static int treeGetCh (FILE *fp) /* get next nonblank, noncomment character */
{ /* treeGetCh */
int ch;
while ((ch = getc(fp)) != EOF) {
if (whitechar(ch)) ;
else if (ch == '[') { /* comment; find its end */
if ((ch = treeFinishCom(fp, (char **) NULL)) == EOF) break;
}
else break;
}
return ch;
} /* treeGetCh */
static boolean lineContainsOnlyWhiteChars(char *line)
{
int i, n = strlen(line);
if(n == 0)
return TRUE;
for(i = 0; i < n; i++)
{
if(!whitechar(line[i]))
return FALSE;
}
return TRUE;
}
static void treeEchoContext (FILE *fp1, FILE *fp2, int n)
{ /* treeEchoContext */
int ch;
boolean waswhite;
waswhite = TRUE;
while (n > 0 && ((ch = getc(fp1)) != EOF)) {
if (whitechar(ch)) {
ch = waswhite ? '\0' : ' ';
waswhite = TRUE;
}
else {
waswhite = FALSE;
}
if (ch > '\0') {putc(ch, fp2); n--;}
}
} /* treeEchoContext */
FILE *
collect(struct header *hp, int printheaders, struct message *mp,
char *quotefile, int doprefix, int tflag)
{
FILE *fbuf;
struct ignoretab *quoteig;
int lc, cc, escape, eofcount;
int c, t;
char *linebuf = NULL, *cp, *quote = NULL;
size_t linesize;
char *tempMail = NULL;
int getfields;
sigset_t oset, nset;
long count;
enum sendaction action;
sighandler_type savedtop;
const char tildehelp[] =
"-------------------- ~ ESCAPES ----------------------------\n\
~~ Quote a single tilde\n\
~@ [file ...] Edit attachment list\n\
~b users Add users to \"blind\" cc list\n\
~c users Add users to cc list\n\
~d Read in dead.letter\n\
~e Edit the message buffer\n\
~f messages Read in messages without indenting lines\n\
~F messages Same as ~f, but keep all header lines\n\
~h Prompt for to list, subject, cc, and \"blind\" cc list\n\
~r file Read a file into the message buffer\n\
~p Print the message buffer\n\
~q Abort message composition and save text to dead.letter\n\
~m messages Read in messages with each line indented\n\
~M messages Same as ~m, but keep all header lines\n\
~s subject Set subject\n\
~t users Add users to to list\n\
~v Invoke display editor on message\n\
~w file Write message onto file\n\
~x Abort message composition and discard text written so far\n\
~!command Invoke the shell\n\
~:command Execute a regular command\n\
-----------------------------------------------------------\n";
(void) &escape;
(void) &eofcount;
(void) &getfields;
(void) &tempMail;
(void) &tflag;
(void) "e;
collf = NULL;
/*
* Start catching signals from here, but we're still die on interrupts
* until we're in the main loop.
*/
sigemptyset(&nset);
sigaddset(&nset, SIGINT);
sigaddset(&nset, SIGHUP);
sigprocmask(SIG_BLOCK, &nset, &oset);
handlerpush(collint);
if ((saveint = safe_signal(SIGINT, SIG_IGN)) != SIG_IGN)
safe_signal(SIGINT, collint);
if ((savehup = safe_signal(SIGHUP, SIG_IGN)) != SIG_IGN)
safe_signal(SIGHUP, collhup);
savetstp = safe_signal(SIGTSTP, collstop);
savettou = safe_signal(SIGTTOU, collstop);
savettin = safe_signal(SIGTTIN, collstop);
if (sigsetjmp(collabort, 1)) {
if (tempMail != NULL) {
rm(tempMail);
Ftfree(&tempMail);
}
goto err;
}
if (sigsetjmp(colljmp, 1)) {
if (tempMail != NULL) {
rm(tempMail);
Ftfree(&tempMail);
}
goto err;
}
sigprocmask(SIG_SETMASK, &oset, (sigset_t *)NULL);
noreset++;
if ((collf = Ftemp(&tempMail, "Rs", "w+", 0600, 1)) == NULL) {
perror(catgets(catd, CATSET, 51, "temporary mail file"));
goto err;
}
unlink(tempMail);
Ftfree(&tempMail);
if ((cp = value("MAILX_HEAD")) != NULL) {
if (is_a_tty[0])
putesc(cp, stdout);
putesc(cp, collf);
}
/*
* If we are going to prompt for a subject,
* refrain from printing a newline after
* the headers (since some people mind).
