int CTGDataset::ReadImagery()
{
if (bHasReadImagery)
return TRUE;
bHasReadImagery = TRUE;
char szLine[81];
char szField[11];
szLine[80] = 0;
int nLine = HEADER_LINE_COUNT;
VSIFSeekL(fp, nLine * 80, SEEK_SET);
int nCells = nRasterXSize * nRasterYSize;
while(VSIFReadL(szLine, 1, 80, fp) == 80)
{
int nZone = atoi(ExtractField(szField, szLine, 0, 3));
if (nZone != nUTMZone)
{
CPLError(CE_Failure, CPLE_AppDefined,
"Read error at line %d, %s. Did not expected UTM zone %d",
nLine, szLine, nZone);
return FALSE;
}
int nX = atoi(ExtractField(szField, szLine, 3, 8)) - nCellSize / 2;
int nY = atoi(ExtractField(szField, szLine, 11, 8)) + nCellSize / 2;
int nDiffX = nX - nNWEasting;
int nDiffY = nNWNorthing - nY;
if (nDiffX < 0 || (nDiffX % nCellSize) != 0 ||
nDiffY < 0 || (nDiffY % nCellSize) != 0)
{
CPLError(CE_Failure, CPLE_AppDefined,
"Read error at line %d, %s. Unexpected cell coordinates",
nLine, szLine);
return FALSE;
}
int nCellX = nDiffX / nCellSize;
int nCellY = nDiffY / nCellSize;
if (nCellX >= nRasterXSize || nCellY >= nRasterYSize)
{
CPLError(CE_Failure, CPLE_AppDefined,
"Read error at line %d, %s. Unexpected cell coordinates",
nLine, szLine);
return FALSE;
}
int i;
for(i=0;i<6;i++)
{
int nVal = atoi(ExtractField(szField, szLine, 20 + 10*i, 10));
if (nVal >= 2000000000)
nVal = 0;
((int*)pabyImage)[i * nCells + nCellY * nRasterXSize + nCellX] = nVal;
}
nLine ++;
}
return TRUE;
}
/*>BOOL blGetSpeciesWholePDBMolID(WHOLEPDB *wpdb, int molid,
PDBSOURCE *source)
-----------------------------------------------------------
*//**
\param[in] *wpdb WHOLEPDB structure
\param[in] molid MOL_ID from PDB-format SOURCE record.
\param[out] *source SOURCE information for chain
\return Success (chain found?)
Extracts the SOURCE data for a specified MOL_ID. Returns FALSE if not
found.
- 12.05.15 Original based on blGetSpeciesWholePDBChain(). By: CTP
*/
BOOL blGetSpeciesWholePDBMolID(WHOLEPDB *wpdb, int molid,
PDBSOURCE *source)
{
STRINGLIST *s,
*molidFirst = NULL,
*molidStart = NULL,
*molidStop = NULL;
/* reset source */
source->scientificName[0] = '\0';
source->commonName[0] = '\0';
source->strain[0] = '\0';
source->taxid = 0;
/* find start of source records */
molidFirst = FindNextMolIDRecord(wpdb->header, "SOURCE");
/* get source record */
for(molidStart=molidFirst; molidStart!=NULL; molidStart=molidStop)
{
molidStop = FindNextMolIDRecord(molidStart, "SOURCE");
for(s=molidStart; s!=molidStop; NEXT(s))
{
char buffer[MAXPDBANNOTATION];
int thisMolid = 0;
ExtractField(molidStart, molidStop, buffer,
"SOURCE", "MOL_ID:");
sscanf(buffer,"%d", &thisMolid);
if(thisMolid == molid)
{
ExtractField(molidStart, molidStop, source->scientificName,
"SOURCE","ORGANISM_SCIENTIFIC:");
ExtractField(molidStart, molidStop, source->commonName,
"SOURCE", "ORGANISM_COMMON:");
ExtractField(molidStart, molidStop, source->strain,
"SOURCE", "STRAIN:");
ExtractField(molidStart, molidStop, buffer,
"SOURCE", "ORGANISM_TAXID:");
sscanf(buffer,"%d",&source->taxid);
return(TRUE);
}
}
}
return(FALSE);
}
int CTGDataset::Identify( GDALOpenInfo * poOpenInfo )
{
