void TRS2Fasta()
{
const char *TRSFileName = RequiredValueOpt("trs2fasta");
const char *SeqFileName = RequiredValueOpt("seq");
const char *Path = ValueOpt("path");
const char *strMaxFam = ValueOpt("maxfam");
const char *Prefix = ValueOpt("prefix");
int MaxFam = DEFAULT_MAX_FAM;
if (strMaxFam != 0)
MaxFam = atoi(strMaxFam);
if (0 == Path)
Path = ".";
ProgressStart("Reading seq file");
int SeqLength;
const char *Seq = ReadMFA(SeqFileName, &SeqLength);
ProgressDone();
Progress("Seq length %d bases, %.3g Mb", SeqLength, SeqLength/1e6);
ProgressStart("Read TRS file");
int TRSCount;
TRSData *TRSs = ReadTRS(TRSFileName, &TRSCount);
ProgressDone();
Progress("%d records", TRSCount);
ProgressStart("Sorting by family");
qsort((void *) TRSs, TRSCount, sizeof(TRSData), CmpTRS);
ProgressDone();
FILE *f = 0;
int CurrentFamily = -1;
int MemberCount = 0;
for (int TRSIndex = 0; TRSIndex < TRSCount; ++TRSIndex)
{
const TRSData &TRS = TRSs[TRSIndex];
if (TRS.FamIndex != CurrentFamily)
{
if (f != 0)
fclose(f);
char *FastaFileName = FamFileName(Path, TRS.FamIndex, TRS.SuperFamIndex);
f = OpenStdioFile(FastaFileName, FILEIO_MODE_WriteOnly);
CurrentFamily = TRS.FamIndex;
MemberCount = 0;
}
++MemberCount;
if (MemberCount > MaxFam)
continue;
const int From = ContigToGlobal(TRS.ContigFrom, TRS.ContigLabel);
const int Length = TRS.ContigTo - TRS.ContigFrom + 1;
char *Label = TRSLabel(Prefix, TRS);
WriteFasta(f, Seq + From, Length, Label, TRS.Rev);
freemem(Label);
}
}
void Tanmotif2Fasta()
{
const char *MotifFileName = RequiredValueOpt("tanmotif2fasta");
const char *SeqFileName = RequiredValueOpt("seq");
const char *Path = ValueOpt("path");
const char *strMaxFam = ValueOpt("maxfam");
const char *Prefix = ValueOpt("prefix");
int MaxFam = DEFAULT_MAX_FAM;
if (strMaxFam != 0)
MaxFam = atoi(strMaxFam);
if (0 == Path)
Path = ".";
ProgressStart("Reading seq file");
int SeqLength;
const char *Seq = ReadMFA(SeqFileName, &SeqLength);
ProgressDone();
Progress("Seq length %d bases, %.3g Mb", SeqLength, SeqLength/1e6);
ProgressStart("Read Motif file");
int MotifCount;
MotifData *Motifs = ReadMotif(MotifFileName, &MotifCount);
ProgressDone();
Progress("%d records", MotifCount);
ProgressStart("Sorting by family");
qsort((void *) Motifs, MotifCount, sizeof(MotifData), CmpMotif);
ProgressDone();
FILE *f = 0;
int CurrentFamily = -1;
int MemberCount = 0;
for (int MotifIndex = 0; MotifIndex < MotifCount; ++MotifIndex)
{
const MotifData &Motif = Motifs[MotifIndex];
if (Motif.FamIndex != CurrentFamily)
{
if (f != 0)
fclose(f);
char *FastaFileName = FamFileName(Path, Motif.FamIndex);
f = OpenStdioFile(FastaFileName, FILEIO_MODE_WriteOnly);
CurrentFamily = Motif.FamIndex;
MemberCount = 0;
}
++MemberCount;
if (MemberCount > MaxFam)
continue;
const int From = ContigToGlobal(Motif.ContigFrom, Motif.ContigLabel);
const int Length = Motif.ContigTo - Motif.ContigFrom + 1;
char *Label = MotifLabel(Prefix, Motif);
WriteFasta(f, Seq + From, Length, Label, false);
freemem(Label);
}
}
hlVoid ExtractItemStartCallback(HLDirectoryItem *pItem)
{
#if 0
PyEval_RestoreThread(g_extract_save);
if( pStartExtractFunc == Py_None )
{
if(!bSilent)
{
if(hlItemGetType(pItem) == HL_ITEM_FILE)
{
PySys_WriteStdout(" Extracting %s: ", hlItemGetName(pItem));
ProgressStart();
}
else
{
PySys_WriteStdout(" Extracting %s:\n", hlItemGetName(pItem));
}
}
}
else
{
PyEval_CallFunction(pStartExtractFunc, "si", hlItemGetName(pItem), hlItemGetType(pItem));
}
g_extract_save = PyEval_SaveThread();
#endif // 0
}
void AnnotEdge()
{
const char *InputFileName = RequiredValueOpt("annotedge");
const char *RepeatFileName = RequiredValueOpt("rep");
const char *OutputFileName = RequiredValueOpt("out");
ProgressStart("Reading repeat file");
int RepCount;
RepData *Reps = ReadReps(RepeatFileName, &RepCount);
ProgressDone();
Progress("%d records", RepCount);
FILE *fInput = OpenStdioFile(InputFileName);
FILE *fOutput = OpenStdioFile(OutputFileName, FILEIO_MODE_WriteOnly);
ProgressStart("Transferring annotation");
GFFRecord Rec;
