String File_appendFileNameChar(String fileName, char ch)
{
assert(fileName != NULL);
if (String_length(fileName) > 0)
{
if (String_index(fileName,String_length(fileName)-1) != FILES_PATHNAME_SEPARATOR_CHAR)
{
String_appendChar(fileName,FILES_PATHNAME_SEPARATOR_CHAR);
}
}
String_appendChar(fileName,ch);
return fileName;
}
void
distance2text (String s, char *species, double dist) {
char distbuffer[32];
String_appendCString(s, species);
String_appendChar(s, ':');
sprintf(distbuffer, "%g", dist);
String_appendCString(s, distbuffer);
}
String File_appendFileNameBuffer(String fileName, const char *buffer, ulong bufferLength)
{
assert(fileName != NULL);
if (String_length(fileName) > 0)
{
if (String_index(fileName,String_length(fileName)-1) != FILES_PATHNAME_SEPARATOR_CHAR)
{
String_appendChar(fileName,FILES_PATHNAME_SEPARATOR_CHAR);
}
}
String_appendBuffer(fileName,buffer,bufferLength);
return fileName;
}
LOCAL bool readProcessIO(int fd, String line)
{
#if defined(PLATFORM_LINUX)
int n;
#elif defined(PLATFORM_WINDOWS)
u_long n;
#endif /* PLATFORM_... */
char ch;
do
{
// check if data available
#if defined(PLATFORM_LINUX)
ioctl(fd,FIONREAD,&n);
#elif defined(PLATFORM_WINDOWS)
// NYI ???
#warning not implemented
#endif /* PLATFORM_... */
// read data until EOL found
while (n > 0)
{
if (read(fd,&ch,1) == 1)
{
switch (ch)
{
case '\n':
case '\r':
case '\b':
if (String_length(line) > 0L) return TRUE;
break;
default:
String_appendChar(line,ch);
break;
}
n--;
}
else
{
n = 0;
}
}
}
while (n > 0);
return FALSE;
}
void
tree2string_node(struct Tnode *node, String s)
{
if (node != NULL) {
if (node->left == NULL && node->right == NULL) {
if (node->clust->clustersize == 0 || node->clust->members == NULL) {
} else if (node->clust->clustersize == 1) {
distance2text(s, node->clust->members[0]->name, node->distance);
} else {
unsigned int i;
for (i=0; i<node->clust->clustersize-1; i++) {
String_appendChar(s, '(');
distance2text(s, node->clust->members[i]->name, 0.0);
}
distance2text(s, node->clust->members[i]->name, 0.0);
String_appendChar(s, ')');
for (i=0; i<node->clust->clustersize-2; i++) {
String_appendChar(s, ':');
distance2text(s, "", 0.0);
String_appendChar(s, ')');
}
String_appendChar(s, ':');
distance2text(s, "", node->distance);
}
} else if (node->left != NULL && node->right != NULL) {
String_appendChar(s, '(');
tree2string_node(node->left, s);
String_appendChar(s, ',');
tree2string_node(node->right, s);
String_appendChar(s, ')');
distance2text(s, "", node->distance);
}
}
}
LOCAL bool readProcessIO(int fd, String line)
{
int n;
char ch;
do
{
// check if data available
ioctl(fd,FIONREAD,&n);
// read data until EOL found
while (n > 0)
{
if (read(fd,&ch,1) == 1)
{
switch (ch)
{
case '\n':
case '\r':
case '\b':
if (String_length(line) > 0L) return TRUE;
break;
default:
String_appendChar(line,ch);
break;
}
n--;
}
else
{
n = 0;
}
}
}
while (n > 0);
return FALSE;
}
Errors File_readLine(FileHandle *fileHandle,
String line
)
{
int ch;
assert(fileHandle != NULL);
assert(fileHandle->file != NULL);
assert(line != NULL);
String_clear(line);
do
{
ch = getc(fileHandle->file);
if (ch >= 0) fileHandle->index += 1;
if (ch < 0)
{
return ERRORX(IO_ERROR,errno,String_cString(fileHandle->name));
}
if (((char)ch != '\n') && ((char)ch != '\r'))
{
String_appendChar(line,ch);
}
}
while (((char)ch != '\r') && ((char)ch != '\n'));
if ((char)ch == '\r')
{
ch = getc(fileHandle->file);
if (ch >= 0) fileHandle->index += 1;
if (ch != '\n')
{
fileHandle->index -= 1;
ungetc(ch,fileHandle->file);
}
}
return ERROR_NONE;
}
String Misc_expandMacros(String string,
const char *macroTemplate,
const TextMacro macros[],
uint macroCount
)
{
#define APPEND_CHAR(string,index,ch) \
do \
{ \
if ((index) < sizeof(string)-1) \
{ \
(string)[index] = ch; \
(index)++; \
} \
} \
while (0)
#define SKIP_SPACES(string,i) \
do \
{ \
while ( ((string)[i] != '\0') \
&& isspace((string)[i]) \
) \
{ \
(i)++; \
} \
} \
while (0)
bool macroFlag;
ulong i;
uint j;
char name[128];
char format[128];
assert(macroTemplate != NULL);
assert((macroCount == 0) || (macros != NULL));
String_clear(string);
i = 0;
do
{
// add prefix string
macroFlag = FALSE;
while ((macroTemplate[i] != '\0') && !macroFlag)
{
if (macroTemplate[i] == '%')
{
if ((macroTemplate[i+1] == '%'))
{
String_appendChar(string,'%');
i+=2;
}
else
{
macroFlag = TRUE;
i++;
}
}
else
{
String_appendChar(string,macroTemplate[i]);
i++;
}
}
if (macroFlag)
{
// skip spaces
SKIP_SPACES(macroTemplate,i);
// get macro name
j = 0;
if ( (macroTemplate[i] != '\0')
&& isalpha(macroTemplate[i])
)
{
APPEND_CHAR(name,j,'%');
do
{
APPEND_CHAR(name,j,macroTemplate[i]);
i++;
}
while ( (macroTemplate[i] != '\0')
&& isalnum(macroTemplate[i])
);
}
name[j] = '\0';
// get format data (if any)
j = 0;
if (macroTemplate[i] == ':')
{
// skip ':'
i++;
// skip spaces
SKIP_SPACES(macroTemplate,i);
// get format string
APPEND_CHAR(format,j,'%');
while ( (macroTemplate[i] != '\0')
&& ( isdigit(macroTemplate[i])
|| (macroTemplate[i] == '-')
|| (macroTemplate[i] == '.')
