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Alignment.cpp
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Alignment.cpp
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/** \file
\brief Contains the methods of the TAlignment class and its helper class, TAlignLine
*/
#include "Alignment.h"
#include <wx/textfile.h>
#ifdef __DEBIAN__
#define USE_EXTERNAL_CLUSTALW
#endif
#ifndef USE_EXTERNAL_CLUSTALW
#include "clustalw/clustalw.h"
int clustalw_main(int argc,char **argv) ;
#endif
BEGIN_EVENT_TABLE(TAlignment, MyChildBase)
EVT_CLOSE(ChildBase::OnClose)
EVT_SET_FOCUS(ChildBase::OnFocus)
EVT_CHECKBOX(ALIGN_HORIZ, TAlignment::OnHorizontal)
EVT_MENU(MDI_FILE_SAVE, TAlignment::OnFileSave)
EVT_MENU(ALIGNMENT_SETTINGS,TAlignment::OnSettings)
EVT_MENU(ALIGN_BOLD,TAlignment::OnMenuBold)
EVT_MENU(ALIGN_MONO,TAlignment::OnMenuMono)
EVT_MENU(ALIGN_NORM,TAlignment::OnMenuNorm)
EVT_MENU(ALIGN_INVS,TAlignment::OnMenuInvs)
EVT_MENU(ALIGN_SOA,TAlignment::OnMenuSoa)
EVT_MENU(ALIGN_SOAI,TAlignment::OnMenuSoaI)
EVT_MENU(ALIGN_SIML,TAlignment::OnMenuSiml)
EVT_MENU(ALIGN_SEQ,TAlignment::OnMenuSeq)
EVT_MENU(ALIGN_FEAT,TAlignment::OnMenuFeat)
EVT_MENU(ALIGN_RNA,TAlignment::OnMenuRNA)
EVT_MENU(ALIGN_CONS,TAlignment::OnMenuCons)
EVT_MENU(ALIGN_IDENT,TAlignment::OnMenuIdent)
EVT_MENU(SEQ_PRINT, TAlignment::OnSeqPrint)
// Dummies
EVT_MENU(MDI_TOGGLE_FEATURES,ChildBase::OnDummy)
EVT_MENU(MDI_TOGGLE_RESTRICTION,ChildBase::OnDummy)
EVT_MENU(MDI_TOGGLE_IDNA,ChildBase::OnDummy)
EVT_MENU(MDI_VIEW_MODE,ChildBase::OnDummy)
EVT_MENU(MDI_ORFS,ChildBase::OnDummy)
EVT_MENU(MDI_CIRCULAR_LINEAR,ChildBase::OnDummy)
EVT_MENU(MDI_UNDO,ChildBase::OnDummy)
EVT_MENU(MDI_CUT,ChildBase::OnDummy)
EVT_MENU(MDI_COPY,ChildBase::OnDummy)
EVT_MENU(MDI_PASTE,ChildBase::OnDummy)
EVT_MENU(MDI_EDIT_MODE,ChildBase::OnDummy)
EVT_MENU(MDI_EXPORT,ChildBase::OnExport)
EVT_MENU(MDI_MARK_ALL,ChildBase::OnDummy)
EVT_MENU(MDI_FIND,ChildBase::OnDummy)
EVT_MENU(AA_NONE,TABIviewer::OnDummy)
EVT_MENU(AA_KNOWN, TABIviewer::OnDummy)
EVT_MENU(AA_ALL, TABIviewer::OnDummy)
EVT_MENU(AA_THREE, TABIviewer::OnDummy)
EVT_MENU(AA_ONE, TABIviewer::OnDummy)
EVT_MENU(AA_THREE_1, TABIviewer::OnDummy)
EVT_MENU(AA_THREE_2, TABIviewer::OnDummy)
EVT_MENU(AA_THREE_3, TABIviewer::OnDummy)
EVT_MENU(AA_THREE_M1, TABIviewer::OnDummy)
EVT_MENU(AA_THREE_M2, TABIviewer::OnDummy)
EVT_MENU(AA_THREE_M3, TABIviewer::OnDummy)
END_EVENT_TABLE()
TAlignment::TAlignment(wxWindow *parent, const wxString& title)
: ChildBase(parent, title)
{
keepIdentity = false ;
threadRunning = false ;
invs = cons = bold = mono = false ;
def = _T("alignment") ;
match = 2 ; // Match value
mismatch = -1 ; // Mismatch score
gap_penalty = -2 ; // Gap penalty
matrix = _T("BLOSUM") ;
gap = _T("-") ;
algorithm = ALG_CW ;
vec = NULL ;
aaa = NULL ;
colCur = NULL ;
readTabColors ( myapp()->homedir + myapp()->slash + _T("default.tab") ) ;
}
TAlignment::~TAlignment ()
{
}
bool TAlignment::isDNA ()
{
wxString s ;
int a , b = 0 ;
for ( a = 0 ; a < lines.size() ; a++ )
{
if ( !lines[a].isIdentity ) s += lines[a].s ;
}
for ( a = 0 ; a < s.length() ; a++ )
{
wxChar c = s.GetChar ( a ) ;
if ( c == 'N' || c == ' ' || c == '-' ) continue ;
if ( c == 'A' || c == 'C' || c == 'G' || c == 'T' ) continue ;
b++ ;
}