while (GetNextGFFRecord(fInput, Rec))
{
const bool Rev = (Rec.Strand == '-');
const char *Annot = MakeAnnotEdge(Rec.SeqName, Rec.Start-1, Rec.End-1, Rev,
Reps, RepCount);
fprintf(fOutput, "%s\t%s\t%s\t%d\t%d\t%.3g\t%c",
// 0 1 2 3 4 5 6
Rec.SeqName, // 0
Rec.Source, // 1
Rec.Feature, // 2
Rec.Start, // 3
Rec.End, // 4
Rec.Score, // 5
Rec.Strand); // 6
if (-1 == Rec.Frame)
fprintf(fOutput, "\t.");
else
fprintf(fOutput, "\t%d", Rec.Frame);
fprintf(fOutput, "\t%s ; Annot \"%s\"\n", Rec.Attrs, Annot);
}
fclose(fInput);
fclose(fOutput);
ProgressDone();
}
hlVoid ExtractItemStartCallback(HLDirectoryItem *pItem)
{
if(!bSilent)
{
if(hlItemGetType(pItem) == HL_ITEM_FILE)
{
printf(" Extracting %s: ", hlItemGetName(pItem));
ProgressStart();
}
else
{
Print(FOREGROUND_RED | FOREGROUND_GREEN | FOREGROUND_BLUE | FOREGROUND_INTENSITY, " Extracting %s:\n", hlItemGetName(pItem));
}
}
}
void Tan()
{
// Image file annotated with from-to pile indexes
// Produced by:
// piler2 -trs banded_hits.gff -images mainband_images.gff
const char *HitFileName = RequiredValueOpt("tan");
const char *OutFileName = RequiredValueOpt("out");
const char *PyramidFileName = ValueOpt("pyramid");
const char *MotifFileName = ValueOpt("motif");
const char *strMinHits = ValueOpt("minhits");
const char *strMaxMargin = ValueOpt("maxmargin");
const char *strMinRatio = ValueOpt("minratio");
if (0 != strMinHits)
MIN_HIT_COUNT = atoi(strMinHits);
if (0 != strMaxMargin)
MAX_FRACT_MARGIN = atof(strMaxMargin);
if (0 != strMinRatio)
MIN_RATIO = atof(strMinRatio);
FILE *fInput = OpenStdioFile(HitFileName);
ProgressStart("Initialize piles");
GFFRecord Rec;
int HitCount = 0;
while (GetNextGFFRecord(fInput, Rec))
{
if (0 != strcmp(Rec.Feature, "hit"))
continue;
int QueryPileIndex = -1;
int TargetPileIndex = -1;
ParsePilesAttrs(Rec.Attrs, &QueryPileIndex, &TargetPileIndex);
if (QueryPileIndex != TargetPileIndex)
continue;
char TargetLabel[128];
int TargetStart;
int TargetEnd;
ParseTargetAttrs(Rec.Attrs, TargetLabel, sizeof(TargetLabel), &TargetStart, &TargetEnd);
if (0 != strcmp(Rec.SeqName, TargetLabel))
Quit("Labels don't match");
const int QueryFrom = Rec.Start - 1;
const int QueryTo = Rec.End - 1;
const int TargetFrom = TargetStart - 1;
const int TargetTo = TargetEnd - 1;
const bool Rev = (Rec.Strand == '-');
AddHit(QueryPileIndex, Rec.SeqName, QueryFrom, QueryTo, TargetFrom, TargetTo, Rev);
++HitCount;
}
ProgressDone();
Progress("%d hits, %d piles", HitCount, PileCount);
ProgressStart("Allocate piles");
for (int PileIndex = 0; PileIndex < PileCount; ++PileIndex)
{
TanPile &Pile = Piles[PileIndex];
Pile.Hits = all(HitData, Pile.HitCount);
Pile.HitCount = 0;
}
ProgressDone();
ProgressStart("Assign hits to piles");
Rewind(fInput);
while (GetNextGFFRecord(fInput, Rec))
{
if (0 != strcmp(Rec.Feature, "hit"))
continue;
int QueryPileIndex = -1;
int TargetPileIndex = -1;
ParsePilesAttrs(Rec.Attrs, &QueryPileIndex, &TargetPileIndex);
if (QueryPileIndex != TargetPileIndex)
continue;
char TargetLabel[128];
int TargetStart;
int TargetEnd;
ParseTargetAttrs(Rec.Attrs, TargetLabel, sizeof(TargetLabel), &TargetStart, &TargetEnd);
if (0 != strcmp(Rec.SeqName, TargetLabel))
Quit("Labels don't match");
const int QueryFrom = Rec.Start - 1;
const int QueryTo = Rec.End - 1;
const int TargetFrom = TargetStart - 1;
const int TargetTo = TargetEnd - 1;
const bool Rev = (Rec.Strand == '-');
AssignHit(QueryPileIndex, Rec.SeqName, QueryFrom, QueryTo, TargetFrom, TargetTo, Rev);
}
ProgressDone();
fOut = OpenStdioFile(OutFileName, FILEIO_MODE_WriteOnly);
fPyramid = (0 == PyramidFileName ? 0 : OpenStdioFile(PyramidFileName, FILEIO_MODE_WriteOnly));
fMotif = (0 == PyramidFileName ? 0 : OpenStdioFile(MotifFileName, FILEIO_MODE_WriteOnly));
ProgressStart("Find pyramids");
for (int PileIndex = 0; PileIndex < PileCount; ++PileIndex)
FindPyramids(PileIndex);
int PyramidCount = PyramidIndex;
ProgressDone();
Progress("%d pyramids", PyramidCount);
}
int main(hlInt argc, hlChar* argv[])
{
hlUInt i;
// Arguments.
