/*******************************************************************
* Function Name: ReadProgramPath
* Return Type : int
* Created On : Feb 23, 2013
* Created By : hrushi
* Comments : Reads the program path. This is the zero-th argument
* Arguments : int argc, char* argv[]
*******************************************************************/
int Args::ReadProgramPath( int argc, char* argv[])
{
string ProgramPath( argv[0]);
m_ProgramPath = ProgramPath;
return EXIT_SUCCESS;
}
Int2 Main (void)
{
AsnIoPtr aop = NULL;
AsnModulePtr amp;
AsnTypePtr atp_bss, atp_ss, atp_se;
BioseqSet bss;
FILE *fp;
ValNodePtr head, vnp;
Char path [PATH_MAX];
CharPtr progname, str, subfile;
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
UseLocalAsnloadDataAndErrMsg ();
ErrPathReset ();
if (! AllObjLoad ()) {
Message (MSG_FATAL, "AllObjLoad failed");
return 1;
}
if (! SubmitAsnLoad ()) {
Message (MSG_FATAL, "SubmitAsnLoad failed");
return 1;
}
if (! SeqCodeSetLoad ()) {
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 1;
}
if (! GeneticCodeTableLoad ()) {
Message (MSG_FATAL, "GeneticCodeTableLoad failed");
return 1;
}
MemSet ((Pointer) &bss, 0, sizeof (BioseqSet));
amp = AsnAllModPtr ();
if (amp == NULL) {
Message (MSG_FATAL, "Unable to load AsnAllModPtr");
return 1;
}
atp_bss = AsnFind ("Bioseq-set");
if (atp_bss == NULL) {
Message (MSG_FATAL, "Unable to find ASN.1 type Bioseq-set");
return 1;
}
atp_ss = AsnFind ("Bioseq-set.seq-set");
if (atp_ss == NULL) {
Message (MSG_FATAL, "Unable to find ASN.1 type Bioseq-set.seq-set");
return 1;
}
atp_se = AsnFind ("Bioseq-set.seq-set.E");
if (atp_se == NULL) {
Message (MSG_FATAL, "Unable to find ASN.1 type Bioseq-set.seq-set.E");
return 1;
}
ProgramPath (path, sizeof (path));
progname = StringRChr (path, DIRDELIMCHR);
if (progname != NULL) {
progname++;
} else {
progname = "idcleanscan";
}
if (! GetArgs (progname, sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
fp = FileOpen (myargs [o_argOutputFile].strvalue, "a");
if (fp == NULL) {
Message (MSG_FATAL, "FileOpen failed");
return 1;
}
if (StringHasNoText (myargs [p_argInputPath].strvalue)) {
str = myargs [i_argInputFile].strvalue;
if (! StringHasNoText (str)) {
DoReleaseFile (str, myargs [b_argBinaryFile].intvalue, myargs [c_argCompressed].intvalue, fp, aop, NULL);
}
} else {
head = DirCatalog (myargs [p_argInputPath].strvalue);
if (! StringHasNoText (myargs [s_argSubset].strvalue)) {
aop = AsnIoOpen (myargs [s_argSubset].strvalue, /* "wb" */ "w");
AsnOpenStruct (aop, atp_bss, (Pointer) &bss);
AsnOpenStruct (aop, atp_ss, (Pointer) bss.seq_set);
/*
av.intvalue = BioseqseqSet_class_genbank;
AsnWrite (aop, atp_cls, &av);
*/
}
for (vnp = head; vnp != NULL; vnp = vnp->next) {
if (vnp->choice == 0) {
str = (CharPtr) vnp->data.ptrvalue;
if (! StringHasNoText (str)) {
subfile = myargs [x_argFileSelect].strvalue;
if (StringHasNoText (subfile) || StringStr (str, subfile) != NULL) {
#ifdef OS_UNIX
/* printf ("%s\n", str); */
#endif
DoReleaseFile (str, myargs [b_argBinaryFile].intvalue, myargs [c_argCompressed].intvalue, fp, aop, atp_se);
}
}
}
}
if (aop != NULL) {
AsnCloseStruct (aop, atp_ss, (Pointer) bss.seq_set);
AsnCloseStruct (aop, atp_bss, (Pointer) &bss);
AsnIoClose (aop);
}
ValNodeFreeData (head);
}
FileClose (fp);
return 0;
}
/*******************************************************************************************
> BOOL BitmapPreviewData::GenerateHTMLStub(BrowserPreviewOptions BrowserOptions)
Author: Stefan_Stoykov (Xara Group Ltd) <*****@*****.**>
Created: 24/6/97
Inputs: BrowserOptions - the options for generating the html page
Purpose: Generate a html file which includes our bitmap, together with some other optional
stuff. Used for browser preview.
