/// @throws AbortError, GetRangesError
void DirectSearch::searchComp(Mem::Random &ram, Comparison::t comp, Async::AbortableProgress &progress) {
assert(mStatus != DirectStatus::NotStarted);
if (mStatus == DirectStatus::SavedBackup) {
Mem::Live live(ram);
Mem::Backup backup(mBackup.get());
mBackup = boost::none;
mStatus = DirectStatus::Started;
Mem::DoubleBlockEnum blocks(backup, live, Number::maxSize);
progress.start(blocks.totalSize());
while (blocks.next()) {
if (mType) {
mLocLists[mType.get()].appendComp(blocks, comp);
}
else {
for (size_t type = 0; type < Number::Type::count; ++type) {
mLocLists[type].appendComp(blocks, comp);
}
}
progress.set(blocks.doneSize());
progress.check();
}
}
else {
Mem::Random::Lock lock(ram);
initProgress(progress);
for (size_t type = 0; type < Number::Type::count; ++type) {
mLocLists[type].filterComp(lock, comp, progress);
}
}
}
/// @throws AbortError, BackupReadError, BackupWriteError, GetRangesError
void DirectSearch::searchExact(Mem::Random &ram, const Number::Untyped &value, Async::AbortableProgress &progress) {
if (mStatus == DirectStatus::Started) {
Mem::Random::Lock lock(ram);
initProgress(progress);
for (size_t type = 0; type < Number::Type::count; ++type) {
mLocLists[type].filterEqual(lock, value, progress);
}
}
else {
Mem::Live live(ram);
Mem::SingleBlockEnum block(live, Number::maxSize, NULL);
mBackup = boost::none;
mStatus = DirectStatus::Started;
progress.start(block.totalSize());
while (block.next()) {
if (mType) {
mLocLists[mType.get()].appendEqual(block, value);
}
else {
for (size_t type = 0; type < Number::Type::count; ++type) {
mLocLists[type].appendEqual(block, value);
}
}
progress.set(block.doneSize());
progress.check();
}
}
}
int MainWindow::readAreaDataBaseFile( const QString &FilenameADB, QVector<AreaItem> &v_Area, QVector<PositionItem> &v_Position )
{
int i = 0;
int n = 0;
int stopProgress = 0;
int i_NumOfAreas = 0;
int i_NumOfPositions = 0;
QStringList sl_Input;
// **********************************************************************************************
// read file
if ( ( n = readFile( FilenameADB, sl_Input, _SYSTEM_, 1, -1 ) ) < 1 )
return( n );
// **********************************************************************************************
i_NumOfAreas = sl_Input.at( 2 ).section( "\t", 1, 1 ).toInt();
i_NumOfPositions = sl_Input.at( 3 ).section( "\t", 1, 1 ).toInt();
for ( i=7; i<i_NumOfAreas+7; i++ )
v_Area.append( AreaItem( sl_Input.at( i ).section( "\t", 0, 0 ), sl_Input.at( i ).section( "\t", 1, 1 ).toInt(), sl_Input.at( i ).section( "\t", 2, 2 ).toInt(), sl_Input.at( i ).section( "\t", 5, 5 ).toFloat(), sl_Input.at( i ).section( "\t", 3, 3 ).toFloat(), sl_Input.at( i ).section( "\t", 6, 6 ).toFloat(), sl_Input.at( i ).section( "\t", 4, 4 ).toFloat() ) );
initProgress( 2, FilenameADB, tr( "Finding area database (read data) ..." ), i_NumOfPositions );
i = i_NumOfAreas+10;
i_NumOfPositions += i;
while ( ( i < i_NumOfPositions ) && ( stopProgress != _APPBREAK_ ) )
{
v_Position.append( PositionItem( sl_Input.at( i ).section( "\t", 0, 0 ).toDouble(), sl_Input.at( i ).section( "\t", 1, 1 ).toDouble() ) );
stopProgress = incProgress( 2, ++i );
}
resetProgress( 2 );
return( i_NumOfAreas );
}
/// @throws AbortError, BackupReadError, BackupWriteError, GetRangesError
void DirectSearch::saveState(Mem::Random &ram, Async::AbortableProgress &progress) {
if (mStatus == DirectStatus::Started) {
Mem::Random::Lock lock(ram);
initProgress(progress);
for (size_t type = 0; type < Number::Type::count; ++type) {
mLocLists[type].refresh(lock, progress);
}
}
else {
Mem::Live live(ram);
std::auto_ptr<Mem::BackupData> data(new Mem::BackupData());
Mem::SingleBlockEnum block(live, 1, data.get());
mBackup = boost::none;
mStatus = DirectStatus::NotStarted;
progress.start(block.totalSize());
while (block.next()) {
progress.set(block.doneSize());
progress.check();
}
mBackup = Mem::Backup(data);
mStatus = DirectStatus::SavedBackup;
}
}
int MainWindow::GaussKruegerConverter( const QString &s_FilenameIn, const QString &s_FilenameOut, const int i_CodecInput, const int i_CodecOutput, const int i_EOL, const int i_ColumnLatitude, const int i_ColumnLongitude, const int i_ColumnHoch, const int i_ColumnRechts, const int i_ColumnStreifen, const int i_NumOfDigits, const int i_DecimalSeparator, const bool b_DeleteInputFile, const int i_NumOfFiles )
{
int i = 0;
int n = 0;
int mode = -1;
int stopProgress = 0;
QString s_EOL = setEOLChar( i_EOL );
QStringList sl_Input;
convertPosition *llc = new convertPosition( i_NumOfDigits, i_DecimalSeparator );
// **********************************************************************************************
// read file
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) < 1 )
return( n );
// **********************************************************************************************
if ( ( i_ColumnHoch > 0 ) && ( i_ColumnRechts > 0 ) && ( i_ColumnStreifen > 0 ) )
mode = _GKLL_;
if ( ( i_ColumnLatitude > 0 ) && ( i_ColumnLongitude > 0 ) )
mode = _LLGK_;
if ( mode < 0 )
return( mode );
// **********************************************************************************************
// open output file
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text) == false )
return( -20 );
QTextStream tout( &fout );
switch ( i_CodecOutput )
{
case _SYSTEM_:
break;
case _LATIN1_:
tout.setCodec( QTextCodec::codecForName( "ISO 8859-1" ) );
break;
case _APPLEROMAN_:
tout.setCodec( QTextCodec::codecForName( "Apple Roman" ) );
break;
default:
tout.setCodec( QTextCodec::codecForName( "UTF-8" ) );
break;
}
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Converting positions..." ), n );
switch( mode )
{
case _GKLL_:
tout << "Latitude\tLongitude\t" << sl_Input.at( i++ ) << s_EOL;
break;
case _LLGK_:
tout << "Hoch [m]\tRechts [m]\tStreifen\t" << sl_Input.at( i++ ) << s_EOL;
break;
}
while ( ( i < n ) && ( stopProgress != _APPBREAK_ ) )
{
switch( mode )
{
case _GKLL_:
llc->convertGKtoLL( sl_Input.at( i ).section( "\t", i_ColumnStreifen-1, i_ColumnStreifen-1 ), sl_Input.at( i ).section( "\t", i_ColumnRechts-1, i_ColumnRechts-1 ), sl_Input.at( i ).section( "\t", i_ColumnHoch-1, i_ColumnHoch-1 ) );
tout << sl_Input.at( i ) << "\t" << llc->Latitude() << "\t" << llc->Longitude() << s_EOL;
break;
case _LLGK_:
if ( ( llc->getMode( sl_Input.at( i ).section( "\t", i_ColumnLatitude-1, i_ColumnLatitude-1 ) ) == 1 ) || ( llc->getMode( sl_Input.at( i ).section( "\t", i_ColumnLongitude-1, i_ColumnLongitude-1 ) ) == 1 ) )
{
llc->setNumOfDigitsLL( 7 );
llc->convertLLtoLL( sl_Input.at( i ).section( "\t", i_ColumnLatitude-1, i_ColumnLatitude-1 ), sl_Input.at( i ).section( "\t", i_ColumnLongitude-1, i_ColumnLongitude-1 ) );
llc->convertLLtoGK( llc->Latitude(), llc->Longitude() );
}
else
{
llc->convertLLtoGK( sl_Input.at( i ).section( "\t", i_ColumnLatitude-1, i_ColumnLatitude-1 ), sl_Input.at( i ).section( "\t", i_ColumnLongitude-1, i_ColumnLongitude-1 ) );
}
tout << QString( "%1" ).arg( llc->Hoch(), 0, 'f', i_NumOfDigits ) << "\t" << QString( "%1" ).arg( llc->Rechts(), 0, 'f', i_NumOfDigits ) << "\t" << llc->Streifen() << "\t" << sl_Input.at( i ) << s_EOL;
break;
}
stopProgress = incProgress( i_NumOfFiles, ++i );
}
resetProgress( i_NumOfFiles );
// **********************************************************************************************
fout.close();
if ( stopProgress == _APPBREAK_ )
return( _APPBREAK_ );
if ( b_DeleteInputFile == true )
removeFile( s_FilenameIn );
return( _NOERROR_ );
}
int MainWindow::CliwocConverter( const QString &s_FilenameIn, const QString &s_FilenameOut, const QString &s_FilenameConf, const int i_NumOfFiles )
{
int k = 0;
int n = 0;
QString InputStr = "";
QString s_EventLabel = "";
QStringList sl_Conf;
unsigned int ui_length = 1;
unsigned int ui_filesize = 1;
// **********************************************************************************************
n = readFile( s_FilenameConf, sl_Conf );
if ( n < 9 )
return( _ERROR_ );
// **********************************************************************************************
// open input file
QFile fin( s_FilenameIn );
if ( fin.open( QIODevice::ReadOnly | QIODevice::Text ) == false )
return( -10 );
ui_filesize = fin.size();
QTextStream tin( &fin );
// **********************************************************************************************
// open output file
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text ) == false )
return( -20 );
QTextStream tout( &fout );
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Converting..." ), 100 );
// **********************************************************************************************
// read file
// Header
tout << k++ << "\t" << "Event label" << "\t" << "Date/Time" << "\t" << "Latitude" << "\t" << "Longitude";
for ( int i=9; i<n; i++ )
{
if ( sl_Conf.at( i ).section( "\t", 0, 0 ) == "x" )
tout << "\t" << sl_Conf.at( i ).section( "\t", 3, 3 ); // Column no 4: Parameter name
}
tout << endl;
while ( ( tin.atEnd() == false ) && ( ui_length != (unsigned int) _APPBREAK_ ) )
{
InputStr = tin.readLine();
ui_length = incProgress( i_NumOfFiles, ui_filesize, ui_length, InputStr );
// Event label
s_EventLabel = "@" + InputStr.mid( 34, 9 ).simplified() + "_" + InputStr.mid( 2597, 8 ).simplified() + "_" + InputStr.mid( 297, 30 ).simplified();
s_EventLabel.replace( "EXTRACT ", "" );
s_EventLabel.replace( ",", "" );
s_EventLabel.replace( ".", "" );
s_EventLabel.replace( "(", "-" );
s_EventLabel.replace( ")", "" );
s_EventLabel.replace( " ", "_" );
s_EventLabel.replace( "_-_", "_" );
s_EventLabel.replace( "_-", "_" );
s_EventLabel.replace( "-_", "_" );
s_EventLabel.replace( "__", "_" );
s_EventLabel.replace( "'", "" );
tout << k++ << "\t" << s_EventLabel << "\t";
// Date/Time
QString s_DateTime = InputStr.mid( 0, 4 ) + tr( "-" ) + InputStr.mid( 4, 2 ) + tr( "-" ) + InputStr.mid( 6, 2 ) + tr( "T" ) + InputStr.mid( 8, 2 ) + tr( ":" ) + InputStr.mid( 10, 2 );
s_DateTime.replace( " ", "0" );