hlUInt uiArgumentCount = (hlUInt)argc;
hlChar *lpPackage = 0;
hlUInt uiExtractItems = 0;
hlChar *lpExtractItems[MAX_ITEMS];
hlUInt uiValidateItems = 0;
hlChar *lpValidateItems[MAX_ITEMS];
hlChar *lpList = 0;
hlBool bDefragment = hlFalse;
hlChar *lpNCFRootPath = 0;
hlBool bList = hlFalse;
hlBool bListFolders = hlFalse;
hlBool bListFiles = hlFalse;
FILE *pFile = 0;
hlBool bConsoleMode = hlFalse;
hlUInt uiConsoleCommands = 0;
hlChar *lpConsoleCommands[MAX_ITEMS];
hlBool bFileMapping = hlFalse;
hlBool bQuickFileMapping = hlFalse;
hlBool bVolatileAccess = hlFalse;
hlBool bOverwriteFiles = hlTrue;
hlBool bForceDefragment = hlFalse;
// Package stuff.
HLPackageType ePackageType = HL_PACKAGE_NONE;
hlUInt uiPackage = HL_ID_INVALID, uiMode = HL_MODE_INVALID;
HLDirectoryItem *pItem = 0;
if(hlGetUnsignedInteger(HL_VERSION) < HL_VERSION_NUMBER)
{
printf("Wrong HLLib version: v%s.\n", hlGetString(HL_VERSION));
return 1;
}
// Process switches.
if(uiArgumentCount == 2)
{
// The user just specified a file, drop into console mode.
lpPackage = argv[1];
bConsoleMode = hlTrue;
bVolatileAccess = hlTrue;
}
else
{
for(i = 1; i < uiArgumentCount; i++)
{
if(stricmp(argv[i], "-p") == 0 || stricmp(argv[i], "--package") == 0)
{
if(lpPackage == 0 && i + 1 < uiArgumentCount)
{
lpPackage = argv[++i];
}
else
{
PrintUsage();
return 2;
}
}
else if(stricmp(argv[i], "-d") == 0 || stricmp(argv[i], "--dest") == 0)
{
if(*lpDestination == 0 && i + 1 < uiArgumentCount)
{
strcpy(lpDestination, argv[++i]);
}
else
{
PrintUsage();
return 2;
}
}
else if(stricmp(argv[i], "-e") == 0 || stricmp(argv[i], "--extract") == 0)
{
if(i + 1 < uiArgumentCount)
{
if(uiExtractItems == MAX_ITEMS)
{
Print(FOREGROUND_RED | FOREGROUND_INTENSITY, "Error loading package:\nMAX_ITEMS\n");
return 2;
}
lpExtractItems[uiExtractItems++] = argv[++i];
}
else
{
PrintUsage();
return 2;
}
}
else if(stricmp(argv[i], "-t") == 0 || stricmp(argv[i], "--validate") == 0)
{
if(i + 1 < uiArgumentCount)
{
if(uiValidateItems == MAX_ITEMS)
{
Print(FOREGROUND_RED | FOREGROUND_INTENSITY, "Error loading package:\nMAX_ITEMS\n");
return 2;
}
lpValidateItems[uiValidateItems++] = argv[++i];
}
else
{
PrintUsage();
return 2;
}
}
else if(strnicmp(argv[i], "-l", 2) == 0 || stricmp(argv[i], "--list") == 0)
{
if(bList)
{
PrintUsage();
return 2;
}
bList = hlTrue;
if(stricmp(argv[i], "-l") == 0 || stricmp(argv[i], "--list") == 0)
{
// By default list everything.
bListFolders = hlTrue;
bListFiles = hlTrue;
}
else
{
// List folders and files if specified.
bListFolders = strcspn(argv[i], "dD") != strlen(argv[i]);
bListFiles = strcspn(argv[i], "fF") != strlen(argv[i]);
}
// Check to see if we need to dump our list to a file.
if(i + 1 < uiArgumentCount && *argv[i + 1] != '-')
{
lpList = argv[++i];
}
}
else if(stricmp(argv[i], "-f") == 0 || stricmp(argv[i], "--defragment") == 0)
{
bDefragment = hlTrue;
}
else if(stricmp(argv[i], "-n") == 0 || stricmp(argv[i], "--ncfroot") == 0)
{
if(lpNCFRootPath == 0 && i + 1 < uiArgumentCount)
{
lpNCFRootPath = argv[++i];
}
else
{
PrintUsage();
return 2;
}
}
else if(stricmp(argv[i], "-s") == 0 || stricmp(argv[i], "--silent") == 0)
{
bSilent = hlTrue;
}
else if(stricmp(argv[i], "-c") == 0 || stricmp(argv[i], "--console") == 0)
{
bConsoleMode = hlTrue;
}
else if(stricmp(argv[i], "-x") == 0 || stricmp(argv[i], "--execute") == 0)
{
if(i + 1 < uiArgumentCount)
{
if(uiConsoleCommands == MAX_ITEMS)
{
Print(FOREGROUND_RED | FOREGROUND_INTENSITY, "Error loading package:\nMAX_ITEMS\n");
return 2;
}
lpConsoleCommands[uiConsoleCommands++] = argv[++i];
}
else
{
PrintUsage();
return 2;
}
}
else if(stricmp(argv[i], "-m") == 0 || stricmp(argv[i], "--filemapping") == 0)
{
bFileMapping = hlTrue;
}
else if(stricmp(argv[i], "-q") == 0 || stricmp(argv[i], "--quick-filemapping") == 0)
{
bFileMapping = hlTrue;
bQuickFileMapping = hlTrue;
}
else if(stricmp(argv[i], "-v") == 0 || stricmp(argv[i], "--volatile") == 0)
{
bVolatileAccess = hlTrue;
}
else if(stricmp(argv[i], "-o") == 0 || stricmp(argv[i], "--overwrite") == 0)
{
bOverwriteFiles = hlFalse;
}
else if(stricmp(argv[i], "-r") == 0 || stricmp(argv[i], "--force-defragment") == 0)
{
bDefragment = hlTrue;
bForceDefragment = hlTrue;
}
else
{
PrintUsage();
return 2;
}
}
}
// Make sure we have something to do.