*******************************************************************************************/
BOOL BitmapPreviewData::GenerateHTMLStub(BrowserPreviewOptions BrowserOptions)
{
PORTNOTE("other","Removed _R(IDD_TIMAPOPTIONS) - isn't wanted yet")
#ifndef EXCLUDE_FROM_XARALX
// sanity checks
// check for export options
ERROR3IF(m_pOptions == NULL, "BitmapPreviewData::GenerateHTMLStub - need export options");
if (m_pOptions == NULL) // we need export options
return FALSE;
// get the path for the exported bitmap from the options
PathName TempPath = m_pOptions->GetPathName();
// check for exported bitmap
ERROR3IF((m_pOptions->HasTempFile() == FALSE) || (TempPath.IsValid() == FALSE),
"BitmapPreviewData::GenerateHTMLStub - need exported bitmap");
if ((m_pOptions->HasTempFile() == FALSE) || (TempPath.IsValid() == FALSE))
return FALSE;
// delete the previous temp file, if any
if (m_pTempHTMLPath != NULL)
FileUtil::DeleteFile(m_pTempHTMLPath);
else
m_pTempHTMLPath = new PathName;
// safety check
if (m_pTempHTMLPath == NULL)
return FALSE;
// create a new temp file
if (FileUtil::GetTemporaryPathName( _T("htm"),m_pTempHTMLPath) == FALSE)
{
delete m_pTempHTMLPath;
m_pTempHTMLPath = NULL;
return FALSE;
}
// start creating the html page
// create a disk file
CCDiskFile TempDiskFile(1024, FALSE, TRUE);
// get path name to server, so we can find the logo bitmaps
CString str;
AfxGetModuleShortFileName(AfxGetInstanceHandle(), str);
String_256 strPathName(str.GetBuffer(0));
// create a path name object from the program name
PathName ProgramPath(strPathName);
try
{
// open it for reading
if (!TempDiskFile.open(*m_pTempHTMLPath, ios::out))
return FALSE;
// output header
String_256 s(_R(IDS_HTML_HEAD));
TempDiskFile.write(s);
// set the background attributes
switch (BrowserOptions.m_Background)
{
case BROWSER_BGR_DOC:
{
// set the background from the document page
if (!SetBackgroundFromPage(TempDiskFile, BrowserOptions.m_pSpread))
ERROR3("Setting the html background from the document page failed\n");
}
break;
case BROWSER_BGR_CHECKER:
{
// display the checkered bitmap as background
// get the checkered bitmap name
String_256 Checker(_R(IDS_HTML_CHECKER));
// set it in the path
ProgramPath.SetFileNameAndType(Checker);
// set the checkered bitmap as background image
s.MakeMsg(_R(IDS_CHECK_BACK), (TCHAR *)ProgramPath.GetWebAddress());
TempDiskFile.write(s);
}
break;
case BROWSER_BGR_BITMAP:
{
// set our bitmap as background image
s.MakeMsg(_R(IDS_BITMAPED_BACKGROUND), (TCHAR *)TempPath.GetWebAddress());
TempDiskFile.write(s);
}
break;
case BROWSER_BGR_NONE:
{
String_256 background(_R(IDS_PLAIN_BACKGROUND));
TempDiskFile.write(background);
}
break;
default:
ERROR3("Unknown type of BrowserOptions.m_Background");
break;
} // end of switch(BrowserOptions.m_Background) block
// Get a pointer to the actual bitmap so that we can get some details from it.
// OILBitmap *pOilBitmap = m_pBitmap->ActualBitmap;
// ERROR3IF(pOilBitmap == NULL,"BitmapPreviewData::GenerateBitmapInfoStrings NULL oil bitmap pointer");
// Get the details from the specified bitmap
// BitmapInfo BmInfo;
// pOilBitmap->GetInfo(&BmInfo);
// output our bitmap, but only if it wasn't already set as background
String_256 s2(_R(IDS_PAGE_TITLE));
TempDiskFile.write(s2);
if (BrowserOptions.m_Background != BROWSER_BGR_BITMAP)
{
// output the bitmap