tout << s_DateTime << "\t";
// Position
// Latitude
if ( InputStr.mid( 12, 5 ) != " " )
tout << InputStr.mid( 12, 5 ).toFloat()/100. << "\t";
else
tout << "\t";
// Longitude
if ( InputStr.mid( 17, 6 ) != " " )
{
float f_Longitude = InputStr.mid( 17, 6 ).toFloat()/100.;
if ( f_Longitude > 180. )
f_Longitude -=360;
tout << f_Longitude;
}
else
tout << "";
for ( int i=9; i<n; i++ )
{
if ( sl_Conf.at( i ).section( "\t", 0, 0 ) == "x" )
{
QString s_Factor = sl_Conf.at( i ).section( "\t", 1, 1 );
QString s_Entry = InputStr.mid( sl_Conf.at( i ).section( "\t", 4, 4 ).toInt()-1, sl_Conf.at( i ).section( "\t", 6, 6 ).toInt() ).simplified();
if ( s_Entry.isEmpty() == true )
{
tout << "\t";
}
else
{
if ( s_Factor == "T" )
{
s_Entry.replace( "\"", "''" );
tout << "\t~@" << s_Entry;
}
else
{
if ( s_Factor.isEmpty() == false )
tout << "\t" << s_Entry.toFloat()*s_Factor.toFloat();
else
tout << "\t" << s_Entry;
}
}
}
}
tout << endl;
}
resetProgress( i_NumOfFiles );
fin.close();
fout.close();
// **********************************************************************************************
if ( ui_length == (unsigned int) _APPBREAK_ )
return( _APPBREAK_ );
return( _NOERROR_ );
}
int MainWindow::findArea( const QString &s_FilenameIn, const QString &s_FilenameOut, const int i_CodecInput, const int i_CodecOutput, const int i_EOL, QVector<AreaItem> &v_Area, QVector<PositionItem> &v_Position, const bool b_DeleteInputFile, const int i_NumOfFiles)
{
int i = 1;
int j = 0;
int n = 0;
int m = 0;
int i_LatID = -1;
int i_LongID = -1;
int stopProgress = -1;
double d_Latitude_dummy = -1000.;
double d_Longitude_dummy = -1000.;
double d_Latitude = -1000.;
double d_Longitude = -1000.;
QString s_AreaName = "???";
QString s_EOL = setEOLChar( i_EOL );
QStringList sl_Input;
// **********************************************************************************************
// read file
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) < 1 )
return( n );
m = NumOfSections( sl_Input.at( 0 ) );
j = 0;
while ( ( i_LatID < 0 ) && ( j < m ) )
{
if ( sl_Input.at( 0 ).section( "\t", j, j ).contains( "Latitude", Qt::CaseInsensitive ) == true )
i_LatID = j;
else
j++;
}
j = 0;
while ( ( i_LongID < 0 ) && ( j < m ) )
{
if ( sl_Input.at( 0 ).section( "\t", j, j ).contains( "Longitude", Qt::CaseInsensitive ) == true )
i_LongID = j;
else
j++;
}
if ( ( i_LatID < 0 ) || ( i_LongID < 0 ) )
return( -40 );
// **********************************************************************************************
// open output file
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text) == false )
return( -20 );
QTextStream tout( &fout );
switch ( i_CodecOutput )
{
case _SYSTEM_:
break;
case _LATIN1_:
tout.setCodec( QTextCodec::codecForName( "ISO 8859-1" ) );
break;
case _APPLEROMAN_:
tout.setCodec( QTextCodec::codecForName( "Apple Roman" ) );
break;
default:
tout.setCodec( QTextCodec::codecForName( "UTF-8" ) );
break;
}
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Finding areas..." ), sl_Input.count() );
// **********************************************************************************************
tout << "Area\t" << sl_Input.at( 0 ) << s_EOL;
while ( ( i < n ) && ( stopProgress != _APPBREAK_ ) )
{
d_Latitude = (double) qMin( sl_Input.at( i ).section( "\t", i_LatID, i_LatID ).toFloat() + 90., 179.99 ); // 0 - 179.99
d_Longitude = (double) qMin( sl_Input.at( i ).section( "\t", i_LongID, i_LongID ).toFloat() + 180., 359.99 ); // 0 - 359.99
if ( ( d_Latitude-d_Latitude_dummy > 0.001 ) || ( d_Longitude-d_Longitude_dummy > 0.001 ) || ( d_Latitude-d_Latitude_dummy < -0.001 ) || ( d_Longitude-d_Longitude_dummy < -0.001 ) )
{
int j = 0;
int k = 0;
int i_InPolygon = 0;
while ( j < v_Area.count() )
{
if ( ( v_Area.at( j ).maxLatitude() > d_Latitude ) && ( d_Latitude > v_Area.at( j ).minLatitude() ) )
{
if ( ( v_Area.at( j ).maxLongitude() > d_Longitude ) && ( d_Longitude > v_Area.at( j ).minLongitude() ) )
{
i_InPolygon = PtInPolygon( d_Latitude, d_Longitude, v_Area.at( j ).StartPosition(), v_Area.at( j ).NumOfPoints(), v_Position );
if ( i_InPolygon == 1 )
{
s_AreaName = v_Area.at( j ).AreaName();
s_AreaName.replace( ", western part", "" );
s_AreaName.replace( ", eastern part", "" );
d_Latitude_dummy = d_Latitude;
d_Longitude_dummy = d_Longitude;
tout << s_AreaName << "\t" << sl_Input.at( i ) << s_EOL;
j = v_Area.count() - 1;
}
}
}
k += v_Area.at( j ).NumOfPoints();
j += 1;
}
if ( i_InPolygon < 1 )
{
d_Latitude_dummy = d_Latitude;
d_Longitude_dummy = d_Longitude;
if ( d_Latitude > 160. )
s_AreaName = "Arctic Ocean";
else
s_AreaName = "???";
tout << s_AreaName << "\t" << sl_Input.at( i ) << s_EOL;
}
}
else
{
tout << s_AreaName << "\t" << sl_Input.at( i ) << s_EOL;
}
stopProgress = incProgress( i_NumOfFiles, ++i );
}
//--------------------------------------------------------------------------------------------
resetProgress( i_NumOfFiles );
fout.close();
if ( stopProgress == _APPBREAK_ )
return( _APPBREAK_ );
if ( b_DeleteInputFile == true )
removeFile( s_FilenameIn );
return( _NOERROR_ );
}
int main(int argc,char* argv[]) {
int width=512;
int height=512;
int max;
int x,y;
int nowProgress=0;
FILE* fp=NULL;
png_structp pngPtr;
png_infop pngInfoPtr;
png_bytepp pngImageData;
/* コマンドライン引数の取得とスクリプトの読み込み */
if(argc<3) {
puts("Usage: 3d_gazou_seisei <script file> <output file> [width [height [params...]]");
return 1;
}
if(argc>=4)sscanf(argv[3],"%d",&width);
if(argc>=5)sscanf(argv[4],"%d",&height);
if(width<=0 || height<=0) {
puts("invalid size");
return 1;
}
if(!loadScript(argv[1],argc>5?argc-5:0,argv+5))return 1;
/* PNGデータを書き込む準備 */
pngPtr=png_create_write_struct(PNG_LIBPNG_VER_STRING,NULL,NULL,NULL);
if(!pngPtr) {
puts("png_create_write_struct failed");
return 1;
}
pngInfoPtr=png_create_info_struct(pngPtr);
if(!pngInfoPtr) {
puts("png_create_info_struct failed");
png_destroy_write_struct(&pngPtr,NULL);
return 1;
}
fp=fopen(argv[2],"wb");
if(setjmp(png_jmpbuf(pngPtr))) {
png_destroy_write_struct(&pngPtr,&pngInfoPtr);
fclose(fp);
return 1;
}
png_init_io(pngPtr,fp);
png_set_IHDR(pngPtr,pngInfoPtr,width,height,8,PNG_COLOR_TYPE_RGB,
PNG_INTERLACE_NONE,PNG_COMPRESSION_TYPE_BASE,PNG_FILTER_TYPE_BASE);
/* 画像を格納するメモリの確保 */
puts("generating image data...");
pngImageData=png_malloc(pngPtr,height*sizeof(png_bytep));
for(y=0;y<height;y++)pngImageData[y]=png_malloc(pngPtr,width*3);
/* 画像生成の計算本体 */
initProgress(height);
max=(width>=height?width:height);
#ifdef _OPENMP
#pragma omp parallel for schedule(dynamic) private(x)
#endif
for(y=0;y<height;y++) {
for(x=0;x<width;x++) {
double xoff=(double)(x-width/2)/(max/2);
double yoff=(double)(height/2-y)/(max/2);
double vec[3]={
theWorld.camera.dir[0]+theWorld.camera.dx[0]*xoff+theWorld.camera.dy[0]*yoff,
theWorld.camera.dir[1]+theWorld.camera.dx[1]*xoff+theWorld.camera.dy[1]*yoff,
theWorld.camera.dir[2]+theWorld.camera.dx[2]*xoff+theWorld.camera.dy[2]*yoff
};
color_t color=getColorOfOnePoint(theWorld.camera.pos,vec,theWorld.ttl);
pngImageData[y][x*3+0]=(int)(color.r*255.0+EPS);
pngImageData[y][x*3+1]=(int)(color.g*255.0+EPS);
pngImageData[y][x*3+2]=(int)(color.b*255.0+EPS);
}
#ifdef _OPENMP
#pragma omp flush(nowProgress)
#pragma omp atomic
#endif
nowProgress++;
#ifdef _OPENMP
#pragma omp flush(nowProgress)
#endif
updateProgress(nowProgress);
}
putchar('\n');
png_set_rows(pngPtr,pngInfoPtr,pngImageData);
/* 画像のファイルへの書き込み */
png_write_png(pngPtr,pngInfoPtr,PNG_TRANSFORM_IDENTITY,NULL);
for(y=0;y<height;y++)png_free(pngPtr,pngImageData[y]);
png_free(pngPtr,pngImageData);
png_destroy_write_struct(&pngPtr,&pngInfoPtr);
fclose(fp);
puts("done");
/* 確保したテクスチャの開放 */
freeTheWorld();
return 0;
}
void NGSD::annotate(VariantList& variants, QString filename)
{
initProgress("NGSD annotation", true);
//get sample ids
QString s_id = sampleId(filename, false);
QString ps_id = processedSampleId(filename, false);
QString sys_id = getValue("SELECT processing_system_id FROM processed_sample WHERE id='" + processedSampleId(filename, false) + "'").toString();
//check if we could determine the sample
bool found_in_db = true;
if (s_id=="" || ps_id=="" || sys_id=="")
{
Log::warn("Could not find processed sample in NGSD by name '" + filename + "'. Annotation will be incomplete because processing system could not be determined!");
found_in_db = false;
}
//get sample ids that have processed samples with the same processing system (not same sample, variants imported, same processing system, good quality of sample, not tumor)
QSet<int> sys_sample_ids;
SqlQuery tmp = getQuery();
tmp.exec("SELECT DISTINCT s.id FROM processed_sample as ps, sample s WHERE ps.processing_system_id='" + sys_id + "' AND ps.sample_id=s.id AND s.tumor='0' AND s.quality='good' AND s.id!='" + s_id + "' AND (SELECT count(id) FROM detected_variant as dv WHERE dv.processed_sample_id = ps.id)>0");
while(tmp.next())
{
sys_sample_ids.insert(tmp.value(0).toInt());
}
//remove all NGSD-specific columns
QList<VariantAnnotationHeader> headers = variants.annotations();
foreach(const VariantAnnotationHeader& header, headers)
{
if (header.name().startsWith("ihdb_"))
{
removeColumnIfPresent(variants, header.name(), true);
}
}
removeColumnIfPresent(variants, "classification", true);
removeColumnIfPresent(variants, "classification_comment", true);
removeColumnIfPresent(variants, "validated", true);
removeColumnIfPresent(variants, "comment", true);
//get required column indices
QString num_samples = QString::number(sys_sample_ids.count());
int ihdb_hom_idx = addColumn(variants, "ihdb_hom", "Homozygous variant counts in NGSD for the same processing system (" + num_samples + " samples).");
int ihdb_het_idx = addColumn(variants, "ihdb_het", "Heterozyous variant counts in NGSD for the same processing system (" + num_samples + " samples).");
int ihdb_wt_idx = addColumn(variants, "ihdb_wt", "Wildtype variant counts in NGSD for the same processing system (" + num_samples + " samples).");
int ihdb_all_hom_idx = addColumn(variants, "ihdb_allsys_hom", "Homozygous variant counts in NGSD independent of the processing system.");