if(lpPackage == 0 || (uiExtractItems == 0 && uiValidateItems == 0 && !bList && !bDefragment && !bConsoleMode))
{
PrintUsage();
return 2;
}
// If the destination directory is not specified, make it the input directory.
if(*lpDestination == 0)
{
const hlChar *pForward = strrchr(lpPackage, '\\');
const hlChar *pBackward = strrchr(lpPackage, '/');
const hlChar *pEnd = pForward > pBackward ? pForward : pBackward;
if(pEnd != 0)
{
strncpy(lpDestination, lpPackage, pEnd - lpPackage);
lpDestination[pEnd - lpPackage] = '\0';
}
}
hlInitialize();
hlSetBoolean(HL_OVERWRITE_FILES, bOverwriteFiles);
hlSetBoolean(HL_FORCE_DEFRAGMENT, bForceDefragment);
hlSetVoid(HL_PROC_EXTRACT_ITEM_START, ExtractItemStartCallback);
hlSetVoid(HL_PROC_EXTRACT_ITEM_END, ExtractItemEndCallback);
hlSetVoid(HL_PROC_EXTRACT_FILE_PROGRESS, FileProgressCallback);
hlSetVoid(HL_PROC_VALIDATE_FILE_PROGRESS, FileProgressCallback);
hlSetVoid(HL_PROC_DEFRAGMENT_PROGRESS_EX, DefragmentProgressCallback);
// Get the package type from the filename extension.
ePackageType = hlGetPackageTypeFromName(lpPackage);
// If the above fails, try getting the package type from the data at the start of the file.
if(ePackageType == HL_PACKAGE_NONE)
{
pFile = fopen(lpPackage, "rb");
if(pFile != 0)
{
hlByte lpBuffer[HL_DEFAULT_PACKAGE_TEST_BUFFER_SIZE];
hlUInt uiBufferSize = (hlUInt)fread(lpBuffer, 1, HL_DEFAULT_PACKAGE_TEST_BUFFER_SIZE, pFile);
ePackageType = hlGetPackageTypeFromMemory(lpBuffer, uiBufferSize);
fclose(pFile);
pFile = 0;
}
}
if(ePackageType == HL_PACKAGE_NONE)
{
Print(FOREGROUND_RED | FOREGROUND_INTENSITY, "Error loading %s:\nUnsupported package type.\n", lpPackage);
hlShutdown();
return 3;
}
// Create a package element, the element is allocated by the library and cleaned
// up by the library. An ID is generated which must be bound to apply operations
// to the package.
if(!hlCreatePackage(ePackageType, &uiPackage))
{
Print(FOREGROUND_RED | FOREGROUND_INTENSITY, "Error loading %s:\n%s\n", lpPackage, hlGetString(HL_ERROR_SHORT_FORMATED));
hlShutdown();
return 3;
}
hlBindPackage(uiPackage);
uiMode = HL_MODE_READ | (bDefragment ? HL_MODE_WRITE : 0);
uiMode |= !bFileMapping ? HL_MODE_NO_FILEMAPPING : 0;
uiMode |= bQuickFileMapping ? HL_MODE_QUICK_FILEMAPPING : 0;
uiMode |= bVolatileAccess ? HL_MODE_VOLATILE : 0;
// Open the package.
// Of the above modes, only HL_MODE_READ is required. HL_MODE_WRITE is present
// only for future use. File mapping is recommended as an efficient way to load
// packages. Quick file mapping maps the entire file (instead of bits as they are
// needed) and thus should only be used in Windows 2000 and up (older versions of
// Windows have poor virtual memory management which means large files won't be able
// to find a continues block and will fail to load). Volatile access allows HLLib
// to share files with other applications that have those file open for writing.
// This is useful for, say, loading .gcf files while Steam is running.
if(!hlPackageOpenFile(lpPackage, uiMode))
{
Print(FOREGROUND_RED | FOREGROUND_INTENSITY, "Error loading %s:\n%s\n", lpPackage, hlGetString(HL_ERROR_SHORT_FORMATED));
hlShutdown();
return 3;
}
// If we have a .ncf file, the package file data is stored externally. In order to
// validate the file data etc., HLLib needs to know where to look. Tell it where.
if(ePackageType == HL_PACKAGE_NCF)
{
hlNCFFileSetRootPath(lpNCFRootPath);
}
if(!bSilent)
Print(FOREGROUND_GREEN | FOREGROUND_INTENSITY, "%s opened.\n", lpPackage);
// Extract the requested items.
for(i = 0; i < uiExtractItems; i++)
{
// Find the item.
pItem = hlFolderGetItemByPath(hlPackageGetRoot(), lpExtractItems[i], HL_FIND_ALL);
if(pItem == 0)
{
printf("%s not found in package.\n", lpExtractItems[i]);
continue;
}
if(!bSilent)
{
Print(FOREGROUND_GREEN | FOREGROUND_INTENSITY, "Extracting %s...\n", hlItemGetName(pItem));
printf("\n");
}
// Extract the item.
