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///////////////////////////////////////////////////////////////////////////////////////////////////
// File : Taxonomy.cpp
// Purpose : Handles the taxonomy functions for ParsInsert
//
// CTaxEntry: Class to manage heirarchy of taxonomic classifications
// Count of number of occurances of given name at given rank
// Keeps list of all entries that were defined to lower ranks
//
// Developer : David Knox (david.knox@colorado.edu) Jan 2011
// Copyright : Copyright (C) 2007-2011 David Knox
//
// Web site : http://parsinsert.sourceforge.net/
//
///////////////////////////////////////////////////////////////////////////////////////////////////
// This file is part of ParsInsert.
//
// ParsInsert is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// ParsInsert is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with ParsInsert. If not, see <http://www.gnu.org/licenses/>.
///////////////////////////////////////////////////////////////////////////////////////////////////
#include "Taxonomy.h"
///////////////////////////////////////////////////////////////////////////////////////////////////
CTaxEntry :: CTaxEntry(LPCSTR _name)
{
name = _name;
count = 0;
entries.clear();
}
///////////////////////////////////////////////////////////////////////////////////////////////////
CTaxEntry :: ~CTaxEntry()
{
// release all the subentries
for (CTaxEntryList::iterator iter=entries.begin() ; iter != entries.end() ; ++iter)
{
delete (*iter).second;
}
entries.clear();
}
///////////////////////////////////////////////////////////////////////////////////////////////////
BOOL CTaxEntry :: Add(LPCSTR tax, int votes)
{
// Add the first name in the taxonomy to this entry
count += votes;
if (strlen(tax) == 0)
return TRUE;
// strip next rank off string
string subentry = tax; // assume whole string is this name
string rest = "";
int len = strcspn(tax, ";/");
if (len < subentry.length())
{
rest = subentry.substr(len+1);
subentry = subentry.substr(0, len);
}
Trim(subentry, " \r\n\t");
// lookup in table to get entry
CTaxEntry *ptr = entries[subentry];
if (ptr == NULL)
{
ptr = new CTaxEntry(subentry.c_str());
entries[subentry] = ptr;
}
// add rest to that entry
ptr->Add(rest.c_str(), votes);
return TRUE;
}
///////////////////////////////////////////////////////////////////////////////////////////////////
BOOL CTaxEntry :: Display(LPCSTR leader, int levels)
{
if (levels <= 0) return FALSE;
--levels;
if (leader != NULL)
DisplayL("%s[%s] %d\n", leader, name.c_str(), count);
string indent = leader;
indent += " ";
// display all the subentries
for (CTaxEntryList::iterator iter=entries.begin() ; iter != entries.end() ; ++iter)
{
string key = (*iter).first;
CTaxEntry *ptr = (*iter).second;
ptr->Display(indent.c_str(), levels);
}
return TRUE;
}
///////////////////////////////////////////////////////////////////////////////////////////////////
int CTaxEntry :: FindBest(int threshPercent, CStringList& taxList)
{
// Find the best taxonomy with at least thresh count
taxList.clear();
int thresh = count * threshPercent / 100;
for (CTaxEntryList::iterator iter=entries.begin() ; iter != entries.end() ; ++iter)
{
string key = (*iter).first;
CTaxEntry *ptr = (*iter).second;
ptr->FindBestSubentry(thresh, "", taxList);
}
return taxList.size();
}
///////////////////////////////////////////////////////////////////////////////////////////////////
void CTaxEntry :: FindBestSubentry(int thresh, LPCSTR lineage, CStringList& taxList)
{
// Find the best taxonomy with at least thresh count
int ntax = 0;
string myLineage = lineage;
if (!myLineage.empty())
myLineage += ";";
myLineage += name;
for (CTaxEntryList::iterator iter=entries.begin() ; iter != entries.end() ; ++iter)
{
string key = (*iter).first;
CTaxEntry *ptr = (*iter).second;
if (ptr->count < thresh)
continue;
++ntax;
ptr->FindBestSubentry(thresh, myLineage.c_str(), taxList);
}
if (ntax == 0)
taxList.push_back(myLineage); // if no other lineage added, add my lineage
}
///////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////////////////////////
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