*/
getfields = 0;
if (!tflag) {
t = GTO|GSUBJECT|GCC|GNL;
if (value("fullnames"))
t |= GCOMMA;
if (hp->h_subject == NULL && value("interactive") != NULL &&
(value("ask") != NULL || value("asksub") != NULL))
t &= ~GNL, getfields |= GSUBJECT;
if (hp->h_to == NULL && value("interactive") != NULL)
t &= ~GNL, getfields |= GTO;
if (value("bsdcompat") == NULL && value("askatend") == NULL &&
value("interactive")) {
if (hp->h_bcc == NULL && value("askbcc"))
t &= ~GNL, getfields |= GBCC;
if (hp->h_cc == NULL && value("askcc"))
t &= ~GNL, getfields |= GCC;
}
if (printheaders) {
puthead(hp, stdout, t, SEND_TODISP, CONV_NONE,
NULL, NULL);
fflush(stdout);
}
}
/*
* Quote an original message
*/
if (mp != NULL && (doprefix || (quote = value("quote")) != NULL)) {
quoteig = allignore;
action = SEND_QUOTE;
if (doprefix) {
quoteig = fwdignore;
if ((cp = value("fwdheading")) == NULL)
cp = "-------- Original Message --------";
if (*cp) {
fprintf(collf, "%s\n", cp);
fprintf(stdout, "%s\n", cp);
}
} else if (strcmp(quote, "noheading") == 0) {
/*EMPTY*/;
} else if (strcmp(quote, "headers") == 0) {
quoteig = ignore;
} else if (strcmp(quote, "allheaders") == 0) {
quoteig = NULL;
action = SEND_QUOTE_ALL;
} else {
cp = hfield("from", mp);
if (cp != NULL) {
mime_write(cp, strlen(cp),
collf, CONV_FROMHDR, TD_NONE,
NULL, (size_t) 0,
NULL, NULL);
mime_write(cp, strlen(cp),
stdout, CONV_FROMHDR, TD_NONE,
NULL, (size_t) 0,
NULL, NULL);
fwrite(catgets(catd, CATSET, 52,
" wrote:\n\n"), sizeof(char), 9, collf);
fwrite(catgets(catd, CATSET, 52,
" wrote:\n\n"), sizeof(char), 9, stdout);
}
}
cp = value("indentprefix");
if (cp != NULL && *cp == '\0')
cp = "\t";
send(mp, collf, quoteig, doprefix ? NULL : cp, action, NULL);
send(mp, stdout, quoteig, doprefix ? NULL : cp, action, NULL);
}
if ((cp = value("escape")) != NULL)
escape = *cp;
else
escape = ESCAPE;
eofcount = 0;
hadintr = 0;
if (!sigsetjmp(colljmp, 1)) {
if (getfields)
grabh(hp, getfields, 1);
if (quotefile != NULL) {
if (include_file(NULL, quotefile, &lc, &cc, 1) != 0)
goto err;
}
} else {
/*
* Come here for printing the after-signal message.
* Duplicate messages won't be printed because
* the write is aborted if we get a SIGTTOU.
*/
cont:
if (hadintr) {
fflush(stdout);
fprintf(stderr, catgets(catd, CATSET, 53,
"\n(Interrupt -- one more to kill letter)\n"));
} else {
printf(catgets(catd, CATSET, 54, "(continue)\n"));
fflush(stdout);
}
}
if (value("interactive") == NULL && tildeflag <= 0 && !is_a_tty[0] &&
!tflag) {
/*
* No tilde escapes, interrupts not expected. Copy
* standard input the simple way.
*/
linebuf = srealloc(linebuf, linesize = BUFSIZ);
while ((count = fread(linebuf, sizeof *linebuf,
linesize, stdin)) > 0) {
if (fwrite(linebuf, sizeof *linebuf,
count, collf) != count)
goto err;
}
goto out;
}
for (;;) {
colljmp_p = 1;
count = readline(stdin, &linebuf, &linesize);
colljmp_p = 0;
if (count < 0) {
if (value("interactive") != NULL &&
value("ignoreeof") != NULL && ++eofcount < 25) {
printf(catgets(catd, CATSET, 55,
"Use \".\" to terminate letter\n"));
continue;
}
break;
}
if (tflag && count == 0) {
rewind(collf);
if (makeheader(collf, hp) != OKAY)
goto err;
rewind(collf);
tflag = 0;
continue;
}
eofcount = 0;
hadintr = 0;
if (linebuf[0] == '.' && linebuf[1] == '\0' &&
value("interactive") != NULL &&
(value("dot") != NULL || value("ignoreeof") != NULL))
break;
if (linebuf[0] != escape || (value("interactive") == NULL &&
tildeflag == 0 ||
tildeflag < 0)) {
if (putline(collf, linebuf, count) < 0)
goto err;
continue;
}
c = linebuf[1];
switch (c) {
default:
/*
* On double escape, just send the single one.
