Esempio n. 1
0
bool CMarkupSTL::OutOfElem()
{
	// Go to parent element
	if ( m_iPosParent )
	{
		x_SetPos( m_aPos[m_iPosParent].iElemParent, m_iPosParent, m_iPos );
		return true;
	}
	return false;
}
Esempio n. 2
0
bool CMarkupSTL::RemoveChildElem()
{
	// Remove current child position element
	if ( m_iPosChild )
	{
		int iPosChild = x_RemoveElem( m_iPosChild );
		x_SetPos( m_iPosParent, m_iPos, iPosChild );
		return true;
	}
	return false;
}
Esempio n. 3
0
bool CMarkupSTL::RemoveElem()
{
	// Remove current main position element
	if ( m_iPos && m_nNodeType == MNT_ELEMENT )
	{
		int iPos = x_RemoveElem( m_iPos );
		x_SetPos( m_iPosParent, iPos, 0 );
		return true;
	}
	return false;
}
Esempio n. 4
0
void CSeqVector_CI::SetRandomizeAmbiguities(CRef<INcbi2naRandomizer> randomizer)
{
    if ( randomizer != m_Randomizer ) {
        TSeqPos pos = GetPos();
        m_Randomizer = randomizer;
        x_ResetBackup();
        if ( x_CacheSize() ) {
            x_ResetCache();
            if ( m_Seg ) {
                x_SetPos(pos);
            }
        }
    }
}
Esempio n. 5
0
void CSeqVector_CI::SetCoding(TCoding coding)
{
    if ( m_Coding != coding ) {
        TSeqPos pos = GetPos();
        m_Coding = coding;
        x_ResetBackup();
        if ( x_CacheSize() ) {
            x_ResetCache();
            if ( m_Seg ) {
                x_SetPos(pos);
            }
        }
    }
}
Esempio n. 6
0
bool CMarkupSTL::RestorePos( const char * szPosName )
{
	// Restore element position if found in saved position map
	if (!szPosName)
		return false;

	std::map<CStdString, SavedPos>::iterator iter=m_mapSavedPos.find( szPosName );

	if ( iter!=m_mapSavedPos.end() )
	{
		x_SetPos( iter->second.iPosParent, iter->second.iPos, iter->second.iPosChild );
		return true;
	}
	return false;
}
Esempio n. 7
0
bool CMarkupSTL::FindElem( const char * szName )
{
	// Change current position only if found
	//
	if ( m_aPos.size() )
	{
		int iPos = x_FindElem( m_iPosParent, m_iPos, szName );
		if ( iPos )
		{
			// Assign new position
			x_SetPos( m_aPos[iPos].iElemParent, iPos, 0 );
			return true;
		}
	}
	return false;
}
Esempio n. 8
0
bool CMarkupSTL::IntoElem()
{
	// If there is no child position and IntoElem is called it will succeed in release 6.3
	// (A subsequent call to FindElem will find the first element)
	// The following short-hand behavior was never part of EDOM and was misleading
	// It would find a child element if there was no current child element position and go into it
	// It is removed in release 6.3, this change is NOT backwards compatible!
	// if ( ! m_iPosChild )
	//	FindChildElem();

	if ( m_iPos && m_nNodeType == MNT_ELEMENT )
	{
		x_SetPos( m_iPos, m_iPosChild, 0 );
		return true;
	}
	return false;
}
Esempio n. 9
0
void CSeqVector_CI::SetStrand(ENa_strand strand)
{
    if ( IsReverse(m_Strand) == IsReverse(strand) ) {
        m_Strand = strand;
        return;
    }

    TSeqPos pos = GetPos();
    m_Strand = strand;
    x_ResetBackup();
    if ( x_CacheSize() ) {
        x_ResetCache();
        if ( m_Seg ) {
            m_Seg = CSeqMap_CI();
            x_SetPos(pos);
        }
    }
}
Esempio n. 10
0
bool CMarkupSTL::FindChildElem( const char * szName )
{
	// Change current child position only if found
	//
	// Shorthand: call this with no current main position
	// means find child under root element
	if ( ! m_iPos )
		FindElem();

	int iPosChild = x_FindElem( m_iPos, m_iPosChild, szName );
	if ( iPosChild )
	{
		// Assign new position
		int iPos = m_aPos[iPosChild].iElemParent;
		x_SetPos( m_aPos[iPos].iElemParent, iPos, iPosChild );
		return true;
	}