CPLString osFilename(poOpenInfo->pszFilename);
GDALOpenInfo* poOpenInfoToDelete = NULL;
/* GZipped grid_cell.gz files are common, so automagically open them */
/* if the /vsigzip/ has not been explicitely passed */
const char* pszFilename = CPLGetFilename(poOpenInfo->pszFilename);
if ((EQUAL(pszFilename, "grid_cell.gz") ||
EQUAL(pszFilename, "grid_cell1.gz") ||
EQUAL(pszFilename, "grid_cell2.gz")) &&
!EQUALN(poOpenInfo->pszFilename, "/vsigzip/", 9))
{
osFilename = "/vsigzip/";
osFilename += poOpenInfo->pszFilename;
poOpenInfo = poOpenInfoToDelete =
new GDALOpenInfo(osFilename.c_str(), GA_ReadOnly,
poOpenInfo->papszSiblingFiles);
}
if (poOpenInfo->nHeaderBytes < HEADER_LINE_COUNT * 80)
{
delete poOpenInfoToDelete;
return FALSE;
}
/* -------------------------------------------------------------------- */
/* Chech that it looks roughly as a CTG dataset */
/* -------------------------------------------------------------------- */
const char* pszData = (const char*)poOpenInfo->pabyHeader;
int i;
for(i=0;i<4 * 80;i++)
{
if (!((pszData[i] >= '0' && pszData[i] <= '9') ||
pszData[i] == ' ' || pszData[i] == '-'))
{
delete poOpenInfoToDelete;
return FALSE;
}
}
char szField[11];
int nRows = atoi(ExtractField(szField, pszData, 0, 10));
int nCols = atoi(ExtractField(szField, pszData, 20, 10));
int nMinColIndex = atoi(ExtractField(szField, pszData+80, 0, 5));
int nMinRowIndex = atoi(ExtractField(szField, pszData+80, 5, 5));
int nMaxColIndex = atoi(ExtractField(szField, pszData+80, 10, 5));
int nMaxRowIndex = atoi(ExtractField(szField, pszData+80, 15, 5));
if (nRows <= 0 || nCols <= 0 ||
nMinColIndex != 1 || nMinRowIndex != 1 ||
nMaxRowIndex != nRows || nMaxColIndex != nCols)
{
delete poOpenInfoToDelete;
return FALSE;
}
delete poOpenInfoToDelete;
return TRUE;
}
/*>int blFindMolID(WHOLEPDB *wpdb, char *chain)
--------------------------------------------
*//**
\param[in] *wpdb WHOLEPDB structure
\param[in] *chain Chain label
\return MOL_ID or 0 if chain not found
Finds the MOL_ID for a specified chain
- 28.04.15 Original By: ACRM
- 04.06.15 Modified to use the ExtractField() routine instead of
duplicating code here. Fixes a bug in dealing with compounds
where the referenced chains span more than one line
*/
int blFindMolID(WHOLEPDB *wpdb, char *chain)
{
STRINGLIST *molidFirst,
*molidStart,
*molidStop;
molidFirst = FindNextMolIDRecord(wpdb->header, "COMPND");
for(molidStart=molidFirst; molidStart!=NULL; molidStart=molidStop)
{
char buffer[MAXPDBANNOTATION],
*chp,
word[MAXWORD];
molidStop = FindNextMolIDRecord(molidStart, "COMPND");
ExtractField(molidStart, molidStop, buffer, "COMPND", "CHAIN:");
/* Check the chains to see if our chain is there */
chp = buffer;
do {
int molid = 0;
chp=blGetWord(chp, word, MAXWORD);
if(!strcmp(word, chain))
{
ExtractField(molidStart, molidStop,
buffer, "COMPND", "MOL_ID:");
sscanf(buffer,"%d", &molid);
return(molid);
}
} while(chp!=NULL);
}
return(0);
}
int CallCommand :: CallOnFields( CSVRow & row, char * buffer ) {
string fields;
int fc = 0;
for ( unsigned int i = 0; i < row.size(); i++ ) {
if ( mFields.size() == 0 || ALib::Contains( mFields, i ) ) {