int ihdb_all_het_idx = addColumn(variants, "ihdb_allsys_het", "Heterozygous variant counts in NGSD independent of the processing system.");
int class_idx = addColumn(variants, "classification", "Classification from the NGSD.");
int clacom_idx = addColumn(variants, "classification_comment", "Classification comment from the NGSD.");
int valid_idx = addColumn(variants, "validated", "Validation information from the NGSD. Validation results of other samples are listed in brackets!");
if (variants.annotationIndexByName("comment", true, false)==-1) addColumn(variants, "comment", "Comments from the NGSD. Comments of other samples are listed in brackets!");
int comment_idx = variants.annotationIndexByName("comment", true, false);
//(re-)annotate the variants
SqlQuery query = getQuery();
for (int i=0; i<variants.count(); ++i)
{
//QTime timer;
//timer.start();
//variant id
Variant& v = variants[i];
QByteArray v_id = variantId(v, false).toLatin1();
//variant classification
QVariant classification = getValue("SELECT class FROM variant_classification WHERE variant_id='" + v_id + "'", true);
if (!classification.isNull())
{
v.annotations()[class_idx] = classification.toByteArray().replace("n/a", "");
v.annotations()[clacom_idx] = getValue("SELECT comment FROM variant_classification WHERE variant_id='" + v_id + "'", true).toByteArray().replace("\n", " ").replace("\t", " ");
}
//int t_v = timer.elapsed();
//timer.restart();
//detected variant infos
int dv_id = -1;
QByteArray comment = "";
if (found_in_db)
{
query.exec("SELECT id, comment FROM detected_variant WHERE processed_sample_id='" + ps_id + "' AND variant_id='" + v_id + "'");
if (query.size()==1)
{
query.next();
dv_id = query.value(0).toInt();
comment = query.value(1).toByteArray();
}
}
//validation info
int vv_id = -1;
QByteArray val_status = "";
if (found_in_db)
{
query.exec("SELECT id, status FROM variant_validation WHERE sample_id='" + s_id + "' AND variant_id='" + v_id + "'");
if (query.size()==1)
{
query.next();
vv_id = query.value(0).toInt();
val_status = query.value(1).toByteArray().replace("n/a", "");
}
}
//int t_dv = timer.elapsed();
//timer.restart();
//validation info other samples
int tps = 0;
int fps = 0;
query.exec("SELECT id, status FROM variant_validation WHERE variant_id='"+v_id+"' AND status!='n/a'");
while(query.next())
{
if (query.value(0).toInt()==vv_id) continue;
if (query.value(1).toByteArray()=="true positive") ++tps;
else if (query.value(1).toByteArray()=="false positive") ++fps;
}
if (tps>0 || fps>0)
{
if (val_status=="") val_status = "n/a";
val_status += " (" + QByteArray::number(tps) + "xTP, " + QByteArray::number(fps) + "xFP)";
}
//int t_val = timer.elapsed();
//timer.restart();
//comments other samples
QList<QByteArray> comments;
query.exec("SELECT id, comment FROM detected_variant WHERE variant_id='"+v_id+"' AND comment IS NOT NULL");
while(query.next())
{
if (query.value(0).toInt()==dv_id) continue;
QByteArray tmp = query.value(1).toByteArray().trimmed();
if (tmp!="") comments.append(tmp);
}
if (comments.size()>0)
{
if (comment=="") comment = "n/a";
comment += " (";
for (int i=0; i<comments.count(); ++i)
{
if (i>0)
{
comment += ", ";
}
comment += comments[i];
}
comment += ")";
}
//int t_com = timer.elapsed();
//timer.restart();
//genotype counts
int allsys_hom_count = 0;
int allsys_het_count = 0;
int sys_hom_count = 0;
int sys_het_count = 0;
QSet<int> s_ids_done;
int s_id_int = s_id.toInt();
query.exec("SELECT dv.genotype, ps.sample_id FROM detected_variant as dv, processed_sample ps WHERE dv.processed_sample_id=ps.id AND dv.variant_id='" + v_id + "'");
while(query.next())
{
//skip this sample id
int current_sample = query.value(1).toInt();
if (current_sample==s_id_int) continue;
//skip already seen samples (there could be several processings of the same sample because of different processing systems or because of experment repeats due to quality issues)
if (s_ids_done.contains(current_sample)) continue;
s_ids_done.insert(current_sample);
QByteArray current_geno = query.value(0).toByteArray();
if (current_geno=="hom")
{
++allsys_hom_count;
if (sys_sample_ids.contains(current_sample))
{
++sys_hom_count;
}
}
else if (current_geno=="het")
{
++allsys_het_count;
if (sys_sample_ids.contains(current_sample))
{
++sys_het_count;
}
}
}
//qDebug() << (v.isSNV() ? "S" : "I") << query.size() << t_v << t_dv << t_val << t_com << timer.elapsed();
v.annotations()[ihdb_all_hom_idx] = QByteArray::number(allsys_hom_count);
v.annotations()[ihdb_all_het_idx] = QByteArray::number(allsys_het_count);
if (found_in_db)
{
v.annotations()[ihdb_hom_idx] = QByteArray::number((double)sys_hom_count / sys_sample_ids.count(), 'f', 4);
v.annotations()[ihdb_het_idx] = QByteArray::number((double)sys_het_count / sys_sample_ids.count(), 'f', 4);
v.annotations()[ihdb_wt_idx] = QByteArray::number((double)(sys_sample_ids.count() - sys_hom_count - sys_het_count) / sys_sample_ids.count(), 'f', 4);
v.annotations()[valid_idx] = val_status;
v.annotations()[comment_idx] = comment.replace("\n", " ").replace("\t", " ");
}
else
{
v.annotations()[ihdb_hom_idx] = "n/a";
v.annotations()[ihdb_het_idx] = "n/a";
v.annotations()[ihdb_wt_idx] = "n/a";
v.annotations()[valid_idx] = "n/a";
v.annotations()[comment_idx] = "n/a";
}
emit updateProgress(100*i/variants.count());
}
}
int MainWindow::buildAreaDatabase( const QString &s_FilenameIn, const int i_CodecInput, const int i_NumOfFiles )
{
int n = 0;
int stopProgress = 0;
int i = 0;
int i_NumOfAreas = 0;
int i_NumOfPositions = 0;
int i_StartPosition = 0;
int i_AreaNamePosition = -1;
int i_LatitudePosition = -1;
int i_LongitudePosition = -1;
double d_Lat = 0.;
double d_Long = 0.;
double d_minLat = 180.;
double d_maxLat = 0.;
double d_minLong = 360.;
double d_maxLong = 0.;
QString s_AreaName = "";
QString s_Header = "";
QStringList sl_Input;
QVector<AreaItem> v_Area;
QVector<PositionItem> v_Position;
// **********************************************************************************************
QFileInfo fi( s_FilenameIn );
QFile fout( fi.absolutePath() + "/" + fi.baseName() + ".adb" );
if ( fout.open( QIODevice::WriteOnly ) == false )
return( -20 );
// **********************************************************************************************
// read file
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) < 1 )
return( n );
if ( sl_Input.at( i ).contains( "/*" ) == true )
{
while ( ( i < n ) && ( sl_Input.at( i ).contains( "*/" ) == false ) )
i++;
}
// **********************************************************************************************
// check file format (plain text or doi:10.1594/PANGAEA.777975)
if ( i > 0 )
{
if ( n-i++ < 4 )
return ( -40 );
}
else
{
if ( n < 4 )
return ( -40 );
}
s_Header = sl_Input.at( i++ );
for ( int j=0; j<s_Header.count(); j++ )
{
if ( ( s_Header.section( "\t", j, j ) == "Name" ) || ( s_Header.section( "\t", j, j ) == "Name of area" ) || ( s_Header.section( "\t", j, j ) == "Campaign" ) )
i_AreaNamePosition = j;
if ( s_Header.section( "\t", j, j ) == "Latitude" )
i_LatitudePosition = j;
if ( s_Header.section( "\t", j, j ) == "Longitude" )
i_LongitudePosition = j;
}
if ( ( i_AreaNamePosition < 0 ) || ( i_LatitudePosition < 0 ) || ( i_LongitudePosition < 0 ) )
return( -40 );
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Building area database (read data) ..." ), n );
while ( ( i < n ) && ( stopProgress != _APPBREAK_ ) )
{
d_minLat = 1000.0;
d_maxLat = -1000.0;
d_minLong = 1000.0;
d_maxLong = -1000.0;
i_NumOfPositions = 0;
i_StartPosition = v_Position.count();
s_AreaName = sl_Input.at( i ).section( "\t", i_AreaNamePosition, i_AreaNamePosition );
while ( ( i < n ) && ( ( sl_Input.at( i ).section( "\t", i_AreaNamePosition, i_AreaNamePosition ) == s_AreaName ) || ( sl_Input.at( i ).section( "\t", i_AreaNamePosition, i_AreaNamePosition ).isEmpty() == true ) ) && ( stopProgress != _APPBREAK_ ) )
{
i_NumOfPositions++;
d_Lat = (double) qMin( sl_Input.at( i ).section( "\t", i_LatitudePosition, i_LatitudePosition ).toFloat() + 90., 179.99 );
d_Long = (double) qMin( sl_Input.at( i ).section( "\t", i_LongitudePosition, i_LongitudePosition ).toFloat() + 180., 359.99 );
v_Position.append( PositionItem( d_Lat, d_Long ) );
d_minLat = qMin( d_minLat, v_Position.last().Latitude() );
d_maxLat = qMax( d_maxLat, v_Position.last().Latitude() );
d_minLong = qMin( d_minLong, v_Position.last().Longitude() );
d_maxLong = qMax( d_maxLong, v_Position.last().Longitude() );
stopProgress = incProgress( i_NumOfFiles, ++i );
}
v_Area.append( AreaItem( s_AreaName, i_StartPosition, i_NumOfPositions, d_minLat, d_maxLat, d_minLong, d_maxLong ) );
}
resetProgress( i_NumOfFiles );
//----------------------------------------------------------------------------------------------------
if ( stopProgress != _APPBREAK_ )
{
i_NumOfAreas = v_Area.count();
i_NumOfPositions = v_Position.count();
QByteArray ba( "PanTool area database\n" ); // 0
ba.append( QString( "Created:\t%1\n" ).arg( QDateTime::currentDateTime().toString( Qt::ISODate ) ) ); // 1
ba.append( QString( "Number of areas:\t%1\n" ).arg( i_NumOfAreas ) ); // 2
ba.append( QString( "Number of positions:\t%1\n" ).arg( i_NumOfPositions ) ); // 3
ba.append( "\n[Areas]\n" );
ba.append( "Name of area\tStart position\tNumber of positions\tmax Lat\tmax Long\tmin Lat\tmin Long\n" ); // 4
for ( i=0; i<i_NumOfAreas; i++ )
{
ba.append( v_Area.at( i ).AreaName() + "\t" );
ba.append( QString( "%1\t%2\t%3\t%4\t%5\t%6\n" ).arg( v_Area.at( i ).StartPosition() ).arg( v_Area.at( i ).NumOfPoints() ).arg( v_Area.at( i ).maxLatitude() ).arg( v_Area.at( i ).maxLongitude() ).arg( v_Area.at( i ).minLatitude() ).arg( v_Area.at( i ).minLongitude() ) );
}
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Building area database (write data) ..." ), i_NumOfPositions );
i = 0;
ba.append( "\n[Positions]\n" );
ba.append( "Latitude\tLongitude\n" );
while ( ( i<i_NumOfPositions ) && ( stopProgress != _APPBREAK_ ) )
{