if (m_pOptions->GetFilterType() == MAKE_BITMAP_FILTER)
{
// GIF animation
s.MakeMsg(_R(IDS_DISPLAY_PIC), (const TCHAR *)TempPath.GetFileName());
}
else
{
if( m_pOptions->GetFilterNameStrID() == _R(IDN_FILTERNAME_GIF) ||
m_pOptions->GetFilterNameStrID() == _R(IDS_JPG_EXP_FILTERNAME) ||
m_pOptions->GetFilterNameStrID() == _R(IDT_FILTERNAME_BMP) )
{
s.MakeMsg(_R(IDS_DISPLAY_BMP), (const TCHAR *)TempPath.GetFileName());
}
else
if( m_pOptions->GetFilterNameStrID() == _R(IDS_FILTERNAME_PNG) )
s.MakeMsg(_R(IDS_DISPLAY_PNG), (const TCHAR *)TempPath.GetFileName());
}
TempDiskFile.write(s);
}
else
{
s.MakeMsg(_R(IDS_EMPTY_BOX));
TempDiskFile.write(s);
}
switch (m_pOptions->GetFilterNameStrID())
{
case _R(IDT_FILTERNAME_BMP):
s2.MakeMsg(_R(IDS_BMP_MESSAGE));
s.MakeMsg(_R(IDS_WARNING_BOX), (TCHAR *)s2);
TempDiskFile.write(s);
break;
case _R(IDS_FILTERNAME_PNG):
s2.MakeMsg(_R(IDS_PNG_MESSAGE));
s.MakeMsg(_R(IDS_WARNING_BOX), (TCHAR *)s2);
TempDiskFile.write(s);
break;
} // end of switch(m_pOptions->GetFilterNameStrID())
s.MakeMsg(_R(IDS_DETAILS_BUILD));
TempDiskFile.write(s);
// output the bitmap info, if requested
if (BrowserOptions.m_bInfo != FALSE)
{
String_64 ImageSize;
String_64 FileSize;
BOOL m_bTransparent = FALSE;
INT32 count;
count=0;
// generate the info strings
if (m_pOptions->GetFilterType() == MAKE_BITMAP_FILTER)
{
// This is actually the export animated GIF using the frame gallery system
MakeBitmapExportOptions* pMkBOptions = (MakeBitmapExportOptions*)m_pOptions;
ERROR3IF(!pMkBOptions->IS_KIND_OF(MakeBitmapExportOptions), "pMkBOptions isn't");
PALETTE Palette = PAL_OPTIMISED;
DITHER DitherType;
UINT32 colDepth;
String_64 sPalette;
String_64 Dither;
UINT32 NoOfColours;
NoOfColours=m_pOptions->GetNumColsInPalette();
// Palette = pMkBOptions->GetPalette();
DitherType = pMkBOptions->GetDither();
colDepth = pMkBOptions->GetDepth();
s2.MakeMsg(_R(IDS_ANIMATED_GIF));
if (pMkBOptions->WantTransparent())
{
s2.MakeMsg(_R(IDS_TRANSPARENT),"animated GIF");
}
s.MakeMsg(_R(IDS_TEXTLINE_BR),(const TCHAR*)s2);
TempDiskFile.write(s);
switch (Palette)
{
case PAL_OPTIMISED:
sPalette.MakeMsg(_R(IDS_OPTIMISED_PAL));
break;
case PAL_BROWSER:
case PAL_STANDARD:
sPalette.MakeMsg(_R(IDS_BROWSER_PAL));
break;
case PAL_GLOBALOPTIMISED:
sPalette.MakeMsg(_R(IDS_GLOBAL_OPT));
break;
}
if (colDepth == 8 && (Palette == PAL_STANDARD || Palette == PAL_BROWSER) )
{
NoOfColours = 216;
}
switch (colDepth)
{
case 32:
case 24:
s2.MakeMsg(_R(IDS_TRUECOLOUR),colDepth);
break;
case 8:
{
// Include the transparent colour in the colour depth check
UINT32 RealNumberOfColours = NoOfColours;
if (colDepth <= 8 && pMkBOptions->WantTransparent())
{
UINT32 MaxColours = UINT32(pow(2,colDepth));
RealNumberOfColours++;
if (RealNumberOfColours > MaxColours)
RealNumberOfColours = MaxColours;
}
// We say 8 but we really mean the number of colours deep
// We cannot say 2 colours = 2bpp as we save it as 10 colours due
// to having 1 transparent colour and the usual lets pick 10 as the
// transparent colour. Cannot allow the user to choose 1 as the code
// then outputs 8bpp as GRenderOptPalette::GetOptimisedPalette has the
// test if (ReservedColours < NumColours), which fails.
/* if (RealNumberOfColours <= 2)
s2.MakeMsg(_R(IDS_PALETTEINFO),2,NoOfColours,(const TCHAR*)sPalette);
else */
if (RealNumberOfColours <= 16)
s2.MakeMsg(_R(IDS_PALETTEINFO),4,NoOfColours,(const TCHAR*)sPalette);
