LytSeqInfo* AceParser::addSeq(char* s, LytCtgData* ctg) {
LytSeqInfo* seq;
if (!startsWith(s, "AF ", 3))
return NULL;
s+=3;
char* p=strchrs(s," \t");
if (p==NULL) return NULL;
p++;
char c;
int offs;
if (sscanf(p,"%c %d", &c, &offs)!=2) return NULL;
p--;
*p='\0';
if ((seq=seqinfo.Find(s))!=NULL) {
GMessage("Sequence '%s' already found for contig '%s (%d nt)'\n"
" so it cannot be added for contig '%s (%d)'\n",
s, seq->contig->name, seq->contig->len,
ctg->name, ctg->len);
return NULL;
}
seq = new LytSeqInfo(s, ctg, offs, (c=='C') ? 1 : 0);
seqinfo.shkAdd(seq->name, seq);
ctg->seqs.Add(seq);
return seq;
}
char* LytCtgData::readName(char* s, GHash<int>& names) {
char* p=strchrs(s, " \t");
if (p!=NULL) {
char* tmp;
char* tmp2;
GMALLOC(tmp, (p-s+30)*sizeof(char));
strncpy(tmp, s,p-s);
tmp[p-s]='\0';
GMALLOC(tmp2, (p-s+30)*sizeof(char));
strcpy(tmp2, tmp);
//make it unique (by simple versioning)
int v=0;
while (names.hasKey(tmp2)) {
v++;
sprintf(tmp2, "%s.%d", tmp, v);
}
name=Gstrdup(tmp2);
GFREE(tmp);
GFREE(tmp2);
names.shkAdd(name, new int(1));
p++;
}
else {
GMessage("LytCtgData::readName: Cannot find the token delimiter in:\n%s\n", s);
}
return p;
}
int
url_check_word (const char *word)
{
laststart = lastend = lasttype = 0;
if (do_an_re (word, &laststart, &lastend, &lasttype))
{
switch (lasttype)
{
char *str;
case WORD_NICK:
if (strchrs (word[laststart], NICKPRE))
laststart++;
str = g_strndup (&word[laststart], lastend - laststart);
if (!userlist_find (current_sess, str))
lasttype = 0;
g_free (str);
return lasttype;
case WORD_EMAIL:
if (!isalnum (word[laststart]))
laststart++;
/* Fall through */
case WORD_URL:
case WORD_HOST:
case WORD_HOST6:
case WORD_CHANNEL:
case WORD_PATH:
return lasttype;
default:
return 0; /* Should not occur */
}
}
else
return 0;
}
void
wrapText( const char* const s, const int x, const int y, const int w,
const int h, const int fc, const int bc )
{
int nCharsPerLine = w/8;
int yPos = y;
// debug( "width: [%d] nCharsPerLine: [%d]", w, nCharsPerLine );
// debug( "s: [%s]", s );
int nCharsToPrint = 0;
char szLineToPrint[ 132 ];
char* szLine = (char*)s;
char* szFollow = szLine;
char* space;
for ( /* ALL THE TEXT */ ;; )
{
while ( *szLine == ' ' )
++szLine;
for ( /* EACH LINE */ ;; )
{
space = strchrs( szFollow, " ." );
if ( space && *space == '.' )
++space;
if ( !space || ( space - szLine > nCharsPerLine ) )
break;
nCharsToPrint = space - szLine;
szFollow = space+1;
if ( *space == '' )
break;
}
if ( !*szLine )
break;
assert( nCharsToPrint < sizeof( szLineToPrint ) );
strncpy( szLineToPrint, szLine, nCharsToPrint );
szLineToPrint[ nCharsToPrint ] = '\0';
// puts( szLineToPrint );
gfx_8x16_text( szLineToPrint, x, yPos, fc, bc );
yPos += 16;
szLine += nCharsToPrint;
if ( *(szFollow-1) == '' )
++szLine;
}
}
/* This function returns a pointer to the first token of the given string,
* seperated by the delimiter. The function does not alter the string. */
char *strntok(char *string, char delimiter, int length)
{
int i, ret, lastCharDelimiter = 0;
for (i = 0; i < length; i++) {
ret = strchrs(delimiter, string + i);
