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/** \file
\brief Contains the methods of the TAlignmentDialog class
*/
#include "TAlignmentDialog.h"
BEGIN_EVENT_TABLE(TAlignmentDialog, wxDialog)
EVT_BUTTON(AL_ADD,TAlignmentDialog::OnAdd)
EVT_BUTTON(AL_DEL,TAlignmentDialog::OnDel)
EVT_BUTTON(AL_UP,TAlignmentDialog::OnUp)
EVT_BUTTON(AL_DOWN,TAlignmentDialog::OnDown)
EVT_BUTTON(AL_OK,TAlignmentDialog::OnOK)
EVT_BUTTON(AL_CANCEL,TAlignmentDialog::OnCancel)
EVT_CHAR_HOOK(TAlignmentDialog::OnCharHook)
END_EVENT_TABLE()
// ******************************************* TAlignmentDialog
TAlignmentDialog::TAlignmentDialog(wxWindow *parent, const wxString& title )
: wxDialog ( myapp()->frame , -1 , title , wxDefaultPosition , wxSize ( 600 , 450 ) )
{
myapp()->frame->push_help ( _T("GENtle:Alignments") ) ; // TODO : Link to dialog help page
bo = 5 ;
th = 15 ;
al = (TAlignment*) parent ;
#ifndef __WXMAC__
Show ( TRUE ) ;
#endif
int w , h ;
#ifdef __WXMSW__
GetClientSize ( &w , &h ) ;
h -= 30 ;
#else
w = -1 ;
h = -1 ;
#endif
nb = new wxNotebook ( this , -1 , wxDefaultPosition , wxSize ( w , h ) );
init_what () ;
init_how () ;
// init_disp () ;
wxButton *b = new wxButton ( this , AL_OK , txt("b_OK") ) ;
wxButton *c = new wxButton ( this , AL_CANCEL , txt("b_cancel") ) ;
#ifndef __WXMSW__
wxBoxSizer *v0 = new wxBoxSizer ( wxVERTICAL ) ;
wxBoxSizer *h0 = new wxBoxSizer ( wxHORIZONTAL ) ;
h0->Add ( b , 1 , wxALL , 5 ) ;
h0->Add ( c , 1 , wxALL , 5 ) ;
v0->Add ( nb , 1 , wxEXPAND|wxALL , 5 ) ;
v0->Add ( h0 , 0 , wxCENTRE , 5 ) ;
SetSizer ( v0 ) ;
#else
b->SetSize ( w / 5 , h + 5 , -1 , -1 ) ;
c->SetSize ( w / 5 * 3 , h + 5 , -1 , -1 ) ;
#endif
nb->SetSelection ( 0 ) ;
b->SetDefault () ;
b->SetFocus () ;
}
TAlignmentDialog::~TAlignmentDialog ()
{
nb->DeleteAllPages() ;
}
void TAlignmentDialog::init_what ()
{
wxBoxSizer *vx = new wxBoxSizer ( wxVERTICAL ) ;
wxBoxSizer *h0 = new wxBoxSizer ( wxHORIZONTAL ) ;
wxBoxSizer *v0 = new wxBoxSizer ( wxVERTICAL ) ;
wxBoxSizer *v1 = new wxBoxSizer ( wxVERTICAL ) ;
wxBoxSizer *v2 = new wxBoxSizer ( wxVERTICAL ) ;
pwhat = new wxPanel ( nb , -1 ) ;
wxPanel *p = pwhat ;
v0->Add ( new wxStaticText ( p , -1 , txt("al_cur") ) , 0 , wxEXPAND ) ;
v2->Add ( new wxStaticText ( p , -1 , txt("al_all") ) , 0 , wxEXPAND ) ;
cur = new wxListBox ( p , AL_CUR ,
wxDefaultPosition ,
wxDefaultSize ,
0 , NULL , wxLB_EXTENDED ) ;
all = new wxListBox ( p , AL_ALL ,
wxDefaultPosition ,
wxDefaultSize ,
0 , NULL , wxLB_EXTENDED ) ;
v0->Add ( cur , 1 , wxEXPAND ) ;
v2->Add ( all , 1 , wxEXPAND ) ;
v1->Add ( new wxStaticText ( p , -1 , _T(" ") ) , 0 , wxALIGN_CENTER_HORIZONTAL ) ;
v1->Add ( new wxButton ( p , AL_ADD , txt("<-- add") ) , 0 , wxALIGN_CENTER_HORIZONTAL ) ;
v1->Add ( new wxButton ( p , AL_DEL , txt("del -->") ) , 0 , wxALIGN_CENTER_HORIZONTAL ) ;
v1->Add ( new wxStaticText ( p , -1 , _T(" ") ) , 0 , wxALIGN_CENTER_HORIZONTAL ) ;
v1->Add ( new wxButton ( p , AL_UP , txt("b_up_in_list") ) , 0 , wxALIGN_LEFT ) ;
v1->Add ( new wxButton ( p , AL_DOWN , txt("b_down_in_list") ) , 0 , wxALIGN_LEFT ) ;
unsigned int a ;
MyFrame *f = myapp()->frame ;
// All
for ( a = 0 ; a < f->children.GetCount() ; a++ )
{
if ( f->children[a]->def == _T("dna") ||
f->children[a]->def == _T("AminoAcids") ||
f->children[a]->def == _T("ABIviewer") )
{
vav.Add ( ((MyChild*)f->children[a])->vec ) ;
van.Add ( f->children[a]->getName() ) ;
all->Append ( f->children[a]->getName() ) ;
}
}
// Current
for ( a = 0 ; a < al->lines.size() ; a++ )
{
if ( al->lines[a].name != txt("t_identity") )
{