ba.append( QString( "%1\t%2\n" ).arg( v_Position.at( i ).Latitude(), 0, 'f', 6 ).arg( v_Position.at( i ).Longitude(), 0, 'f', 6 ) );
stopProgress = incProgress( i_NumOfFiles, ++i );
}
resetProgress( i_NumOfFiles );
fout.write( qCompress( ba, 9 ) );
fout.close();
}
return( _NOERROR_ );
}
int MainWindow::addLine( const QString &s_FilenameIn, const QString &s_FilenameOut, const int i_CodecInput, const int i_CodecOutput, const int i_EOL,
const QStringList &sl_Text, const int i_LineNo, const bool b_AddFilename, const bool b_AddFullPath, const bool b_AddOrdinalNumber,
const bool b_PrependMetadataColumn, const bool b_AppendMetadataColumn, const bool b_SkipEmptyLines, const bool b_SkipCommentLines, const int i_NumOfFiles )
{
int i = 0;
int k = 0;
int n = 0;
int e = 0;
int stopProgress = 0;
QString s_EOL = setEOLChar( i_EOL );
QStringList sl_Input;
// **********************************************************************************************
// read file
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) < 1 )
return( n );
// **********************************************************************************************
// open output file
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text) == false )
return( -20 );
QTextStream tout( &fout );
switch ( i_CodecOutput )
{
case _SYSTEM_:
break;
case _LATIN1_:
tout.setCodec( QTextCodec::codecForName( "ISO 8859-1" ) );
break;
case _APPLEROMAN_:
tout.setCodec( QTextCodec::codecForName( "Apple Roman" ) );
break;
default:
tout.setCodec( QTextCodec::codecForName( "UTF-8" ) );
break;
}
QFileInfo fi( s_FilenameIn );
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Adding lines..." ), sl_Input.count() );
e = i_LineNo - 1;
if ( b_PrependMetadataColumn == true )
{
if ( b_AddFilename == true )
tout << "Event label" << "\t";
if ( b_AddFullPath == true )
tout << "Filename" << "\t";
if ( b_AddOrdinalNumber == true )
tout << "No" << "\t";
}
tout << sl_Input.at( 0 );
if ( b_AppendMetadataColumn == true )
{
if ( b_AddFilename == true )
tout << "\t" << "Event label";
if ( b_AddFullPath == true )
tout << "\t"<< "Filename";
if ( b_AddOrdinalNumber == true )
tout << "\t" << "No";
}
tout << s_EOL;
stopProgress = incProgress( i_NumOfFiles, ++i );
while ( ( i<e ) && ( stopProgress != _APPBREAK_ ) )
{
if ( LineCanBeWritten( sl_Input.at( i ), b_SkipEmptyLines, b_SkipCommentLines ) == true )
{
if ( b_PrependMetadataColumn == true )
{
if ( b_AddFilename == true )
tout << fi.baseName() << "\t";
if ( b_AddFullPath == true )
tout << fi.absoluteFilePath() << "\t";
if ( b_AddOrdinalNumber == true )
tout << QString( "%1" ).arg( ++k ) << "\t";
}
tout << sl_Input.at( i );
if ( b_AppendMetadataColumn == true )
{
if ( b_AddFilename == true )
tout << "\t" << fi.baseName();
if ( b_AddFullPath == true )
tout << "\t" << fi.absoluteFilePath();
if ( b_AddOrdinalNumber == true )
{
if ( b_PrependMetadataColumn == false )
tout << "\t" << QString( "%1" ).arg( ++k );
else
tout << "\t" << QString( "%1" ).arg( k );
}
}
tout << s_EOL;
}
stopProgress = incProgress( i_NumOfFiles, ++i );
}
for ( int j=0; j<sl_Text.count(); j++ )
{
if ( b_PrependMetadataColumn == true )
{
if ( b_AddFilename == true )
tout << fi.baseName() << "\t";
if ( b_AddFullPath == true )
tout << fi.absoluteFilePath() << "\t";
if ( b_AddOrdinalNumber == true )
tout << QString( "%1" ).arg( ++k ) << "\t";
}
tout << sl_Text.at( j );
if ( b_AppendMetadataColumn == true )
{
if ( b_AddFilename == true )
tout << "\t" << fi.baseName();
if ( b_AddFullPath == true )
tout << "\t" << fi.absoluteFilePath();
if ( b_AddOrdinalNumber == true )
{
if ( b_PrependMetadataColumn == false )
tout << "\t" << QString( "%1" ).arg( ++k );
else
tout << "\t" << QString( "%1" ).arg( k );
}
}
tout << s_EOL;
}
while ( ( i < n ) && ( stopProgress != _APPBREAK_ ) )
{
if ( LineCanBeWritten( sl_Input.at( i ), b_SkipEmptyLines, b_SkipCommentLines ) == true )
{
if ( b_PrependMetadataColumn == true )
{
if ( b_AddFilename == true )
tout << fi.baseName() << "\t";
if ( b_AddFullPath == true )
tout << fi.absoluteFilePath() << "\t";
if ( b_AddOrdinalNumber == true )
tout << QString( "%1" ).arg( ++k ) << "\t";
}
tout << sl_Input.at( i );
if ( b_AppendMetadataColumn == true )
{
if ( b_AddFilename == true )
tout << "\t" << fi.baseName();
if ( b_AddFullPath == true )
tout << "\t" << fi.absoluteFilePath();
if ( b_AddOrdinalNumber == true )
{
if ( b_PrependMetadataColumn == false )
tout << "\t" << QString( "%1" ).arg( ++k );
else
tout << "\t" << QString( "%1" ).arg( k );
}
}
tout << s_EOL;
}
stopProgress = incProgress( i_NumOfFiles, ++i );
}
resetProgress( i_NumOfFiles );
// **********************************************************************************************
fout.close();
if ( stopProgress == _APPBREAK_ )
return( _APPBREAK_ );
return( _NOERROR_ );
}
int MainWindow::getDataMetadata( const int i_CodecInput, const int i_OutputFormat, const QString &s_MetadataIn, QStringList &sl_DataMetadataList, structURL URL[], const int i_NumOfFiles )
{
int n = 0;
int j = 0;
int i_line = 0;
int stopProgress = 0;
int i_DatePos = -1;
int i_TimePos = -1;
int i_DateTimePos = -1;
int i_ElevationPos = -1;
int i_EventLabelPos = -1;
int i_CampaignLabelPos = -1;
int i_AreaNamePos = -1;
int i_GearNamePos = -1;
int i_LatitudePos = -1;
int i_LongitudePos = -1;
QStringList sl_Input;
QString s_Metadata = "";
QString s_EventLabel = "";
QString s_Header = "";
QString s_LatLon = "";
bool b_containsPosition = false;
sl_DataMetadataList.clear();
//-----------------------------------------------------------------------------------------------------------------------
b_containsPosition = getDataMetadataPosition( s_MetadataIn, i_DatePos, i_TimePos, i_DateTimePos, i_ElevationPos, i_EventLabelPos, i_CampaignLabelPos, i_AreaNamePos, i_GearNamePos, i_LatitudePos, i_LongitudePos );
//-----------------------------------------------------------------------------------------------------------------------
if ( ( n = readFile( s_MetadataIn.section( "\t", _FILENAMEPOS, _FILENAMEPOS ), sl_Input, i_CodecInput ) ) < 1 )
return( n );
//-----------------------------------------------------------------------------------------------------------------------
switch ( i_OutputFormat )
{
case _FORMAT_KMLFILE:
initProgress( i_NumOfFiles, s_MetadataIn.section( "\t", _FILENAMEPOS, _FILENAMEPOS ), tr( "Creating Google Earth import file" ), n );
break;
case _FORMAT_SHAPE_METADATA:
case _FORMAT_SHAPE_DATA:
initProgress( i_NumOfFiles, s_MetadataIn.section( "\t", _FILENAMEPOS, _FILENAMEPOS ), tr( "Creating shapefile" ), n );
break;
default:
initProgress( i_NumOfFiles, s_MetadataIn.section( "\t", _FILENAMEPOS, _FILENAMEPOS ), tr( "Creating file" ), n );
break;
}
//-----------------------------------------------------------------------------------------------------------------------
i_line = s_MetadataIn.section( "\t", _NUMOFHEADERLINESPOS, _NUMOFHEADERLINESPOS ).toInt()-1;
if ( sl_Input.at( i_line ) == "*/" )
++i_line;
for ( int i=0; i<NumOfSections( sl_Input.at( i_line ) ); ++i )
{
s_Header = sl_Input.at( i_line ).section( "\t", i, i );
if ( ( s_Header.startsWith( "url", Qt::CaseInsensitive ) == true ) || ( s_Header.startsWith( "uri", Qt::CaseInsensitive ) == true ) || ( s_Header.startsWith( "persistent identifier", Qt::CaseInsensitive ) == true ) )
{
if ( ++j <= _MAX_NUM_OF_URLS )
{
URL[j].position = i;
if ( s_Header.contains( "@" ) == true )
URL[j].TitleURL = s_Header.section( "@", 1, 1 );
else
URL[j].TitleURL = s_Header;
}
}
}
stopProgress = incProgress( i_NumOfFiles, i_line );
//-----------------------------------------------------------------------------------------------------------------------
++i_line;
parseData( i_line, sl_Input.at( i_line ), s_MetadataIn, i_AreaNamePos, i_CampaignLabelPos, i_EventLabelPos, i_GearNamePos, i_DatePos, i_TimePos, i_DateTimePos, i_LatitudePos, i_LongitudePos, i_ElevationPos, URL, s_Metadata );
addToMetadataList( s_Metadata, s_EventLabel, s_LatLon, sl_DataMetadataList );
stopProgress = incProgress( i_NumOfFiles, i_line );
if ( b_containsPosition == true )
{
while ( ( ++i_line < n ) && ( stopProgress != _APPBREAK_ ) )
{
parseData( i_line, sl_Input.at( i_line ), s_MetadataIn, i_AreaNamePos, i_CampaignLabelPos, i_EventLabelPos, i_GearNamePos, i_DatePos, i_TimePos, i_DateTimePos, i_LatitudePos, i_LongitudePos, i_ElevationPos, URL, s_Metadata );
addToMetadataList( s_Metadata, s_EventLabel, s_LatLon, sl_DataMetadataList );
stopProgress = incProgress( i_NumOfFiles, i_line );
}
}
//-----------------------------------------------------------------------------------------------------------------------
resetProgress( i_NumOfFiles );
return( _NOERROR_ );
}
int MainWindow::createKmlFile( const QString &s_FilenameIn,
int &i_IconColor, int &i_IconSize,
int &i_TracklineColor, int &i_TracklineWidth,
QString &s_FilenameGoogleEarthProgram, bool &b_startGoogleEarth,
QString &s_FilenameOut, const int i_NumOfFiles )
{
int i = 0;
int n = 0;
int stopProgress = 0;
int i_ID = 0;
int i_StartID = 0;
int i_EndID = 0;
double d_Distance = 0.0;
double d_Speed = 0.0;
double d_Latitude = 0.0;
double d_Longitude = 0.0;
double d_Latitude_old = 0.0;
double d_Longitude_old = 0.0;
double d_Seconds_old = 0.0;
double d_PlotDistance = 100.0;
QString s_Date = "";
QString s_Time = "";
QString s_Latitude = "";
QString s_Longitude = "";
QString s_TrackName = "";
QStringList sl_Input;
QFileInfo fi( s_FilenameIn );
// **********************************************************************************************
// read file
QFile fin( s_FilenameIn );
if ( fin.open( QIODevice::ReadOnly | QIODevice::Text ) == false )
return( -10 );
QTextStream tin( &fin );
while ( tin.atEnd() == false )
sl_Input.append( tin.readLine().replace( QChar( 0x00 ), "" ) );
fin.close();
n = sl_Input.count();
// **********************************************************************************************
if ( ( n<2 ) || ( sl_Input.at( i++ ) != "INDEX,TAG,DATE,TIME,LATITUDE N/S,LONGITUDE E/W,HEIGHT,SPEED,HEADING,VOX" ) )
return( _APPBREAK_ );