/* If the current character is a delimiter, set the corresponding flag */
if (ret)
lastCharDelimiter = 1;
/* If the current character isn't a delimiter, but the last was, return the pointer.*/
if (!ret && lastCharDelimiter)
return string + i;
}
return NULL;
}
int GFastaIndex::loadIndex(const char* finame) { //load record info from existing fasta index
if (finame==NULL) finame=fai_name;
if (finame!=fai_name) {
fai_name=Gstrdup(finame);
}
if (fai_name==NULL) GError("Error: GFastaIndex::loadIndex() called with no file name!\n");
records.Clear();
haveFai=false;
FILE* fi=fopen(fai_name,"rb");
if (fi==NULL) {
GMessage("Warning: cannot open fasta index file: %s!\n",fai_name);
return 0;
}
GLineReader fl(fi);
char* s=NULL;
while ((s=fl.nextLine())!=NULL) {
if (*s=='#') continue;
char* p=strchrs(s,"\t ");
if (p==NULL) GError(ERR_FAIDXLINE,s);
*p=0; //s now holds the genomic sequence name
p++;
uint len=0;
int line_len=0, line_blen=0;
#ifdef __WIN32__
long offset=-1;
sscanf(p, "%d%ld%d%d", &len, &offset, &line_len, &line_blen);
#else
long long offset=-1;
sscanf(p, "%d%lld%d%d", &len, &offset, &line_len, &line_blen);
#endif
if (len==0 || line_len==0 || line_blen==0 || line_blen<line_len)
GError(ERR_FAIDXLINE,p);
addRecord(s,len,offset,line_len, line_blen);
}
fclose(fi);
haveFai=(records.Count()>0);
return records.Count();
}
bool AceParser::loadContig(int ctgidx, fnLytSeq* seqfn, bool re_pos) {
bool forgetCtg = false;
if (ctgidx>=contigs.Count())
GError("LayoutParser: invalid contig index '%d'\n", ctgidx);
LytCtgData* ctgdata=contigs[ctgidx];
if (re_pos && currentContig!=NULL) { //free previously loaded contig data
currentContig->seqs.Clear(); // unless it was a parse() call
seqinfo.Clear();
}
currentContig=ctgdata;
int ctg_numSeqs=ctgdata->numseqs;
if (re_pos) {
seek(ctgdata->fpos); //position right where the contig definition starts
char *r = linebuf->getLine(f,f_pos);
if (r==NULL) return false;
}
if (seqfn!=NULL) { //process the contig sequence!
char* ctgseq=readSeq();
forgetCtg=(*seqfn)(numContigs, ctgdata, NULL, ctgseq);
GFREE(ctgseq); //obviously the caller should have made a copy
}
//now look for all the component sequences
if (fskipTo("AF ")<0) {
GMessage("AceParser: error finding sequence offsets (AF)"
" for contig '%s' (%d)\n", ctgdata->name, ctgdata->len);
return false;
}
int numseqs=0;
while (startsWith(linebuf->chars(), "AF ",3)) {
if (addSeq(linebuf->chars(), ctgdata)==NULL) {
GMessage("AceParser: error parsing AF entry:\n%s\n",linebuf->chars());
return false;
}
numseqs++;
//read next line:
linebuf->getLine(f,f_pos);
}
if (numseqs!=ctg_numSeqs) {
GMessage("Invalid number of AF entries found (%d) for contig '%s' "
"(length %d, numseqs %d)\n", numseqs,
ctgdata->name, ctgdata->len, ctg_numSeqs);
return false;
}
//now read each sequence entry
off_t seqpos=fskipTo("RD ");
numseqs=0; //count again, now the RD entries
if (seqpos<0) {
GMessage("AceParser: error locating first RD entry for contig '%s'\n",
ctgdata->name);
return false;
}
//int numseqs=0;
//reading the actual component sequence details