else
s2.MakeMsg(_R(IDS_AN_PALINFO),colDepth,NoOfColours,(const TCHAR*)sPalette);
break;
}
case 1:
s2.MakeMsg(_R(IDS_MONO),colDepth);
break;
case 4:
default:
s2.MakeMsg(_R(IDS_PALETTEINFO),colDepth,NoOfColours,(const TCHAR*)sPalette);
break;
}
TempDiskFile.write(s2);
s.MakeMsg(_R(IDS_NODITHER));
switch (DitherType)
{
case XARADITHER_ORDERED:
case XARADITHER_ORDERED_GREY:
Dither.MakeMsg(_R(IDS_DITH_ORDER));
s.MakeMsg(_R(IDS_DITHERING),(const TCHAR*) Dither);
break;
case XARADITHER_ERROR_DIFFUSION:
case XARADITHER_SIMPLE:
Dither.MakeMsg(_R(IDS_DITH_ERROR));
s.MakeMsg(_R(IDS_DITHERING),(const TCHAR*) Dither);
break;
case XARADITHER_NONE:
s.MakeMsg(_R(IDS_NODITHER));
break;
}
TempDiskFile.write(s);
} // if (m_pOptions->GetFilterType() == MAKE_BITMAP_FILTER) block ends
else
{
switch (m_pOptions->GetFilterNameStrID())
{
case _R(IDN_FILTERNAME_GIF):
{
GIFExportOptions* pGIFOptions = (GIFExportOptions*)m_pOptions;
ERROR3IF(!pGIFOptions->IS_KIND_OF(GIFExportOptions), "pGIFOptions isn't");
PALETTE Palette = PAL_OPTIMISED;
DITHER DitherType;
UINT32 colDepth;
String_64 sPalette;
String_64 Dither;
UINT32 NoOfColours;
NoOfColours=m_pOptions->GetNumColsInPalette();
// Palette = pGIFOptions->GetPalette();
DitherType = pGIFOptions->GetDither();
colDepth = pGIFOptions->GetDepth();
if (pGIFOptions->WantTransparent())
count=count+1;
if (pGIFOptions->WantInterlaced())
count=count+2;
s.MakeMsg(_R(IDS_GIF));
s2.MakeMsg(_R(IDS_A), (const TCHAR*)s);
switch (count)
{
case 1:
s2.MakeMsg(_R(IDS_TRANSPARENT),"GIF");
break;
case 2:
s2.MakeMsg(_R(IDS_INTERLACED),"GIF");
break;
case 3:
s2.MakeMsg(_R(IDS_INTER_TRANS),"GIF");
break;
case 0:
break;
}
s.MakeMsg(_R(IDS_TEXTLINE_BR),(const TCHAR*)s2);
TempDiskFile.write(s);
switch (Palette)
{
case PAL_OPTIMISED:
sPalette.MakeMsg(_R(IDS_OPTIMISED_PAL));
break;
case PAL_BROWSER:
case PAL_STANDARD:
sPalette.MakeMsg(_R(IDS_BROWSER_PAL));
break;
case PAL_GLOBALOPTIMISED:
sPalette.MakeMsg(_R(IDS_GLOBAL_OPT));
break;
}
if (colDepth == 8 && (Palette == PAL_STANDARD || Palette == PAL_BROWSER) )
{
NoOfColours = 216;
}
s2.MakeMsg(_R(IDS_PALETTEINFO),colDepth,NoOfColours,(const TCHAR*)sPalette);
if (colDepth == 8)
s2.MakeMsg(_R(IDS_AN_PALINFO),colDepth,NoOfColours,(const TCHAR*)sPalette);
if (colDepth == 1)
s2.MakeMsg(_R(IDS_MONO),colDepth);
if (colDepth > 8)
s2.MakeMsg(_R(IDS_TRUECOLOUR),colDepth);
TempDiskFile.write(s2);
s.MakeMsg(_R(IDS_NODITHER));
switch (DitherType)
{
case XARADITHER_ORDERED:
case XARADITHER_ORDERED_GREY:
Dither.MakeMsg(_R(IDS_DITH_ORDER));
s.MakeMsg(_R(IDS_DITHERING),(const TCHAR*) Dither);
break;
case XARADITHER_ERROR_DIFFUSION:
case XARADITHER_SIMPLE:
Dither.MakeMsg(_R(IDS_DITH_ERROR));
s.MakeMsg(_R(IDS_DITHERING),(const TCHAR*) Dither);
break;
case XARADITHER_NONE:
s.MakeMsg(_R(IDS_NODITHER));
break;
}
TempDiskFile.write(s);
} // end case _R(IDN_FILTERNAME_GIF)
break;
case _R(IDS_JPG_EXP_FILTERNAME):
{
JPEGExportOptions* pJPEGOptions = (JPEGExportOptions *)m_pOptions;
ERROR3IF(!pJPEGOptions->IS_KIND_OF(JPEGExportOptions), "pJPEGOptions isn't");
INT32 Quality = pJPEGOptions->GetQuality(); // Default Quality
BOOL Progressive = pJPEGOptions->DoAsProgressive();
if (Quality > 100)
Quality = 100;
s.MakeMsg(_R(IDS_JPEG));
s2.MakeMsg(_R(IDS_A), (const TCHAR*)s);
if (Progressive)
s2.MakeMsg(_R(IDS_PROGRESSIVE));
s.MakeMsg(_R(IDS_TEXTLINE_BR),(const TCHAR*)s2);