// Guess : if more than 1/4 of the sequence are not ACTGN, it's an amino acid sequence
if ( b >= s.length() / 4 ) return false ;
return true ;
}
bool TAlignment::isAA ()
{
return !isDNA() ;
}
void TAlignment::readTabColors ( wxString filename )
{
// Now we read a color scheme in BioEdit format
wxString fn = filename ;
wxTextFile in ( fn ) ;
in.Open ( *(myapp()->isoconv) ) ;
int a ;
wxColour *c = NULL ;
for ( a = 0 ; a < 256 ; a++ )
{
c = colDNA ;
c[a].Set ( 0 , 100 , 0 ) ;
c = colAA ;
c[a].Set ( 0 , 100 , 0 ) ;
}
bool initial = true ;
while ( !in.Eof() )
{
wxString s ;
if ( initial ) s = in.GetFirstLine() ;
else s = in.GetNextLine() ;
initial = false ;
if ( s.IsEmpty() ) ;
else if ( s.GetChar(0) == '/' )
{
if ( s == _T("/amino acids/") ) c = colAA ;
else if ( s == _T("/nucleotides/") ) c = colDNA ;
else c = NULL ;
}
else if ( c )
{
wxString t = in.GetNextLine () ; // s in int, t is list of chars
int x = atoi ( s.mb_str() ) ;
for ( unsigned int b = 0 ; b < t.length() ; b++ )
{
unsigned char ch = (unsigned char)t.GetChar(b) ;
int red = ( x >> 16 ) & 255 ;
int green = ( x >> 8 ) & 255 ;
int blue = x & 255 ;
c[ch].Set ( red , green , blue ) ;
}
}
}
colCur = colAA ;
}
wxColour TAlignment::findColors ( char c1 , char c2 , bool fg )
{
wxColour r ;
if ( invs && c1 != '-' ) fg = !fg ;
if ( fg )
{
int cc = (unsigned char) c1 ;
if ( !colCur ) r = *wxBLACK ;
else if ( cc < 0 || cc >= 256 ) r = *wxBLACK ;
else r = colCur[cc] ;
}
else r = *wxWHITE ;
// if ( fg && c1 != '-' && c2 != '-' && c1 != c2 )
// r = wxColour ( 200 , 0 , 0 ) ;
return r ;
}
void TAlignment::initme ()
{
// Menus
wxMenu *file_menu = myapp()->frame->getFileMenu ( FILE_MENU_SAVE|FILE_MENU_EXPORT ) ;
wxMenu *tool_menu = myapp()->frame->getToolMenu () ;
wxMenu *help_menu = myapp()->frame->getHelpMenu () ;
wxMenu *view_menu = new wxMenu ;
view_menu->Append(ALIGN_BOLD, txt("m_align_bold") , _T("") , true ) ;
view_menu->Append(ALIGN_MONO, txt("m_align_mono") , _T("") , true ) ;
view_menu->Append(ALIGN_CONS, txt("m_align_cons") , _T("") , true ) ;
view_menu->AppendSeparator();
view_menu->Append(ALIGN_NORM, txt("m_align_norm") , _T("") , true ) ;
view_menu->Append(ALIGN_INVS, txt("m_align_invs") , _T("") , true ) ;
view_menu->Append(ALIGN_SOA , txt("m_align_soa") , _T("") , true ) ;
view_menu->Append(ALIGN_SOAI, txt("m_align_soai") , _T("") , true ) ;
view_menu->Append(ALIGN_SIML, txt("m_align_siml") , _T("") , true ) ;
view_menu->Append(ALIGN_SEQ , txt("m_align_seq") , _T("") , true ) ;
view_menu->Append(ALIGN_FEAT, txt("m_align_feat") , _T("") , true ) ;
view_menu->Append(ALIGN_RNA , txt("m_align_rna") , _T("") , true ) ;
view_menu->AppendSeparator();
view_menu->Append(ALIGN_IDENT, txt("m_align_ident") , _T("") , true ) ;
wxMenuBar *menu_bar = new wxMenuBar;
menu_bar->Append(file_menu, txt("m_file") );
menu_bar->Append(view_menu, txt("m_view") );
menu_bar->Append(tool_menu, txt("m_tools") );
menu_bar->Append(help_menu, txt("m_help") );
SetMenuBar(menu_bar);
menu_bar->FindItem(ALIGN_NORM)->Check ( true ) ;
menu_bar->FindItem(ALIGN_CONS)->Check ( true ) ;
menu_bar->FindItem(ALIGN_IDENT)->Check ( true ) ;
// Not implemented yet
menu_bar->FindItem(ALIGN_SOA )->Enable ( false ) ;
menu_bar->FindItem(ALIGN_SOAI)->Enable ( false ) ;
menu_bar->FindItem(ALIGN_SIML)->Enable ( false ) ;