i_StartID = sl_Input.at( 1 ).section( ",", 0, 0 ).toInt();
i_EndID = sl_Input.at( sl_Input.count() - 1 ).section( ",", 0, 0 ).toInt();
s_TrackName = fi.baseName();
if ( doGPStoKmlOptionsDialog( i_StartID, i_EndID, i_IconColor, i_IconSize, i_TracklineColor, i_TracklineWidth, s_TrackName, s_FilenameGoogleEarthProgram, b_startGoogleEarth ) == QDialog::Rejected )
return( _APPBREAK_ );
// **********************************************************************************************
// open output file
s_FilenameOut = fi.absolutePath() + "/" + s_TrackName + ".kml";
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text) == false )
{
s_FilenameOut = "";
return( -20 );
}
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Creating KML file..." ), 2*sl_Input.count() );
// **********************************************************************************************
QTextStream tout( &fout );
tout.setCodec( "UTF-8" );
tout << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << endl;
tout << "<kml xmlns=\"http://earth.google.com/kml/2.1\">" << endl;
tout << "<Document>" << endl;
/*
tout << " <ScreenOverlay>" << endl;
tout << " <name>Pan2Applic logo</name>" << endl;
tout << " <Icon><href>http://epic.awi.de/40953/121/Pan2Applic_logo.png</href></Icon>" << endl;
tout << " <overlayXY x=\"0\" y=\"1\" xunits=\"fraction\" yunits=\"fraction\"/>" << endl;
tout << " <screenXY x=\"5\" y=\"5\" xunits=\"pixels\" yunits=\"insetPixels\"/>" << endl;
tout << " <size x=\"200\" y=\"88\" xunits=\"pixel\" yunits=\"pixel\"/>" << endl;
tout << " </ScreenOverlay>" << endl;
*/
tout << " <Style id=\"circle-blue\"><IconStyle><Icon><href>http://epic.awi.de/40953/1/circle-blue.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"circle-green\"><IconStyle><Icon><href>http://epic.awi.de/40953/2/circle-green.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"circle-orange\"><IconStyle><Icon><href>http://epic.awi.de/40953/3/circle-orange.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"circle-red\"><IconStyle><Icon><href>http://epic.awi.de/40953/4/circle-red.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"circle-white\"><IconStyle><Icon><href>http://epic.awi.de/40953/5/circle-white.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"circle-yellow\"><IconStyle><Icon><href>http://epic.awi.de/40953/6/circle-yellow.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"square-blue\"><IconStyle><Icon><href>http://epic.awi.de/40953/7/square-blue.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"square-green\"><IconStyle><Icon><href>http://epic.awi.de/40953/8/square-green.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"square-orange\"><IconStyle><Icon><href>http://epic.awi.de/40953/9/square-orange.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"square-red\"><IconStyle><Icon><href>http://epic.awi.de/40953/10/square-red.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"square-white\"><IconStyle><Icon><href>http://epic.awi.de/40953/11/square-white.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"square-yellow\"><IconStyle><Icon><href>http://epic.awi.de/40953/12/square-yellow.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"star-blue\"><IconStyle><Icon><href>http://epic.awi.de/40953/13/star-blue.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"star-green\"><IconStyle><Icon><href>http://epic.awi.de/40953/14/star-green.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"star-orange\"><IconStyle><Icon><href>http://epic.awi.de/40953/15/star-orange.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"star-red\"><IconStyle><Icon><href>http://epic.awi.de/40953/16/star-red.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"star-white\"><IconStyle><Icon><href>http://epic.awi.de/40953/17/star-white.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"star-yellow\"><IconStyle><Icon><href>http://epic.awi.de/40953/18/star-yellow.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"triangle-blue\"><IconStyle><Icon><href>http://epic.awi.de/40953/19/triangle-blue.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"triangle-green\"><IconStyle><Icon><href>http://epic.awi.de/40953/20/triangle-green.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"triangle-orange\"><IconStyle><Icon><href>http://epic.awi.de/40953/21/triangle-orange.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"triangle-red\"><IconStyle><Icon><href>http://epic.awi.de/40953/22/triangle-red.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"triangle-white\"><IconStyle><Icon><href>http://epic.awi.de/40953/23/triangle-white.png</href></Icon></IconStyle></Style>" << endl;
tout << " <Style id=\"triangle-yellow\"><IconStyle><Icon><href>http://epic.awi.de/40953/24/triangle-yellow.png</href></Icon></IconStyle></Style>" << endl;
// **********************************************************************************************
// Way points
tout << "<Folder>" << endl;
tout << "<name>Point Set</name>" << endl;
tout << "<open>0</open>" << endl;
while ( ( i<n ) && ( stopProgress != _APPBREAK_ ) )
{
if ( sl_Input.at( i ).section( ",", 1, 1 ) == "T" )
{
i_ID = sl_Input.at( i ).section( ",", 0, 0 ).toInt();
if ( ( i_StartID <= i_ID ) && ( i_ID <= i_EndID ) )
{
s_Time = sl_Input.at( i ).section( ",", 3, 3 ).left( 2 ) + ":" + sl_Input.at( i ).section( ",", 3, 3 ).mid( 2, 2 ) + ":" + sl_Input.at( i ).section( ",", 3, 3 ).mid( 4, 2 );
s_Date = "20" + sl_Input.at( i ).section( ",", 2, 2 ).left( 2 ) + "-" + sl_Input.at( i ).section( ",", 2, 2 ).mid( 2, 2 ) + "-" + sl_Input.at( i ).section( ",", 2, 2 ).mid( 4, 2 );
s_Latitude = extractLatitude( sl_Input.at(i) );
s_Longitude = extractLongitude( sl_Input.at(i) );
d_Latitude = s_Latitude.toDouble();
d_Longitude = s_Longitude.toDouble();
d_Distance = calculateDistance( d_Latitude, d_Longitude, d_Latitude_old, d_Longitude_old ); // [m]
if ( ( i_ID == i_StartID ) || ( i_ID == i_EndID ) || ( d_Distance > d_PlotDistance ) )
{
d_Speed = 3.6 * d_Distance/( (double) i - d_Seconds_old ); // [m/s] -> [km/h]
tout << "<Placemark>";
// tout << "<name>" << s_Time << "</name>";
switch ( i_IconColor )
{
case _RED_:
tout << "<styleUrl>#red</styleUrl>";
break;
case _GREEN_:
tout << "<styleUrl>#green</styleUrl>";
break;
case _BLUE_:
tout << "<styleUrl>#blue</styleUrl>";
break;
case _ORANGE_:
tout << "<styleUrl>#orange</styleUrl>";
break;
case _YELLOW_:
tout << "<styleUrl>#yellow</styleUrl>";
break;
default:
tout << "<styleUrl>#red</styleUrl>";
break;
}
tout << "<Style><IconStyle>" << QString( "<scale>%1</scale>" ).arg( (float) i_IconSize/100. ) << "</IconStyle></Style>";
tout << "<Point><coordinates>" << s_Longitude << "," << s_Latitude << "</coordinates></Point>";
tout << "<description>" << endl;
tout << "<![CDATA[Time: " << s_Time << "<br />Date: " << s_Date << "<br />Latitude: " << d_Latitude << "° N<br />Longitude: " << d_Longitude << "° E<br />Altitude: " << sl_Input.at( i ).section( ",", 6, 6 ).simplified() << " m<br />Speed: " << d_Speed << " km/h<br />ID: " << i_ID << "<br />]]>" << endl;
tout << "</description>" << endl;
tout << "</Placemark>" << endl;
d_Latitude_old = d_Latitude;
d_Longitude_old = d_Longitude;
d_Seconds_old = (double) i;
if ( d_Speed < 50. )
d_PlotDistance = 100;
else
d_PlotDistance = 1000;
}
}
}
stopProgress = incProgress( i_NumOfFiles, ++i );
}
tout << "</Folder>" << endl;
// **********************************************************************************************
// Track line
tout << "<Placemark><name>Trackline</name>" << endl;
switch ( i_TracklineColor )
{
case _RED_:
tout << "<Style><LineStyle><color>ff0000ff</color>";
break;
case _GREEN_:
tout << "<Style><LineStyle><color>ff00ff00</color>";
break;
case _BLUE_:
tout << "<Style><LineStyle><color>ffff0000</color>";
break;
case _ORANGE_:
tout << "<Style><LineStyle><color>ff0099ff</color>";
break;
case _YELLOW_:
tout << "<Style><LineStyle><color>ff33ffff</color>";
break;
default:
tout << "<Style><LineStyle><color>ff0099ff</color>";
break;
}
tout << "<width>" << (float) i_TracklineWidth/10. << "</width></LineStyle></Style>" << endl;
tout << "<LineString>" << endl;
tout << "<tessellate>1</tessellate>" << endl;
tout << "<coordinates>" << endl;
i = 1;
while ( ( i<n ) && ( stopProgress != _APPBREAK_ ) )
{
if ( sl_Input.at( i ).section( ",", 1, 1 ) == "T" )
{
i_ID = sl_Input.at( i ).section( ",", 0, 0 ).toInt();
if ( ( i_StartID <= i_ID ) && ( i_ID <= i_EndID ) )
{
s_Latitude = extractLatitude( sl_Input.at(i) );
s_Longitude = extractLongitude( sl_Input.at(i) );
tout << s_Longitude << "," << s_Latitude << "," << sl_Input.at( i ).section( ",", 6, 6 ).simplified() << endl;
}
}
stopProgress = incProgress( i_NumOfFiles, ++i+n );
}
tout << "</coordinates>" << endl;
tout << "</LineString>" << endl;
tout << "</Placemark>" << endl;
tout << "</Document>" << endl;
tout << "</kml>" << endl;
fout.close();
resetProgress( i_NumOfFiles );
if ( stopProgress == _APPBREAK_ )
return( _APPBREAK_ );
return( _NOERROR_ );
}
bool SurfaceNetworkBuilder::build(model::Model &model)
{
bool first = true;
bool nowarnings = true;
QVector<openstudio::Handle> used;
m_logSink.setThreadId(QThread::currentThread());
m_logSink.resetStringStream();
std::vector<model::Surface> surfaces = model.getConcreteModelObjects<model::Surface>();
initProgress(surfaces.size(),"Processing surfaces for network creation");
for (model::Surface surface : surfaces) {
if(!first) {
progress();
}
first=false;
std::string bc = surface.outsideBoundaryCondition();
if(bc == "Outdoors") {
// Get the associated thermal zone
boost::optional<openstudio::model::Space> space = surface.space();
if(!space) {
LOG(Warn, "Unattached surface '" << openstudio::toString(surface.handle()) << "'");
nowarnings = false;
continue;
}
boost::optional<openstudio::model::ThermalZone> thermalZone = space->thermalZone();
if(!thermalZone) {
LOG(Warn, "Unzoned space '" << openstudio::toString(space->handle()) << "'");
nowarnings = false;
continue;
}
// If we made it to here, then the exterior surface is good.