)
)
{
APPEND_CHAR(format,j,macroTemplate[i]);
i++;
}
while ( (macroTemplate[i] != '\0')
&& (strchr("l",macroTemplate[i]) != NULL)
)
{
APPEND_CHAR(format,j,macroTemplate[i]);
i++;
}
if ( (macroTemplate[i] != '\0')
&& (strchr("duxfsS",macroTemplate[i]) != NULL)
)
{
APPEND_CHAR(format,j,macroTemplate[i]);
i++;
}
}
format[j] = '\0';
// find macro
if (strlen(name) > 0)
{
// find macro
j = 0;
while ( (j < macroCount)
&& (strcmp(name,macros[j].name) != 0)
)
{
j++;
}
if (j < macroCount)
{
// get default format if no format given
if (strlen(format) == 0)
{
switch (macros[j].type)
{
case TEXT_MACRO_TYPE_INTEGER:
strcpy(format,"%d");
break;
case TEXT_MACRO_TYPE_INTEGER64:
strcpy(format,"%lld");
break;
case TEXT_MACRO_TYPE_DOUBLE:
strcpy(format,"%lf");
break;
case TEXT_MACRO_TYPE_CSTRING:
strcpy(format,"%s");
break;
case TEXT_MACRO_TYPE_STRING:
strcpy(format,"%S");
break;
#ifndef NDEBUG
default:
HALT_INTERNAL_ERROR_UNHANDLED_SWITCH_CASE();
break; /* not reached */
#endif /* NDEBUG */
}
}
// expand macro
switch (macros[j].type)
{
case TEXT_MACRO_TYPE_INTEGER:
String_format(string,format,macros[j].value.i);
break;
case TEXT_MACRO_TYPE_INTEGER64:
String_format(string,format,macros[j].value.l);
break;
case TEXT_MACRO_TYPE_DOUBLE:
String_format(string,format,macros[j].value.d);
break;
case TEXT_MACRO_TYPE_CSTRING:
String_format(string,format,macros[j].value.s);
break;
case TEXT_MACRO_TYPE_STRING:
String_format(string,format,macros[j].value.string);
break;
#ifndef NDEBUG
default:
HALT_INTERNAL_ERROR_UNHANDLED_SWITCH_CASE();
break; /* not reached */
#endif /* NDEBUG */
}
}
else
{
// keep unknown macro
String_appendCString(string,name);
}
}
else
{
// empty macro: add empty string
String_format(string,format,"");
}
}
}
while (macroFlag);
return string;
#undef SKIP_SPACES
#undef APPEND_CHAR
}
char *
tree2string (struct Tree *tree) {
String s;
s = String_new();
if (tree != NULL) {
if (tree->child[0] != NULL) {
if (tree->child[1] == NULL) {
if (tree->child[0]->left != NULL && tree->child[0]->right != NULL) {
String_appendChar(s, '(');
tree2string_node(tree->child[0]->left, s);
String_appendChar(s, ',');
tree2string_node(tree->child[0]->right, s);
String_appendCString(s, ");");
} else {
if (tree->child[0]->clust->clustersize == 1) {
String_appendCString(s, "0;");
} else {
unsigned int i;
for (i=0; i<tree->child[0]->clust->clustersize-1; i++) {
String_appendChar(s, '(');
distance2text(s, tree->child[0]->clust->members[i]->name, 0.0);
}
distance2text(s, tree->child[0]->clust->members[i]->name, 0.0);
for (i=0; i<tree->child[0]->clust->clustersize-2; i++) {
String_appendCString(s, "):0.0)");
}
String_appendCString(s, ");");
}
}
}
}
}
// unsigned int strlen = String_length(s);
char *buffer = NULL;
// buffer = malloc(sizeof(char) * (strlen+1));
// strncpy(buffer, String_cString(s), strlen);
char *position;
const char *cString = String_cString(s);
// fprintf(stderr, "[TREE]: ### %s ###\n", cString);
position = strchr(cString, ';');
if (position == NULL) {
fprintf(stderr, "Error in trees\n");
exit(-1);
}
int index = cString - position;
if (index < 0) {
index = -index;
}
// fprintf(stderr, "\tindex: %d\n", index);
buffer = malloc(sizeof(char) * (index+2));
strncpy(buffer, cString, index+1);
buffer[index+1] = '\0';
// fprintf(stderr, "\tbuffer: %s\n", buffer);
String_delete(s);
return buffer;
}