menu_bar->FindItem(ALIGN_SEQ )->Enable ( false ) ;
menu_bar->FindItem(ALIGN_FEAT)->Enable ( false ) ;
menu_bar->FindItem(ALIGN_RNA )->Enable ( false ) ;
cons = true ;
showIdentity = true ;
Hide () ;
// hs = new wxSplitterWindow ( this , SPLIT_ALIGNMENT ) ;
// Sequence Canvas
sc = new SequenceCanvas ( this , wxPoint ( 0 , 0 ) , wxSize ( -1 , -1 ) ) ;
sc->blankline = 1 ;
sc->child = this ;
sc->EnableScrolling ( true , true ) ;
wxToolBar *toolBar = CreateToolBar(wxNO_BORDER | wxTB_FLAT | wxTB_HORIZONTAL |wxTB_DOCKABLE);
toolBar->Reparent ( this ) ;
toolbar = toolBar ;
myapp()->frame->InitToolBar(toolBar);
toolBar->AddTool( MDI_TEXT_IMPORT ,
myapp()->frame->bitmaps[0] ,
txt("m_new_sequence") ) ;
toolBar->AddTool( MDI_FILE_OPEN,
myapp()->frame->bitmaps[1] ,
txt("m_open") , txt("m_opentxt") );
toolBar->AddTool( MDI_FILE_SAVE,
myapp()->frame->bitmaps[2],
txt("m_store_in_db") ,
txt("m_txt_store_in_db"));
toolBar->AddTool( SEQ_PRINT,
myapp()->frame->bitmaps[16],
txt("m_print_sequence") ) ;
toolBar->AddSeparator () ;
toolBar->AddTool( ALIGNMENT_SETTINGS,
wxBitmap (myapp()->bmpdir + myapp()->slash + _T("alignment.bmp") , wxBITMAP_TYPE_BMP),
txt("t_settings") ) ;
toolBar->AddSeparator () ;
wxCheckBox *mycb = new wxCheckBox ( toolBar , ALIGN_HORIZ , txt("t_horizontal") ) ;
toolBar->AddControl ( mycb ) ;
toolBar->AddSeparator () ;
mmb = new wxChoice ( toolBar , -1 ) ;
mmb->Append ( txt("t_mmb_insert_gap") ) ;
mmb->Append ( txt("t_mmb_delete_gap") ) ;
mmb->Append ( txt("t_mmb_insert_gap_others") ) ;
mmb->Append ( txt("t_mmb_delete_gap_others") ) ;
mmb->SetStringSelection ( txt("t_mmb_insert_gap") ) ;
toolBar->AddControl ( new wxStaticText ( toolBar , -1 , txt("t_mmb") ) ) ;
toolBar->AddControl ( mmb ) ;
myapp()->frame->addDefaultTools ( toolBar ) ;
toolbar = toolBar ;
toolBar->Realize() ;
wxBoxSizer *v0 = new wxBoxSizer ( wxVERTICAL ) ;
v0->Add ( toolbar , 0 , wxEXPAND , 5 ) ;
v0->Add ( sc , 1 , wxEXPAND , 5 ) ;
SetSizer ( v0 ) ;
v0->Fit ( this ) ;
// Maximize () ;
sc->SetFocus() ;
myapp()->frame->setChild ( this ) ;
readTabColors ( myapp()->homedir + myapp()->slash + _T("default.tab") ) ;
}
void* TAlignment::Entry()
{
int a ;
TAlignLine line ;
wxString cwt = _T("clustalw.txt") ;
wxString hd = myapp()->homedir ;
wxString tx = hd + _T("/") + cwt ;
wxFile out ( tx , wxFile::write ) ;
for ( a = 0 ; a < lines.size() ; a++ )
{
out.Write ( wxString::Format ( _T(">%d\n") , a ) ) ;
out.Write ( lines[a].v->getSequence() + _T("\n") ) ;
}
out.Close() ;
#ifdef USE_EXTERNAL_CLUSTALW // Use external ClustalW
wxString bn ;
#ifdef __WXMSW__
// This is not used anymore under Windows
bn = hd + _T("\\clustalw.bat") ;
wxFile bat ( bn , wxFile::write ) ;
bat.Write ( _T("@echo off\n") ) ;
bat.Write ( _T("cd ") + hd + _T("\n") ) ;
bat.Write ( _T("clustalw.exe clustalw.txt") +
wxString::Format ( _T(" /gapopen=%d") , gap_penalty ) +
wxString::Format ( _T(" /gapext=%d") , mismatch ) + _T("\n") ) ;
bat.Close() ;
#else
// External call to be used by Debian
bn = _T("clustalw clustalw.txt") +
wxString::Format ( _T(" /gapopen=%d") , gap_penalty ) +
wxString::Format ( _T(" /gapext=%d") , mismatch ) + _T("\n") ;
// cout << "Executing " << bn.mb_str() << endl ;
#endif
wxExecute ( bn , wxEXEC_SYNC ) ;
#else // Using internal ClustalW - cool!