while (startsWith(linebuf->chars(), "RD ",3)) {
char* s=linebuf->chars()+3;
char* p=strchrs(s, " \t");
LytSeqInfo* seq;
if (p==NULL) {
GMessage("AceParser: Error parsing RD header line:\n%s\n", linebuf->chars());
return false;
}
*p='\0';
if ((seq=seqinfo.Find(s))==NULL) {
GMessage("AceParser: unknown RD encountered: '%s'\n", s);
return false;
}
p++; //now p is in linebuf after the RD name
seq->fpos=seqpos;
int len;
if (sscanf(p, "%d", &len)!=1) {
GMessage("AceParser: cannot parse RD length for '%s'\n", s);
return false;
}
seq->setLength(len);
//read the sequence data here if a callback fn was given:
char* sseq=NULL;
if (seqfn!=NULL)
sseq=readSeq(seq); //read full sequence here
if (fskipTo("QA ")<0) {
GMessage("AceParser: Error finding QA entry for read %s! (fpos=%llu)\n", seq->name, (unsigned long long)f_pos);
return false;
}
//parse QA entry:
int tmpa, tmpb;
if (sscanf(linebuf->chars()+3, "%d %d %d %d", &tmpa, &tmpb, &seq->left,&seq->right)!=4 ||
seq->left<=0 || seq->right<=0) {
GMessage("AceParser: Error parsing QA entry.\n");
return false;
}
/*
if (fskipTo("DS")<0) {
GMessage("AceParser: Error closing RD entry ('DS' not found).\n");
return false;
}
*/
seqpos=getFilePos()+1;
bool forgetSeq=false;
if (seqfn!=NULL) {
forgetSeq=(*seqfn)(numContigs, ctgdata, seq, sseq);
GFREE(sseq);
}
if (forgetSeq) { //parsing the whole stream -- aceconv)
ctg_numSeqs--;
seqinfo.Remove(seq->name);
ctgdata->seqs.RemovePtr(seq);
}
numseqs++;
if (numseqs<ctgdata->numseqs)
seqpos=fskipTo("RD ", "CO "); //more sequences left to read
}
if (numseqs!=ctgdata->numseqs) {
GMessage("Error: Invalid number of RD entries found (%d) for contig '%s' "
"(length %d, numseqs %d)\n", numseqs,
ctgdata->name, ctgdata->len, ctg_numSeqs);
return false;
}
if (forgetCtg) {
ctgIDs.Remove(ctgdata->name);
ctgdata->seqs.Clear();
seqinfo.Clear();
contigs.RemovePtr(ctgdata);
}
return true;
}
LytSeqInfo* LayoutParser::addSeq(char* s, LytCtgData* ctg) {
LytSeqInfo* seq;
//s must be the line with sequence data
char* p=strchrs(s," \t");
if (p==NULL) return NULL;
p++;
char c;
int slen, soffs, clpL, clpR;
clpL=0;clpR=0;
if (sscanf(p,"%c %d %d %d %d", &c, &slen, &soffs, &clpL, &clpR)<3) return NULL;
p--;
*p='\0';
if ((seq=seqinfo.Find(s))!=NULL) {
GMessage("Sequence '%s' already found for contig '%s (%d nt)'\n"
" so it cannot be added for contig '%s (%d nt)'\n",
s, seq->contig->name, seq->contig->len,
ctg->name, ctg->len);
return NULL;
}
seq = new LytSeqInfo(s, ctg, soffs, (c=='-') ? 1 : 0, slen, clpL, clpR);
seqinfo.shkAdd(seq->name, seq);
ctg->seqs.Add(seq);
//parse optional extensions, if any
p+=strlen(s); //position p after the seqname
char* m=NULL;
int segEnd, segRclip,nextsegStart, nextsegLclip, prevSegStart;
char segSplice, nextsegSplice;
while ((m=strchr(p,':'))!=NULL) {
switch (*(m-1)) {
case 'G': //segmenting info
prevSegStart=soffs+clpL-1;
p=m+1; //p to the beginning of G: data
//accumulate the total length in lenSegs
while (*p>='1' && *p<='9') {
segEnd=0;
segRclip=0;
nextsegStart=0;
nextsegLclip=0;
segSplice=0;
nextsegSplice=0;
if (!parseInt(p,segEnd))
