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|
// Copyright (C) 1999-2003 Paul O. Lewis
//
// This file is part of NCL (Nexus Class Library) version 2.0.
//
// NCL 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 2 of the License, or
// (at your option) any later version.
//
// NCL 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 NCL; if not, write to the Free Software Foundation, Inc.,
// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
#include "ncl.h"
/*----------------------------------------------------------------------------------------------------------------------
| Initializes all pointer data members to NULL, and all bool data members to true except isUserSupplied, which is
| initialized to false.
*/
NxsBlock::NxsBlock()
{
next = NULL;
nexus = NULL;
isEmpty = true;
isEnabled = true;
isUserSupplied = false;
id.clear();
errormsg.clear();
}
/*----------------------------------------------------------------------------------------------------------------------
| Nothing to be done.
*/
NxsBlock::~NxsBlock()
{
}
/*----------------------------------------------------------------------------------------------------------------------
| This base class version simply returns 0 but a derived class should override this function if it needs to construct
| and run a NxsSetReader object to read a set involving characters. The NxsSetReader object may need to use this
| function to look up a character label encountered in the set. A class that overrides this method should return the
| character index in the range [1..nchar].
*/
unsigned NxsBlock::CharLabelToNumber(
NxsString s) /* the character label to be translated to the character's number */
{
# if defined(HAVE_PRAGMA_UNUSED)
# pragma unused(s)
# endif
return 0;
}
/*----------------------------------------------------------------------------------------------------------------------
| Sets the value of isEnabled to false. A NxsBlock can be disabled (by calling this method) if blocks of that type
| are to be skipped during execution of the NEXUS file. If a disabled block is encountered, the virtual
| NxsReader::SkippingDisabledBlock function is called, giving your application the opportunity to inform the user
| that a block was skipped.
*/
void NxsBlock::Disable()
{
isEnabled = false;
}
/*----------------------------------------------------------------------------------------------------------------------
| Sets the value of isEnabled to true. A NxsBlock can be disabled (by calling Disable) if blocks of that type are to
| be skipped during execution of the NEXUS file. If a disabled block is encountered, the virtual
| NxsReader::SkippingDisabledBlock function is called, giving your application the opportunity to inform the user
| that a block was skipped.
*/
void NxsBlock::Enable()
{
isEnabled = true;
}
/*----------------------------------------------------------------------------------------------------------------------
| Returns value of isEnabled, which can be controlled through use of the Enable and Disable member functions. A
| NxsBlock should be disabled if blocks of that type are to be skipped during execution of the NEXUS file. If a
| disabled block is encountered, the virtual NxsReader::SkippingDisabledBlock function is called, giving your
| application the opportunity to inform the user that a block was skipped.
*/
bool NxsBlock::IsEnabled()
{
return isEnabled;
}
/*----------------------------------------------------------------------------------------------------------------------
| Returns value of isUserSupplied, which is true if and only if this block's Read function is called to process a
| block of this type appearing in a data file. This is useful because in some cases, a block object may be created
| internally (e.g. a NxsTaxaBlock may be populated using taxon names provided in a DATA block), and such blocks do
| not require permission from the user to delete data stored therein.
*/
bool NxsBlock::IsUserSupplied()
{
return isUserSupplied;
}
/*----------------------------------------------------------------------------------------------------------------------
| Returns true if Read function has not been called since the last Reset. This base class version simply returns the
| value of the data member isEmpty. If you derive a new block class from NxsBlock, be sure to set isEmpty to true in
| your Reset function and isEmpty to false in your Read function.
*/
bool NxsBlock::IsEmpty()
{
return isEmpty;
}
/*----------------------------------------------------------------------------------------------------------------------
| Returns the id NxsString.
*/
NxsString NxsBlock::GetID()
{
return id;
}
/*----------------------------------------------------------------------------------------------------------------------
| This virtual function must be overridden for each derived class to provide the ability to read everything following
| the block name (which is read by the NxsReader object) to the end or endblock statement. Characters are read from
| the input stream 'in'. Note that to get output comments displayed, you must derive a class from NxsToken, override
| the member function OutputComment to display a supplied comment, and then pass a reference to an object of the
| derived class to this function.
*/
void NxsBlock::Read(
NxsToken &token) /* the NxsToken to use for reading block */
{
# if defined(HAVE_PRAGMA_UNUSED)
# pragma unused(token)
# endif
}
/*----------------------------------------------------------------------------------------------------------------------
| This virtual function should be overridden for each derived class to completely reset the block object in
| preparation for reading in another block of this type. This function is called by the NxsReader object just prior to
| calling the block object's Read function.
*/
void NxsBlock::Reset()
{
}
/*----------------------------------------------------------------------------------------------------------------------
| This virtual function provides a brief report of the contents of the block.
*/
void NxsBlock::Report(
ostream &out) /* the output stream to which the report is sent */
{
# if defined(HAVE_PRAGMA_UNUSED)
# pragma unused(out)
# endif
}
/*----------------------------------------------------------------------------------------------------------------------
| Sets the nexus data member of the NxsBlock object to 'nxsptr'.
*/
void NxsBlock::SetNexus(
NxsReader *nxsptr) /* pointer to a NxsReader object */
{
nexus = nxsptr;
}
/*----------------------------------------------------------------------------------------------------------------------
| This function is called when an unknown command named commandName is about to be skipped. This version of the
| function does nothing (i.e., no warning is issued that a command was unrecognized). Override this virtual function
| in a derived class to provide such warnings to the user.
*/
void NxsBlock::SkippingCommand(
NxsString commandName) /* the name of the command being skipped */
{
# if defined(HAVE_PRAGMA_UNUSED)
# pragma unused(commandName)
# endif
}
/*----------------------------------------------------------------------------------------------------------------------
| This base class version simply returns 0, but a derived class should override this function if it needs to construct
| and run a NxsSetReader object to read a set involving taxa. The NxsSetReader object may need to use this function to
| look up a taxon label encountered in the set. A class that overrides this method should return the taxon index in
| the range [1..ntax].
*/
unsigned NxsBlock::TaxonLabelToNumber(
NxsString s) /* the taxon label to be translated to a taxon number */
{
# if defined(HAVE_PRAGMA_UNUSED)
# pragma unused(s)
# endif
return 0;
}
|
