bool constructSafeLabels(const NxsTaxaBlock & tb, std::vector<std::string> * vs, std::set<std::string> & safeLabelSet)
{
if (vs == 0L)
return false;
const unsigned numTaxa = tb.GetNTaxTotal();
bool changed = false;
for (unsigned i = 0; i < numTaxa; ++i)
{
NxsString oldName = tb.GetTaxonLabel(i);
unsigned oldOffset = 0;
unsigned newOffset = 0;
std::string prefix;
for (; newOffset < 10 && oldOffset < oldName.length(); ++oldOffset)
{
char c = oldName[oldOffset];
if ((isgraph(c)) && (strchr("!@#$%^&*.?|()[]{}/\\,;:=*\'\"`-+<>", c) == NULL))
{
if (newOffset == 0 && isdigit(c))
{
prefix.append(1, 't');
newOffset += 1;
}
prefix.append(1, toupper(c));
newOffset += 1;
}
}
std::string newLabel = assignUniqueName(prefix, 10, safeLabelSet);
safeLabelSet.insert(newLabel);
vs->push_back(newLabel);
if (newLabel != oldName)
changed = true;
}
return changed;
}
/*----------------------------------------------------------------------------------------------------------------------
| Right-justifies `x' in a field `w' characters wide with precision `p', using blank spaces to fill in unused
| portions on the left-hand side of the field. Specify true for `clear_first' to first empty the string. Assumes that
| the specified width is enough to accommodate the string representation of `x'.
*/
NxsString &NxsString::RightJustifyDbl(
double x, /* double value to right justify */
unsigned w, /* width of field */
unsigned p, /* precision to use when displaying `x' */
bool clear_first) /* if true, initialize stored string first to the empty string */
{
if (clear_first)
erase();
char fmtstr[81];
sprintf(fmtstr, "%%.%df", p);
NxsString tmp;
tmp.PrintF(fmtstr, x);
NCL_ASSERT(w >= tmp.length());
unsigned num_spaces = w - tmp.length();
for (unsigned k = 0; k < num_spaces; k++)
*this += ' ';
*this += tmp;
return *this;
}
bool formLegalPhylipName(const std::string & origName, const NxsString & numericExtension, const std::set<std::string> & used, std::string & toReturn)
{
const unsigned MAX_PHYLIP_NAME_LENGTH = 10;
unsigned postLen = numericExtension.length();
if (postLen > MAX_PHYLIP_NAME_LENGTH)
throw NxsException("Number of duplicate names exceed the capacity of our poorly thought out mechanism for avoiding name clashes");
const unsigned unPaddedLen = postLen + origName.length();
if (unPaddedLen <= MAX_PHYLIP_NAME_LENGTH)
toReturn = origName;
else if (postLen == MAX_PHYLIP_NAME_LENGTH)
toReturn.clear();
else
toReturn.assign(origName.c_str(), MAX_PHYLIP_NAME_LENGTH - postLen);
toReturn.append(numericExtension.c_str());
if (unPaddedLen < MAX_PHYLIP_NAME_LENGTH)
toReturn.append(MAX_PHYLIP_NAME_LENGTH - unPaddedLen, ' ');
const std::string cap = NxsString::get_upper(toReturn);
return (used.find(cap) == used.end());
}
/*----------------------------------------------------------------------------------------------------------------------
| Shortens stored string to `n' - 3 characters, making the last three characters "...". If string is already less than
| `n' characters in length, this function has no effect. This is useful when it is desirable to show some of the
| contents of a string, even when the string will not fit in its entirety into the space available for displaying it.
| Assumes that `n' is at least 4.
*/
NxsString &NxsString::ShortenTo(
unsigned n) /* maximum number of characters available for displaying the string */
{
NCL_ASSERT(n > 3);
if (length() <= static_cast<unsigned>(n))
return *this;
NxsString s;
for (NxsString::iterator sIt = begin(); sIt != end(); sIt++)
{
s += (*sIt);
if (s.length() >= n - 3)
break;
}
s += "...";
*this = s;
return *this;
}
std::string assignUniqueName(const std::string & prefix, unsigned maxLen, const std::set<std::string> & safeLabelSet)
{
NxsString s;
s << prefix;
std::set<std::string>::const_iterator sIt = safeLabelSet.find(s);
if (sIt == safeLabelSet.end())
return s;
unsigned i = 1;
for (;;)
{
NxsString numAsStr;
numAsStr << i++;
s.clear();
unsigned concatLen = numAsStr.length() + prefix.length();
if (concatLen > maxLen)
s << prefix.substr(0, 2*maxLen - 1 - concatLen);
else
s << prefix;
s << numAsStr;
sIt = safeLabelSet.find(s);
if (sIt == safeLabelSet.end())
return s;
}
}