wxString a1 = wxString::Format ( _T("/gapopen=%d") , gap_penalty ) ;
wxString a2 = wxString::Format ( _T("/gapext=%d") , mismatch ) ;
char *av[4] ;
av[0] = new char[100] ; strcpy ( av[0] , "clustalw.exe" ) ;
av[1] = new char[100] ; strcpy ( av[1] , "clustalw.txt" ) ;
av[2] = new char[100] ; strcpy ( av[2] , a1.mb_str() ) ;
av[3] = new char[100] ; strcpy ( av[3] , a2.mb_str() ) ;
clustalw_main ( 4 , av ) ;
#endif
wxString aln = hd + _T("/clustalw.aln") ;
wxTextFile in ( aln ) ;
in.Open ( *(myapp()->isoconv) ) ;
wxString s = in.GetFirstLine() ;
do {
s = in.GetNextLine() ;
} while ( s.IsEmpty() ) ;
int off ;
for ( off = s.length()-1 ; s.GetChar(off-1) != ' ' ; off-- ) ;
line.isIdentity = true ;
line.name = txt("t_identity") ;
lines.push_back ( line ) ;
bool first = true ;
for ( a = 0 ; a < lines.size() ; a++ ) lines[a].s = _T("") ;
while ( !in.Eof() )
{
for ( a = 0 ; a < lines.size() ; a++ )
{
if ( !first ) s = in.GetNextLine() ;
else first = false ;
long index ;
wxString i = s.substr ( 0 , off-1 ) ;
i.ToLong ( &index ) ;
if ( s.GetChar(0) == ' ' ) index = lines.size()-1 ;
lines[index].s += s.substr ( off , s.length() ) ;
}
if ( !in.Eof() ) s = in.GetNextLine() ; // Blank line
}
#ifndef __WXMSW__
wxMutexGuiEnter() ;
#endif
keepIdentity = true ;
redoAlignments ( true ) ;
keepIdentity = false ;
#ifndef __WXMSW__
wxMutexGuiLeave() ;
#endif
}
// Calculating alignments; all changes are lost!
void TAlignment::recalcAlignments ()
{
if ( !keepIdentity )
{
while ( lines.size() && lines[lines.size()-1].isIdentity )
lines.pop_back () ;
}
if ( lines.size() == 0 ) return ;
// Align
int a ;
TAlignLine line ;
SetCursor ( *wxHOURGLASS_CURSOR ) ;
if ( lines.size() <= 1 ) // Just one sequence
{
lines[0].ResetSequence() ;
}
else if ( algorithm == ALG_CW ) // Clustal-W
{
if ( threadRunning )
{
generateConsensusSequence ( false ) ;
threadRunning = false ;
// SetCursor ( *wxSTANDARD_CURSOR ) ;
}
else
{
SetCursor ( *wxSTANDARD_CURSOR ) ;
threadRunning = true ;
sc->Refresh () ;
// sc->SilentRefresh() ;
// wxSafeYield() ;
wxThreadHelper::Create () ;
GetThread()->Run() ;
return ;
}
}
else // Internal routines
{
myass ( lines.size() > 0 , "Alignment::recalcAlignments:internal1" ) ;
// while ( lines.size() > 2 ) lines.pop_back () ;
for ( a = 0 ; a < lines.size() ; a++ ) lines[a].ResetSequence () ;
for ( a = 1 ; a < lines.size() ; a++ )
{
wxString s0 = lines[0].s ;
if ( algorithm == ALG_NW )
NeedlemanWunsch ( s0 , lines[a].s ) ;
else if ( algorithm == ALG_SW )
SmithWaterman ( s0 , lines[a].s ) ;
if ( lines[0].s == s0 ) continue ; // No gaps were introduced into first sequence
int b ;
for ( b = 0 ; b <= a ; b++ ) // All lines get the same length
{
while ( lines[b].s.length() < s0.length() )
lines[b].s += _T(" ") ;
}
for ( b = 0 ; b < s0.length() ; b++ ) // Insert gaps
{
if ( lines[0].s.GetChar(b) != s0.GetChar(b) ) // New gap
{
for ( int c = 0 ; c < a ; c++ )
{
for ( int d = s0.length()-1 ; d > b && d >= 0 ; d-- )