	return false;
}
Esempio n. 11
0
CSeqVector_CI::CSeqVector_CI(const CSeqVector& seq_vector, TSeqPos pos)
    : m_Scope(seq_vector.m_Scope),
      m_SeqMap(seq_vector.m_SeqMap),
      m_TSE(seq_vector.m_TSE),
      m_Strand(seq_vector.m_Strand),
      m_Coding(seq_vector.m_Coding),
      m_CaseConversion(eCaseConversion_none),
      m_Cache(0),
      m_CachePos(0),
      m_CacheData(),
      m_CacheEnd(0),
      m_BackupPos(0),
      m_BackupData(),
      m_BackupEnd(0),
      m_Randomizer(seq_vector.m_Randomizer),
      m_ScannedStart(0),
      m_ScannedEnd(0)
{
    x_SetPos(pos);
}
Esempio n. 12
0
bool CMarkupSTL::x_AddSubDoc( const char * szSubDoc, bool bInsert, bool bAddChild )
{
	// Add subdocument, parse, and modify positions of affected elements
	//
	int nOffset = 0, iPosParent, iPosBefore;
	if ( bAddChild )
	{
		// Add a subdocument under main position, after current child position
		if ( ! m_iPos )
			return false;
		iPosParent = m_iPos;
		iPosBefore = m_iPosChild;
	}
	else
	{
		iPosParent = m_iPosParent;
		iPosBefore = m_iPos;
	}
	int nFlags = bInsert?1:0;
	x_LocateNew( iPosParent, iPosBefore, nOffset, 0, nFlags );
	bool bEmptyParent = m_aPos[iPosParent].IsEmptyElement();
	if ( bEmptyParent )
		nOffset += 2; // include CRLF

	// if iPosBefore is NULL, insert as first element under parent
	int nParentEndLBeforeAdd = m_aPos[iPosParent].nEndL;
	int iPosFreeBeforeAdd = m_iPosFree;

	// Skip version tag or DTD at start of subdocument
	TokenPos token( szSubDoc );
	int nNodeType = x_ParseNode( token );
	while ( nNodeType && nNodeType != MNT_ELEMENT )
	{
		token.szDoc = &szSubDoc[token.nNext];
		token.nNext = 0;
		nNodeType = x_ParseNode( token );
	}
	CStdString csInsert = token.szDoc;

	// Insert subdocument
	m_aPos[iPosParent].nEndL = nOffset;
	int nReplace = 0, nLeft = nOffset;
	CStdString csParentTagName;
	if ( bEmptyParent )
	{
		csParentTagName = x_GetTagName(iPosParent);
		CStdString csFormat;
		csFormat = _T(">\r\n");
		csFormat += csInsert;
		csFormat += _T("</");
		csFormat += csParentTagName;
		csInsert = csFormat;
		m_aPos[iPosParent].nEndL = m_aPos[iPosParent].nStartR + 2;
		nLeft = m_aPos[iPosParent].nStartR - 1;
		nReplace = 1;
	}
	x_DocChange( nLeft, nReplace, csInsert );

	// Parse subdocument
	int iPos = x_ParseElem(iPosParent);
	m_aPos[iPosParent].nEndL = nParentEndLBeforeAdd;
	if ( iPos <= 0 )
	{
		// Abort because not well-formed
		CStdString csRevert = bEmptyParent?_T("/"):_T("");
		x_DocChange( nLeft, csInsert.GetLength(), csRevert );
		m_iPosFree = iPosFreeBeforeAdd;
		return false;
	}
	else
	{
		// Link in parent and siblings
		m_aPos[iPos].iElemParent = iPosParent;
		if ( iPosBefore )
		{
			m_aPos[iPos].iElemNext = m_aPos[iPosBefore].iElemNext;
			m_aPos[iPosBefore].iElemNext = iPos;
		}
		else
		{
			m_aPos[iPos].iElemNext = m_aPos[iPosParent].iElemChild;
			m_aPos[iPosParent].iElemChild = iPos;
		}

		// Make empty parent pre-adjustment
		if ( bEmptyParent )
		{
			m_aPos[iPosParent].nStartR -= 1;
			m_aPos[iPosParent].nEndL -= (csParentTagName.GetLength() + 1);
		}

		// Adjust, but don't adjust children of iPos (bAfterPos=true)
		x_Adjust( iPos, csInsert.GetLength() - nReplace, true );
	}

