void AaptDir::print() const
{
const size_t ND=getDirs().size();
size_t i;
for (i=0; i<ND; i++) {
getDirs().valueAt(i)->print();
}
const size_t NF=getFiles().size();
for (i=0; i<NF; i++) {
getFiles().valueAt(i)->print();
}
}
static bool maybeAddDirectory(const std::string& newPath, Array<Directory>& directoryArray, bool recurse = true) {
if (fileExists(newPath)) {
Directory& d = directoryArray.next();
d.path = newPath;
getFiles(pathConcat(newPath, "*"), d.contents);
Array<std::string> dirs;
getDirs(pathConcat(newPath, "*"), dirs);
d.contents.append(dirs);
if (recurse) {
// Look for subdirectories
static const std::string subdirs[] =
{"font", "gui", "SuperShader", "cubemap", "icon", "material", "image", "md2", "md3", "ifs", "3ds", "sky", ""};
for (int j = 0; j < dirs.size(); ++j) {
for (int i = 0; ! subdirs[i].empty(); ++i) {
if (dirs[j] == subdirs[i]) {
maybeAddDirectory(pathConcat(newPath, dirs[j]), directoryArray, false);
}
}
}
}
return true;
} else {
return false;
}
}
void FileUtils::getDirs(const std::string& dirPath, std::vector<std::string>& dirs, bool includeChild)const
{
std::string finallyPath = dirPath;
if (*(finallyPath.end() - 1) != '/' && *(finallyPath.end() - 1) != '\\')
{
finallyPath.append("/");
}
DIR* dir = opendir(finallyPath.c_str());
if (!dir) return;
dirent* entry = readdir(dir);
while (entry)
{
if (strcmp(entry->d_name, ".") == 0 || strcmp(entry->d_name, "..") == 0)
{
entry = readdir(dir);
continue;
}
if (entry->d_type == DT_DIR)
{
dirs.push_back(finallyPath+entry->d_name);
if (includeChild)
{
getDirs(finallyPath + entry->d_name, dirs, includeChild);
}
}
entry = readdir(dir);
}
closedir(dir);
}
struct wormFeature *wormGenesInRange(char *chromId, int start, int end)
/* Get names of all genes that overlap the range. */
{
/* This routine looks through the .PGO files made by makePgo
*/
getDirs();
return wormSomeGenesInRange(chromId, start, end, sangerDir);
}
FILE *wormOpenGoodAli()
/* Opens good alignment file and reads signature.
* (You can then cdaLoadOne() it.) */
{
char fileName[512];
getDirs();
sprintf(fileName, "%sgood.ali", cdnaDir);
return cdaOpenVerify(fileName);
}
struct wormFeature *wormCosmidsInRange(char *chromId, int start, int end)
/* Get names of all genes that overlap the range. */
{
/* This routine looks through the .COO files made by makePgo
*/
getDirs();
return scanChromOffsetFile(featDir, ".coo", pgoSig, 2*sizeof(int)+1,
chromId, start, end, 1);
}
struct wormFeature *wormCdnasInRange(char *chromId, int start, int end)
/* Get all cDNAs that overlap the range. freeDnaSeqList the returned
* list when you are through with it. */
{
/* This routine looks through the .CDO files made by cdnaOff
*/
getDirs();
return scanChromOffsetFile(cdnaDir, ".cdo", cdoSig, 2*sizeof(int)+1,
chromId, start, end, 0);
}
boolean wormSearchAllCdna(struct wormCdnaIterator **retSi)
/* Set up to search entire database or worm cDNA */
{
char buf[512];
struct wormCdnaIterator *it;
it = needMem(sizeof(*it));
getDirs();
sprintf(buf, "%s%s", cdnaDir, "allcdna.fa");
it->faFile = mustOpen(buf, "rb");
*retSi = it;
return TRUE;
}
static void wormCdnaCache()
/* Set up to read cDNAs */
{
getDirs();
if (cdnaSnof == NULL)
{
char buf[512];
sprintf(buf, "%s%s", cdnaDir, "allcdna");
cdnaSnof = snofMustOpen(buf);