// Item is extracted to cDestination\Item->GetName().
hlItemExtract(pItem, lpDestination);
if(!bSilent)
{
printf("\n");
printf("Done.\n");
}
}
// Validate the requested items.
for(i = 0; i < uiValidateItems; i++)
{
// Find the item.
pItem = hlFolderGetItemByPath(hlPackageGetRoot(), lpValidateItems[i], HL_FIND_ALL);
if(pItem == 0)
{
printf("%s not found in package.\n", lpValidateItems[i]);
continue;
}
if(!bSilent)
{
Print(FOREGROUND_GREEN | FOREGROUND_INTENSITY, "Validating %s...\n", hlItemGetName(pItem));
printf("\n");
}
// Validate the item.
Validate(pItem);
if(!bSilent)
{
printf("\n");
printf("Done.\n");
}
}
// List items in package.
if(bList)
{
if(!bSilent)
{
printf("Listing...\n");
printf("\n");
}
pFile = stdout;
if(lpList != 0)
{
pFile = fopen(lpList, "wt");
if(pFile == 0)
{
Print(FOREGROUND_RED | FOREGROUND_INTENSITY, "Error opening %s:\n%s\n", lpList, "fopen() failed.");
pFile = stdout;
}
}
List(pFile, hlPackageGetRoot(), bListFolders, bListFiles);
if(lpList != 0)
{
fclose(pFile);
pFile = 0;
}
if(!bSilent)
{
printf("\n");
printf("Done.\n");
}
}
if(bDefragment)
{
if(!bSilent)
{
printf("Defragmenting...\n");
printf("\n");
ProgressStart();
printf(" Progress: ");
}
if(!hlPackageDefragment())
{
Print(FOREGROUND_RED | FOREGROUND_INTENSITY, " %s", hlGetString(HL_ERROR_SHORT_FORMATED));
}
if(!bSilent)
{
printf("\n");
printf("\n");
printf("Done.\n");
}
}
// Interactive console mode.
// Commands: dir, cd, root, info, extract, find, type, cls, help, exit.
if(bConsoleMode)
{
EnterConsole(uiPackage, uiConsoleCommands, lpConsoleCommands);
}
// Close the package.
hlPackageClose();
if(!bSilent)
Print(FOREGROUND_GREEN | FOREGROUND_INTENSITY, "%s closed.\n", lpPackage);
// Free up the allocated memory.
hlDeletePackage(uiPackage);
hlShutdown();
return 0;
}
HLValidation Validate(HLDirectoryItem *pItem)
{
hlUInt i, uiItemCount;
hlChar lpPath[512] = "";
HLValidation eValidation = HL_VALIDATES_OK, eTest;
switch(hlItemGetType(pItem))
{
case HL_ITEM_FOLDER:
if(!bSilent)
{
Print(FOREGROUND_RED | FOREGROUND_GREEN | FOREGROUND_BLUE | FOREGROUND_INTENSITY, " Validating %s:\n", hlItemGetName(pItem));
}
uiItemCount = hlFolderGetCount(pItem);
for(i = 0; i < uiItemCount; i++)
{
eTest = Validate(hlFolderGetItem(pItem, i));
if(eTest > eValidation)
{
eValidation = eTest;
}
}
if(!bSilent)
{
Print(FOREGROUND_RED | FOREGROUND_GREEN | FOREGROUND_BLUE | FOREGROUND_INTENSITY, " Done %s: ", hlItemGetName(pItem));
PrintValidation(eValidation);
printf("\n");
}
break;
case HL_ITEM_FILE:
if(!bSilent)
{
printf(" Validating %s: ", hlItemGetName(pItem));
ProgressStart();
}
eValidation = hlFileGetValidation(pItem);
if(bSilent)
{
switch(eValidation)
{
case HL_VALIDATES_INCOMPLETE:
case HL_VALIDATES_CORRUPT:
hlItemGetPath(pItem, lpPath, sizeof(lpPath));
printf(" Validating %s: ", lpPath);
PrintValidation(eValidation);
printf("\n");
break;
}
}
else
{
PrintValidation(eValidation);
printf(" \n");
}
break;
}
return eValidation;
}
void TR()
{
#if defined(DEBUG) && defined(_MSC_VER)
_CrtSetDbgFlag(0); // too expensive
#endif
const char *HitFileName = RequiredValueOpt("tr");
const char *OutFileName = RequiredValueOpt("out");
const char *CandFileName = ValueOpt("cand");
const char *strMinTrSpacing = ValueOpt("mintrspacing");
const char *strMaxTrSpacing = ValueOpt("maxtrspacing");
const char *strMinTrLength = ValueOpt("mintrlength");
const char *strMaxTrLength = ValueOpt("minspacingratio");
const char *strMinFam = ValueOpt("minfam");
const char *strMinHitRatio = ValueOpt("minhitratio");
const char *strMinDistPairs = ValueOpt("mindistpairs");
if (0 != strMinTrSpacing)
MIN_LENGTH_LINE = atoi(strMinTrSpacing);
if (0 != strMaxTrSpacing)
MAX_LENGTH_LINE = atoi(strMaxTrSpacing);