fields += row[i];
fields += '\0';
fc++;
}
}
int ofc = 0;
int rv = mFunc( fc, fields.c_str(), &ofc, buffer, mOutBufSize );
if ( rv == 0 ) {
int pos = 0;
while( ofc-- ) {
string field = ExtractField( buffer, pos );
pos++;
row.push_back( field );
}
}
return rv;
}
OGRFeature *OGRSEGP1Layer::GetNextRawFeature()
{
if( bEOF )
return nullptr;
const char* pszLine = nullptr;
while( true )
{
pszLine = CPLReadLine2L(fp,81,nullptr);
if (pszLine == nullptr || STARTS_WITH_CI(pszLine, "EOF"))
{
bEOF = true;
return nullptr;
}
int nLineLen = static_cast<int>(strlen(pszLine));
while(nLineLen > 0 && pszLine[nLineLen-1] == ' ')
{
((char*)pszLine)[nLineLen-1] = '\0';
nLineLen --;
}
char* pszExpandedLine = ExpandTabs(pszLine);
pszLine = pszExpandedLine;
nLineLen = static_cast<int>(strlen(pszLine));
OGRFeature* poFeature = new OGRFeature(poFeatureDefn);
poFeature->SetFID(nNextFID ++);
OGRGeometry* poGeom = nullptr;
if (nLatitudeCol-1 + 19 <= nLineLen)
{
char szDeg[3+1];
char szMin[2+1];
char szSec[4+1];
ExtractField(szDeg, pszLine, nLatitudeCol-1, 2);
ExtractField(szMin, pszLine, nLatitudeCol+2-1, 2);
ExtractField(szSec, pszLine, nLatitudeCol+2+2-1, 4);
double dfLat = atoi(szDeg) + atoi(szMin) / 60.0 + atoi(szSec) / 100.0 / 3600.0;
if (pszLine[nLatitudeCol+2+2+4-1] == 'S')
dfLat = -dfLat;
poFeature->SetField(SEGP1_FIELD_LATITUDE, dfLat);
ExtractField(szDeg, pszLine, nLatitudeCol+9-1, 3);
ExtractField(szMin, pszLine, nLatitudeCol+9+3-1, 2);
ExtractField(szSec, pszLine, nLatitudeCol+9+3+2-1, 4);
double dfLon = atoi(szDeg) + atoi(szMin) / 60.0 + atoi(szSec) / 100.0 / 3600.0;
if (pszLine[nLatitudeCol+9+3+2+4-1] == 'W')
dfLon = -dfLon;
poFeature->SetField(SEGP1_FIELD_LONGITUDE, dfLon);
if (!bUseEastingNorthingAsGeometry)
poGeom = new OGRPoint(dfLon, dfLat);
}
/* Normal layout -> extract other fields */
if (nLatitudeCol == 27 && nLineLen >= 26-1+1)
{
char szLineName[16 + 1];
ExtractField(szLineName, pszLine, 2-1, 16);
int i = 15;
while (i >= 0)
{
if (szLineName[i] == ' ')
szLineName[i] = '\0';
else
break;
i --;
}
poFeature->SetField(SEGP1_FIELD_LINENAME, szLineName);
char szPointNumber[8+1];
ExtractField(szPointNumber, pszLine, 18-1, 8);
poFeature->SetField(SEGP1_FIELD_POINTNUMBER, atoi(szPointNumber));
char szReshootCode[1+1];
ExtractField(szReshootCode, pszLine, 26-1, 1);
poFeature->SetField(SEGP1_FIELD_RESHOOTCODE, szReshootCode);
if (nLineLen >= 61)
{
char szEasting[8+1];
ExtractField(szEasting, pszLine, 46-1, 8);
double dfEasting = CPLAtof(szEasting);
poFeature->SetField(SEGP1_FIELD_EASTING, dfEasting);
char szNorthing[8+1];
ExtractField(szNorthing, pszLine, 54-1, 8);
double dfNorthing = CPLAtof(szNorthing);
poFeature->SetField(SEGP1_FIELD_NORTHING, dfNorthing);
if (bUseEastingNorthingAsGeometry)
poGeom = new OGRPoint(dfEasting, dfNorthing);
}
if (nLineLen >= 66)
{
char szDepth[5+1];
ExtractField(szDepth, pszLine, 62-1, 5);
double dfDepth = CPLAtof(szDepth);
poFeature->SetField(SEGP1_FIELD_DEPTH, dfDepth);
}
}
if (poGeom)
{
if (poSRS)
poGeom->assignSpatialReference(poSRS);
poFeature->SetGeometryDirectly(poGeom);
}
CPLFree(pszExpandedLine);