sprintf(buf, "%s%s", cdnaDir, "allcdna.fa");
cdnaFa = mustOpen(buf, "rb");
}
}
/*
* Steps recursively through a directory and collects all music files in a list
* curdir: current directory path
* files: the list to store filenames in
* returns the LAST entry of the list. So the next item is the first in the list
*/
mptitle *recurse( char *curdir, mptitle *files ) {
char dirbuff[2*MAXPATHLEN];
struct dirent **entry;
int num, i;
if( '/' == curdir[strlen( curdir )-1] ) {
curdir[strlen( curdir )-1]=0;
}
addMessage( 3, "Checking %s", curdir );
/* get all music files */
num = getMusic( curdir, &entry );
if( num < 0 ) {
addMessage( 0, "getMusic failed in %s", curdir );
return files;
}
for( i=0; i<num; i++ ) {
activity( "Scanning" );
sprintf( dirbuff, "%s/%s", curdir, entry[i]->d_name );
files=insertTitle( files, dirbuff );
free( entry[i] );
}
free( entry );
/* step down subdirectories */
num=getDirs( curdir, &entry );
if( num < 0 ) {
addMessage( 0, "getDirs failed on %s", curdir );
return files;
}
for( i=0; i<num; i++ ) {
sprintf( dirbuff, "%s/%s", curdir, entry[i]->d_name );
files=recurse( dirbuff, files );
free( entry[i] );
}
free( entry );
return files;
}
static void wormCacheSomeGdf(struct wormGdfCache *cache)
/* Cache one gene prediction set. */
{
if (cache->snof == NULL)
{
char fileName[512];
char *dir;
bits32 sig;
getDirs();
dir = *(cache->pDir);
sprintf(fileName, "%sgenes", dir);
cache->snof = snofMustOpen(fileName);
sprintf(fileName, "%sgenes.gdf", dir);
cache->file = mustOpen(fileName, "rb");
mustReadOne(cache->file, sig);
if (sig != glSig)
errAbort("%s is not a good file", fileName);
}
}
int DirectoryDAO::addDirectory(const QString& newDir) {
// Do nothing if the dir to add is a child of a directory that is already in
// the db.
ScopedTransaction transaction(m_database);
QStringList dirs = getDirs();
QString childDir;
QString parentDir;
foreach (const QString& dir, dirs) {
if (isChildDir(newDir, dir)) {
childDir = dir;
}
if (isChildDir(dir, newDir)) {
parentDir = dir;
}
}
if (!childDir.isEmpty()) {
qDebug() << "return already watching";
return ALREADY_WATCHING;
}
if (!parentDir.isEmpty()) {
// removeing the old directory won't harm because we are adding the
// parent later in this function
removeDirectory(parentDir);
}
QSqlQuery query(m_database);
query.prepare("INSERT INTO " % DIRECTORYDAO_TABLE %
" (" % DIRECTORYDAO_DIR % ") VALUES (:dir)");
query.bindValue(":dir", newDir);
if (!query.exec()) {
LOG_FAILED_QUERY(query) << "Adding new dir (" % newDir % ") failed.";
return SQL_ERROR;
}
transaction.commit();
return ALL_FINE;
}
static void makeChromFileName(char *chromId, char *buf)
{
getDirs();
sprintf(buf, "%s%s.nt4", nt4Dir, chromId);
}
/*!\brief Gets all the file names of every .png image found in the given directory. Outputs a series of power 2 sized textures which contain all
* the individual images as one sheet (or several depending on how many images you have and what your max sized square is). It also outputs
* a single textfile which lists which texture pack contains which images. They are listed using their file names minus the png extension.
* If a series of images are found, they are listed as an animation with a single reference name. So if you have cat_1.png cat_2.png cat_3.png
* you will get animation 'cat' with 3 frames.
