
{
PrintHelp();
return 0;
}
int i,j;
char modmfile[MAX_PATH+1] = "";
char modmfilelist[MAX_PATH+1] = "";
char outfile[MAX_PATH+1] = "";
char suppliedAlphabet[SIZE_ALPHABET+1] = ""; /*force supplied alphabet to the alphabet in the output binary file*/
char outpath[MAX_PATH+1] = ""; /*default output path for the binary file is the same as the ascii file*/
double value = 0.0;
int mode = 0;
const char control_option[] = "bp"; //options which control the program, and does not take parameters
char tmpfile[MAX_PATH+1] = "/tmp/fileXXXXXX";
if (mkstemp(tmpfile) == -1)
{
fprintf(stderr, "Error! No temporary file can be created\n");
return -1;
}
FILE *fptmp = fopen(tmpfile,"w");
bool isIDsSet = false;
bool isOutputTimeInfo = true;
i = 1;
while(i < argc)/*{{{*/
{
if(argv[i][0] == '-' && !isNonOptionArg) //options
{
isNonOptionArg = false;
if(IsInCharSet(argv[i][1], control_option))//if argv[i][1] is in control_option, it might be used as -aqs
{
for(j = 1 ; j < strlen(argv[i]); j++)
{
switch (argv[i][j])
{
case 'b': isWriteBinaryFile = true; break;
case 'p': isPrintOut = true; break;
default : fprintf(stderr,"Invalid option, non-control option '%c' can be used together with contorl-option\n", argv[j]); return -1;
}
}
i ++;
}
else if(strcmp(argv[i],"-h") == 0 ||strcmp(argv[i],"--help")==0 )
{
PrintHelp();
return 0;
}
else if(strcmp(argv[i],"-H") == 0 )
{
PrintVerboseHelp();
return 0;
}
else if(strcmp(argv[i],"-a") == 0 )
{
my_strcpy(suppliedAlphabet, argv[i+1], SIZE_ALPHABET);
i += 2;
}
else if( (strcmp(argv[i],"-o") == 0) || (strcmp(argv[i], "--out") == 0))
{
if( ( i = option_parser_filename(argc, argv, i, outfile)) == -1)
return -1;
}
else if( (strcmp(argv[i], "--outpath") == 0))
{
if( ( i = option_parser_filename(argc, argv, i, outpath)) == -1)
return -1;
}
else if( (strcmp(argv[i],"-l") == 0) )
{
if( ( i = option_parser_filename(argc, argv, i, modmfilelist)) == -1)
return -1;
}
else if( (strcmp(argv[i], "--mode") == 0))
{
if( ( i = option_parser_numeric(argc, argv, i, mode, true, 0, 1)) == -1)
return -1;
}
else if (strcmp(argv[i], "--sad") == 0)/*indicating the modm file contains SAD information*/
{
isHaveSAD = true;
i ++;
}
else if (strcmp(argv[i], "--notime") == 0)/*do not output time info*/
{
isOutputTimeInfo = false;
i ++;
}
else if (strcmp(argv[i], "--") == 0)//next item is non option argument
{
isNonOptionArg = true;
i ++;
continue;
}
else
{
fprintf(stderr,"Error! Invalid argument '%s'\n", argv[i]);
return -1;
}
}
else //non-option argument
{
if(!isIDsSet)
{
fptmp = fopen(tmpfile,"w");
if(fptmp == NULL)
{
fprintf(stderr,"can not open file '%s' for write\n", tmpfile);
assert( fptmp != NULL);
}
}
fprintf(fptmp,"%s\n",argv[i]);
isIDsSet = true;
i ++;
}
}/*}}}*/
if(isIDsSet) fclose(fptmp);
if(!isIDsSet && strcmp(modmfilelist, "") == 0)
{
fprintf(stderr,"Error! neither ids and idListFile set\n");