return poFeature;
}
}
OGRFeature *OGRUKOOAP190Layer::GetNextRawFeature()
{
if( bEOF )
return nullptr;
while( true )
{
const char* pszLine = CPLReadLine2L(fp, 81, nullptr);
if (pszLine == nullptr || STARTS_WITH_CI(pszLine, "EOF"))
{
bEOF = true;
return nullptr;
}
int nLineLen = static_cast<int>(strlen(pszLine));
while(nLineLen > 0 && pszLine[nLineLen-1] == ' ')
{
((char*)pszLine)[nLineLen-1] = '\0';
nLineLen --;
}
if (pszLine[0] == 'H' || nLineLen < 46)
continue;
OGRFeature* poFeature = new OGRFeature(poFeatureDefn);
poFeature->SetFID(nNextFID ++);
char szLineName[12 + 1];
ExtractField(szLineName, pszLine, 2-1, 12);
int i = 11;
while (i >= 0)
{
if (szLineName[i] == ' ')
szLineName[i] = '\0';
else
break;
i --;
}
poFeature->SetField(FIELD_LINENAME, szLineName);
char szVesselId[1+1];
szVesselId[0] = pszLine[17-1];
if (szVesselId[0] != ' ')
{
szVesselId[1] = '\0';
poFeature->SetField(FIELD_VESSEL_ID, szVesselId);
}
char szSourceId[1+1];
szSourceId[0] = pszLine[18-1];
if (szSourceId[0] != ' ')
{
szSourceId[1] = '\0';
poFeature->SetField(FIELD_SOURCE_ID, szSourceId);
}
char szOtherId[1+1];
szOtherId[0] = pszLine[19-1];
if (szOtherId[0] != ' ')
{
szOtherId[1] = '\0';
poFeature->SetField(FIELD_OTHER_ID, szOtherId);
}
char szPointNumber[6+1];
ExtractField(szPointNumber, pszLine, 20-1, 6);
poFeature->SetField(4, atoi(szPointNumber));
char szDeg[3+1];
char szMin[2+1];
char szSec[5+1];
ExtractField(szDeg, pszLine, 26-1, 2);
ExtractField(szMin, pszLine, 26+2-1, 2);
ExtractField(szSec, pszLine, 26+2+2-1, 5);
double dfLat = atoi(szDeg) + atoi(szMin) / 60.0 + CPLAtof(szSec) / 3600.0;
if (pszLine[26+2+2+5-1] == 'S')
dfLat = -dfLat;
poFeature->SetField(FIELD_LATITUDE, dfLat);
ExtractField(szDeg, pszLine, 36-1, 3);
ExtractField(szMin, pszLine, 36+3-1, 2);
ExtractField(szSec, pszLine, 36+3+2-1, 5);
double dfLon = atoi(szDeg) + atoi(szMin) / 60.0 + CPLAtof(szSec) / 3600.0;
if (pszLine[36+3+2+5-1] == 'W')
dfLon = -dfLon;
poFeature->SetField(FIELD_LONGITUDE, dfLon);
OGRGeometry* poGeom = nullptr;
if (!bUseEastingNorthingAsGeometry)
poGeom = new OGRPoint(dfLon, dfLat);
if (nLineLen >= 64)
{
char szEasting[9+1];
ExtractField(szEasting, pszLine, 47-1, 9);
double dfEasting = CPLAtof(szEasting);
poFeature->SetField(FIELD_EASTING, dfEasting);
char szNorthing[9+1];
ExtractField(szNorthing, pszLine, 56-1, 9);
double dfNorthing = CPLAtof(szNorthing);
poFeature->SetField(FIELD_NORTHING, dfNorthing);
if (bUseEastingNorthingAsGeometry)
poGeom = new OGRPoint(dfEasting, dfNorthing);
}
if (poGeom)
{
if (poSRS)
poGeom->assignSpatialReference(poSRS);
poFeature->SetGeometryDirectly(poGeom);
}
if (nLineLen >= 70)
{
char szDepth[6+1];
ExtractField(szDepth, pszLine, 65-1, 6);
double dfDepth = CPLAtof(szDepth);
poFeature->SetField(FIELD_DEPTH, dfDepth);
}
int nDayOfYear = 0;
if (nLineLen >= 73)
{
char szDayOfYear[3+1];
ExtractField(szDayOfYear, pszLine, 71-1, 3);
nDayOfYear = atoi(szDayOfYear);
poFeature->SetField(FIELD_DAYOFYEAR, nDayOfYear);
}
if (nLineLen >= 79)
{
char szH[2+1], szM[2+1], szS[2+1];
ExtractField(szH, pszLine, 74-1, 2);
ExtractField(szM, pszLine, 74-1+2, 2);