*/
int main(int argc, const char *argv[], const char **envp ){
char const *refstrSourceDir = DEFAULT_SOURCE;
char const *refstrOutputFile = DEFAULT_OUTPUT;
char const *refstrJavapak = NULL;
char const *refstrManClass = NULL;
unsigned int maxSquare = 1024;
eOutputFormat format = eFormatDefault;
char ignoreOutputFiles[256]; memset(ignoreOutputFiles, 0, sizeof(ignoreOutputFiles));
short usePadding=FALSE;
bool enforcePow2=FALSE;
printf("---Texture Cram---\n");
/** parse command arguments */
while(argc > 0){
if(argc > 1 && strncmp(argv[argc-2], SWITCH_DIR, 2)==0 ){
refstrSourceDir = argv[argc-1];
printf("Source directory is %s\n", refstrSourceDir);
--argc;
}else if(argc > 1 && strncmp(argv[argc-2], SWITCH_OUTPUT, 2)==0 ){
refstrOutputFile = argv[argc-1];
printf("Output path is %s\n", refstrOutputFile);
--argc;
}else if(argc > 1 && strncmp(argv[argc-2], SWITCH_MAXSQUARE, 2)==0 ){
maxSquare = atoi(argv[argc-1]);
--argc;
}else if(argc > 1 && strncmp(argv[argc-2], SWITCH_MAN_FORMAT, 2)==0 ){
if( strncmp(argv[argc-1], MAN_FORMAT_C, strlen(MAN_FORMAT_C) ) == 0 ){
format = eFormatC;
printf("Manifest is C\n");
}else if( strncmp(argv[argc-1], MAN_FORMAT_JAVA, strlen(MAN_FORMAT_JAVA) ) == 0 ){
format = eFormatJava;
printf("Manifest is java\n");
}else{
printf("Manifest is default\n");
}
//- todo others
--argc;
}else if(argc > 1 && strncmp(argv[argc-2], SWITCH_JAVAPAK, 5)==0 ){
refstrJavapak = argv[argc-1];
printf("Java pack is: %s\n", refstrJavapak);
--argc;
}else if(argc > 1 && strncmp(argv[argc-2], SWITCH_CLASS, 5)==0 ){
refstrManClass = argv[argc-1];
printf("parent class is: %s\n", refstrManClass);
--argc;
}else if(argc > 1 && strncmp(argv[argc-2], SWITCH_PAD, 4)==0 ){
usePadding=TRUE;
printf("Padding used\n");
--argc;
}else if(strncmp(argv[argc-1], SWITCH_NEARPOW2, 2)==0){
enforcePow2 = TRUE;
}
--argc;
}
printf("The max size is %i\n", maxSquare);
char *strBaseOut=NULL;
getBaseDir(&strBaseOut, refstrOutputFile);
char *strBaseName=NULL;
getOutputNameFromFullPath(&strBaseName, refstrOutputFile);
char **subDirs = calloc(2, sizeof(char*));
size_t numDirs = 1;
copyString(&subDirs[0], refstrSourceDir);
subDirs[1] = NULL;
char buffCurOut[256];
size_t iDir;
for(iDir=0; iDir < numDirs; ++iDir){
sTex **dynarrTextures = NULL;
sSheetList sheets; memset(&sheets, 0, sizeof(sheets));
sFileList files; memset(&files, 0, sizeof(files));
sStillList stills; memset(&stills, 0, sizeof(stills));
sSeqList seqs; memset(&seqs, 0, sizeof(seqs));
sFontList fonts; memset(&fonts, 0, sizeof(fonts));
sManifest theMan; memset(&theMan, 0, sizeof(theMan));
if(getFiles(subDirs[iDir], &files, ignoreOutputFiles, SEARCH_PATTERN) != NOPROB)
continue;
if(strBaseName == NULL)
getOutputNameFromFullPath(&strBaseName, subDirs[iDir]);
snprintf(ignoreOutputFiles, 256, "%s*", strBaseName);
if(strBaseOut != NULL)
snprintf(buffCurOut, 256, "%s%s", strBaseOut, strBaseName);
else
strncpy(buffCurOut, strBaseName, 256);
if(files.num > 0){
if(genTextures(subDirs[iDir], &files, &dynarrTextures) != NOPROB)
goto LOOP_PROB;
}
if(dynarrTextures != NULL){ /** we only need to sort sequences and stills */
