/*! \fn void Filter::Print()
* \brief to write the filter features
*/
void Filter::Print()
{
std::cerr << "The filter has the following features \n";
PrintId();
PrintHost();
PrintPort();
}
static void PrintModules (const cc65_moduleinfo* M)
/* Output a list of modules */
{
unsigned I;
const cc65_moduledata* D;
/* Modules */
for (I = 0, D = M->data; I < M->count; ++I, ++D) {
PrintId (D->module_id, 8);
Print ("%-24s", D->module_name);
PrintId (D->source_id, 8);
PrintId (D->library_id, 9);
PrintId (D->scope_id, 6);
NewLine ();
}
}
/*! \fn void Synchronizer::Print()
* \brief to write the synchronizer features
*/
void Synchronizer::Print()
{
std::cerr << "The synchronizer has the following features \n";
PrintId();
PrintHost();
PrintPort();
}
static void PrintLines (const cc65_lineinfo* L)
/* Output a list of lines */
{
unsigned I;
const cc65_linedata* D;
/* Lines */
for (I = 0, D = L->data; I < L->count; ++I, ++D) {
PrintId (D->line_id, 8);
PrintId (D->source_id, 8);
PrintNumber (D->source_line, 6, 9);
PrintNumber (D->line_type, 4, 6);
PrintNumber (D->count, 3, 0);
NewLine ();
}
}
/*! \fn void Module::Print()
* \brief to write the module features
*/
void Module::Print()
{
std::cerr << "The module has the following features \n";
PrintId();
PrintHost();
PrintPort();
}
static void PrintSpans (const cc65_spaninfo* S)
/* Output a list of spans */
{
unsigned I;
const cc65_spandata* D;
/* Segments */
for (I = 0, D = S->data; I < S->count; ++I, ++D) {
PrintId (D->span_id, 7);
PrintAddr (D->span_start, 8);
PrintAddr (D->span_end, 9);
PrintId (D->segment_id, 7);
PrintId (D->type_id, 6);
PrintNumber (D->line_count, 6, 7);
PrintNumber (D->scope_count, 7, 0);
NewLine ();
}
}
static void PrintScopes (const cc65_scopeinfo* S)
/* Output a list of scopes */
{
unsigned I;
const cc65_scopedata* D;
/* Segments */
for (I = 0, D = S->data; I < S->count; ++I, ++D) {
PrintId (D->scope_id, 8);
Print ("%-24s", D->scope_name);
PrintNumber (D->scope_type, 4, 8); /* ## */
PrintSize (D->scope_size, 8);
PrintId (D->parent_id, 8);
PrintId (D->symbol_id, 8);
PrintId (D->module_id, 0);
NewLine ();
}
}
/*! \fn void RoutingNode::Print()
* \brief to write the RoutingNode features
*/
void RoutingNode::Print()
{
std::cerr << "The routing node has the following features \n";
PrintId();
PrintHost();
PrintSource();
PrintPrevious();
PrintType();
PrintFull();
}
static void PrintCSymbols (const cc65_csyminfo* S)
/* Output a list of C symbols */
{
unsigned I;
const cc65_csymdata* D;
/* Segments */
for (I = 0, D = S->data; I < S->count; ++I, ++D) {
PrintId (D->csym_id, 6);
Print ("%-28s", D->csym_name);
PrintId (D->type_id, 6);
PrintNumber (D->csym_kind, 4, 6);
PrintNumber (D->csym_sc, 4, 6);
PrintNumber (D->csym_offs, 4, 8);
PrintId (D->symbol_id, 6);
PrintId (D->scope_id, 0);
NewLine ();
}
}
static void PrintSymbols (const cc65_symbolinfo* S)
/* Output a list of symbols */
{
unsigned I;
const cc65_symboldata* D;
/* Segments */
for (I = 0, D = S->data; I < S->count; ++I, ++D) {
PrintId (D->symbol_id, 6);
Print ("%-24s", D->symbol_name);
PrintNumber (D->symbol_type, 4, 6);
PrintNumber (D->symbol_size, 4, 6);
PrintNumber (D->symbol_value, 5, 7);
PrintId (D->export_id, 7);
PrintId (D->segment_id, 6);
PrintId (D->scope_id, 6);
PrintId (D->parent_id, 0);
NewLine ();
}
}
static void PrintType (unsigned Id, const cc65_typedata* T)
/* Output one type */
{
/* Output the id */
PrintId (Id, 6);
while (1) {
switch (T->what) {
case CC65_TYPE_VOID:
Print ("VOID");