ExtractField(szS, pszLine, 74-1+2+2, 2);
poFeature->SetField(FIELD_TIME, 0, 0, 0, atoi(szH), atoi(szM), static_cast<float>(atoi(szS)) );
if( nYear != 0 )
{
constexpr int mon_lengths[2][12] = {
{31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31},
{31, 29, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31}
} ;
const bool bIsLeap = isleap(nYear);
int nMonth = 0;
int nDays = 0;
if ((bIsLeap && nDayOfYear >= 1 && nDayOfYear <= 366) ||
(!bIsLeap && nDayOfYear >= 1 && nDayOfYear <= 365))
{
const int leap_offset = bIsLeap ? 1 : 0;
while( nDayOfYear >
nDays +
mon_lengths[leap_offset][nMonth] )
{
nDays += mon_lengths[leap_offset][nMonth];
nMonth ++;
}
const int nDayOfMonth = nDayOfYear - nDays;
nMonth++;
poFeature->SetField(FIELD_DATETIME,
nYear, nMonth, nDayOfMonth,
atoi(szH), atoi(szM),
static_cast<float>(atoi(szS)) );
}
}
}
return poFeature;
}
}
void OGRUKOOAP190Layer::ParseHeaders()
{
while( true )
{
const char* pszLine = CPLReadLine2L(fp,81,nullptr);
if (pszLine == nullptr || STARTS_WITH_CI(pszLine, "EOF"))
{
break;
}
int nLineLen = static_cast<int>(strlen(pszLine));
while(nLineLen > 0 && pszLine[nLineLen-1] == ' ')
{
((char*)pszLine)[nLineLen-1] = '\0';
nLineLen --;
}
if (pszLine[0] != 'H')
break;
if (nLineLen < 33)
continue;
if (!bUseEastingNorthingAsGeometry &&
STARTS_WITH(pszLine, "H1500") && poSRS == nullptr)
{
if (STARTS_WITH(pszLine + 33 - 1, "WGS84") ||
STARTS_WITH(pszLine + 33 - 1, "WGS-84"))
{
poSRS = new OGRSpatialReference(SRS_WKT_WGS84_LAT_LONG);
poSRS->SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
}
else if (STARTS_WITH(pszLine + 33 - 1, "WGS72"))
{
poSRS = new OGRSpatialReference();
poSRS->SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
poSRS->SetFromUserInput("WGS72");
}
}
else if (!bUseEastingNorthingAsGeometry &&
STARTS_WITH(pszLine, "H1501") && poSRS != nullptr &&
nLineLen >= 32 + 6 * 6 + 10)
{
char aszParams[6][6+1];
char szZ[10+1];
for( int i = 0; i < 6; i++ )
{
ExtractField(aszParams[i], pszLine, 33 - 1 + i * 6, 6);
}
ExtractField(szZ, pszLine, 33 - 1 + 6 * 6, 10);
poSRS->SetTOWGS84(CPLAtof(aszParams[0]),
CPLAtof(aszParams[1]),
CPLAtof(aszParams[2]),
CPLAtof(aszParams[3]),
CPLAtof(aszParams[4]),
CPLAtof(aszParams[5]),
CPLAtof(szZ));
}
else if (STARTS_WITH(pszLine, "H0200"))
{
char** papszTokens = CSLTokenizeString(pszLine + 33 - 1);
for(int i = 0; papszTokens[i] != nullptr; i++)
{
if (strlen(papszTokens[i]) == 4)
{
int nVal = atoi(papszTokens[i]);
if (nVal >= 1900)
{
if( nYear != 0 && nYear != nVal )
{
CPLDebug("SEGUKOOA",
"Several years found in H0200. Ignoring them!");
nYear = 0;
break;
}
nYear = nVal;
}
}
}
CSLDestroy(papszTokens);
}
}
VSIFSeekL( fp, 0, SEEK_SET );
}
void OGRUKOOAP190Layer::ParseHeaders()
{
while(TRUE)
{
const char* pszLine = CPLReadLine2L(fp,81,NULL);
if (pszLine == NULL || EQUALN(pszLine, "EOF", 3))
{
break;
}
int nLineLen = strlen(pszLine);
while(nLineLen > 0 && pszLine[nLineLen-1] == ' ')
{
((char*)pszLine)[nLineLen-1] = '\0';
nLineLen --;
}
if (pszLine[0] != 'H')
break;
if (nLineLen < 33)
continue;
if (!bUseEastingNorthingAsGeometry &&