if (0 != strMinTrLength)
MIN_LENGTH_LTR = atoi(strMinTrLength);
if (0 != strMaxTrLength)
MAX_LENGTH_LTR = atoi(strMaxTrLength);
if (0 != strMinFam)
MIN_FAM_SIZE = atoi(strMinFam);
if (0 != strMinHitRatio)
MIN_HIT_LENGTH_RATIO = atoi(strMinHitRatio);
if (0 != strMinDistPairs)
MIN_DIST_EDGE = atoi(strMinDistPairs);
FILE *fHit = OpenStdioFile(HitFileName, FILEIO_MODE_ReadOnly);
ProgressStart("Index hits");
GLIX HitGlix;
HitGlix.Init();
HitGlix.FromGFFFile(fHit);
HitGlix.MakeGlobalToLocalIndex();
ProgressDone();
const int GlobalLength = HitGlix.GetGlobalLength();
IIX IntervalIndex;
IntervalIndex.Init(GlobalLength);
ProgressStart("Find candidate TRs");
Rewind(fHit);
GFFRecord Rec;
while (GetNextGFFRecord(fHit, Rec))
{
HitData Hit;
GFFRecordToHit(HitGlix, Rec, Hit);
if (IsCandLTR(Hit))
AddCand(Hit, IntervalIndex);
}
ProgressDone();
Progress("%d candidates", CandCount);
if (0 != CandFileName)
{
ProgressStart("Write candidates");
FILE *fCand = OpenStdioFile(CandFileName, FILEIO_MODE_WriteOnly);
WriteCands(fCand, HitGlix);
ProgressDone();
}
ProgressStart("Make graph");
Rewind(fHit);
while (GetNextGFFRecord(fHit, Rec))
{
HitData Hit;
GFFRecordToHit(HitGlix, Rec, Hit);
FindEdges(Hit, HitGlix, IntervalIndex);
}
fclose(fHit);
fHit = 0;
ProgressDone();
Progress("%d edges", (int) Edges.size());
ProgressStart("Find families");
FamList Fams;
FindConnectedComponents(Edges, Fams, MIN_FAM_SIZE);
ProgressDone();
Progress("%d families", (int) Fams.size());
FILE *fOut = OpenStdioFile(OutFileName, FILEIO_MODE_WriteOnly);
WriteOutputFile(fOut, HitGlix, Fams);
}
void TRS()
{
const char *InputFileName = RequiredValueOpt("trs");
const char *OutputFileName = ValueOpt("out");
const char *PilesFileName = ValueOpt("piles");
const char *ImagesFileName = ValueOpt("images");
const char *strMinFamSize = ValueOpt("famsize");
const char *strMaxLengthDiffPct = ValueOpt("maxlengthdiffpct");
g_paramSingleHitCoverage = !FlagOpt("multihit");
if (0 == OutputFileName && 0 == PilesFileName && 0 == ImagesFileName)
Quit("No output file specified, must be at least one of -out, -piles, -images");
if (0 != strMinFamSize)
g_paramMinFamSize = atoi(strMinFamSize);
if (0 != strMaxLengthDiffPct)
g_paramMaxLengthDiffPct = atoi(strMaxLengthDiffPct);
Log("singlehit=%s famsize=%d maxlengthdiffpct=%d\n",
g_paramSingleHitCoverage ? "True" : "False",
g_paramMinFamSize,
g_paramMaxLengthDiffPct);
ProgressStart("Read hit file");
int HitCount;
int SeqLength;
HitData *Hits = ReadHits(InputFileName, &HitCount, &SeqLength);
ProgressDone();
Progress("%d hits", HitCount);
SeqLengthChunks = (SeqLength + CHUNK_LENGTH - 1)/CHUNK_LENGTH;
const int BitVectorLength = (SeqLengthChunks + BITS_PER_INT - 1)/BITS_PER_INT;
int *CopyCount = all(int, BitVectorLength);
zero(CopyCount, int, BitVectorLength);
ProgressStart("Compute copy counts");
for (int i = 0; i < HitCount; ++i)
IncCopyCount(CopyCount, Hits[i]);
ProgressDone();
ProgressStart("Identify piles");
PILE_INDEX_TYPE *PileIndexes = IdentifyPiles(CopyCount);
ProgressDone();
Progress("%d stacks", PileCount);
freemem(CopyCount);
CopyCount = 0;
CreatePiles(Hits, HitCount, PileIndexes);
if (0 != ImagesFileName)
{
ProgressStart("Writing images file");
WriteImages(ImagesFileName, Hits, HitCount, PileIndexes);
ProgressDone();
}
freemem(Hits);
Hits = 0;
if (0 != PilesFileName)
{
ProgressStart("Writing piles file");
WritePiles(PilesFileName, Piles, PileCount);
ProgressDone();
}
freemem(PileIndexes);
PileIndexes = 0;
if (0 == OutputFileName)
return;
ProgressStart("Find edges");
EdgeList Edges;
FindGlobalEdges(Edges, MaxImageCount);
ProgressDone();
Progress("%d edges", (int) Edges.size());
ProgressStart("Find families");
FamList Fams;