lines[c].s.SetChar ( d , lines[c].s.GetChar(d-1) ) ;
myass ( lines[c].s.length() > b , "Alignment::recalcAlignments:internal2" ) ;
lines[c].s.SetChar ( b , '-' ) ;
}
}
}
}
generateConsensusSequence ( true ) ;
}
for ( a = 0 ; a < 1 ; a++ )
{
if ( !lines[a].isIdentity && lines[a].v->items.size() > 0 )
lines[a].showFeatures () ;
}
SetCursor ( *wxSTANDARD_CURSOR ) ;
}
void TAlignment::redoAlignments ( bool doRecalc )
{
int a ;
// Cleaning up
CLEAR_DELETE ( sc->seq ) ;
if ( doRecalc ) recalcAlignments () ;
if ( threadRunning ) return ;
// Display
sc->maxendnumberlength = txt("t_identity").length() ;
for ( a = 0 ; a < lines.size() ; a++ )
{
if ( lines[a].hasFeatures() )
{
lines[a].showFeatures () ;
SeqFeature *f = new SeqFeature ( sc ) ;
f->id = a ;
sc->seq.Add ( f ) ;
}
SeqAlign *d = new SeqAlign ( sc ) ;
sc->seq.Add ( d ) ;
d->id = a ;
d->s = lines[a].s ;
d->myname = lines[a].name ;
}
// Features
for ( int g = 0 ; g < lines.size() ; g++ )
{
if ( !lines[g].isIdentity && lines[g].hasFeatures() )
{
// lines[g].showFeatures () ;
for ( a = 0 ; a < lines[g].s.length() ; a++ )
{
if ( lines[g].s.GetChar(a) == '-' )
lines[g].getFeatures()->insert_char ( '-' , a+1 , false ) ;
}
}
}
updateSequence () ;
}
void TAlignment::generateConsensusSequence ( bool addit )
{
int a , b ;
// The stars'n'stripes sequence ;-)
TAlignLine line ;
line.isIdentity = true ;
line.name = txt("t_identity") ;
wxString s ;
for ( a = 0 ; a < lines[0].s.length() ; a++ )
{
char c = '*' ;
for ( b = 1 ; b < lines.size() && c == '*' ; b++ )
{
if ( lines[0].s.GetChar(a) != lines[b].s.GetChar(a) /*&&
lines[0].s.GetChar(a) != '-' &&
lines[b].s.GetChar(a) != '-' */) c = ' ' ;
}
s += (wxChar) c ;
}
line.s = s ;
if ( addit ) lines.push_back ( line ) ;
// The REAL consensus sequence
consensusSequence = lines[0].s ;
for ( a = 0 ; a < consensusSequence.length() ; a++ )
{
int c[256] ;
for ( b = 0 ; b < 256 ; b++ ) c[b] = 0 ;
for ( b = 0 ; b + 1 < lines.size() ; b++ ) c[lines[b].s.GetChar(a)]++ ;
consensusSequence.SetChar ( a , ' ' ) ;
for ( b = 0 ; b < 256 ; b++ )
{
float f = 100 * c[b] ;
f /= lines.size() - 1 ;
if ( f >= 60 ) consensusSequence.SetChar ( a , b ) ;
}
}
}
void TAlignment::myInsert ( int line , int pos , char what )
{
if ( lines[line].hasFeatures() )
{
lines[line].getFeatures()->insert_char ( '-' , pos , false ) ;
lines[line].s = lines[line].getFeatures()->getSequence() ;
}
else lines[line].s.insert ( pos-1 , wxString ( (wxChar) what ) ) ;
}
void TAlignment::myDelete ( int line , int pos )
{
if ( lines[line].hasFeatures() )
{
lines[line].getFeatures()->doRemoveNucleotide ( pos - 1 ) ;
lines[line].s = lines[line].getFeatures()->getSequence() ;
}
else lines[line].s.erase ( pos-1 , 1 ) ;
}
void TAlignment::callMiddleMouseButton ( int id , int pos , wxString _mode )
{
wxString mode = mmb->GetStringSelection () ;
if ( !_mode.IsEmpty() ) mode = txt(_mode) ;
unsigned int a , line = id ;
if ( lines[line].s.GetChar(pos-1) != '-' && mode == txt("t_mmb_delete_gap") )