* Otherwise, it's an error.
*/
if (c == escape) {
if (putline(collf, &linebuf[1], count - 1) < 0)
goto err;
else
break;
}
printf(catgets(catd, CATSET, 56,
"Unknown tilde escape.\n"));
break;
#ifdef DEBUG_COMMANDS
case 'C':
/*
* Dump core.
*/
core(NULL);
break;
#endif /* DEBUG_COMMANDS */
case '!':
/*
* Shell escape, send the balance of the
* line to sh -c.
*/
shell(&linebuf[2]);
break;
case ':':
case '_':
/*
* Escape to command mode, but be nice!
*/
inhook = 0;
execute(&linebuf[2], 1, count - 2);
goto cont;
case '.':
/*
* Simulate end of file on input.
*/
goto out;
case 'x':
/*
* Same as 'q', but no dead.letter saving.
*/
hadintr++;
collint(0);
exit(1);
/*NOTREACHED*/
case 'q':
/*
* Force a quit of sending mail.
* Act like an interrupt happened.
*/
hadintr++;
collint(SIGINT);
exit(1);
/*NOTREACHED*/
case 'h':
/*
* Grab a bunch of headers.
*/
do
grabh(hp, GTO|GSUBJECT|GCC|GBCC,
value("bsdcompat") != NULL &&
value("bsdorder") != NULL);
while (hp->h_to == NULL);
goto cont;
case 'H':
/*
* Grab extra headers.
*/
do
grabh(hp, GEXTRA, 0);
while (check_from_and_sender(hp->h_from, hp->h_sender));
goto cont;
case 't':
/*
* Add to the To list.
*/
while ((hp->h_to = checkaddrs(cat(hp->h_to,
sextract(&linebuf[2], GTO|GFULL))))
== NULL);
break;
case 's':
/*
* Set the Subject list.
*/
cp = &linebuf[2];
while (whitechar(*cp & 0377))
cp++;
hp->h_subject = savestr(cp);
break;
case '@':
/*
* Edit the attachment list.
*/
if (linebuf[2] != '\0')
hp->h_attach = append_attachments(hp->h_attach,
&linebuf[2]);
else
hp->h_attach = edit_attachments(hp->h_attach);
break;
case 'c':
/*
* Add to the CC list.
*/
hp->h_cc = checkaddrs(cat(hp->h_cc,
sextract(&linebuf[2], GCC|GFULL)));
break;
case 'b':
/*
* Add stuff to blind carbon copies list.
*/
hp->h_bcc = checkaddrs(cat(hp->h_bcc,
sextract(&linebuf[2], GBCC|GFULL)));
break;
case 'd':
strncpy(linebuf + 2, getdeadletter(), linesize - 2);
linebuf[linesize-1]='\0';
/*FALLTHRU*/
case 'r':
case '<':
/*
* Invoke a file:
* Search for the file name,
* then open it and copy the contents to collf.
*/
cp = &linebuf[2];
while (whitechar(*cp & 0377))
cp++;
if (*cp == '\0') {
printf(catgets(catd, CATSET, 57,
"Interpolate what file?\n"));
break;
}
if (*cp == '!') {
insertcommand(collf, cp + 1);
break;
}
cp = expand(cp);
if (cp == NULL)
break;
if (is_dir(cp)) {
printf(catgets(catd, CATSET, 58,
"%s: Directory\n"), cp);
break;
}
if ((fbuf = Fopen(cp, "r")) == NULL) {
perror(cp);
break;
}
printf(catgets(catd, CATSET, 59, "\"%s\" "), cp);
fflush(stdout);
if (include_file(fbuf, cp, &lc, &cc, 0) != 0)
goto err;
printf(catgets(catd, CATSET, 60, "%d/%d\n"), lc, cc);
break;
case 'i':
/*
* Insert an environment variable into the file.
*/
cp = &linebuf[2];
while (whitechar(*cp & 0377))
cp++;
if ((cp = value(cp)) == NULL || *cp == '\0')
break;
if (is_a_tty[0])
putesc(cp, stdout);
putesc(cp, collf);
break;
case 'a':
case 'A':
/*
* Insert the contents of a signature variable.