goto ExitPoint;
case CC65_TYPE_BYTE:
Print ("BYTE");
goto ExitPoint;
case CC65_TYPE_WORD:
Print ("WORD");
goto ExitPoint;
case CC65_TYPE_DBYTE:
Print ("DBYTE");
goto ExitPoint;
case CC65_TYPE_DWORD:
Print ("DWORD");
goto ExitPoint;
case CC65_TYPE_FARPTR:
Print ("FAR ");
/* FALLTHROUGH */
case CC65_TYPE_PTR:
Print ("POINTER TO ");
T = T->data.ptr.ind_type;
break;
case CC65_TYPE_ARRAY:
Print ("ARRAY[%u] OF ", T->data.array.ele_count);
T = T->data.array.ele_type;
break;
default:
/* Anything else is currently not implemented */
Print ("***NOT IMPLEMENTED***");
goto ExitPoint;
}
}
ExitPoint:
NewLine ();
}
static void PrintLibraries (const cc65_libraryinfo* L)
/* Output a list of libraries */
{
unsigned I;
const cc65_librarydata* D;
/* Libraries */
for (I = 0, D = L->data; I < L->count; ++I, ++D) {
PrintId (D->library_id, 8);
Print ("%-24s", D->library_name);
NewLine ();
}
}
static void PrintSources (const cc65_sourceinfo* S)
/* Output a list of sources */
{
unsigned I;
const cc65_sourcedata* D;
/* Segments */
for (I = 0, D = S->data; I < S->count; ++I, ++D) {
PrintId (D->source_id, 8);
Print ("%-30s", D->source_name);
PrintNumber (D->source_size, 7, 9);
PrintTime (D->source_mtime, 0);
NewLine ();
}
}
//-------------------------------------------------------------------------
void CMaskWriterFasta::Print( objects::CBioseq_Handle& bsh,
const TMaskList & mask,
bool parsed_id )
{
PrintId( bsh, parsed_id );
os << endl;
CSeqVector data = bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac);
/// FIXME: this can be implemented as a call to CFastaOstream, which
/// understands masking via a seq-loc
// if( dest->GetIupacna().CanGet() )
if( true )
{
string accumulator;
TMaskList::const_iterator imask = mask.begin();
for( TSeqPos i = 0; i < data.size(); ++i )
{
char letter = data[i];
if( imask != mask.end() && i >= imask->first ) {
if( i <= imask->second )
letter = tolower((unsigned char) letter);
else
{
++imask;
if( imask != mask.end()
&& i >= imask->first && i <= imask->second )
letter = tolower((unsigned char) letter);
}
}
accumulator.append( 1, letter );
if( !((i + 1)%60) )
{
os << accumulator << "\n";
accumulator = "";
}
}
if( accumulator.length() ) os << accumulator << "\n";
}
}
static void PrintSegments (const cc65_segmentinfo* S)
/* Output a list of segments */
{
unsigned I;
const cc65_segmentdata* D;
/* Segments */
for (I = 0, D = S->data; I < S->count; ++I, ++D) {
PrintId (D->segment_id, 8);
Print ("%-16s", D->segment_name);
PrintAddr (D->segment_start, 9);
PrintSize (D->segment_size, 7);
Print ("%-16s", D->output_name? D->output_name : "");
PrintSize (D->output_offs, 6);
NewLine ();
}
}
void CAlnVecPrinter::PopsetStyle(int scrn_width,
EAlgorithm algorithm)
{
x_SetChars();
switch(algorithm) {
case eUseSeqString:
{
TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1;
const CAlnMap::TNumrow nrows = m_NumRows;
const CAlnMap::TNumseg nsegs = m_AlnVec.GetNumSegs();
const CDense_seg::TStarts& starts = m_AlnVec.GetDenseg().GetStarts();
const CDense_seg::TLens& lens = m_AlnVec.GetDenseg().GetLens();
vector<string> buffer(nrows);
for (CAlnMap::TNumrow row = 0; row < nrows; row++) {
// allocate space for the row
buffer[row].reserve(aln_len + 1);
string buff;
int seg, pos, left_seg = -1, right_seg = -1;
TSignedSeqPos start;
TSeqPos len;
// determine the ending right seg
for (seg = nsegs - 1, pos = seg * nrows + row;
seg >= 0; --seg, pos -= nrows) {
if (starts[pos] >= 0) {
right_seg = seg;
break;
}
}