{
wxBell() ;
return ;
}
wxArrayInt l2s ;
l2s.Alloc ( lines.size() ) ;
while ( l2s.GetCount() < lines.size() ) l2s.Add ( 0 ) ;
for ( a = 0 ; a < sc->seq.GetCount() ; a++ )
{
if ( sc->seq[a]->whatsthis() == _T("ALIGN") )
{
SeqAlign *b = (SeqAlign*) sc->seq[a] ;
l2s[b->id] = a ;
}
}
for ( a = 0 ; a < lines.size() ; a++ )
{
if ( lines[a].isIdentity ) {}
else if ( mode == txt("t_mmb_insert_gap") )
{
if ( line == a ) myInsert ( a , pos , '-' ) ;
else myInsert ( a , lines[a].s.length()+1 , '-' ) ;
}
else if ( mode == txt("t_mmb_delete_gap") )
{
if ( line == a )
{
myDelete ( a , pos ) ;
myInsert ( a , lines[a].s.length()+1 , '-' ) ;
}
}
else if ( mode == txt("t_mmb_insert_gap_others") )
{
if ( line != a ) myInsert ( a , pos , '-' ) ;
else myInsert ( a , lines[a].s.length()+1 , '-' ) ;
}
else if ( mode == txt("t_mmb_delete_gap_others") )
{
if ( line != a && lines[a].s.GetChar(pos-1) == '-' )
{
myDelete ( a , pos ) ;
myInsert ( a , lines[a].s.length()+1 , '-' ) ;
}
}
SeqAlign *d = (SeqAlign*) sc->seq[l2s[a]] ;
d->id = a ;
d->s = lines[a].s ;
}
// Cleanup of '-' ends
bool again = true ;
while ( again )
{
int max = 0 ;
for ( a = 0 ; a < lines.size() && !lines[a].isIdentity ; a++ ) max++ ;
for ( a = 0 ; a < lines.size() && !lines[a].isIdentity && lines[a].s[lines[a].s.length()-1] == '-' ; a++ ) ;
if ( a == max )
{
for ( a = 0 ; a < lines.size() ; a++ )
if ( !lines[a].isIdentity )
myDelete ( a , lines[a].s.length() ) ;
}
else again = false ;
}
updateSequence () ;
}
void TAlignment::updateSequence ()
{
if ( threadRunning ) return ;
for ( unsigned int g = 0 ; g < sc->seq.GetCount() ; g++ )
{
if ( sc->seq[g]->whatsthis() != _T("FEATURE") ) continue ;
SeqFeature *f = (SeqFeature*) sc->seq[g] ;
int id = f->id ;
if ( lines[id].getFeatures()->getType() == TYPE_AMINO_ACIDS )
{
colCur = colAA ;
if ( aaa ) delete aaa ;
aaa = new SeqAA ( NULL ) ;
sc->seq[g] = aaa ;
aaa->initFromString ( lines[id].getFeatures()->getSequence() ) ;
// aaa->fixOffsets ( lines[id].getFeatures() ) ;
aaa->can = sc ;
sc->arrange () ;
sc->seq[g] = f ;
f->initFromTVector ( lines[id].getFeatures() ) ;
f->aaa = aaa ;
}
else if ( lines[id].getFeatures()->getType() == TYPE_VECTOR )
{
colCur = colDNA ;
if ( aaa ) delete aaa ;
aaa = new SeqAA ( NULL ) ;
sc->seq[g] = aaa ;
aaa->mode = AA_KNOWN ;
aaa->disp = AA_ONE ;
aaa->initFromTVector ( lines[id].getFeatures() ) ;
aaa->showNumbers = false ;
aaa->can = sc ;
sc->arrange () ;
sc->seq[g] = f ;
f->initFromTVector ( lines[id].getFeatures() ) ;
f->aaa = aaa ;
}
else f->initFromTVector ( lines[id].getFeatures() ) ;
}
sc->arrange () ;
sc->SilentRefresh() ;
}
wxString TAlignment::getName ()
{
return _T("Alignment") ;
}
void TAlignment::OnSettings ( wxCommandEvent &ev )
{
TAlignmentDialog ad ( this , txt("t_settings") ) ;
int r = ad.ShowModal () ;
if ( r != wxID_OK ) return ;
lines.clear () ;
for ( unsigned int a = 0 ; a < ad.vcn.GetCount() ; a++ )
{
TAlignLine line ;
line.name = ad.vcn[a] ;