linkExteriorSurface(thermalZone.get(),space.get(),surface);
for(model::SubSurface subSurface : surface.subSurfaces()) {
linkExteriorSubSurface(thermalZone.get(),space.get(),surface,subSurface);
}
} else if(!used.contains(surface.handle()) && bc == "Surface") {
// Get the associated thermal zone
boost::optional<openstudio::model::Space> space = surface.space();
if(!space) {
LOG(Warn, "Unattached surface '" << openstudio::toString(surface.handle()) << "'");
nowarnings = false;
continue;
}
boost::optional<openstudio::model::ThermalZone> thermalZone = space->thermalZone();
if(!thermalZone) {
LOG(Warn, "Unzoned space '" << openstudio::toString(space->handle()) << "'");
nowarnings = false;
continue;
}
boost::optional<openstudio::model::Surface> adjacentSurface = surface.adjacentSurface();
if(!adjacentSurface) {
LOG(Error, "Unable to find adjacent surface for surface '" << openstudio::toString(surface.handle()) << "'");
nowarnings = false;
continue;
}
boost::optional<openstudio::model::Space> adjacentSpace = adjacentSurface->space();
if(!adjacentSpace) {
LOG(Error, "Unattached adjacent surface '" << openstudio::toString(adjacentSurface->handle()) << "'");
nowarnings = false;
continue;
}
boost::optional<openstudio::model::ThermalZone> adjacentZone = adjacentSpace->thermalZone();
if(!thermalZone) {
LOG(Warn, "Unzoned adjacent space '" << openstudio::toString(adjacentSpace->handle()) << "'");
nowarnings = false;
continue;
}
// We could punt the checking of subsurfaces until later, but it is best to get this out of the way now
for(model::SubSurface subSurface : surface.subSurfaces()) {
boost::optional<model::SubSurface> adjacentSubSurface = subSurface.adjacentSubSurface();
if(!adjacentSubSurface) {
LOG(Warn, "Unable to find adjacent subsurface for subsurface of '" << openstudio::toString(surface.handle()) << "'");
nowarnings = false;
continue;
}
if(adjacentSubSurface->surface() != adjacentSurface) {
LOG(Warn, "Adjacent subsurface for subsurface of '" << openstudio::toString(surface.handle()) << "' is not attached to the expected surface");
nowarnings = false;
continue;
}
}
// Ok, now we a surface, a space, a zone, an adjacent surface, an adjacent space, and an adjacent zone. Finally.
used.push_back(adjacentSurface->handle());
if(thermalZone == adjacentZone) {
continue;
}
// Now have a surface that is fully connected and separates two zones so it can be linked
linkInteriorSurface(thermalZone.get(),space.get(),surface,adjacentSurface.get(),adjacentSpace.get(),adjacentZone.get());
// Link subsurfaces
for(model::SubSurface subSurface : surface.subSurfaces()) {
// Now we need to check the connections as we did with the surface
boost::optional<model::SubSurface> adjacentSubSurface = subSurface.adjacentSubSurface();
if(!adjacentSubSurface) {
LOG(Warn, "Unable to find adjacent subsurface for subsurface of '" << openstudio::toString(surface.handle()) << "'");
nowarnings = false;
continue;
}
if(adjacentSubSurface->surface() != adjacentSurface) {
LOG(Warn, "Adjacent subsurface for subsurface of '" << openstudio::toString(surface.handle()) << "' is not attached to the expected surface");
nowarnings = false;
continue;
}
// If we made it here, then the subsurface is fully connected and can be linked
linkInteriorSubSurface(thermalZone.get(),space.get(),surface,subSurface,adjacentSubSurface.get(),adjacentSurface.get(),
adjacentSpace.get(),adjacentZone.get());
}
}
}
if(surfaces.size()>0) {
progress();
}
return nowarnings;
}
int MainWindow::convertTSG( const QString &s_FilenameIn, const QString &s_FilenameOut, const int i_CodecInput, const int i_CodecOutput, const int i_EOL, const int i_NumOfFiles )
{
int i = 1;
int n = 0;
int stopProgress = 0;
QString s = "";
QString s_DateTime = "";
QString s_Position = "";
QString s_EOL = setEOLChar( i_EOL );
QStringList sl_Input;
// **********************************************************************************************
// read file
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) < 1 )
return( -10 );
// **********************************************************************************************
// open output file
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text) == false )
return( -20 );
QTextStream tout( &fout );
switch ( i_CodecOutput )
{
case _SYSTEM_:
break;
case _LATIN1_:
tout.setCodec( QTextCodec::codecForName( "ISO 8859-1" ) );
break;
case _APPLEROMAN_:
tout.setCodec( QTextCodec::codecForName( "Apple Roman" ) );
break;
default:
tout.setCodec( QTextCodec::codecForName( "UTF-8" ) );
break;
}
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Converting TSG data..." ), sl_Input.count() );
// **********************************************************************************************
tout << "Event label" << "\t" << "Date/Time" << "\t" << "Latitude" << "\t" << "Longitude" << "\t";
tout << "Depth, water [m]" << "\t" << "Temperature, water [C]@ITS-90" << "\t" << "Salinity []" << s_EOL;
tout << "PS-track";
while ( ( i<sl_Input.count() ) && ( stopProgress != _APPBREAK_ ) )
{
s_DateTime = sl_Input.at( i ).section( "\t", 0, 0 );
s_DateTime.replace( " ", "T" );
s_Position = sl_Input.at( i ).section( "\t", 1, 2 );
s_Position.replace( " ", "" );
s = sl_Input.at( i ).section( "\t", 3, 4 );
s.replace( " ", "" );
s.replace( "-999.000000", "" );
if ( s != "\t" )
tout << "\t" + s_DateTime << "\t" << s_Position << "\t5\t" << s << s_EOL;
s = sl_Input.at( i ).section( "\t", 5, 6 );
s.replace( " ", "" );
s.replace( "-999.000000", "" );
if ( s != "\t" )
tout << "\t" + s_DateTime << "\t" << s_Position << "\t11\t" << s << s_EOL;
stopProgress = incProgress( i_NumOfFiles, ++i );
}
fout.close();
resetProgress( i_NumOfFiles );
if ( stopProgress == _APPBREAK_ )
return( _APPBREAK_ );
return( _NOERROR_ );
}
int MainWindow::createOceanDataViewFile( QStringList &sl_MetadataList, QStringList &sl_ParameterList, const QString &s_FilenameOut,
const int i_CodecInput, const int i_Env, const int i_DeviceTypeOceanDataView,
const bool b_showShortName, const bool b_showMethod, const bool b_showComment,
const bool b_usePANGAEAQualityFlags, const bool b_setGeocode, const bool b_addLineNo,
const float f_GEOCODE_min, const float f_GEOCODE_max, const QString &s_GEOCODE_min,
const QString &s_GEOCODE_max, const bool b_setGearID, const int i_GearID, const int i_NumOfFiles )
{
QVector<int> vi_pos;
QVector<int> vi_posQV;
QVector<int> vi_SpecialPos;
int i_NumOfRemovedLines = 0;
int i_NumOfHeaderItems = 0;
int i_GeocodePos = -1;
int i_GearIDPos = -1;
int i_File = 0;
int i_stopFileProgress = 0;
int stopProgress = 0;
int err = _NOERROR_;
int i = 0;
int n = 0;
bool b_containsDOI = false;
QString s_FieldDelimiter = "\t";
QString s_Environment = "";
QString s_DeviceType = "*";
QString s_Output = "";
QString s_FilenameIn = sl_MetadataList.at( 1 ).section( "\t", _FILENAMEPOS, _FILENAMEPOS );
QStringList sld_ParameterList;
QStringList sl_Input;
QStringList sl_Output;
QDateTime dt_GEOCODE_min( QDateTime::fromString( (QString) s_GEOCODE_min, Qt::ISODate ) );
QDateTime dt_GEOCODE_max( QDateTime::fromString( (QString) s_GEOCODE_max, Qt::ISODate ) );
//-----------------------------------------------------------------------------------------------------------------------
if ( sl_ParameterList.count() == 0 )
return( -60 );
//-----------------------------------------------------------------------------------------------------------------------
i_NumOfHeaderItems = buildODVHeader( sl_Output, sl_ParameterList, vi_posQV, i_Env, b_showShortName, b_showMethod, b_showComment, b_usePANGAEAQualityFlags );
if ( i_NumOfHeaderItems < 0 )
return( i_NumOfHeaderItems ); // return as error, -70 = Latitude/Longitude not given, -71 = Latitude not given, -72 = Longitude not given
//-----------------------------------------------------------------------------------------------------------------------
QFile ftext( s_FilenameOut );
if ( ftext.open( QIODevice::WriteOnly | QIODevice::Text) == false )
return( -20 );
QTextStream tout( &ftext );
//-----------------------------------------------------------------------------------------------------------------------
initFileProgress( i_NumOfFiles, s_FilenameIn, tr( "Creating Ocean Data View file..." ) );
//-----------------------------------------------------------------------------------------------------------------------
// write header
tout << "//<Version>ODV Spreadsheet V4.0</Version>" << endl;
tout << "//<Creator>" << "</Creator>" << endl;
tout << "//<CreateTime>" << QDateTime::currentDateTime().toString( "yyyy-MM-ddThh:mm" ) << "</CreateTime>" << endl;
tout << "//<Software>" << getApplicationName( true ) << " " << _VERSION_ << "</Software>" << endl;
tout << "//<Source>" << QDir::toNativeSeparators( s_FilenameOut ) << "</Source>" << endl;
tout << "//<SourceLastModified>" << QDateTime::currentDateTime().toString( "yyyy-MM-ddThh:mm" ) << "</SourceLastModified>" << endl;
tout << "//<DataField>GeneralField</DataField>" << endl;
tout << "//<DataType>GeneralType</DataType>" << endl;
tout << "//" << endl;
//-----------------------------------------------------------------------------------------------------------------------
i_GeocodePos = getGeocodePosition( sl_ParameterList, i_Env );
i_GearIDPos = getGearIDPosition( sl_ParameterList );
b_containsDOI = sl_Output.contains( "DOI:METAVAR:TEXT:51" );
tout << sl_Output.join( s_FieldDelimiter ) << endl;
//-----------------------------------------------------------------------------------------------------------------------
// find position of date/time parameters
getSpecialPos( sl_ParameterList, vi_SpecialPos );
//-----------------------------------------------------------------------------------------------------------------------
s_DeviceType = setDeviceType( i_DeviceTypeOceanDataView );
//-----------------------------------------------------------------------------------------------------------------------
i_File = 1;
while ( ( i_File <= i_NumOfFiles ) && ( err == _NOERROR_ ) && ( i_stopFileProgress != _APPBREAK_ ) )
{