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_JCOMPRESSION),Quality);
TempDiskFile.write(s);
} // end case _R(IDS_JPG_EXP_FILTERNAME)
break;
case _R(IDT_FILTERNAME_BMP):
{
BMPExportOptions* pBMPOptions = (BMPExportOptions*)m_pOptions;
ERROR3IF(!pBMPOptions->IS_KIND_OF(BMPExportOptions), "pBMPOptions isn't");
PALETTE Palette;
DITHER DitherType;
UINT32 colDepth;
String_64 sPalette;
String_64 Dither;
UINT32 NoOfColours;
NoOfColours=m_pOptions->GetNumColsInPalette();
Palette = pBMPOptions->GetPalette();
DitherType = pBMPOptions->GetDither();
colDepth = pBMPOptions->GetDepth();
s.MakeMsg(_R(IDS_BMP));
s2.MakeMsg(_R(IDS_A), (const TCHAR*)s);
s.MakeMsg(_R(IDS_TEXTLINE_BR),(const TCHAR*)s2);
TempDiskFile.write(s);
switch (Palette)
{
case PAL_OPTIMISED:
sPalette.MakeMsg(_R(IDS_OPTIMISED_PAL));
break;
case PAL_BROWSER:
case PAL_STANDARD:
sPalette.MakeMsg(_R(IDS_BROWSER_PAL));
break;
case PAL_GLOBALOPTIMISED:
sPalette.MakeMsg(_R(IDS_GLOBAL_OPT));
break;
}
if (colDepth == 8 && (Palette == PAL_STANDARD || Palette == PAL_BROWSER) )
{
NoOfColours = 216;
}
if (colDepth == 8 && NoOfColours > 256)
NoOfColours = 256;
s2.MakeMsg(_R(IDS_PALETTEINFO),colDepth,NoOfColours,(const TCHAR*)sPalette);
if (colDepth == 8)
s2.MakeMsg(_R(IDS_AN_PALINFO),colDepth,NoOfColours,(const TCHAR*)sPalette);
if (colDepth == 1)
s2.MakeMsg(_R(IDS_MONO),colDepth);
if (colDepth > 8)
s2.MakeMsg(_R(IDS_TRUECOLOUR),colDepth);
TempDiskFile.write(s2);
s.MakeMsg(_R(IDS_NODITHER));
switch (DitherType)
{
case XARADITHER_ORDERED:
case XARADITHER_ORDERED_GREY:
Dither.MakeMsg(_R(IDS_DITH_ORDER));
s.MakeMsg(_R(IDS_DITHERING),(const TCHAR*) Dither);
break;
case XARADITHER_ERROR_DIFFUSION:
case XARADITHER_SIMPLE:
Dither.MakeMsg(_R(IDS_DITH_ERROR));
s.MakeMsg(_R(IDS_DITHERING),(const TCHAR*) Dither);
break;
case XARADITHER_NONE:
s.MakeMsg(_R(IDS_NODITHER));
break;
}
TempDiskFile.write(s);
} // end case _R(IDT_FILTERNAME_BMP)
break;
case _R(IDS_FILTERNAME_PNG):
{
PNGExportOptions* pPNGOptions = (PNGExportOptions*)m_pOptions;
ERROR3IF(!pPNGOptions->IS_KIND_OF(PNGExportOptions), "pPNGOptions isn't");
PALETTE Palette = PAL_OPTIMISED;
DITHER DitherType;
UINT32 colDepth;
String_64 sPalette;
String_64 Dither;
UINT32 NoOfColours;
NoOfColours=m_pOptions->GetNumColsInPalette();
// Palette = pPNGOptions->GetPalette();
DitherType = pPNGOptions->GetDither();
colDepth = pPNGOptions->GetDepth();
if (pPNGOptions->WantTransparent())
count=count+1;
if (pPNGOptions->WantInterlaced())
count=count+2;
s.MakeMsg(_R(IDS_PNG));
s2.MakeMsg(_R(IDS_A), (const TCHAR*)s);
switch (count)
{
case 1:
s2.MakeMsg(_R(IDS_TRANSPARENT),"PNG");
break;
case 2:
s2.MakeMsg(_R(IDS_INTERLACED),"PNG");
break;
case 3:
s2.MakeMsg(_R(IDS_INTER_TRANS),"PNG");
break;
case 0:
break;
}
s.MakeMsg(_R(IDS_TEXTLINE_BR),(const TCHAR*)s2);
TempDiskFile.write(s);
switch (Palette)
{
case PAL_OPTIMISED:
sPalette.MakeMsg(_R(IDS_OPTIMISED_PAL));
break;
case PAL_BROWSER:
case PAL_STANDARD:
sPalette.MakeMsg(_R(IDS_BROWSER_PAL));
break;
case PAL_GLOBALOPTIMISED:
sPalette.MakeMsg(_R(IDS_GLOBAL_OPT));
break;
}
if (colDepth == 8 && (Palette == PAL_STANDARD || Palette == PAL_BROWSER) )
{
NoOfColours = 216;
}
s2.MakeMsg(_R(IDS_PALETTEINFO),colDepth,NoOfColours,(const TCHAR*)sPalette);
if (colDepth == 8)
s2.MakeMsg(_R(IDS_AN_PALINFO),colDepth,NoOfColours,(const TCHAR*)sPalette);
if (colDepth == 1)
s2.MakeMsg(_R(IDS_MONO),colDepth);