PrintHelp();
return -1;
}
else if(isIDsSet && strcmp(modmfilelist,"") == 0)
{
my_strcpy(modmfilelist,tmpfile,MAX_PATH);
}
FILE *fpout = NULL;
if(strcmp(outfile,"") == 0 || strcasecmp(outfile, "stdout") == 0)
{
fpout = stdout;
}
else
{
fpout = fopen(outfile, "w");
checkfilestream(fpout, outfile,"w");
}
clock_t start, finish;
double duration;
int tmp;
start = clock();
FILE *fpFileList = fopen(modmfilelist, "r");
checkfilestream(fpFileList, modmfilelist, "r");
int linesize;
int maxline = 300;
Array1D <char> line_1darray(maxline+1);
char *line = line_1darray.array1D;
int sizeAlphabet = 0;
char alphabet[SIZE_ALPHABET+1] = "";
int numRes = 0;
Array1D <Profile> profile_1darray(2000);
Profile *profile = profile_1darray.array1D;
Array1D <ProfileSAD> profileSAD_1darray(2000);
ProfileSAD *profileSAD = profileSAD_1darray.array1D;
double parameter[8];
int status_sscanf = 0;
int cntFile = 0;
while((linesize = fgetline(fpFileList,line, maxline)) != EOF)
{
my_strcpy(modmfile, line, MAX_PATH);
for(j = 0; j < 8; j ++)
{
parameter[j] = 0.0;
}
strcpy(alphabet,"");
if(mode == 0) /*read text file*/
{
FILE *fpin = fopen(modmfile,"r");
checkfilestream(fpin,modmfile,"r");
char str[100] = "";
char first_non_blank_char = ' ';
int cntRes = 0;
while((linesize = fgetline(fpin, line, maxline)) != EOF)
{
if(line[0] == '#' || linesize <=0 )
{
continue;
}
sscanf(line, " %c", &first_non_blank_char);
if (first_non_blank_char == 'N')/*alphabet line*/
{
SpanExcluding(line, str);
if(!isHaveSAD)
{
my_strcpy(alphabet, str+5, SIZE_ALPHABET);
}
else
{
my_strcpy(alphabet, str+8, SIZE_ALPHABET);
}
}
else if (isdigit(first_non_blank_char))
{
if(!isHaveSAD)
{
profile[cntRes].score1 = 0.0;
profile[cntRes].score2 = 0.0;
status_sscanf = sscanf(line,"%d %c %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f",/*{{{*/
&profile[cntRes].aaSeqIndex,
&profile[cntRes].aa,
&profile[cntRes].p[0],
&profile[cntRes].p[1],
&profile[cntRes].p[2],
&profile[cntRes].p[3],
&profile[cntRes].p[4],
&profile[cntRes].p[5],
&profile[cntRes].p[6],
&profile[cntRes].p[7],
&profile[cntRes].p[8],
&profile[cntRes].p[9],
&profile[cntRes].p[10],
&profile[cntRes].p[11],
&profile[cntRes].p[12],
&profile[cntRes].p[13],
&profile[cntRes].p[14],
&profile[cntRes].p[15],
&profile[cntRes].p[16],
&profile[cntRes].p[17],
&profile[cntRes].p[18],
&profile[cntRes].p[19],
&profile[cntRes].score1,
&profile[cntRes].score2
);/*}}}*/
if(status_sscanf < 22)
{
fprintf(stderr,"current line=%s\n!", line );
fprintf(stderr,"The profile maybe incomplete, status_sscanf = %d, number %d, file %s\n!", status_sscanf, cntRes+1, modmfile );
assert (status_sscanf >= 22);
}
}
else
{
profileSAD[cntRes].score1 = 0.0;
profileSAD[cntRes].score2 = 0.0;
status_sscanf = sscanf(line,"%d %c %1c%1d%1c %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f",/*{{{*/
&profileSAD[cntRes].aaSeqIndex,