*/
if ((cp = value(c == 'a' ? "sign" : "Sign")) != NULL &&
*cp != '\0') {
if (is_a_tty[0])
putesc(cp, stdout);
putesc(cp, collf);
}
break;
case 'w':
/*
* Write the message on a file.
*/
cp = &linebuf[2];
while (blankchar(*cp & 0377))
cp++;
if (*cp == '\0') {
fprintf(stderr, catgets(catd, CATSET, 61,
"Write what file!?\n"));
break;
}
if ((cp = expand(cp)) == NULL)
break;
rewind(collf);
exwrite(cp, collf, 1);
break;
case 'm':
case 'M':
case 'f':
case 'F':
/*
* Interpolate the named messages, if we
* are in receiving mail mode. Does the
* standard list processing garbage.
* If ~f is given, we don't shift over.
*/
if (forward(linebuf + 2, collf, c) < 0)
goto err;
goto cont;
case '?':
fputs(tildehelp, stdout);
break;
case 'p':
/*
* Print out the current state of the
* message without altering anything.
*/
print_collf(collf, hp);
goto cont;
case '|':
/*
* Pipe message through command.
* Collect output as new message.
*/
rewind(collf);
mespipe(&linebuf[2]);
goto cont;
case 'v':
case 'e':
/*
* Edit the current message.
* 'e' means to use EDITOR
* 'v' means to use VISUAL
*/
rewind(collf);
mesedit(c, value("editheaders") ? hp : NULL);
goto cont;
}
}
goto out;
err:
if (collf != NULL) {
Fclose(collf);
collf = NULL;
}
out:
if (collf != NULL) {
if ((cp = value("MAILX_TAIL")) != NULL) {
if (is_a_tty[0])
putesc(cp, stdout);
fflush(collf);
putesc(cp, collf);
}
rewind(collf);
}
handlerpop();
noreset--;
sigemptyset(&nset);
sigaddset(&nset, SIGINT);
sigaddset(&nset, SIGHUP);
#ifndef OLDBUG
sigprocmask(SIG_BLOCK, &nset, (sigset_t *)NULL);
#else
sigprocmask(SIG_BLOCK, &nset, &oset);
#endif
safe_signal(SIGINT, saveint);
safe_signal(SIGHUP, savehup);
safe_signal(SIGTSTP, savetstp);
safe_signal(SIGTTOU, savettou);
safe_signal(SIGTTIN, savettin);
sigprocmask(SIG_SETMASK, &oset, (sigset_t *)NULL);
return collf;
}
void handleExcludeFile(tree *tr, analdef *adef, rawdata *rdta)
{
FILE *f;
char buf[256];
int
ch,
j, value, i,
state = 0,
numberOfModels = 0,
l = -1,
excludeRegion = 0,
excludedColumns = 0,
modelCounter = 1;
int
*excludeArray, *countArray, *modelList;
int
**partitions;
printf("\n\n");
f = myfopen(excludeFileName, "rb");
while((ch = getc(f)) != EOF)
{
if(ch == '-')
numberOfModels++;
}
excludeArray = (int*)malloc(sizeof(int) * (rdta->sites + 1));
countArray = (int*)malloc(sizeof(int) * (rdta->sites + 1));
modelList = (int *)malloc((rdta->sites + 1)* sizeof(int));
partitions = (int **)malloc(sizeof(int *) * numberOfModels);
for(i = 0; i < numberOfModels; i++)
partitions[i] = (int *)malloc(sizeof(int) * 2);
rewind(f);
while((ch = getc(f)) != EOF)
{
switch(state)
{
case 0: /* get first number */
if(!whitechar(ch))
{
if(!isNum(ch))
{
printf("exclude file must have format: number-number [number-number]*\n");
exit(-1);
}
l = 0;
buf[l++] = ch;
state = 1;
}
break;
case 1: /*get the number or detect - */
if(!isNum(ch) && ch != '-')
{
printf("exclude file must have format: number-number [number-number]*\n");
exit(-1);
}
if(isNum(ch))
{
buf[l++] = ch;
}
else
{
buf[l++] = '\0';
value = atoi(buf);
partitions[excludeRegion][0] = value;
state = 2;
}
break;
case 2: /*get second number */
if(!isNum(ch))
{
printf("exclude file must have format: number-number [number-number]*\n");
exit(-1);
}
l = 0;
buf[l++] = ch;
state = 3;
break;
case 3: /* continue second number or find end */
if(!isNum(ch) && !whitechar(ch))
{