if (colDepth > 8)
s2.MakeMsg(_R(IDS_TRUECOLOUR),colDepth);
TempDiskFile.write(s2);
s.MakeMsg(_R(IDS_NODITHER));
switch (DitherType)
{
case XARADITHER_ORDERED:
case XARADITHER_ORDERED_GREY:
Dither.MakeMsg(_R(IDS_DITH_ORDER));
s.MakeMsg(_R(IDS_DITHERING),(const TCHAR*) Dither);
break;
case XARADITHER_ERROR_DIFFUSION:
case XARADITHER_SIMPLE:
Dither.MakeMsg(_R(IDS_DITH_ERROR));
s.MakeMsg(_R(IDS_DITHERING),(const TCHAR*) Dither);
break;
case XARADITHER_NONE:
s.MakeMsg(_R(IDS_NODITHER));
break;
}
TempDiskFile.write(s);
} // end case _R(IDS_FILTERNAME_PNG)
break;
} // end switch (m_pOptions->GetFilterNameStrID())
} // end else block
GenerateBitmapInfoStrings(ImageSize, FileSize);
// output the bitmap info
s.MakeMsg(_R(IDS_HTML_INFO1), (TCHAR *)ImageSize);
TempDiskFile.write(s);
// output the bitmap file size info
s.MakeMsg(_R(IDS_HTML_INFO2), (TCHAR *)FileSize);
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_CLOSE_CENTER));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_TDTR_CLOSE));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_BANNER_BOX));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_SPEED_BUILD));
TempDiskFile.write(s);
// s.MakeMsg(_R(IDS_SPEED_BUILD2));
// TempDiskFile.write(s);
s.MakeMsg(_R(IDS_ES_TR));
TempDiskFile.write(s);
String_64 times;
s.MakeMsg(_R(IDS_TIME_ENTRY),"14.4k");
TempDiskFile.write(s);
CalculateTime(times,14400.0);
TempDiskFile.write(times);
s.MakeMsg(_R(IDS_ES_TR));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_TIME_ENTRY),"28.8k");
TempDiskFile.write(s);
CalculateTime(times,28800.0);
TempDiskFile.write(times);
s.MakeMsg(_R(IDS_ES_TR));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_TIME_ENTRY),"33.6k");
TempDiskFile.write(s);
CalculateTime(times,33600.0);
TempDiskFile.write(times);
s.MakeMsg(_R(IDS_ES_TR));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_TIME_ENTRY),"57.6k");
TempDiskFile.write(s);
CalculateTime(times,57600.0);
TempDiskFile.write(times);
s.MakeMsg(_R(IDS_ES_TR));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_TIME_ENTRY),"64k");
TempDiskFile.write(s);
CalculateTime(times,65536.0);
TempDiskFile.write(times);
s.MakeMsg(_R(IDS_ES_TR));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_TIME_ENTRY),"128k");
TempDiskFile.write(s);
CalculateTime(times,131072.0);
TempDiskFile.write(times);
// s.MakeMsg(_R(IDS_ES_TR));
// TempDiskFile.write(s);
s.MakeMsg(_R(IDS_SPEED_END));
TempDiskFile.write(s);
TRACE( _T("m_FileSize = %d"), m_FileSize);
} // end of if (BrowserOptions.m_bInfo != FALSE)
String_64 webaddy(_R(IDS_HTML_URL_PROGRAM));
//Mark Howitt, 29/10/97. Setup the _R(IDS_HTML_URL_VISITMSG) To be a TCHAR* Also. It likes it that way!
String_64 webvmess(_R(IDS_HTML_URL_VISITMSG));
s.MakeMsg(_R(IDS_LINK_BOX),(TCHAR *)webaddy,(TCHAR *)webvmess);
TempDiskFile.write(s);
//end of my stuff
s.MakeMsg(_R(IDS_END_TABLE));
TempDiskFile.write(s);
s.MakeMsg(_R(IDS_CLOSE_CENTER));
TempDiskFile.write(s);
// output the "Exported from" string
// get the xara logo file name
String_256 Logo(_R(IDS_HTML_XARALOGO));
// set it in the path
ProgramPath.SetFileNameAndType(Logo);
// get the xara link
String_256 URL(_R(IDS_HTML_URL_XARA));
// output the xara link and the xara logo
s.MakeMsg(_R(IDS_HTML_XARA), (TCHAR *)URL, (TCHAR *)ProgramPath.GetWebAddress());
TempDiskFile.write(s);
// Do not display the Xara X logo bottom right...