GError("Error [segment] at LayoutParser for %s at: %s\n",
s, m-1);
if (*p=='c') {
p++;
if (!parseInt(p,segRclip))
GError("Error [segment] at LayoutParser for %s at: %s\n",
s, m-1);
}
if (*p=='S' || *p=='s') {
segSplice=*p; p++;
}
if (*p!='-')
GError("Error [segment] at LayoutParser for %s at: %s\n",
s, m-1);
else p++;
if (!parseInt(p,nextsegStart))
GError("Error [segment] at LayoutParser for %s at: %s\n",
s, m-1);
if (*p=='c') {
p++;
if (!parseInt(p,nextsegLclip))
GError("Error [segment] at LayoutParser for %s at: %s\n",
s, m-1);
}
if (*p=='S' || *p=='s') {
nextsegSplice=*p; p++;
}
seq->addInterSeg(segEnd,nextsegStart,segRclip,nextsegLclip,
segSplice, nextsegSplice);
prevSegStart=nextsegStart;
//
if (*p==',') p++;
else break;
} //while inter-segment parsing
break; // 'G:' case
case 'L': //clone mates list
p=m+1; //p to the beginning of L: data
break;
case 'D': //difference sequence
p=m+1; //p to the beginning of D: data
break;
case 'S': //actual sequence
p=m+1; //p to the beginning of S: data
break;
default:
p=m+1;//next attribute
}
}
return seq;
}
static void
add_clicked_cb (GtkWidget *widget,
DialogData *data)
{
FrWindow *window = data->window;
char *archive_name;
char *archive_dir;
char *archive_file;
char *tmp;
const char *archive_ext;
gboolean do_not_add = FALSE;
GError *error = NULL;
data->add_clicked = TRUE;
/* Collect data */
archive_name = g_uri_escape_string (gtk_entry_get_text (GTK_ENTRY (data->a_add_to_entry)), NULL, FALSE);
/* Check whether the user entered a valid archive name. */
if ((archive_name == NULL) || (*archive_name == '\0')) {
GtkWidget *d;
d = _gtk_error_dialog_new (GTK_WINDOW (window),
GTK_DIALOG_DESTROY_WITH_PARENT,
NULL,
_("Could not create the archive"),
"%s",
_("You have to specify an archive name."));
gtk_dialog_run (GTK_DIALOG (d));
gtk_widget_destroy (GTK_WIDGET (d));
g_free (archive_name);
return;
}
else if (strchrs (archive_name, BAD_CHARS)) {
GtkWidget *d;
char *utf8_name = g_filename_display_name (archive_name);
d = _gtk_error_dialog_new (GTK_WINDOW (window),
GTK_DIALOG_DESTROY_WITH_PARENT,
NULL,
_("Could not create the archive"),
_("The name \"%s\" is not valid because it cannot contain the characters: %s\n\n%s"),
utf8_name,
BAD_CHARS,
_("Please use a different name."));
gtk_dialog_run (GTK_DIALOG (d));
gtk_widget_destroy (GTK_WIDGET (d));
g_free (utf8_name);
g_free (archive_name);
return;
}
/* Check directory existence. */
archive_dir = gtk_file_chooser_get_uri (GTK_FILE_CHOOSER (data->a_location_filechooserbutton));
if (archive_dir == NULL) {
g_free (archive_dir);
g_free (archive_name);
return;
}
if (! check_permissions (archive_dir, R_OK|W_OK|X_OK)) {
GtkWidget *d;
d = _gtk_error_dialog_new (GTK_WINDOW (window),
GTK_DIALOG_DESTROY_WITH_PARENT,
NULL,
_("Could not create the archive"),
"%s",
_("You don't have the right permissions to create an archive in the destination folder."));
gtk_dialog_run (GTK_DIALOG (d));
gtk_widget_destroy (GTK_WIDGET (d));
g_free (archive_dir);
g_free (archive_name);
return;
}
if (! uri_is_dir (archive_dir)) {
GtkWidget *d;
int r;