if ( containsSelectedEnvironment( _SELECTPARAMETER, sl_MetadataList.at( i_File ).section( "\t", _ENVIRONMENTPOS, _ENVIRONMENTPOS ).toInt(), i_Env ) == true )
{
s_FilenameIn = sl_MetadataList.at( i_File ).section( "\t", _FILENAMEPOS, _FILENAMEPOS );
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) > 0 )
{
i = 0;
sld_ParameterList.clear();
vi_pos.clear();
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Ocean Data View converter is working..." ), n );
setStatusBarFileInProgress( s_FilenameIn );
//-----------------------------------------------------------------------------------------------------------------------
// read header and find position of parameter
s_Environment = sl_MetadataList.at( i_File ).section( "\t", _ENVIRONMENTPOS, _ENVIRONMENTPOS ) + _PSEPARATOR_;
stopProgress = incProgress( i_NumOfFiles, i );
if ( sl_Input.at( i ).startsWith( "/* DATA DESCRIPTION:" ) == true ) // file starts with PANGAEA header
{
while ( ( i < n ) && ( sl_Input.at( i ).startsWith( "*/" ) == false ) )
{
if ( sl_Input.at( i ).startsWith( "Parameter(s):" ) == true )
{
while ( ( i < n ) && ( ( sl_Input.at( i ).startsWith( "Parameter(s):" ) == true ) || ( sl_Input.at( i ).startsWith( "\t" ) == true ) ) )
{
sld_ParameterList.append( s_Environment + buildParameter( sl_Input.at( i ).section( "\t", 1, 1 ) ) );
if ( ++i < n )
stopProgress = incProgress( i_NumOfFiles, i );
}
}
if ( ++i < n )
stopProgress = incProgress( i_NumOfFiles, i );
}
for ( int j=0; j<sl_ParameterList.count(); ++j )
vi_pos.append( containsParameter( true, sld_ParameterList, sl_ParameterList.at( j ), b_showShortName, b_showMethod, b_showComment ) );
if ( ++i < n )
stopProgress = incProgress( i_NumOfFiles, i );
}
else
{
sld_ParameterList = buildParameterList( s_Environment, sl_Input.at( i ) ); // not a PANGAEA dataset
for ( int j=0; j<sl_ParameterList.count(); ++j )
vi_pos.append( containsParameter( false, sld_ParameterList, sl_ParameterList.at( j ), b_showShortName, b_showMethod, b_showComment ) );
}
//-----------------------------------------------------------------------------------------------------------------------
// write output string
if ( ( b_setGeocode == true ) || ( b_setGearID == true ) )
{
while ( ( ++i < n ) && ( stopProgress != _APPBREAK_ ) )
{
sl_Output = buildODVOutputStr( i+1, b_addLineNo, sl_Input.at( i ), sl_MetadataList.at( i_File ), vi_pos, vi_posQV, vi_SpecialPos, b_usePANGAEAQualityFlags, b_containsDOI, s_DeviceType, s_FieldDelimiter );
if ( writeDataLine( b_setGeocode, b_setGearID, i_GeocodePos, i_GearIDPos, sl_Output, i_Env, dt_GEOCODE_min, dt_GEOCODE_max, f_GEOCODE_min, f_GEOCODE_max, i_GearID ) == true )
{
s_Output = sl_Output.join( s_FieldDelimiter );
if ( s_Output.contains( "delete line" ) == false )
tout << s_Output << endl;
else
++i_NumOfRemovedLines;
}
stopProgress = incProgress( i_NumOfFiles, i );
}
}
else
{
while ( ( ++i < n ) && ( stopProgress != _APPBREAK_ ) )
{
sl_Output = buildODVOutputStr( i+1, b_addLineNo, sl_Input.at( i ), sl_MetadataList.at( i_File ), vi_pos, vi_posQV, vi_SpecialPos, b_usePANGAEAQualityFlags, b_containsDOI, s_DeviceType, s_FieldDelimiter );
s_Output = sl_Output.join( s_FieldDelimiter );
if ( s_Output.contains( "delete line" ) == false )
tout << s_Output << endl;
else
++i_NumOfRemovedLines;
stopProgress = incProgress( i_NumOfFiles, i );
}
}
resetProgress( i_NumOfFiles );
}
}
i_stopFileProgress = incFileProgress( i_NumOfFiles, i_File++ );
}
//-----------------------------------------------------------------------------------------------------------------------
resetFileProgress( i_NumOfFiles );
ftext.close();
return( i_NumOfRemovedLines );
}
int MainWindow::RadiosondeEquipmentConverter( const QString &s_FilenameIn, QStringList &sl_FilenameOut, structMethod *Method_ptr, structStation *Station_ptr, const int i_NumOfFiles )
{
int i_Year = 2000;
int i_Month = 1;
int i_Day = 1;
int i_StationNumber = 0;
int i_MethodID = 0;
QString InputStr = "";
QString s_RadiosondeIdentification = "";
QString SearchString1 = "*C0005";
QString SearchString2 = "*U0005";
QString s_StationName = "";
QString s_EventLabel = "";
unsigned int ui_length = 1;
unsigned int ui_filesize = 1;
bool b_Stop = false;
// ***********************************************************************************************************************
QFileInfo fi( s_FilenameIn );
if ( ( fi.exists() == false ) || ( fi.suffix().toLower() == "zip" ) || ( fi.suffix().toLower() == "gz" ) )
return( _FILENOEXISTS_ );
// ***********************************************************************************************************************
QFile fin( s_FilenameIn );
if ( fin.open( QIODevice::ReadOnly | QIODevice::Text ) == false )
return( -10 );
ui_filesize = fin.size();
// ***********************************************************************************************************************
QTextStream tin( &fin );
// ***********************************************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Radiosonde equipment converter working ..." ), 100 );
// ***********************************************************************************************************************
InputStr = tin.readLine();
ui_length = incProgress( i_NumOfFiles, ui_filesize, ui_length, InputStr );
if ( ( InputStr.startsWith( "*C0001" ) == false ) && ( InputStr.startsWith( "*U0001" ) == false ) )
{
resetProgress( i_NumOfFiles );
fin.close();
return( -40 );
}
// ***********************************************************************************************************************
InputStr = tin.readLine();
ui_length = incProgress( i_NumOfFiles, ui_filesize, ui_length, InputStr );
i_StationNumber = InputStr.left( 3 ).toInt();
s_StationName = findStationName( i_StationNumber, Station_ptr );
s_EventLabel = findEventLabel( i_StationNumber, Station_ptr );
// ***********************************************************************************************************************
i_Day = 1;
i_Month = InputStr.mid( 4, 2 ).toInt();
i_Year = InputStr.mid( 7, 4 ).toInt();
QDateTime dt = QDateTime().toUTC();
dt.setDate( QDate( i_Year, i_Month, i_Day ) );
dt.setTime( QTime( 0, 0, 0 ) );
// ***********************************************************************************************************************
if ( checkFilename( fi.fileName(), s_EventLabel, InputStr.mid( 4, 2 ), InputStr.mid( 9, 2 ) ) == false )
{
resetProgress( i_NumOfFiles );
fin.close();
return( -41 );
}
// ***********************************************************************************************************************
QFile fout( fi.absolutePath() + "/" + s_EventLabel + "_" + dt.toString( "yyyy-MM" ) + "_0005.txt" );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text ) == false )
{
resetProgress( i_NumOfFiles );
fin.close();
return( -20 );
}
QTextStream tout( &fout );
appendItem( sl_FilenameOut, fout.fileName() );
// ***********************************************************************************************************************
// LR0005
tout << "File name\tStation ID\tEvent label\tStation\tYYYY-MM\t";
tout << "Manufacturer\tLocation\tDistance from radiation site [km]\t";
tout << "Time of 1st launch [hh]\tTime of 2nd launch [hh]\tTime of 3rd launch [hh]\t";
tout << "Time of 4th launch [hh]\tIdentification of radiosonde\tRemarks\t";
tout << "PANGAEA method\tPANGAEA method ID" << endl;
while ( ( tin.atEnd() == false ) && ( ui_length != (unsigned int) _APPBREAK_ ) && ( b_Stop == false ) )
{
InputStr = tin.readLine();
ui_length = incProgress( i_NumOfFiles, ui_filesize, ui_length, InputStr );
if ( ( InputStr.startsWith( SearchString1 ) == true ) || ( InputStr.startsWith( SearchString2 ) == true ) )
{
tout << s_EventLabel.toLower() << dt.toString( "MMyy" ) << ".dat" << "\t";
tout << i_StationNumber << "\t" << s_EventLabel << "\t" << s_StationName << "\t" << dt.toString( "yyyy-MM" ) << "\t";
InputStr = tin.readLine();
ui_length = incProgress( i_NumOfFiles, ui_filesize, ui_length, InputStr );
if ( InputStr.simplified().right( 1 ) == "Y" )
{
InputStr = tin.readLine();
ui_length = incProgress( i_NumOfFiles, ui_filesize, ui_length, InputStr );
tout << InputStr.left( 30 ).simplified() << "\t";
tout << InputStr.mid( 30, 25 ).simplified() << "\t";
tout << InputStr.mid( 57, 3 ) << "\t";
tout << InputStr.mid( 61, 2 ) << "\t";
tout << InputStr.mid( 64, 2 ) << "\t";
tout << InputStr.mid( 67, 2 ) << "\t";
tout << InputStr.mid( 70, 2 ) << "\t";
tout << InputStr.mid( 73, 5 ).simplified() << "\t";
s_RadiosondeIdentification = InputStr.left( 30 ).simplified();
if ( InputStr.mid( 73, 5 ).simplified().isEmpty() == false )
s_RadiosondeIdentification += ", " + InputStr.mid( 73, 5 ).simplified();
i_MethodID = findMethodID( s_RadiosondeIdentification, Method_ptr );
InputStr = tin.readLine();
ui_length = incProgress( i_NumOfFiles, ui_filesize, ui_length, InputStr );
tout << InputStr.simplified() << "\t" << "Radiosonde, " << s_RadiosondeIdentification << "\t";
tout << i_MethodID << endl;
}
b_Stop = true;
}
// Abort if first data record reached
if ( ( InputStr.startsWith( "*C0100" ) == true ) || ( InputStr.startsWith( "*U0100" ) == true ) )
b_Stop = true;
}
//---------------------------------------------------------------------------------------------------
resetProgress( i_NumOfFiles );
fin.close();
fout.close();
if ( ui_length == (unsigned int) _APPBREAK_ )
return( _APPBREAK_ );
return( _NOERROR_ );
}
int MainWindow::convertSPE( const QString &s_FilenameIn, const QString &s_FilenameOut, const int i_CodecInput, const int i_CodecOutput, const int i_EOL, const int i_NumOfFiles )
{
int i = 1;
int j = 0;
int k = 0;
int n = 0;
int stopProgress = 0;
bool b_datafound = false;
QString tempStr = "";
QString s_EOL = setEOLChar( i_EOL );
QStringList sl_Input;
// **********************************************************************************************
// read file
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) < 1 )
return( -10 );
// **********************************************************************************************
// open output file
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text) == false )