/*
// get the program logo file name
Logo.Load(_R(IDS_HTML_PROGRAMLOGO));
// set it in the path
ProgramPath.SetFileNameAndType(Logo);
// output the program link
URL.Load(_R(IDS_HTML_URL_PROGRAM));
s.MakeMsg(_R(IDS_HTML_PROGRAM), (TCHAR *)URL, (TCHAR *)ProgramPath.GetWebAddress());
TempDiskFile.write(s);
*/
// output the end of the file
s.Load(_R(IDS_HTML_END));
TempDiskFile.write(s);
// close the file
TempDiskFile.close();
// now export the image map, if the option for that is set
if (BrowserOptions.m_bImagemap != FALSE)
{
// export the image map
ExportImagemap( TempDiskFile,
m_pTempHTMLPath,
m_pOptions->GetSelectionType(),
m_pOptions->GetDPI(),
BrowserOptions.m_ifoImagemapOptions);
}
TCHAR *FileWebAddress = m_pTempHTMLPath->GetWebAddress();
//Graham 17/9/97
ProgramPath.SetFileNameAndType(PRODUCT_WEBLINKEXENAME);
const TCHAR *PathToWebLink = (const TCHAR *)ProgramPath.GetPath();
String_256 CmdLine = PathToWebLink + String_256(" -f ") + FileWebAddress;
//TCHAR *CommandLine = (TCHAR *)CmdLine;
if (!InvokeWeblink(CmdLine))
return FALSE;
} // end of TRY block
catch( CFileException )
{
// any disk problems - come here
// not much we can do really - just close the file and return FALSE
if (TempDiskFile.isOpen())
TempDiskFile.close();
return FALSE;
}
#endif
return TRUE;
}
PCSAN LIBCALL LoadCSAN(CharPtr pcFile)
{
FILE *f;
Char fullpath [PATH_MAX];
CharPtr ptr;
PCSAN pcsanHead = NULL;
PCSAN pcsanTemp = NULL;
Char pcBuf[250];
CharPtr ppcParse[125];
CharPtr pcTemp = NULL;
CharPtr pcTest = NULL;
CharPtr pcSeqPart = NULL;
ValNodePtr pvn = NULL;
long int val = 0;
Int4 i = 0;
Int4 iString = 0;
Int4 iLen =0;
Int4 iWC =0;
Int4 iWL = 0;
Int4 iGi = 0;
if (!pcFile) return(NULL);
ProgramPath (fullpath, sizeof (fullpath) - 1);
ptr = StringRChr (fullpath, DIRDELIMCHR);
if (ptr != NULL) {
*ptr = '\0';
}
/* printf("FULLPATH[%s]\n",IsNullStr(fullpath)); */
FileBuildPath (fullpath, NULL, pcFile);
/* printf("FULLPATH[%s]\n",IsNullStr(fullpath)); */
if ((f = FileOpen (fullpath, "r")) == NULL)
{
if (FindPath ("NCBI", "NCBI", "DATA", fullpath, sizeof (fullpath) - 1))
{
FileBuildPath (fullpath, NULL, pcFile);
f = FileOpen (fullpath, "r");
if (f == NULL)
{
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s] in LoadCSA", IsNullStr(fullpath));
return (NULL);
}
}
else
{
ErrPost(CTX_NCBIOBJ, 1, "FindPath failed in LoadNeighbors");
return (NULL);
}
}
do /* get each line, tokenize into ppcParse */
{
pcBuf[0] = '\0';
pcTest = fgets(pcBuf, (size_t)250, f);
/* printf("[%s]\n",IsNullStr(pcTest)); */
if (pcTest)
{
iLen = StringLen(pcTest);
/* Break into words delimited by whitespace or "|" */
/* gi|123456| */
/* printf("LineLength %d\n",(int) iLen); */
for (i=0; i < 125; i++) ppcParse[i] = NULL;
pcTemp = pcTest;
ppcParse[0] = pcTest;
iWC = 1;
while ((*pcTemp != '\0') && (iWC < 125))
{
if ((*pcTemp == '|') || (*pcTemp == ' ') || (*pcTemp == '\t') || (*pcTemp == '\n'))
{
*pcTemp = '\0'; /* terminate current word */
do {
pcTemp++; /* skip whitespace to next word */
} while ((*pcTemp == '|') || (*pcTemp == ' ') || (*pcTemp == '\t') || (*pcTemp == '\n'));
ppcParse[iWC] = pcTemp; /* start next word */
iWC++;
}
else
pcTemp++;
}
/* DEBUG TEST */
/* for (i=0; i<125; i++)
if (ppcParse[i] != NULL)
{
printf("%ld/%ld [%s]\n",i,iWC, IsNullStr(ppcParse[i]));
} */
/* If ppcParse[0] is "gi" then this is a VALID sequence line and the last
word parsed is the sequence */
if (ppcParse[0][0] != '\0')
{
iWL = StringLen(ppcParse[0]);
if (iWL == 2)
if (((ppcParse[0][0] == 'g') ||
(ppcParse[0][0] == 'G')) &&
((ppcParse[0][1] == 'i') ||
(ppcParse[0][1] == 'I')))
{
/* next word should be GI */
iGi = 0;
if (StrToInt4 (ppcParse[1], &iGi))
{
/* printf("GI is (%ld)\n",iGi); */
if (iGi == 0) goto parserr;
/* find the 2nd last string = sequence */
/* last string is stripped off line terminator, by the way... */
iString=2; /* start after GI */
while (ppcParse[iString+1] != NULL)
{ /* iString is the LAST sting - line terminator */
iString++;
}
pcsanTemp = pcsanHead;
while (pcsanTemp)
{ /* look for existing pcsan */
if (iGi == pcsanTemp->iGi)
{
break;
}
pcsanTemp = pcsanTemp->next;
}
if (!pcsanTemp) /* otherwise add a new one */
{
pcsanTemp = NewCSAN();
pcsanTemp->next = pcsanHead;
pcsanHead = pcsanTemp; /* put at head of list */