line.v = ad.vcv[a] ;
line.ResetSequence() ;
lines.push_back ( line ) ;
}
match = ad.alg_match->GetValue() ;
mismatch = ad.alg_mismatch->GetValue() ;
gap_penalty = ad.alg_penalty->GetValue() ;
matrix = ad.alg_matrix->GetStringSelection() ;
algorithm = ad.alg->GetSelection () ;
redoAlignments () ;
}
void TAlignment::prealigned ( wxArrayString &vs , wxArrayChildBase &vc )
{
lines.clear () ;
for ( unsigned int a = 0 ; a < vc.GetCount() ; a++ )
{
TAlignLine line ;
line.name = vc[a]->getName() ;
line.v = vc[a]->vec ;
line.ResetSequence() ;
line.s = vs[a] ;
lines.push_back ( line ) ;
}
redoAlignments ( false ) ;
}
// HOMEMADE ALIGNMENT ALGORITHMS
int TAlignment::NeedlemanWunsch ( wxString &s1 , wxString &s2 )
{
return MatrixAlignment ( s1 , s2 , false ) ;
}
int TAlignment::SmithWaterman ( wxString &s1 , wxString &s2 )
{
return MatrixAlignment ( s1 , s2 , true ) ;
}
int TAlignment::MatrixAlignment ( wxString &_s1 , wxString &_s2 , bool local )
{
wxString s1 = _s1 ;
wxString s2 = _s2 ;
int a , b ;
int M = s1.length() ;
int N = s2.length() ;
// Initializing backlink matrix
vector <wxArrayInt> back ;
wxArrayInt blank_b ;
blank_b.Alloc ( N+1 ) ;
back.reserve ( M+1 ) ;
while ( blank_b.GetCount() < N+1 ) blank_b.Add ( 0 ) ;
while ( back.size() < M+1 ) back.push_back ( blank_b ) ;
// Initializing pseudo-matrix (simulated by two altering lines)
int *matrix0 , *matrix1 , *matrix2 ;
matrix0 = new int[N+1] ;
matrix1 = new int[N+1] ;
for ( a = 0 ; a < N+1 ; a++ ) matrix1[a] = 0 ;
// Filling
int i , j ;
int max = -999999 ;
wxArrayInt vi , vj ;
int mi = M , mj = N ;
for ( i = 0 ; i < M ; i++ )
{
matrix2 = matrix0 ;
matrix0 = matrix1 ;
matrix1 = matrix2 ;
*matrix1 = 0 ;
for ( j = 0 ; j < N ; j++ )
{
int x = i+1 ;
int y = j+1 ;
int s = (s1.GetChar(i)==s2.GetChar(j))?match:mismatch ;
// Maxima
int m1 = matrix0[j] + s ;
int m2 = matrix1[j] + gap_penalty ;
int m3 = matrix0[y] + gap_penalty ;
// Determining maximum
int r = m1 > m2 ? m1 : m2 ;
r = r > m3 ? r : m3 ;
if ( local ) r = r > 0 ? r : 0 ;
matrix1[y] = r ;
if ( local && r >= max )
{
if ( r > max )
{
max = r ;
mi = x ;
mj = y ;
vi.Clear() ;
vj.Clear() ;
}
vi.Add ( x ) ;
vj.Add ( y ) ;
}
// The way back
int n = 0 ;
if ( r == m1 ) n |= BACK_LU ;
if ( r == m2 ) n |= BACK_UP ;
if ( r == m3 ) n |= BACK_LEFT ;
back[x][y] = n ;
}
}
// Backtracking
wxString t1 , t2 ;
if ( local )
{
for ( a = b = 0 ; a < vi.GetCount() ; a++ )
{
MatrixBacktrack ( back , s1 , s2 , t1 , t2 , vi[a] , vj[a] ) ;
if ( t1.length() > b )
{
b = t1.length() ;
mi = vi[a] ;
mj = vj[a] ;
}
}
}
else
{
mi = M ;
mj = N ;
}
MatrixBacktrack ( back , s1 , s2 , t1 , t2 , mi , mj ) ;
wxString k1 , k2 ;
// The beginning
char gap0 = gap.GetChar(0) ;
for ( a = b = 0 ; a < t1.size() ; a++ )
if ( t1.GetChar(a) != gap0 ) b++ ;
k1 = s1.substr ( 0 , mi - b ) ;
for ( a = b = 0 ; a < t2.size() ; a++ )
if ( t2.GetChar(a) != gap0 ) b++ ;
k2 = s2.substr ( 0 , mj - b ) ;
while ( k1.length() < k2.length() ) k1 = _T("-") + k1 ;