printf("exclude file must have format: number-number [number-number]*\n");
exit(-1);
}
if(isNum(ch))
{
buf[l++] = ch;
}
else
{
buf[l++] = '\0';
value = atoi(buf);
partitions[excludeRegion][1] = value;
excludeRegion++;
state = 0;
}
break;
default:
assert(0);
}
}
if(state == 3)
{
buf[l++] = '\0';
value = atoi(buf);
partitions[excludeRegion][1] = value;
excludeRegion++;
}
assert(excludeRegion == numberOfModels);
for(i = 0; i <= rdta->sites; i++)
{
excludeArray[i] = -1;
countArray[i] = 0;
modelList[i] = -1;
}
for(i = 0; i < numberOfModels; i++)
{
int lower = partitions[i][0];
int upper = partitions[i][1];
if(lower > upper)
{
printf("Misspecified exclude region %d\n", i);
printf("lower bound %d is greater than upper bound %d\n", lower, upper);
exit(-1);
}
if(lower == 0)
{
printf("Misspecified exclude region %d\n", i);
printf("lower bound must be greater than 0\n");
exit(-1);
}
if(upper > rdta->sites)
{
printf("Misspecified exclude region %d\n", i);
printf("upper bound %d must be smaller than %d\n", upper, (rdta->sites + 1));
exit(-1);
}
for(j = lower; j <= upper; j++)
{
if(excludeArray[j] != -1)
{
printf("WARNING: Exclude regions %d and %d overlap at position %d (already excluded %d times)\n",
excludeArray[j], i, j, countArray[j]);
}
excludeArray[j] = i;
countArray[j] = countArray[j] + 1;
}
}
for(i = 1; i <= rdta->sites; i++)
{
if(excludeArray[i] != -1)
excludedColumns++;
else
{
modelList[modelCounter] = tr->model[i];
modelCounter++;
}
}
printf("You have excluded %d out of %d columns\n", excludedColumns, rdta->sites);
if(excludedColumns == rdta->sites)
{
printf("Error: You have excluded all sites\n");
exit(-1);
}
if(adef->useSecondaryStructure && (excludedColumns > 0))
{
char mfn[2048];
int countColumns;
FILE *newFile;
assert(adef->useMultipleModel);
strcpy(mfn, secondaryStructureFileName);
strcat(mfn, ".");
strcat(mfn, excludeFileName);
newFile = myfopen(mfn, "wb");
printBothOpen("\nA secondary structure file with analogous structure assignments for non-excluded columns is printed to file %s\n", mfn);
for(i = 1, countColumns = 0; i <= rdta->sites; i++)
{
if(excludeArray[i] == -1)
fprintf(newFile, "%c", tr->secondaryStructureInput[i - 1]);
else
countColumns++;
}
assert(countColumns == excludedColumns);
fprintf(newFile,"\n");
fclose(newFile);
}
if(adef->useMultipleModel && (excludedColumns > 0))
{
char mfn[2048];
FILE *newFile;
strcpy(mfn, modelFileName);
strcat(mfn, ".");
strcat(mfn, excludeFileName);
newFile = myfopen(mfn, "wb");
printf("\nA partition file with analogous model assignments for non-excluded columns is printed to file %s\n", mfn);
for(i = 0; i < tr->NumberOfModels; i++)
{
boolean modelStillExists = FALSE;
for(j = 1; (j <= rdta->sites) && (!modelStillExists); j++)
{
if(modelList[j] == i)
modelStillExists = TRUE;
}
if(modelStillExists)
{
int k = 1;
int lower, upper;
int parts = 0;
switch(tr->partitionData[i].dataType)
{
case AA_DATA:
{
char AAmodel[1024];
strcpy(AAmodel, protModels[tr->partitionData[i].protModels]);
if(tr->partitionData[i].protFreqs)
strcat(AAmodel, "F");
fprintf(newFile, "%s, ", AAmodel);
}
break;
case DNA_DATA:
fprintf(newFile, "DNA, ");
break;
case BINARY_DATA:
fprintf(newFile, "BIN, ");
break;
case GENERIC_32:
fprintf(newFile, "MULTI, ");
break;
case GENERIC_64:
fprintf(newFile, "CODON, ");
break;
default:
assert(0);
}
fprintf(newFile, "%s = ", tr->partitionData[i].partitionName);
while(k <= rdta->sites)
{