pcsanTemp->iGi = iGi;
}
/* Initialize fields */
pcSeqPart = NULL;
pcSeqPart = StringSave(ppcParse[iString-1]);
/* printf("SEQ [%ld]= [%s]\n",(long) iString-1, IsNullStr(pcSeqPart)); */
ValNodeAddStr(&pcsanTemp->pvnSeqAlnPart, 0, pcSeqPart);
} /* if GI */
} /* if line starts with GI */
} /* if line starts with a word */
} /* if pcTest */
} while (pcTest);
printf("REPORT\n");
pcsanTemp = pcsanHead;
while (pcsanTemp)
{
printf("GI = [%ld]\n", (long) pcsanTemp->iGi);
pvn = pcsanTemp->pvnSeqAlnPart;
while (pvn)
{
printf(">%s<\n",(char *) IsNullStr(pvn->data.ptrvalue));
pvn = pvn->next;
}
pcsanTemp = pcsanTemp->next;
}
FileClose(f);
return pcsanHead;
parserr:
FileClose(f);
ErrPostEx(SEV_FATAL,0,0, "Error in input format \n");
FreeCSAN(pcsanHead);
return NULL;
}
Int2 Main (void)
{
Int2 db = -1;
Int2 i;
Boolean makeCDS;
Char path [PATH_MAX];
CharPtr progname;
FILE *fp;
Int2 rsult;
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
UseLocalAsnloadDataAndErrMsg ();
ErrPathReset ();
if (! AllObjLoad ()) {
Message (MSG_FATAL, "AllObjLoad failed");
return 1;
}
if (! SeqCodeSetLoad ()) {
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 1;
}
if (! GeneticCodeTableLoad ()) {
Message (MSG_FATAL, "GeneticCodeTableLoad failed");
return 1;
}
ProgramPath (path, sizeof (path));
progname = StringRChr (path, DIRDELIMCHR);
if (progname != NULL) {
progname++;
} else {
progname = "fetchent";
}
/* GetArgs is a portable way of obtaining arguments */
if (! GetArgs (progname, NUMARG, myargs)) {
Message (MSG_FATAL, "GetArgs failed");
return 1;
}
/* Map database argument to TYP_XX value */
for (i = 0; databases [i] != NULL; i++) {
if (StringICmp (myargs [0].strvalue, databases [i]) == 0) {
db = i;
}
}
/* Convert M, P, or N alternative database symbols to proper code */
if (db >= 3 && db <= 5) {
db -= 3;
}
if (db < 0 || db > 2) {
Message (MSG_FATAL, "Database must be ML, AA, or NT");
return 1;
}
if (! EntrezInit (progname, FALSE, NULL)) {
Message (MSG_FATAL, "EntrezInit failed");
return 1;
}
fp = FileOpen (myargs [2].strvalue, "w");
if (fp == NULL) {
Message (MSG_FATAL, "FileOpen failed");
return 1;
}
makeCDS = (Boolean) myargs [3].intvalue;
if (makeCDS && db != TYP_NT) {
Message (MSG_ERROR, "Coding region extraction inappropriate");
makeCDS = FALSE;
}
rsult = ProcessQuery (db, myargs [1].strvalue, makeCDS, fp);
FileClose (fp);
EntrezFini ();
return rsult;
}
/*****************************************************************************
*
* PrintTemplateSetPtr PrintTemplateSetLoad()
* loads PrintTemplates
* If path== NULL, looks for "prt.prt" in the "data" directory
*
*****************************************************************************/
static Boolean PrintTemplateSetLoadInt ( CharPtr path, Boolean verbose )
{
AsnIoPtr aip;
FILE *f;
Boolean retval;
Char filename [80];
Char fullpath [PATH_MAX];
CharPtr ptr;
ErrSev lastLevel;
aip = NULL;
if (path != NULL && *path != '\0' && StringRChr (path, DIRDELIMCHR) != NULL) {
StringNCpy (fullpath, path, sizeof (fullpath) - 1);
if ((aip = AsnIoOpen (fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
} else {
if (path != NULL && *path != '\0') {
StringNCpy (filename, path, sizeof (filename) - 1);
} else {
StringCpy (filename, "prt.prt");
}
ProgramPath (fullpath, sizeof (fullpath) - 1);
ptr = StringRChr (fullpath, DIRDELIMCHR);
if (ptr != NULL) {
*ptr = '\0';
}
FileBuildPath (fullpath, NULL, filename);
/* silence SEV_INFO errors from FileOpen() */
if ((lastLevel = ErrGetMessageLevel()) < SEV_WARNING)
ErrSetMessageLevel (SEV_WARNING);
if ((f = FileOpen (fullpath, "r")) == NULL) {
ErrSetMessageLevel (lastLevel);
if (FindPath ("NCBI", "NCBI", "DATA", fullpath, sizeof (fullpath) - 1)) {
FileBuildPath (fullpath, NULL, filename);
if ((aip = AsnIoOpen (fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
} else {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "FindPath failed in PrintTemplateSetLoad - ncbi configuration file missing or incorrect");
}
return FALSE;
}
} else {
ErrSetMessageLevel (lastLevel);
FileClose (f);
if ((aip = AsnIoOpen(fullpath, "r")) == NULL) {
if (verbose) {
ErrPost(CTX_NCBIOBJ, 1, "Couldn't open [%s]", fullpath);
}
return FALSE;
}
}
}
retval = PrintTemplateSetAsnRead(aip);
AsnIoClose(aip);
return retval;
}