return( -20 );
QTextStream tout( &fout );
switch ( i_CodecOutput )
{
case _SYSTEM_:
break;
case _LATIN1_:
tout.setCodec( QTextCodec::codecForName( "ISO 8859-1" ) );
break;
case _APPLEROMAN_:
tout.setCodec( QTextCodec::codecForName( "Apple Roman" ) );
break;
default:
tout.setCodec( QTextCodec::codecForName( "UTF-8" ) );
break;
}
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Converting SPE data..." ), sl_Input.count() );
// **********************************************************************************************
while ( ( b_datafound == false ) && ( i<sl_Input.count() ) && ( stopProgress != _APPBREAK_ ) )
{
if ( sl_Input.at( i ).startsWith( "$DATA:") == true )
b_datafound = true;
stopProgress = incProgress( i_NumOfFiles, ++i );
}
if ( b_datafound == true )
{
tempStr = sl_Input.at( i++ ).split( QRegularExpression( "\\s+" ) ).join( "\t" );
k = tempStr.section( "\t", 1, 1 ).toInt();
tout << "Channel" << "\t" << "cps" << s_EOL;
while ( ( i<sl_Input.count() ) && ( stopProgress != _APPBREAK_ ) )
{
tempStr = sl_Input.at( i ).split( QRegularExpression( "\\s+" ) ).join( "\t" );
n = NumOfSections( tempStr );
for ( j=1; j<n; j++ )
tout << QString( "%1\t%2" ).arg( k++ ).arg( tempStr.section( "\t", j, j ) ) << s_EOL;
stopProgress = incProgress( i_NumOfFiles, ++i );
}
}
else
{
tout << "No data found! Wrong format." << s_EOL;
}
// **********************************************************************************************
fout.close();
resetProgress( i_NumOfFiles );
if ( stopProgress == _APPBREAK_ )
return( _APPBREAK_ );
return( _NOERROR_ );
}
int MainWindow::replaceCharactersAtPosition( const QString &s_FilenameIn, const QString &s_FilenameOut, const int i_CodecInput, const int i_CodecOutput, const int i_EOL, const QString &s_CharacterPositionsList, const QString &ReplaceStr, const bool b_SkipEmptyLines, const bool b_SkipCommentLines, const int i_NumOfFiles )
{
int i = 0;
int n = 0;
int m = 0;
int stopProgress = 0;
QString s_Output = "";
QString s_EOL = setEOLChar( i_EOL );
QStringList sl_Input;
QList<int> il_PositionList;
// **********************************************************************************************
// read file
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) < 1 )
return( n );
if ( ( m = sl_Input.at( 0 ).length() ) < 1 )
return( -80 );
il_PositionList = scanList( _REPLACECHARS, 99999, s_CharacterPositionsList );
if ( il_PositionList.count() < 1 )
{
QFile::remove( s_FilenameOut ); // if exists from older run
return( -81 );
}
// **********************************************************************************************
// open output file
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text) == false )
return( -20 );
QTextStream tout( &fout );
switch ( i_CodecOutput )
{
case _SYSTEM_:
break;
case _LATIN1_:
tout.setCodec( QTextCodec::codecForName( "ISO 8859-1" ) );
break;
case _APPLEROMAN_:
tout.setCodec( QTextCodec::codecForName( "Apple Roman" ) );
break;
default:
tout.setCodec( QTextCodec::codecForName( "UTF-8" ) );
break;
}
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Replace characters at position..." ), sl_Input.count() );
while ( ( i < n ) && ( stopProgress != _APPBREAK_ ) )
{
s_Output = sl_Input.at( i ).left( il_PositionList.at( 0 ) );
for ( int j=0; j<il_PositionList.count()-1; j++ )
s_Output.append( ReplaceStr + sl_Input.at( i ).mid( il_PositionList.at( j ) + 1, il_PositionList.at( j+1 ) - il_PositionList.at( j ) - 1 ) );
s_Output.append( ReplaceStr + sl_Input.at( i ).mid( il_PositionList.last() + 1 ) );
s_Output.replace( "^t", "\t" );
s_Output.replace( "^n", "\n" );
if ( LineCanBeWritten( s_Output, b_SkipEmptyLines, b_SkipCommentLines ) == true )
tout << s_Output << s_EOL;
stopProgress = incProgress( i_NumOfFiles, ++i );
}
resetProgress( i_NumOfFiles );
// **********************************************************************************************
fout.close();
if ( stopProgress == _APPBREAK_ )
return( _APPBREAK_ );
return( _NOERROR_ );
}
MainWindow::MainWindow() :
m_workspace( NULL ),
m_templatesMenu( NULL ),
m_recentlyOpenedProjectsMenu( NULL ),
m_toolsMenu( NULL ),
m_autoSaveTimer( this ),
m_viewMenu( NULL ),
m_metronomeToggle( 0 ),
m_session( Normal )
{
setAttribute( Qt::WA_DeleteOnClose );
QWidget * main_widget = new QWidget( this );
QVBoxLayout * vbox = new QVBoxLayout( main_widget );
vbox->setSpacing( 0 );
vbox->setMargin( 0 );
QWidget * w = new QWidget( main_widget );
QHBoxLayout * hbox = new QHBoxLayout( w );
hbox->setSpacing( 0 );
hbox->setMargin( 0 );
SideBar * sideBar = new SideBar( Qt::Vertical, w );
QSplitter * splitter = new QSplitter( Qt::Horizontal, w );
splitter->setChildrenCollapsible( false );
ConfigManager* confMgr = ConfigManager::inst();
emit initProgress(tr("Preparing plugin browser"));
sideBar->appendTab( new PluginBrowser( splitter ) );
emit initProgress(tr("Preparing file browsers"));
sideBar->appendTab( new FileBrowser(
confMgr->userProjectsDir() + "*" +
confMgr->factoryProjectsDir(),
"*.mmp *.mmpz *.xml *.mid",
tr( "My Projects" ),
embed::getIconPixmap( "project_file" ).transformed( QTransform().rotate( 90 ) ),
splitter, false, true ) );
sideBar->appendTab( new FileBrowser(
confMgr->userSamplesDir() + "*" +
confMgr->factorySamplesDir(),
"*", tr( "My Samples" ),
embed::getIconPixmap( "sample_file" ).transformed( QTransform().rotate( 90 ) ),
splitter, false, true ) );
sideBar->appendTab( new FileBrowser(
confMgr->userPresetsDir() + "*" +
confMgr->factoryPresetsDir(),
"*.xpf *.cs.xml *.xiz",
tr( "My Presets" ),
embed::getIconPixmap( "preset_file" ).transformed( QTransform().rotate( 90 ) ),
splitter , false, true ) );
sideBar->appendTab( new FileBrowser( QDir::homePath(), "*",
tr( "My Home" ),
embed::getIconPixmap( "home" ).transformed( QTransform().rotate( 90 ) ),
splitter, false, false ) );
QStringList root_paths;
QString title = tr( "Root directory" );
bool dirs_as_items = false;
#ifdef LMMS_BUILD_APPLE
title = tr( "Volumes" );
root_paths += "/Volumes";
#elif defined(LMMS_BUILD_WIN32)
title = tr( "My Computer" );
dirs_as_items = true;
#endif
#if ! defined(LMMS_BUILD_APPLE)
QFileInfoList drives = QDir::drives();
for( const QFileInfo & drive : drives )
{
root_paths += drive.absolutePath();
}
#endif
sideBar->appendTab( new FileBrowser( root_paths.join( "*" ), "*", title,
embed::getIconPixmap( "computer" ).transformed( QTransform().rotate( 90 ) ),
splitter, dirs_as_items) );
m_workspace = new QMdiArea( splitter );
// Load background
emit initProgress(tr("Loading background artwork"));
QString bgArtwork = ConfigManager::inst()->backgroundArtwork();
QImage bgImage;
if( !bgArtwork.isEmpty() )
{
bgImage = QImage( bgArtwork );
}
if( !bgImage.isNull() )
{
m_workspace->setBackground( bgImage );
}
else
{
m_workspace->setBackground( Qt::NoBrush );
}
m_workspace->setOption( QMdiArea::DontMaximizeSubWindowOnActivation );
m_workspace->setHorizontalScrollBarPolicy( Qt::ScrollBarAsNeeded );
m_workspace->setVerticalScrollBarPolicy( Qt::ScrollBarAsNeeded );
hbox->addWidget( sideBar );
hbox->addWidget( splitter );
// create global-toolbar at the top of our window
m_toolBar = new QWidget( main_widget );
m_toolBar->setObjectName( "mainToolbar" );
m_toolBar->setFixedHeight( 64 );
m_toolBar->move( 0, 0 );
// add layout for organizing quite complex toolbar-layouting
m_toolBarLayout = new QGridLayout( m_toolBar/*, 2, 1*/ );
m_toolBarLayout->setMargin( 0 );
m_toolBarLayout->setSpacing( 0 );
vbox->addWidget( m_toolBar );
vbox->addWidget( w );
setCentralWidget( main_widget );
m_updateTimer.start( 1000 / 20, this ); // 20 fps
if( !ConfigManager::inst()->value( "ui", "disableautosave" ).toInt() )
{
// connect auto save
connect(&m_autoSaveTimer, SIGNAL(timeout()), this, SLOT(autoSave()));
m_autoSaveInterval = ConfigManager::inst()->value(
"ui", "saveinterval" ).toInt() < 1 ?
DEFAULT_AUTO_SAVE_INTERVAL :
ConfigManager::inst()->value(
"ui", "saveinterval" ).toInt();
// The auto save function mustn't run until there is a project
// to save or it will run over recover.mmp if you hesitate at the
// recover messagebox for a minute. It is now started in main.
// See autoSaveTimerReset() in MainWindow.h
}
connect( Engine::getSong(), SIGNAL( playbackStateChanged() ),
this, SLOT( updatePlayPauseIcons() ) );
}
int MainWindow::transposeTable( const QString &s_FilenameIn, const QString &s_FilenameOut, const int i_CodecInput, const int i_CodecOutput, const int i_EOL, const int i_NumOfFiles )
{
int j = 0;
int n = 0;
int m = 0;
int stopProgress = 0;
QString s_EOL = setEOLChar( i_EOL );
QStringList sl_Input;
// **********************************************************************************************
// read file
if ( ( n = readFile( s_FilenameIn, sl_Input, i_CodecInput ) ) < 1 )
return( n );
// **********************************************************************************************
// open output file
QFile fout( s_FilenameOut );
if ( fout.open( QIODevice::WriteOnly | QIODevice::Text) == false )
return( -20 );
QTextStream tout( &fout );
switch ( i_CodecOutput )
{
case _SYSTEM_:
break;
case _LATIN1_:
tout.setCodec( QTextCodec::codecForName( "ISO 8859-1" ) );
break;
case _APPLEROMAN_:
tout.setCodec( QTextCodec::codecForName( "Apple Roman" ) );
break;
default:
tout.setCodec( QTextCodec::codecForName( "UTF-8" ) );
break;
}
// **********************************************************************************************
initProgress( i_NumOfFiles, s_FilenameIn, tr( "Transposing table..." ), n );
for ( int i=0; i<n; i++ )
m = qMax( m, NumOfSections( sl_Input.at( i ) ) );
while ( ( j < m ) && ( stopProgress != _APPBREAK_ ) )
{
QString s_Output = sl_Input.at( 0 ).section( "\t", j, j );
for ( int i=1; i<n; i++ )
s_Output.append( "\t" ).append( sl_Input.at( i ).section( "\t", j, j ) );
tout << s_Output << s_EOL;
stopProgress = incProgress( i_NumOfFiles, ++j );
}
resetProgress( i_NumOfFiles );
// **********************************************************************************************
fout.close();
if ( stopProgress == _APPBREAK_ )
{
fout.remove();
return( _APPBREAK_ );
}
return( stopProgress );
}