strncmp(pszLine, "H1500", 5) == 0 && poSRS == NULL)
{
if (strncmp(pszLine + 33 - 1, "WGS84", 5) == 0 ||
strncmp(pszLine + 33 - 1, "WGS-84", 6) == 0)
{
poSRS = new OGRSpatialReference(SRS_WKT_WGS84);
}
else if (strncmp(pszLine + 33 - 1, "WGS72", 5) == 0)
{
poSRS = new OGRSpatialReference();
poSRS->SetFromUserInput("WGS72");
}
}
else if (!bUseEastingNorthingAsGeometry &&
strncmp(pszLine, "H1501", 5) == 0 && poSRS != NULL &&
nLineLen >= 32 + 6 * 6 + 10)
{
char aszParams[6][6+1];
char szZ[10+1];
int i;
for(i=0;i<6;i++)
{
ExtractField(aszParams[i], pszLine, 33 - 1 + i * 6, 6);
}
ExtractField(szZ, pszLine, 33 - 1 + 6 * 6, 10);
poSRS->SetTOWGS84(CPLAtof(aszParams[0]),
CPLAtof(aszParams[1]),
CPLAtof(aszParams[2]),
CPLAtof(aszParams[3]),
CPLAtof(aszParams[4]),
CPLAtof(aszParams[5]),
CPLAtof(szZ));
}
else if (strncmp(pszLine, "H0200", 5) == 0)
{
char** papszTokens = CSLTokenizeString(pszLine + 33 - 1);
for(int i = 0; papszTokens[i] != NULL; i++)
{
if (strlen(papszTokens[i]) == 4)
{
int nVal = atoi(papszTokens[i]);
if (nVal >= 1900)
{
if (nYear != 0 && nYear != nVal)
{
CPLDebug("SEGUKOOA",
"Several years found in H0200. Ignoring them!");
nYear = 0;
break;
}
nYear = nVal;
}
}
}
CSLDestroy(papszTokens);
}
}
VSIFSeekL( fp, 0, SEEK_SET );
}
/*>BOOL blGetCompoundWholePDBMolID(WHOLEPDB *wpdb, int molid,
COMPND *compnd)
------------------------------------------------------------
*//**
\param[in] *wpdb WHOLEPDB structure
\param[in] molid MOL_ID from PDB-format COMPND record.
\param[out] *compnd Data from the COMPND records
\return BOOL Success
Extracts the COMPND data for a specified MOL_ID. Returns FALSE if the
MOL_ID isn't found
- 13.05.15 Original based on blGetCompoundWholePDBChain(). By: CTP
*/
BOOL blGetCompoundWholePDBMolID(WHOLEPDB *wpdb, int molid,
COMPND *compnd)
{
STRINGLIST *molidFirst,
*molidStart,
*molidStop,
*s;
/* reset compnd */
compnd->molid = 0;
compnd->molecule[0] = '\0';
compnd->chain[0] = '\0';
compnd->fragment[0] = '\0';
compnd->synonym[0] = '\0';
compnd->ec[0] = '\0';
compnd->engineered[0] = '\0';
compnd->mutation[0] = '\0';
compnd->other[0] = '\0';
/* find start of compnd records */
molidFirst = FindNextMolIDRecord(wpdb->header, "COMPND");
/* get compound record */
for(molidStart=molidFirst; molidStart!=NULL; molidStart=molidStop)
{
molidStop = FindNextMolIDRecord(molidStart, "COMPND");
for(s=molidStart; s!=molidStop; NEXT(s))
{
char buffer[MAXPDBANNOTATION];
int thisMolid = 0;
ExtractField(molidStart, molidStop,
buffer, "COMPND", "MOL_ID:");
sscanf(buffer,"%d", &thisMolid);
if(thisMolid == molid)
{
ExtractField(molidStart, molidStop,
compnd->molecule, "COMPND","MOLECULE:");
ExtractField(molidStart, molidStop,
compnd->chain, "COMPND", "CHAIN:");
ExtractField(molidStart, molidStop,
compnd->fragment, "COMPND", "FRAGMENT:");
ExtractField(molidStart, molidStop,
compnd->synonym, "COMPND", "SYNONYM:");
ExtractField(molidStart, molidStop,
compnd->ec, "COMPND", "EC:");
ExtractField(molidStart, molidStop,
compnd->engineered, "COMPND", "ENGINEERED:");
ExtractField(molidStart, molidStop,
compnd->mutation, "COMPND", "MUTATION:");
