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;
}
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;
}
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;
}
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);
}
}
}
}
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);
}
}
}
}
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;
}
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;
}
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;
}
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);
}
}
}
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;
}
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);
}
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;
}
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;
}