for (seg = 0, pos = row; seg < nsegs; ++seg, pos += nrows) {
len = lens[seg];
if ((start = starts[pos]) >= 0) {
left_seg = seg; // ending left seg is at most here
m_AlnVec.GetSeqString(buff,
row,
start,
start + len * m_AlnVec.GetWidth(row) - 1);
buffer[row] += buff;
} else {
// add appropriate number of gap/end chars
char* ch_buff = new char[len+1];
char fill_ch;
if (left_seg < 0 || seg > right_seg && right_seg > 0) {
fill_ch = m_AlnVec.GetEndChar();
} else {
fill_ch = m_AlnVec.GetGapChar(row);
}
memset(ch_buff, fill_ch, len);
ch_buff[len] = 0;
buffer[row] += ch_buff;
delete[] ch_buff;
}
}
}
TSeqPos pos = 0;
do {
for (CAlnMap::TNumrow row = 0; row < nrows; row++) {
PrintNumRow(row);
PrintId(row);
PrintSeqPos(m_AlnVec.GetSeqPosFromAlnPos(row, pos, CAlnMap::eLeft));
*m_Out << buffer[row].substr(pos, scrn_width)
<< " "
<< m_AlnVec.GetSeqPosFromAlnPos(row, pos + scrn_width - 1,
CAlnMap::eLeft)
<< endl;
}
*m_Out << endl;
pos += scrn_width;
if (pos + scrn_width > aln_len) {
scrn_width = aln_len - pos;
}
} while (pos < aln_len);
break;
}
case eUseAlnSeqString:
{
TSeqPos aln_pos = 0;
CAlnMap::TSignedRange rng;
do {
// create range
rng.Set(aln_pos, aln_pos + scrn_width - 1);
string aln_seq_str;
aln_seq_str.reserve(scrn_width + 1);
// for each sequence
for (CAlnMap::TNumrow row = 0; row < m_NumRows; row++) {
PrintNumRow(row);
PrintId(row);
PrintSeqPos(m_AlnVec.GetSeqPosFromAlnPos(row, rng.GetFrom(),
CAlnMap::eLeft));
*m_Out << m_AlnVec.GetAlnSeqString(aln_seq_str, row, rng)
<< " "
<< m_AlnVec.GetSeqPosFromAlnPos(row, rng.GetTo(),
CAlnMap::eLeft)
<< endl;
}
*m_Out << endl;
aln_pos += scrn_width;
} while (aln_pos < m_AlnVec.GetAlnStop());
break;
}
case eUseWholeAlnSeqString:
{
CAlnMap::TNumrow row, nrows = m_NumRows;
vector<string> buffer(nrows);
vector<CAlnMap::TSeqPosList> insert_aln_starts(nrows);
vector<CAlnMap::TSeqPosList> insert_starts(nrows);
vector<CAlnMap::TSeqPosList> insert_lens(nrows);
vector<CAlnMap::TSeqPosList> scrn_lefts(nrows);
vector<CAlnMap::TSeqPosList> scrn_rights(nrows);
// Fill in the vectors for each row
for (row = 0; row < nrows; row++) {
m_AlnVec.GetWholeAlnSeqString
(row,
buffer[row],
&insert_aln_starts[row],
&insert_starts[row],
&insert_lens[row],
scrn_width,
&scrn_lefts[row],
&scrn_rights[row]);
}
// Visualization
TSeqPos pos = 0, aln_len = m_AlnVec.GetAlnStop() + 1;
do {
for (row = 0; row < nrows; row++) {
PrintNumRow(row);
PrintId(row);
PrintSeqPos(scrn_lefts[row].front());
*m_Out << buffer[row].substr(pos, scrn_width)
<< " "
<< scrn_rights[row].front()
<< endl;
scrn_lefts[row].pop_front();
scrn_rights[row].pop_front();
}
*m_Out << endl;
pos += scrn_width;
if (pos + scrn_width > aln_len) {
scrn_width = aln_len - pos;
}
} while (pos < aln_len);
break;
}
}
x_UnsetChars();
}
void CAlnVecPrinter::ClustalStyle(int scrn_width,
EAlgorithm algorithm)
{
x_SetChars();
*m_Out << "CLUSTAL W (1.83) multiple sequence alignment" << endl << endl;
switch(algorithm) {
case eUseSeqString:
{
TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1;
const CAlnMap::TNumseg nsegs = m_AlnVec.GetNumSegs();
const CDense_seg::TStarts& starts = m_AlnVec.GetDenseg().GetStarts();
const CDense_seg::TLens& lens = m_AlnVec.GetDenseg().GetLens();
CAlnMap::TNumrow row;
vector<string> buffer(m_NumRows+1);
for (row = 0; row < m_NumRows; row++) {
// allocate space for the row
buffer[row].reserve(aln_len + 1);
string buff;
int seg, pos, left_seg = -1, right_seg = -1;
TSignedSeqPos start;
TSeqPos len;