ExtractField(molidStart, molidStop,
compnd->other, "COMPND", "OTHER_DETAILS:");
ExtractField(molidStart, molidStop,
buffer, "COMPND", "MOL_ID:");
sscanf(buffer,"%d", &(compnd->molid));
return(TRUE);
}
}
}
return(FALSE);
}
/*>BOOL blGetCompoundWholePDBChain(WHOLEPDB *wpdb, char *chain,
COMPND *compnd)
------------------------------------------------------------
*//**
\param[in] *wpdb WHOLEPDB structure
\param[in] *chain Chain label of interest
\param[out] *compnd Data from the COMPND records
\return BOOL Success
Extracts the COMPND data for a specified chain. Returns FALSE if the
chain isn't found
- 28.04.15 Original By: ACRM
- 04.06.15 Modified to use the ExtractField() routine instead of
duplicating code here. Fixes a bug in dealing with compounds
where the referenced chains span more than one line
*/
BOOL blGetCompoundWholePDBChain(WHOLEPDB *wpdb, char *chain,
COMPND *compnd)
{
STRINGLIST *molidFirst,
*molidStart,
*molidStop;
int molid;
compnd->molid = 0;
compnd->molecule[0] = '\0';
compnd->chain[0] = '\0';
compnd->fragment[0] = '\0';
compnd->synonym[0] = '\0';
compnd->ec[0] = '\0';
compnd->engineered[0] = '\0';
compnd->mutation[0] = '\0';
compnd->other[0] = '\0';
#ifdef DEBUG
molid = blFindMolID(wpdb, chain);
fprintf(stderr,"DEBUG: Chain %s molid %d\n", chain, molid);
if(molid == 0)
return(FALSE);
#else
if((molid = blFindMolID(wpdb, chain)) == 0)
return(FALSE);
#endif
molidFirst = FindNextMolIDRecord(wpdb->header, "COMPND");
for(molidStart=molidFirst; molidStart!=NULL; molidStart=molidStop)
{
char buffer[MAXPDBANNOTATION];
int thisMolid = 0;
molidStop = FindNextMolIDRecord(molidStart, "COMPND");
ExtractField(molidStart, molidStop,
buffer, "COMPND", "MOL_ID:");
sscanf(buffer,"%d", &thisMolid);
if(thisMolid == molid)
{
ExtractField(molidStart, molidStop,
compnd->molecule, "COMPND","MOLECULE:");
ExtractField(molidStart, molidStop,
compnd->chain, "COMPND", "CHAIN:");
ExtractField(molidStart, molidStop,
compnd->fragment, "COMPND", "FRAGMENT:");
ExtractField(molidStart, molidStop,
compnd->synonym, "COMPND", "SYNONYM:");
ExtractField(molidStart, molidStop,
compnd->ec, "COMPND", "EC:");
ExtractField(molidStart, molidStop,
compnd->engineered, "COMPND", "ENGINEERED:");
ExtractField(molidStart, molidStop,
compnd->mutation, "COMPND", "MUTATION:");
ExtractField(molidStart, molidStop,
compnd->other, "COMPND", "OTHER:");
ExtractField(molidStart, molidStop,
buffer, "COMPND", "MOL_ID:");
sscanf(buffer,"%d", &(compnd->molid));
return(TRUE);
}
}
return(FALSE);
}
GDALDataset *CTGDataset::Open( GDALOpenInfo * poOpenInfo )
{
int i;
if (!Identify(poOpenInfo))
return NULL;
CPLString osFilename(poOpenInfo->pszFilename);
/* GZipped grid_cell.gz files are common, so automagically open them */
/* if the /vsigzip/ has not been explicitely passed */
const char* pszFilename = CPLGetFilename(poOpenInfo->pszFilename);
if ((EQUAL(pszFilename, "grid_cell.gz") ||
EQUAL(pszFilename, "grid_cell1.gz") ||
EQUAL(pszFilename, "grid_cell2.gz")) &&
!EQUALN(poOpenInfo->pszFilename, "/vsigzip/", 9))
{
osFilename = "/vsigzip/";
osFilename += poOpenInfo->pszFilename;
}