FindConnectedComponents(Edges, Fams, g_paramMinFamSize);
AssignFamsToPiles(Fams);
ProgressDone();
Progress("%d families", (int) Fams.size());
ProgressStart("Find superfamilies");
EdgeList SuperEdges;
FindSuperFamEdges(Fams, SuperEdges);
FamList SuperFams;
FindConnectedComponents(SuperEdges, SuperFams, 1);
FindSingletonSuperFams(Fams, SuperFams);
AssignSuperFamsToPiles(Fams, SuperFams);
ProgressDone();
Progress("%d superfamilies", (int) SuperFams.size());
ProgressStart("Write TRS output file");
WriteTRSFile(OutputFileName, Piles, PileCount);
ProgressDone();
}
static void CreatePiles(const HitData *Hits, int HitCount,
PILE_INDEX_TYPE *PileIndexes)
{
Piles = all(PileData, PileCount);
zero(Piles, PileData, PileCount);
for (int i = 0; i < PileCount; ++i)
{
Piles[i].FamIndex = -1;
Piles[i].SuperFamIndex = -1;
Piles[i].Rev = -1;
}
// Count images in stack
ProgressStart("Create stacks: count images");
for (int HitIndex = 0; HitIndex < HitCount; ++HitIndex)
{
const HitData &Hit = Hits[HitIndex];
int Pos = Hit.QueryFrom/CHUNK_LENGTH;
PILE_INDEX_TYPE PileIndex = PileIndexes[Pos];
assert(PileIndex == PileIndexes[Hit.QueryTo/CHUNK_LENGTH]);
assert(PileIndex >= 0 && PileIndex < PileCount);
++(Piles[PileIndex].ImageCount);
Pos = Hit.TargetFrom/CHUNK_LENGTH;
PileIndex = PileIndexes[Pos];
assert(PileIndex >= 0 && PileIndex < PileCount);
assert(PileIndex == PileIndexes[Hit.TargetTo/CHUNK_LENGTH]);
++(Piles[PileIndex].ImageCount);
}
ProgressDone();
// Allocate memory for image list
int TotalImageCount = 0;
ProgressStart("Create stacks: allocate image memory");
for (int PileIndex = 0; PileIndex < PileCount; ++PileIndex)
{
PileData &Pile = Piles[PileIndex];
const int ImageCount = Pile.ImageCount;
TotalImageCount += ImageCount;
assert(ImageCount > 0);
Pile.Images = all(PileImageData, ImageCount);
}
ProgressDone();
// Build image list
ProgressStart("Create stacks: build image list");
for (int PileIndex = 0; PileIndex < PileCount; ++PileIndex)
{
PileData &Pile = Piles[PileIndex];
Pile.ImageCount = 0;
Pile.From = -1;
Pile.To = -1;
}
for (int HitIndex = 0; HitIndex < HitCount; ++HitIndex)
{
const HitData &Hit = Hits[HitIndex];
const bool Rev = Hit.Rev;
const int Length1 = Hit.QueryTo - Hit.QueryFrom;
const int Length2 = Hit.TargetTo - Hit.TargetFrom;
const int From1 = Hit.QueryFrom;
const int From2 = Hit.TargetFrom;
const int To1 = Hit.QueryTo;
const int To2 = Hit.TargetTo;
const int Pos1 = From1/CHUNK_LENGTH;
const int Pos2 = From2/CHUNK_LENGTH;
PILE_INDEX_TYPE PileIndex1 = PileIndexes[Pos1];
PILE_INDEX_TYPE PileIndex2 = PileIndexes[Pos2];
assert(PileIndex1 == PileIndexes[(From1 + Length1 - 1)/CHUNK_LENGTH]);
assert(PileIndex1 >= 0 && PileIndex1 < PileCount);
assert(PileIndex2 == PileIndexes[(From2 + Length2 - 1)/CHUNK_LENGTH]);
assert(PileIndex2 >= 0 && PileIndex2 < PileCount);
PileData &Pile1 = Piles[PileIndex1];
PileImageData &Image1 = Pile1.Images[Pile1.ImageCount++];
Image1.SILength = Length2;
Image1.SIPile = PileIndex2;
Image1.SIRev = Rev;
PileData &Pile2 = Piles[PileIndex2];
PileImageData &Image2 = Pile2.Images[Pile2.ImageCount++];
Image2.SILength = Length1;
Image2.SIPile = PileIndex1;
Image2.SIRev = Rev;
if (Pile1.From == -1 || From1 < Pile1.From)
Pile1.From = From1;
if (Pile1.To == -1 || To1 > Pile1.To)
Pile1.To = To1;
if (Pile2.From == -1 || From2 < Pile2.From)
Pile2.From = From2;
if (Pile2.To == -1 || To2 > Pile2.To)
Pile2.To = To2;
if (Pile1.ImageCount > MaxImageCount)
MaxImageCount = Pile1.ImageCount;
if (Pile2.ImageCount > MaxImageCount)
MaxImageCount = Pile2.ImageCount;
}
ProgressDone();
}
////////////////////////////////////////////////////////////////////////////////
// Предварительная обработка