	// Set position to top element of subdocument
	if ( bAddChild )
		x_SetPos( m_iPosParent, iPosParent, iPos );
	else // Main
		x_SetPos( m_iPosParent, iPos, 0 );
	return true;
}
Esempio n. 13
0
bool CMarkupSTL::x_AddElem( const char * szName, const char * szValue, bool bInsert, bool bAddChild )
{
	if ( bAddChild )
	{
		// Adding a child element under main position
		if ( ! m_iPos )
			return false;
	}
	else if ( m_iPosParent == 0 )
	{
		// Adding root element
		if ( IsWellFormed() )
			return false;

		// Locate after any version and DTD
		m_aPos[0].nEndL = m_csDoc.GetLength();
	}

	// Locate where to add element relative to current node
	int iPosParent, iPosBefore, nOffset = 0, nLength = 0;
	if ( bAddChild )
	{
		iPosParent = m_iPos;
		iPosBefore = m_iPosChild;
	}
	else
	{
		iPosParent = m_iPosParent;
		iPosBefore = m_iPos;
	}
	int nFlags = bInsert?1:0;
	x_LocateNew( iPosParent, iPosBefore, nOffset, nLength, nFlags );
	bool bEmptyParent = m_aPos[iPosParent].IsEmptyElement();
	if ( bEmptyParent )
		nOffset += 2; // include CRLF

	// Create element and modify positions of affected elements
	// If no szValue is specified, an empty element is created
	// i.e. either <NAME>value</NAME> or <NAME/>
	//
	int iPos = x_GetFreePos();
	m_aPos[iPos].nStartL = nOffset;

	// Set links
	m_aPos[iPos].iElemParent = iPosParent;
	m_aPos[iPos].iElemChild = 0;
	m_aPos[iPos].iElemNext = 0;
	if ( iPosBefore )
	{
		// Link in after iPosBefore
		m_aPos[iPos].iElemNext = m_aPos[iPosBefore].iElemNext;
		m_aPos[iPosBefore].iElemNext = iPos;
	}
	else
	{
		// First child
		m_aPos[iPos].iElemNext = m_aPos[iPosParent].iElemChild;
		m_aPos[iPosParent].iElemChild = iPos;
	}

	// Create string for insert
	CStdString csInsert;
	int nLenName = _tcslen(szName);
	int nLenValue = szValue? _tcslen(szValue) : 0;
	if ( ! nLenValue )
	{
		// <NAME/> empty element
		csInsert = _T("<");
		csInsert += szName;
		csInsert += _T("/>\r\n");
		m_aPos[iPos].nStartR = m_aPos[iPos].nStartL + nLenName + 2;
		m_aPos[iPos].nEndL = m_aPos[iPos].nStartR - 1;
		m_aPos[iPos].nEndR = m_aPos[iPos].nEndL + 1;
	}
	else
	{
		// <NAME>value</NAME>
		CStdString csValue = x_TextToDoc( szValue );
		nLenValue = csValue.GetLength();
		csInsert = _T("<");
		csInsert += szName;
		csInsert += _T(">");
		csInsert += csValue;
		csInsert += _T("</");
		csInsert += szName;
		csInsert += _T(">\r\n");
		m_aPos[iPos].nStartR = m_aPos[iPos].nStartL + nLenName + 1;
		m_aPos[iPos].nEndL = m_aPos[iPos].nStartR + nLenValue + 1;
		m_aPos[iPos].nEndR = m_aPos[iPos].nEndL + nLenName + 2;
	}

	// Insert
	int nReplace = 0, nLeft = m_aPos[iPos].nStartL;
	if ( bEmptyParent )
	{
		CStdString csParentTagName = x_GetTagName(iPosParent);
		CStdString csFormat;
		csFormat = _T(">\r\n");
		csFormat += csInsert;
		csFormat += _T("</");
		csFormat += csParentTagName;
		csInsert = csFormat;
		nLeft -= 3;
		nReplace = 1;
		// x_Adjust is going to update all affected indexes by one amount
		// This will satisfy all except the empty parent
		// Here we pre-adjust for the empty parent
		// The empty tag slash is removed
		m_aPos[iPosParent].nStartR -= 1;
		// For the newly created end tag, see the following example:
		// <A/> (len 4) becomes <A><B/></A> (len 11)
		// In x_Adjust everything will be adjusted 11 - 4 = 7
		// But the nEndL of element A should only be adjusted 5
		m_aPos[iPosParent].nEndL -= (csParentTagName.GetLength() + 1);
	}
	x_DocChange( nLeft, nReplace, csInsert );
	x_Adjust( iPos, csInsert.GetLength() - nReplace );

	if ( bAddChild )
		x_SetPos( m_iPosParent, iPosParent, iPos );
	else
		x_SetPos( iPosParent, iPos, 0 );
	return true;
}