if (poOpenInfo->eAccess == GA_Update)
{
CPLError( CE_Failure, CPLE_NotSupported,
"The CTG driver does not support update access to existing"
" datasets.\n" );
return NULL;
}
/* -------------------------------------------------------------------- */
/* Find dataset characteristics */
/* -------------------------------------------------------------------- */
VSILFILE* fp = VSIFOpenL(osFilename.c_str(), "rb");
if (fp == NULL)
return NULL;
char szHeader[HEADER_LINE_COUNT * 80+1];
szHeader[HEADER_LINE_COUNT * 80] = 0;
if (VSIFReadL(szHeader, 1, HEADER_LINE_COUNT * 80, fp) != HEADER_LINE_COUNT * 80)
{
VSIFCloseL(fp);
return NULL;
}
for(i=HEADER_LINE_COUNT * 80 - 1;i>=0;i--)
{
if (szHeader[i] == ' ')
szHeader[i] = 0;
else
break;
}
char szField[11];
int nRows = atoi(ExtractField(szField, szHeader, 0, 10));
int nCols = atoi(ExtractField(szField, szHeader, 20, 10));
/* -------------------------------------------------------------------- */
/* Create a corresponding GDALDataset. */
/* -------------------------------------------------------------------- */
CTGDataset *poDS;
poDS = new CTGDataset();
poDS->fp = fp;
fp = NULL;
poDS->nRasterXSize = nCols;
poDS->nRasterYSize = nRows;
poDS->SetMetadataItem("TITLE", szHeader + 4 * 80);
poDS->nCellSize = atoi(ExtractField(szField, szHeader, 35, 5));
if (poDS->nCellSize <= 0 || poDS->nCellSize >= 10000)
{
delete poDS;
return NULL;
}
poDS->nNWEasting = atoi(ExtractField(szField, szHeader + 3*80, 40, 10));
poDS->nNWNorthing = atoi(ExtractField(szField, szHeader + 3*80, 50, 10));
poDS->nUTMZone = atoi(ExtractField(szField, szHeader, 50, 5));
if (poDS->nUTMZone <= 0 || poDS->nUTMZone > 60)
{
delete poDS;
return NULL;
}
OGRSpatialReference oSRS;
oSRS.importFromEPSG(32600 + poDS->nUTMZone);
oSRS.exportToWkt(&poDS->pszProjection);
if (!GDALCheckDatasetDimensions(poDS->nRasterXSize, poDS->nRasterYSize))
{
delete poDS;
return NULL;
}
/* -------------------------------------------------------------------- */
/* Read the imagery */
/* -------------------------------------------------------------------- */
GByte* pabyImage = (GByte*)VSICalloc(nCols * nRows, 6 * sizeof(int));
if (pabyImage == NULL)
{
delete poDS;
return NULL;
}
poDS->pabyImage = pabyImage;
/* -------------------------------------------------------------------- */
/* Create band information objects. */
/* -------------------------------------------------------------------- */
poDS->nBands = 6;
for( i = 0; i < poDS->nBands; i++ )
{
poDS->SetBand( i+1, new CTGRasterBand( poDS, i+1 ) );
poDS->GetRasterBand(i+1)->SetDescription(apszBandDescription[i]);
}
/* -------------------------------------------------------------------- */
/* Initialize any PAM information. */
/* -------------------------------------------------------------------- */
poDS->SetDescription( poOpenInfo->pszFilename );
poDS->TryLoadXML();
/* -------------------------------------------------------------------- */
/* Support overviews. */
/* -------------------------------------------------------------------- */
poDS->oOvManager.Initialize( poDS, poOpenInfo->pszFilename );
return( poDS );
}