if(modelList[k] == i)
{
lower = k;
while((modelList[k + 1] == i) && (k <= rdta->sites))
k++;
upper = k;
if(lower == upper)
{
if(parts == 0)
fprintf(newFile, "%d", lower);
else
fprintf(newFile, ",%d", lower);
}
else
{
if(parts == 0)
fprintf(newFile, "%d-%d", lower, upper);
else
fprintf(newFile, ",%d-%d", lower, upper);
}
parts++;
}
k++;
}
fprintf(newFile, "\n");
}
}
fclose(newFile);
}
{
FILE *newFile;
char mfn[2048];
strcpy(mfn, seq_file);
strcat(mfn, ".");
strcat(mfn, excludeFileName);
newFile = myfopen(mfn, "wb");
printf("\nAn alignment file with excluded columns is printed to file %s\n\n\n", mfn);
fprintf(newFile, "%d %d\n", tr->mxtips, rdta->sites - excludedColumns);
for(i = 1; i <= tr->mxtips; i++)
{
unsigned char *tipI = &(rdta->y[i][1]);
fprintf(newFile, "%s ", tr->nameList[i]);
for(j = 0; j < rdta->sites; j++)
{
if(excludeArray[j + 1] == -1)
fprintf(newFile, "%c", getInverseMeaning(tr->dataVector[j + 1], tipI[j]));
}
fprintf(newFile, "\n");
}
fclose(newFile);
}
fclose(f);
for(i = 0; i < numberOfModels; i++)
free(partitions[i]);
free(partitions);
free(excludeArray);
free(countArray);
free(modelList);
}
void parseSecondaryStructure(tree *tr, analdef *adef, int sites)
{
if(adef->useSecondaryStructure)
{
FILE *f = myfopen(secondaryStructureFileName, "rb");
int
i,
k,
countCharacters = 0,
ch,
*characters,
**brackets,
opening,
closing,
depth,
numberOfSymbols,
numSecondaryColumns;
unsigned char bracketTypes[4][2] = {{'(', ')'}, {'<', '>'}, {'[', ']'}, {'{', '}'}};
numberOfSymbols = 4;
tr->secondaryStructureInput = (char*)malloc(sizeof(char) * sites);
while((ch = fgetc(f)) != EOF)
{
if(ch == '(' || ch == ')' || ch == '<' || ch == '>' || ch == '[' || ch == ']' || ch == '{' || ch == '}' || ch == '.')
countCharacters++;
else
{
if(!whitechar(ch))
{
printf("Secondary Structure file %s contains character %c at position %d\n", secondaryStructureFileName, ch, countCharacters + 1);
printf("Allowed Characters are \"( ) < > [ ] { } \" and \".\" \n");
errorExit(-1);
}
}
}
if(countCharacters != sites)
{
printf("Error: Alignment length is: %d, secondary structure file has length %d\n", sites, countCharacters);
errorExit(-1);
}
characters = (int*)malloc(sizeof(int) * countCharacters);
brackets = (int **)malloc(sizeof(int*) * numberOfSymbols);
for(k = 0; k < numberOfSymbols; k++)
brackets[k] = (int*)calloc(countCharacters, sizeof(int));
rewind(f);
countCharacters = 0;
while((ch = fgetc(f)) != EOF)
{
if(!whitechar(ch))
{
tr->secondaryStructureInput[countCharacters] = ch;
characters[countCharacters++] = ch;
}
}
assert(countCharacters == sites);
for(k = 0; k < numberOfSymbols; k++)
{
for(i = 0, opening = 0, closing = 0, depth = 0; i < countCharacters; i++)
{
if((characters[i] == bracketTypes[k][0] || characters[i] == bracketTypes[k][1]) &&
(tr->extendedDataVector[i+1] == AA_DATA || tr->extendedDataVector[i+1] == BINARY_DATA ||
tr->extendedDataVector[i+1] == GENERIC_32 || tr->extendedDataVector[i+1] == GENERIC_64))
{
printf("Secondary Structure only for DNA character positions \n");
printf("I am at position %d of the secondary structure file and this is not part of a DNA partition\n", i+1);
errorExit(-1);
}
if(characters[i] == bracketTypes[k][0])
{
depth++;
/*printf("%d %d\n", depth, i);*/
brackets[k][i] = depth;
opening++;
}
if(characters[i] == bracketTypes[k][1])
{
brackets[k][i] = depth;
/*printf("%d %d\n", depth, i); */
depth--;