&profileSAD[cntRes].aa,
&profileSAD[cntRes].shape,
&profileSAD[cntRes].waterAcc,
&profileSAD[cntRes].dsspSec,
&profileSAD[cntRes].p[0],
&profileSAD[cntRes].p[1],
&profileSAD[cntRes].p[2],
&profileSAD[cntRes].p[3],
&profileSAD[cntRes].p[4],
&profileSAD[cntRes].p[5],
&profileSAD[cntRes].p[6],
&profileSAD[cntRes].p[7],
&profileSAD[cntRes].p[8],
&profileSAD[cntRes].p[9],
&profileSAD[cntRes].p[10],
&profileSAD[cntRes].p[11],
&profileSAD[cntRes].p[12],
&profileSAD[cntRes].p[13],
&profileSAD[cntRes].p[14],
&profileSAD[cntRes].p[15],
&profileSAD[cntRes].p[16],
&profileSAD[cntRes].p[17],
&profileSAD[cntRes].p[18],
&profileSAD[cntRes].p[19],
&profileSAD[cntRes].score1,
&profileSAD[cntRes].score2
);/*}}}*/
if(status_sscanf < 25)
{
fprintf(stderr,"current line=%s\n!", line );
fprintf(stderr,"The profile maybe incomplete, status_sscanf = %d, number %d, file %s\n!", status_sscanf, cntRes+1, modmfile );
assert (status_sscanf >= 25);
}
}
cntRes ++;
}
else if (first_non_blank_char == 'K')
{
int j = 0 ;
while((linesize = fgetline(fpin, line, maxline)) != EOF)
{
status_sscanf = sscanf(line,"%s %s %lf %lf", str, str, ¶meter[j], ¶meter[j+1]);
if(status_sscanf < 4)
{
fprintf(stderr,"Warning, file %s may not have psi-blast parameters\n", modmfile);
}
j += 2;
if (j >= 8 ) break;
}
}
}
fclose(fpin);
numRes = cntRes;
if (isWriteBinaryFile)
{
char binaryfile[MAX_PATH+1] = "";
if(strcmp(outpath, "") == 0) /*if outpath is not set, output to the same folder as the ascii file*/
{
sprintf(binaryfile, "%sbin", modmfile); /*if outpath is set*/
}
else
{
char rtname[MAX_PATH+1] = "";
char fileext[MAX_PATH+1] = "";
rootname(modmfile, rtname);
getfileext(modmfile, fileext);
sprintf(binaryfile, "%s/%s.%sbin", outpath, rtname, fileext);
}
// fprintf(stdout,"%d \t write out binary file to %s\n", cntFile, binaryfile) ;
if(strcmp(suppliedAlphabet,"") != 0)
{
my_strcpy(alphabet, suppliedAlphabet, SIZE_ALPHABET);
}
if(!isHaveSAD)
{
WriteBinaryMODM(binaryfile, alphabet, numRes, profile, parameter);
}
else
{
WriteBinaryMODM(binaryfile, alphabet, numRes, profileSAD, parameter);
}
}
}
else if(mode == 1)
{
if(!isHaveSAD)
{
GetBinaryMODM(modmfile, alphabet, numRes, profile, parameter);
if (isPrintOut)
{
WriteMODM(alphabet, profile, numRes, parameter, fpout);
}
}
else
{
GetBinaryMODM(modmfile, alphabet, numRes, profileSAD, parameter);
if (isPrintOut)
{
WriteMODM(alphabet, profileSAD, numRes, parameter, fpout);
}
}
}
cntFile ++;
}
finish = clock();
duration = double(finish-start) /double(CLOCKS_PER_SEC);
//printf("CLOCKS_PER_SEC=%d, start=%lf, finish=%lf\n", CLOCKS_PER_SEC, start, finish);
if (isOutputTimeInfo)
{
if(mode == 0)
{
fprintf(stdout,"reading text file cost %lf seconds\n", duration);
}
else if(mode == 1)
{
fprintf(stdout,"reading bindary file cost %lf seconds\n", duration);
}
}
if(fpout != NULL && fpout != stdout) fclose(fpout);
return 0;
}