if(sortTextures(dynarrTextures, &seqs, &stills) != NOPROB)
goto LOOP_PROB;
}
{ /** fonts */
sTex **dynarrFntTexs =NULL;
sFontInfo **dynarrFntIfo = genFontInfos(subDirs[iDir], ignoreOutputFiles);
if(dynarrFntIfo != NULL && genTexFromFonts(dynarrFntIfo, &dynarrFntTexs, &fonts) != NOPROB)
goto LOOP_PROB;
unsigned int startIdx;
if(dynarrTextures == NULL){
startIdx = 0;
}else{
for(startIdx=0; dynarrTextures[startIdx] != NULL; ++startIdx)
;
}
appendTexArr(&dynarrTextures, dynarrFntTexs);
genFontFromInfo((const sFontInfo **)dynarrFntIfo, &fonts, startIdx);
cleanupFontInfos(&dynarrFntIfo);
}
if(dynarrTextures == NULL){
DBUG_WARN("No textures found");
goto LOOP_PROB;
}
if(arrangeTextures(dynarrTextures, &seqs, &stills, &fonts, &sheets, maxSquare) != NOPROB)
goto LOOP_PROB;
if(genMan(
strBaseName,
&seqs,
&stills,
&fonts,
&sheets,
(const sTex **)dynarrTextures,
&theMan
) != NOPROB)
goto LOOP_PROB;
switch(format){
case eFormatDefault:
if(writeManifestInTxt(buffCurOut, &theMan, (const sTex **)dynarrTextures) != NOPROB)
goto LOOP_PROB;
break;
case eFormatC:
if(writeManifestInC(buffCurOut, &theMan, (const sTex **)dynarrTextures) != NOPROB)
goto LOOP_PROB;
break;
case eFormatJava:
if(writeManifestInJava(buffCurOut, refstrJavapak, refstrManClass, &theMan, (const sTex **)dynarrTextures)!=NOPROB)
goto LOOP_PROB;
break;
default:
break;
}
if(writeSheets(strBaseOut, strBaseName, dynarrTextures, &sheets) != NOPROB)
goto LOOP_PROB;
{
char **moreDirs = NULL;
getDirs(subDirs[iDir], &moreDirs);
if(moreDirs != NULL){
size_t iMore;
for(iMore = 0; moreDirs[iMore] != NULL; ++iMore){
++numDirs;
subDirs = realloc(subDirs, (numDirs + 1) * sizeof(char*));
snprintf(buffCurOut, 245, "%s/%s", subDirs[iDir], moreDirs[iMore]);
SAFE_DELETE(moreDirs[iMore]);
copyString(&subDirs[ numDirs - 1], buffCurOut);
subDirs[numDirs] = NULL;
}
}
SAFE_DELETE(moreDirs);
}
LOOP_PROB:
cleanupFileList(&files);
cleanupTextures(&dynarrTextures);
cleanupSheetList(&sheets);
cleanupStillList(&stills);
cleanupSeqList(&seqs);
cleanupManifest(&theMan);
SAFE_DELETE(subDirs[iDir]);
SAFE_DELETE(strBaseName);
}
SAFE_DELETE(strBaseName);
SAFE_DELETE(strBaseOut);
SAFE_DELETE(subDirs);
LOG("Finished!\n");
return 0;
}
char *wormFeaturesDir()
/* Return the features directory. (Includes trailing slash.) */
{
getDirs();
return featDir;
}
boolean wormGeneRange(char *name, char **retChrom, char *retStrand, int *retStart, int *retEnd)
/* Return chromosome position of a chrom range, gene, ORF, cosmid, or nameless cluster. */
{
static struct snof *c2gSnof = NULL, *c2cSnof = NULL;
static FILE *c2gFile = NULL, *c2cFile = NULL;
long offset;
char fileName[512];
struct slName *syn = NULL;
boolean ok;
if (wormIsChromRange(name))
{
*retStrand = '.';
return wormParseChromRange(name, retChrom, retStart, retEnd);
}
getDirs();
/* Translate biologist type name to cosmid.N name */
if (wormIsGeneName(name))
{
syn = wormGeneToOrfNames(name);
if (syn != NULL)
{
name = syn->name;
}
}
if (wormFixupOrfName(name)) /* See if ORF, and if so make nice. */
{
if (c2gSnof == NULL)
{
sprintf(fileName, "%sc2g", featDir);
c2gSnof = snofMustOpen(fileName);
sprintf(fileName, "%sc2g", featDir);