char *folder_name;
char *msg;
folder_name = g_filename_display_name (archive_dir);
msg = g_strdup_printf (_("Destination folder \"%s\" does not exist.\n\nDo you want to create it?"), folder_name);
g_free (folder_name);
d = _gtk_message_dialog_new (GTK_WINDOW (data->dialog),
GTK_DIALOG_MODAL,
GTK_STOCK_DIALOG_QUESTION,
msg,
NULL,
GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL,
_("Create _Folder"), GTK_RESPONSE_YES,
NULL);
gtk_dialog_set_default_response (GTK_DIALOG (d), GTK_RESPONSE_YES);
r = gtk_dialog_run (GTK_DIALOG (d));
gtk_widget_destroy (GTK_WIDGET (d));
g_free (msg);
do_not_add = (r != GTK_RESPONSE_YES);
}
if (! do_not_add && ! ensure_dir_exists (archive_dir, 0755, &error)) {
GtkWidget *d;
d = _gtk_error_dialog_new (GTK_WINDOW (window),
GTK_DIALOG_DESTROY_WITH_PARENT,
NULL,
_("Could not create the archive"),
_("Could not create the destination folder: %s."),
error->message);
gtk_dialog_run (GTK_DIALOG (d));
gtk_widget_destroy (GTK_WIDGET (d));
g_error_free (error);
g_free (archive_dir);
g_free (archive_name);
return;
}
if (do_not_add) {
GtkWidget *d;
d = _gtk_message_dialog_new (GTK_WINDOW (window),
GTK_DIALOG_DESTROY_WITH_PARENT,
GTK_STOCK_DIALOG_WARNING,
_("Archive not created"),
NULL,
GTK_STOCK_OK, GTK_RESPONSE_OK,
NULL);
gtk_dialog_set_default_response (GTK_DIALOG (d), GTK_RESPONSE_OK);
gtk_dialog_run (GTK_DIALOG (d));
gtk_widget_destroy (GTK_WIDGET (d));
g_free (archive_dir);
g_free (archive_name);
return;
}
/**/
archive_ext = get_ext (data);
tmp = archive_name;
archive_name = g_strconcat (tmp, archive_ext, NULL);
g_free (tmp);
archive_file = g_strconcat (archive_dir, "/", archive_name, NULL);
if (uri_is_dir (archive_file)) {
GtkWidget *d;
d = _gtk_error_dialog_new (GTK_WINDOW (window),
GTK_DIALOG_DESTROY_WITH_PARENT,
NULL,
_("Could not create the archive"),
"%s",
_("You have to specify an archive name."));
gtk_dialog_run (GTK_DIALOG (d));
gtk_widget_destroy (GTK_WIDGET (d));
g_free (archive_name);
g_free (archive_dir);
g_free (archive_file);
return;
}
if (uri_exists (archive_file)) {
GtkWidget *d;
int r;
d = _gtk_message_dialog_new (GTK_WINDOW (data->dialog),
GTK_DIALOG_MODAL,
GTK_STOCK_DIALOG_QUESTION,
_("The archive is already present. Do you want to overwrite it?"),
NULL,
GTK_STOCK_NO, GTK_RESPONSE_NO,
_("_Overwrite"), GTK_RESPONSE_YES,
NULL);
gtk_dialog_set_default_response (GTK_DIALOG (d), GTK_RESPONSE_YES);
r = gtk_dialog_run (GTK_DIALOG (d));
gtk_widget_destroy (GTK_WIDGET (d));
if (r == GTK_RESPONSE_YES) {
GFile *file;
GError *err = NULL;
/* FIXME: convert this code in a function in file-utils.c */
file = g_file_new_for_uri (archive_file);
g_file_delete (file, NULL, &err);
if (err != NULL) {
g_warning ("Failed to delete file %s: %s",
archive_file,
err->message);
g_clear_error (&err);
}
g_object_unref (file);
}
else {
g_free (archive_name);
g_free (archive_dir);
g_free (archive_file);
return;
}
}
set_archive_options (data);
gtk_widget_destroy (data->dialog);
fr_window_archive_new (window, archive_file);
g_free (archive_name);
g_free (archive_dir);
g_free (archive_file);
}