// determine the ending right seg
for (seg = nsegs - 1, pos = seg * m_NumRows + row;
seg >= 0; --seg, pos -= m_NumRows) {
if (starts[pos] >= 0) {
right_seg = seg;
break;
}
}
for (seg = 0, pos = row; seg < nsegs; ++seg, pos += m_NumRows) {
len = lens[seg];
if ((start = starts[pos]) >= 0) {
left_seg = seg; // ending left seg is at most here
m_AlnVec.GetSeqString(buff,
row,
start,
start + len * m_AlnVec.GetWidth(row) - 1);
buffer[row] += buff;
} else {
// add appropriate number of gap/end chars
char* ch_buff = new char[len+1];
char fill_ch;
if (left_seg < 0 || seg > right_seg && right_seg > 0) {
fill_ch = m_AlnVec.GetEndChar();
} else {
fill_ch = m_AlnVec.GetGapChar(row);
}
memset(ch_buff, fill_ch, len);
ch_buff[len] = 0;
buffer[row] += ch_buff;
delete[] ch_buff;
}
}
}
// Find identities
buffer[m_NumRows].resize(aln_len);
for (TSeqPos pos = 0; pos < aln_len; pos++) {
bool identity = true;
char residue = buffer[0][pos];
for (row = 1; row < m_NumRows; row++) {
if (buffer[row][pos] != residue) {
identity = false;
break;
}
}
buffer[m_NumRows][pos] = (identity ? '*' : ' ');
}
TSeqPos aln_pos = 0;
do {
for (CAlnMap::TNumrow row = 0; row < m_NumRows; row++) {
PrintId(row);
*m_Out << buffer[row].substr(aln_pos, scrn_width)
<< endl;
}
m_Out->width(m_IdFieldLen);
*m_Out << "";
*m_Out << buffer[m_NumRows].substr(aln_pos, scrn_width)
<< endl << endl;
aln_pos += scrn_width;
if (aln_pos + scrn_width > aln_len) {
scrn_width = aln_len - aln_pos;
}
} while (aln_pos < aln_len);
break;
}
case eUseAlnSeqString:
{
TSeqPos aln_pos = 0;
TSeqPos aln_stop = m_AlnVec.GetAlnStop();
CAlnMap::TSignedRange rng;
string identities_str;
identities_str.reserve(scrn_width + 1);
do {
// create range
rng.Set(aln_pos, min(aln_pos + scrn_width - 1, aln_stop));
string aln_seq_str;
aln_seq_str.reserve(scrn_width + 1);
// for each sequence
for (CAlnMap::TNumrow row = 0; row < m_NumRows; row++) {
PrintId(row);
*m_Out << m_AlnVec.GetAlnSeqString(aln_seq_str, row, rng)
<< endl;
if (row == 0) {
identities_str = aln_seq_str;
} else {
for (size_t i = 0; i < aln_seq_str.length(); i++) {
if (aln_seq_str[i] != identities_str[i]) {
identities_str[i] = ' ';
}
}
}
}
for (size_t i = 0; i < identities_str.length(); i++) {
if (identities_str[i] != ' ') {
identities_str[i] = '*';
}
}
m_Out->width(m_IdFieldLen);
*m_Out << "";
*m_Out << identities_str
<< endl << endl;
aln_pos += scrn_width;
} while (aln_pos < m_AlnVec.GetAlnStop());
break;
}
case eUseWholeAlnSeqString:
{
CAlnMap::TNumrow row;
vector<string> buffer(m_NumRows+1);
// Fill in the vectors for each row
for (row = 0; row < m_NumRows; row++) {
m_AlnVec.GetWholeAlnSeqString(row, buffer[row]);
}
TSeqPos pos = 0;
const TSeqPos aln_len = m_AlnVec.GetAlnStop() + 1;
// Find identities
buffer[m_NumRows].resize(aln_len);
for (pos = 0; pos < aln_len; pos++) {
bool identity = true;
char residue = buffer[0][pos];
for (row = 1; row < m_NumRows; row++) {
if (buffer[row][pos] != residue) {
identity = false;
break;
}
}
buffer[m_NumRows][pos] = (identity ? '*' : ' ');
}
// Visualization
pos = 0;
do {
for (row = 0; row < m_NumRows; row++) {
PrintId(row);
*m_Out << buffer[row].substr(pos, scrn_width)
<< endl;
}
m_Out->width(m_IdFieldLen);
*m_Out << "";
*m_Out << buffer[m_NumRows].substr(pos, scrn_width)
<< endl << endl;
pos += scrn_width;
if (pos + scrn_width > aln_len) {
scrn_width = aln_len - pos;
}
} while (pos < aln_len);
break;
}
}
x_UnsetChars();
}
void FnIdGenerator::OnInput(wxCommandEvent &event)
{
PrintId();
event.Skip();
}