c2gFile = mustOpen(fileName, "rb");
}
ok = findAltSpliceRange(name, c2gSnof, c2gFile, retChrom, retStart, retEnd, retStrand);
}
else /* Lets say it's a cosmid. */
{
char lineBuf[128];
char *words[3];
int wordCount;
touppers(name);
if (c2cSnof == NULL)
{
sprintf(fileName, "%sc2c", featDir);
c2cSnof = snofMustOpen(fileName);
sprintf(fileName, "%sc2c", featDir);
c2cFile = mustOpen(fileName, "rb");
}
if (!snofFindOffset(c2cSnof, name, &offset) )
return FALSE;
fseek(c2cFile, offset, SEEK_SET);
mustGetLine(c2cFile, lineBuf, sizeof(lineBuf));
wordCount = chopLine(lineBuf, words);
assert(wordCount == 3);
assert(strcmp(words[2], name) == 0);
assert(wormIsChromRange(words[0]));
*retStrand = words[1][0];
ok = wormParseChromRange(words[0], retChrom, retStart, retEnd);
}
slFreeList(&syn);
return ok;
}
char *wormGenieDir()
/* Return directory with Genie specific gene predictions. */
{
getDirs();
return genieDir;
}
char *wormSangerDir()
/* Return directory with Sanger specific gene predictions. */
{
getDirs();
return sangerDir;
}
char *wormCdnaDir()
/* Return directory with cDNA data. */
{
getDirs();
return cdnaDir;
}
char *wormXenoDir()
/* Return directory with cross-species alignments. */
{
getDirs();
return xenoDir;
}
char *wormChromDir()
/* Return the directory with the chromosomes. */
{
getDirs();
return nt4Dir;
}
/*
* Steps recursively through a directory and collects all music files in a list
* curdir: current directory path
* files: the list to store filenames in
*/
struct entry_t *recurse( char *curdir, struct entry_t *files ) {
struct entry_t *buff=NULL;
char dirbuff[MAXPATHLEN];
DIR *directory;
FILE *file;
struct dirent **entry;
int num, i;
char *pos;
if( _ftverbosity > 2 ) {
printf("Checking %s\n", curdir );
}
// get all music files according to the blacklist
num = getMusic( curdir, &entry );
if( num < 0 ) {
fail( "getMusic", curdir, errno );
}
for( i=0; i<num; i++ ) {
activity("Scanning");
strncpy( dirbuff, curdir, MAXPATHLEN );
if( '/' != dirbuff[strlen(dirbuff)] ) {
strncat( dirbuff, "/", MAXPATHLEN );
}
strncat( dirbuff, entry[i]->d_name, MAXPATHLEN );
if( isValid(dirbuff) ) {
int alen;
file=fopen( dirbuff, "r");
if( NULL == file ) fail("Couldn't open file ", dirbuff, errno);
if( -1 == fseek( file, 0L, SEEK_END ) ) fail( "fseek() failed on ", dirbuff, errno );
buff=(struct entry_t *)calloc(1, sizeof(struct entry_t));
if(buff == NULL) fail("Out of memory!", "", errno);
strncpy( buff->name, entry[i]->d_name, MAXPATHLEN );
alen=genPathName( buff->display, dirbuff, MAXPATHLEN );
// strncpy( buff->title, entry[i]->d_name, MAXPATHLEN );
strncpy( buff->path, curdir, MAXPATHLEN );
strncpy( buff->artist, buff->display, alen );
buff->artist[alen+1]=0;
buff->prev=files;
buff->next=NULL;
if(files != NULL)files->next=buff;
buff->size=ftell( file )/1024;
files=buff;
fclose(file);
}
free(entry[i]);
}
free(entry);
num=getDirs( curdir, &entry );
if( num < 0 ) {
fail( "getDirs", curdir, errno );
}
for( i=0; i<num; i++ ) {
// activity("Scanning");
sprintf( dirbuff, "%s/%s", curdir, entry[i]->d_name );
files=recurse( dirbuff, files );
free(entry[i]);
}
free(entry);
return files;
}