// (07.07.2000) Изначально взято из puma.dll без изменений
// сильно привязана к пуме
// в начале окучиваем выделение компонент
Bool32 PreProcessImage( PRSPreProcessImage Image )
{
Bool32 gbAutoRotate = Image->gbAutoRotate;
puchar *gpRecogDIB = Image->pgpRecogDIB;
Handle hCPAGE = Image->hCPAGE;
const char * glpRecogName = *Image->pglpRecogName;
PCIMAGEBITMAPINFOHEADER info = (PCIMAGEBITMAPINFOHEADER)Image->pinfo;
/////////////////////////////////
Bool32 rc = TRUE;
//char * lpRecogName = NULL;
uint32_t Angle = 0;
hWndTurn = 0;
if(InitPRGTIME())
ProgressStart();
if(!ProgressStep(1,5))
rc = FALSE;
// Andrey 12.11.01
// Проинициализируем контейнер CPAGE
//
if(rc)
{
PAGEINFO PInfo = {0};
GetPageInfo(hCPAGE,&PInfo);
strcpy((char*)PInfo.szImageName, glpRecogName);
PInfo.BitPerPixel = info->biBitCount;
PInfo.DPIX = info->biXPelsPerMeter*254L/10000;
// PInfo.DPIX = PInfo.DPIX < 200 ? 200 : PInfo.DPIX;
PInfo.DPIY = info->biYPelsPerMeter*254L/10000;
// PInfo.DPIY = PInfo.DPIY < 200 ? 200 : PInfo.DPIY;
PInfo.Height = info->biHeight;
PInfo.Width = info->biWidth;
// PInfo.X = 0; Уже установлено
// PInfo.Y = 0;
PInfo.Incline2048 = 0;
PInfo.Page = 1;
PInfo.Angle = Angle;
SetPageInfo(hCPAGE,PInfo);
}
////////////////////////////////////////////////////////
// Выделим компоненты
//
if(!ProgressStep(2,65))
rc = FALSE;
if(rc)
{
if(LDPUMA_Skip(Image->hDebugCancelComponent)/*DPumaSkipComponent()*/)
{
// uchar ori;
PRGTIME prev = StorePRGTIME(65, 85);
rc = ExtractComponents( gbAutoRotate, NULL, (puchar)glpRecogName, Image);
RestorePRGTIME(prev);
/* if(rc && gbAutoRotate)
{
//if(!REXC_GetOrient(&ori))
//if(!REXC_GetOrient(&ori) && db_spec_prj!=SPEC_PRJ_GIP )
if(!RNORM_GetOrient(&ori, *(Image->phCCOM)) && db_spec_prj!=SPEC_PRJ_GIP )
{
SetReturnCode_rstuff(RNORM_GetReturnCode());
rc = FALSE;
}
else
{
//if(ori)
if(ori && !(db_spec_prj==SPEC_PRJ_GIP&&ori==4))
{
uint32_t dwTurn = 0;
switch(ori)
{
case 1:
Angle = 270;
dwTurn = RIMAGE_TURN_270;
break;
case 2:
Angle = 90;
dwTurn = RIMAGE_TURN_90;
break;
case 3:
Angle = 180;
dwTurn = RIMAGE_TURN_180;
break;
}
if( LDPUMA_Skip(Image->hDebugCancelTurn) /*umaSkipTurn()*/ /*)
{
if(!RIMAGE_Turn((puchar)glpRecogName,(puchar)PUMA_IMAGE_TURN,dwTurn,0))
{
SetReturnCode_rstuff_rstuff(RIMAGE_GetReturnCode());
rc = FALSE;
}
else
{
if(!CIMAGE_ReadDIB((puchar)PUMA_IMAGE_TURN,(Handle*)gpRecogDIB,TRUE))
{
SetReturnCode_rstuff_rstuff(CIMAGE_GetReturnCode());
rc = FALSE;
}
else
{
//
// удалим общий контейнер
//
glpRecogName = PUMA_IMAGE_TURN;
hWndTurn = LDPUMA_CreateWindow(PUMA_IMAGE_TURN,(*gpRecogDIB));
PRGTIME prev = StorePRGTIME(85, 100);
rc = ExtractComponents( FALSE, NULL, (puchar)glpRecogName, Image);
PAGEINFO info = {0};
GetPageInfo(hCPAGE,&info);
info.Images|=IMAGE_TURN;
// strcpy((char*)info.szImageName,PUMA_IMAGE_TURN);
SetPageInfo(hCPAGE,info);
RestorePRGTIME(prev);
}
}
}
}
}
}*/
//проверим наличие разрешения и попытаемся определить по компонентам, если его нет
checkResolution(*(Image->phCCOM), hCPAGE);
if(!ProgressStep(2,100))
rc = FALSE;
}
else
LDPUMA_Console("Пропущен этап выделения компонент.\n");
}
//
// Переинициализируем контейнер CPAGE
//
if(rc)
{
PAGEINFO PInfo = {0};
GetPageInfo(hCPAGE,&PInfo);
strcpy((char*)PInfo.szImageName, glpRecogName);
PInfo.BitPerPixel = info->biBitCount;
// PInfo.DPIX = info->biXPelsPerMeter*254L/10000;
PInfo.DPIX = PInfo.DPIX < 200 ? 200 : PInfo.DPIX;
// PInfo.DPIY = info->biYPelsPerMeter*254L/10000;
PInfo.DPIY = PInfo.DPIY < 200 ? 200 : PInfo.DPIY;
PInfo.Height = info->biHeight;
PInfo.Width = info->biWidth;
// PInfo.X = 0; Уже установлено
// PInfo.Y = 0;
PInfo.Incline2048 = 0;
PInfo.Page = 1;
PInfo.Angle = Angle;
SetPageInfo(hCPAGE,PInfo);
}
if(DonePRGTIME())
ProgressFinish();
return rc;
}