closing++;
}
if(closing > opening)
{
printf("at position %d there is a closing bracket too much\n", i+1);
errorExit(-1);
}
}
assert(depth == 0 && countCharacters == sites);
if(closing != opening)
{
printf("Number of opening brackets %d should be equal to number of closing brackets %d\n", opening, closing);
errorExit(-1);
}
}
for(i = 0, numSecondaryColumns = 0; i < countCharacters; i++)
{
int checkSum = 0;
for(k = 0; k < numberOfSymbols; k++)
{
if(brackets[k][i] > 0)
{
checkSum++;
switch(tr->secondaryStructureModel)
{
case SEC_16:
case SEC_16_A:
case SEC_16_B:
case SEC_16_C:
case SEC_16_D:
case SEC_16_E:
case SEC_16_F:
case SEC_16_I:
case SEC_16_J:
case SEC_16_K:
tr->extendedDataVector[i+1] = SECONDARY_DATA;
break;
case SEC_6_A:
case SEC_6_B:
case SEC_6_C:
case SEC_6_D:
case SEC_6_E:
tr->extendedDataVector[i+1] = SECONDARY_DATA_6;
break;
case SEC_7_A:
case SEC_7_B:
case SEC_7_C:
case SEC_7_D:
case SEC_7_E:
case SEC_7_F:
tr->extendedDataVector[i+1] = SECONDARY_DATA_7;
break;
default:
assert(0);
}
numSecondaryColumns++;
}
}
assert(checkSum <= 1);
}
assert(numSecondaryColumns % 2 == 0);
/*printf("Number of secondary columns: %d merged columns: %d\n", numSecondaryColumns, numSecondaryColumns / 2);*/
tr->numberOfSecondaryColumns = numSecondaryColumns;
if(numSecondaryColumns > 0)
{
int model = tr->NumberOfModels;
int countPairs;
pInfo *partBuffer = (pInfo*)malloc(sizeof(pInfo) * tr->NumberOfModels);
for(i = 1; i <= sites; i++)
{
for(k = 0; k < numberOfSymbols; k++)
{
if(brackets[k][i-1] > 0)
tr->model[i] = model;
}
}
/* now make a copy of partition data */
for(i = 0; i < tr->NumberOfModels; i++)
{
partBuffer[i].partitionName = (char*)malloc((strlen(tr->extendedPartitionData[i].partitionName) + 1) * sizeof(char));
strcpy(partBuffer[i].partitionName, tr->extendedPartitionData[i].partitionName);
partBuffer[i].dataType = tr->extendedPartitionData[i].dataType;
partBuffer[i].protModels= tr->extendedPartitionData[i].protModels;
partBuffer[i].protFreqs= tr->extendedPartitionData[i].protFreqs;
}
for(i = 0; i < tr->NumberOfModels; i++)
free(tr->extendedPartitionData[i].partitionName);
free(tr->extendedPartitionData);
tr->extendedPartitionData = (pInfo*)malloc(sizeof(pInfo) * (tr->NumberOfModels + 1));
for(i = 0; i < tr->NumberOfModels; i++)
{
tr->extendedPartitionData[i].partitionName = (char*)malloc((strlen(partBuffer[i].partitionName) + 1) * sizeof(char));
strcpy(tr->extendedPartitionData[i].partitionName, partBuffer[i].partitionName);
tr->extendedPartitionData[i].dataType = partBuffer[i].dataType;
tr->extendedPartitionData[i].protModels= partBuffer[i].protModels;
tr->extendedPartitionData[i].protFreqs= partBuffer[i].protFreqs;
free(partBuffer[i].partitionName);
}
free(partBuffer);
tr->extendedPartitionData[i].partitionName = (char*)malloc(64 * sizeof(char));
switch(tr->secondaryStructureModel)
{
case SEC_16:
case SEC_16_A:
case SEC_16_B:
case SEC_16_C:
case SEC_16_D:
case SEC_16_E:
case SEC_16_F:
case SEC_16_I:
case SEC_16_J:
case SEC_16_K:
strcpy(tr->extendedPartitionData[i].partitionName, "SECONDARY STRUCTURE 16 STATE MODEL");
tr->extendedPartitionData[i].dataType = SECONDARY_DATA;
break;
case SEC_6_A:
case SEC_6_B:
case SEC_6_C:
case SEC_6_D:
case SEC_6_E:
strcpy(tr->extendedPartitionData[i].partitionName, "SECONDARY STRUCTURE 6 STATE MODEL");
tr->extendedPartitionData[i].dataType = SECONDARY_DATA_6;
break;
case SEC_7_A:
case SEC_7_B:
case SEC_7_C:
case SEC_7_D:
case SEC_7_E:
case SEC_7_F:
strcpy(tr->extendedPartitionData[i].partitionName, "SECONDARY STRUCTURE 7 STATE MODEL");
tr->extendedPartitionData[i].dataType = SECONDARY_DATA_7;
break;
default:
assert(0);
}
tr->extendedPartitionData[i].protModels= -1;
tr->extendedPartitionData[i].protFreqs= -1;
tr->NumberOfModels++;
if(adef->perGeneBranchLengths)
{
if(tr->NumberOfModels > NUM_BRANCHES)
{
printf("You are trying to use %d partitioned models for an individual per-gene branch length estimate.\n", tr->NumberOfModels);
printf("Currently only %d are allowed to improve efficiency.\n", NUM_BRANCHES);
printf("Note that the number of partitions has automatically been incremented by one to accomodate secondary structure models\n");
printf("\n");
printf("In order to change this please replace the line \"#define NUM_BRANCHES %d\" in file \"axml.h\" \n", NUM_BRANCHES);
printf("by \"#define NUM_BRANCHES %d\" and then re-compile RAxML.\n", tr->NumberOfModels);
exit(-1);
}
else
{
tr->multiBranch = 1;
tr->numBranches = tr->NumberOfModels;
}
}
assert(countCharacters == sites);
tr->secondaryStructurePairs = (int*)malloc(sizeof(int) * countCharacters);
for(i = 0; i < countCharacters; i++)
tr->secondaryStructurePairs[i] = -1;
/*
for(i = 0; i < countCharacters; i++)
printf("%d", brackets[i]);
printf("\n");
*/
countPairs = 0;
for(k = 0; k < numberOfSymbols; k++)
{
i = 0;
while(i < countCharacters)
{
int
j = i,
bracket,
openBracket,
closeBracket;
while(j < countCharacters && ((bracket = brackets[k][j]) == 0))
{
i++;
j++;
}
if(j == countCharacters)
{
assert(bracket == 0);
break;
}
openBracket = j;
j++;
while(bracket != brackets[k][j] && j < countCharacters)
j++;
assert(j < countCharacters);
closeBracket = j;
assert(closeBracket < countCharacters && openBracket < countCharacters);
assert(brackets[k][closeBracket] > 0 && brackets[k][openBracket] > 0);
/*printf("%d %d %d\n", openBracket, closeBracket, bracket);*/
brackets[k][closeBracket] = 0;
brackets[k][openBracket] = 0;
countPairs++;
tr->secondaryStructurePairs[closeBracket] = openBracket;
tr->secondaryStructurePairs[openBracket] = closeBracket;
}
assert(i == countCharacters);
}
assert(countPairs == numSecondaryColumns / 2);
/*for(i = 0; i < countCharacters; i++)
printf("%d ", tr->secondaryStructurePairs[i]);
printf("\n");*/
adef->useMultipleModel = TRUE;
}
for(k = 0; k < numberOfSymbols; k++)
free(brackets[k]);
free(brackets);
free(characters);
fclose(f);
}
}
/*
* Get the last, possibly quoted part of linebuf.
*/
char *
laststring(char *linebuf, int *flag, int strip)
{
char *cp, *p;
char quoted;
*flag = 1;
cp = strlen(linebuf) + linebuf - 1;
/*
* Strip away trailing blanks.
*/
while (cp > linebuf && whitechar(*cp & 0377))
cp--;
*++cp = 0;
if (cp == linebuf) {
*flag = 0;
return NULL;
}
/*
* Now search for the beginning of the command name.
*/
quoted = *(cp - 1);
if (quoted == '\'' || quoted == '\"') {
cp--;
if (strip)
*cp = '\0';
cp--;
while (cp > linebuf) {
if (*cp != quoted) {
cp--;
} else if (*(cp - 1) != '\\') {
break;
} else {
p = --cp;
do {
*p = *(p + 1);
} while (*p++);
cp--;
}
}
if (cp == linebuf)
*flag = 0;
if (*cp == quoted) {
if (strip)
*cp++ = 0;
} else
*flag = 0;
} else {
while (cp > linebuf && !whitechar(*cp & 0377))
cp--;
if (whitechar(*cp & 0377))
*cp++ = 0;
else
*flag = 0;
}
if (*cp == '\0') {
return(NULL);
}
return(cp);
}