while ( k2.length() < k1.length() ) k2 = _T("-") + k2 ;
t1 = k1 + t1 ;
t2 = k2 + t2 ;
// The end
k1 = s1.substr ( mi ) ;
k2 = s2.substr ( mj ) ;
while ( k1.length() < k2.length() ) k1 += _T("-") ;
while ( k2.length() < k1.length() ) k2 += _T("-") ;
t1 += k1 ;
t2 += k2 ;
_s1 = t1 ;
_s2 = t2 ;
return max ;
}
void TAlignment::MatrixBacktrack ( vector <wxArrayInt> &back ,
wxString s1 , wxString s2 ,
wxString &t1 , wxString &t2 ,
int i , int j )
{
t1 = _T("") ;
t2 = _T("") ;
while ( i > 0 || j > 0 )
{
if ( (back[i][j]&BACK_LU) == BACK_LU ) // upper left
{
t1 = s1.GetChar(--i) + t1 ;
t2 = s2.GetChar(--j) + t2 ;
}
else if ( (back[i][j]&BACK_LEFT) > 0 ) // left
{
t1 = s1.GetChar(--i) + t1 ;
t2 = gap + t2 ;
}
else if ( ( back[i][j]&BACK_UP ) > 0 ) // up
{
t1 = gap + t1 ;
t2 = s2.GetChar(--j) + t2 ;
}
else break ;
}
}
void TAlignment::invokeOriginal ( int id , int pos )
{
ChildBase *c = NULL ;
c = lines[id].FindOrigin() ;
if ( !c ) return ;
myapp()->frame->mainTree->SelectItem ( c->inMainTree ) ;
if ( c->def == _T("dna") )
{
MyChild *c1 = ((MyChild*)c) ;
c1->cSequence->mark ( _T("DNA") , pos , pos , 1 ) ;
c1->cSequence->ensureVisible ( pos ) ;
}
else if ( c->def == _T("AminoAcids") )
{
TAminoAcids *c1 = ((TAminoAcids*)c) ;
c1->sc->mark ( _T("AA") , pos , pos , 1 ) ;
c1->sc->ensureVisible ( pos ) ;
}
else if ( c->def == _T("ABIviewer") )
{
TABIviewer *c1 = ((TABIviewer*)c) ;
c1->sc->mark ( _T("ABI") , pos , pos , 1 ) ;
c1->sc->ensureVisible ( pos ) ;
}
}
void TAlignment::fixMenus ( int i )
{
wxMenuBar *mb = GetMenuBar () ;
mb->FindItem(ALIGN_BOLD)->Check ( bold ) ;
mb->FindItem(ALIGN_MONO)->Check ( mono ) ;
mb->FindItem(ALIGN_NORM)->Check ( false ) ;
mb->FindItem(ALIGN_INVS)->Check ( false ) ;
mb->FindItem(ALIGN_SOA)->Check ( false ) ;
mb->FindItem(ALIGN_SOAI)->Check ( false ) ;
mb->FindItem(ALIGN_SIML)->Check ( false ) ;
mb->FindItem(ALIGN_SEQ)->Check ( false ) ;
mb->FindItem(ALIGN_FEAT)->Check ( false ) ;
mb->FindItem(ALIGN_RNA)->Check ( false ) ;
mb->FindItem(i)->Check ( true ) ;
invs = mb->FindItem(ALIGN_INVS)->IsChecked () ;
if ( threadRunning ) return ;
sc->arrange () ;
sc->SilentRefresh() ;
}
void TAlignment::OnMenuBold ( wxCommandEvent &ev )
{
bold = !bold ;
if ( threadRunning ) return ;
sc->arrange () ;
sc->SilentRefresh() ;
}
void TAlignment::OnMenuMono ( wxCommandEvent &ev )
{
mono = !mono ;
if ( threadRunning ) return ;
sc->arrange () ;
sc->SilentRefresh() ;
}
void TAlignment::OnMenuNorm ( wxCommandEvent &ev )
{
fixMenus ( ALIGN_NORM ) ;
}
void TAlignment::OnMenuInvs ( wxCommandEvent &ev )
{
fixMenus ( ALIGN_INVS ) ;
}
void TAlignment::OnMenuSoa ( wxCommandEvent &ev )
{
for ( unsigned int a = 0 ; a < sc->seq.GetCount() ; a++ )
{
SeqAlign *x = (SeqAlign*) sc->seq[a] ;
}
}
void TAlignment::OnMenuSoaI ( wxCommandEvent &ev )
{
for ( unsigned int a = 0 ; a < sc->seq.GetCount() ; a++ )
{
SeqAlign *x = (SeqAlign*) sc->seq[a] ;
}
}
void TAlignment::OnMenuSiml ( wxCommandEvent &ev )