vcv.Add ( al->lines[a].v ) ;
vcn.Add ( al->lines[a].name ) ;
cur->Append ( al->lines[a].name ) ;
}
}
/*
// Add all when dialog is first opened
if ( vcn.GetCount() == 0 )
{
for ( a = 0 ; a < van.GetCount() ; a++ )
{
vcn.Add ( van[a] ) ;
vcv.Add ( vav[a] ) ;
cur->Append ( van[a] ) ;
}
}
*/
h0->Add ( v0 , 1 , wxEXPAND|wxALL , 5 ) ;
h0->Add ( v1 , 1 , wxALL , 5 ) ;
h0->Add ( v2 , 1 , wxEXPAND|wxALL , 5 ) ;
vx->Add ( h0 , 1 , wxEXPAND ) ;
vx->Add ( new wxStaticText ( p , -1 , txt("t_alignment_txt") ) , 0 , wxEXPAND|wxALIGN_CENTER_HORIZONTAL ) ;
p->SetSizer ( vx ) ;
nb->AddPage ( pwhat , txt("t_sequences") ) ;
}
void TAlignmentDialog::init_how ()
{
phow = new wxPanel ( nb , -1 ) ;
wxPanel *p = phow ;
int w = 600 , h = 400 ;
wxStaticText *st ;
wxRect r ;
st = new wxStaticText ( p , -1 , txt("t_algorithm") , wxPoint ( bo , th ) ) ;
r = st->GetRect () ;
alg = new wxListBox ( p , AL_ALG ,
wxPoint ( bo , r.GetBottom()+bo ) ,
wxSize ( w/2-bo , h/2 ) ,
0 , NULL , wxLB_SINGLE ) ;
alg->Append ( txt("t_clustal_w") ) ;
alg->Append ( txt("t_smith_waterman") ) ;
alg->Append ( txt("t_needleman_wunsch") ) ;
alg->SetSelection ( al->algorithm ) ;
new wxStaticText ( p , -1 , txt("t_alg_param") , wxPoint ( w/2+bo , th ) ) ;
st = new wxStaticText ( p , -1 , txt("t_match") , wxPoint ( w/2+bo , th*2+bo ) ) ;
r = st->GetRect() ;
int xo = r.GetRight() ;
st = new wxStaticText ( p , -1 , txt("t_mismatch") , wxPoint ( w/2+bo , th*4+bo ) ) ;
r = st->GetRect() ;
if ( xo < r.GetRight() ) xo = r.GetRight() ;
st = new wxStaticText ( p , -1 , txt("t_gap_penalty") , wxPoint ( w/2+bo , th*6+bo ) ) ;
r = st->GetRect() ;
if ( xo < r.GetRight() ) xo = r.GetRight() ;
xo += bo ;
alg_match = new wxSpinCtrl ( p , AL_MATCH , _T("") ,
wxPoint ( xo , th*2 ) ,
wxSize ( MYSPINBOXSIZE /*w/5*/ , th*3/2 ) ) ;
alg_match->SetRange ( -100 , 100 ) ;
alg_match->SetValue ( al->match ) ;
alg_mismatch = new wxSpinCtrl ( p , AL_MISMATCH , _T("") ,
wxPoint ( xo , th*4 ) ,
wxSize ( MYSPINBOXSIZE /*w/5*/ , th*3/2 ) ) ;
alg_mismatch->SetRange ( -100 , 100 ) ;
alg_mismatch->SetValue ( al->mismatch ) ;
alg_penalty = new wxSpinCtrl ( p , AL_PENALTY , _T("") ,
wxPoint ( xo , th*6 ) ,
wxSize ( MYSPINBOXSIZE /*w/5*/ , th*3/2 ) ) ;
alg_penalty->SetRange ( -100 , 100 ) ;
alg_penalty->SetValue ( al->gap_penalty ) ;
alg_matrix = new wxChoice ( p , AL_MATRIX , wxPoint ( xo , th*8 ) ) ;
alg_matrix->Append ( txt("t_matrix_blosum") ) ;
alg_matrix->Append ( txt("t_matrix_pam") ) ;
alg_matrix->Append ( txt("t_matrix_gonnet") ) ;
alg_matrix->Append ( txt("t_matrix_id") ) ;
alg_matrix->SetSelection ( 0 ) ;
nb->AddPage ( phow , txt("t_algorithm") ) ;
}
void TAlignmentDialog::init_disp ()
{
pdisp = new wxPanel ( this , -1 ) ;
nb->AddPage ( pdisp , txt("t_display") ) ;
wxPanel *p = pdisp ;
int w , h ;
p->GetClientSize ( &w , &h ) ;
}
void TAlignmentDialog::OnOK ( wxCommandEvent &ev )
{
EndModal ( wxID_OK ) ; // wxDialog::OnOK ( ev ) ;
}
void TAlignmentDialog::OnCancel ( wxCommandEvent &ev )
{
EndModal ( wxID_CANCEL ) ; // wxDialog::OnCancel ( ev ) ;
}
void TAlignmentDialog::OnCharHook ( wxKeyEvent& event )
{
int k = event.GetKeyCode () ;
wxCommandEvent ev ;
if ( k == WXK_ESCAPE ) OnCancel ( ev ) ;
else if ( k == WXK_F1 ) myapp()->frame->OnHelp(ev) ;
else event.Skip() ;
}
void TAlignmentDialog::OnAdd ( wxCommandEvent &ev )
{
wxArrayInt sel ;
unsigned int a , b , n = all->GetSelections ( sel ) ;
for ( a = 0 ; a < n ; a++ )
{
for ( b = 0 ; b < vcv.GetCount() && vcv[b] != vav[sel[a]] ; b++ ) ;
if ( b == vcv.GetCount() )
{
vcv.Add ( vav[sel[a]] ) ;
vcn.Add ( van[sel[a]] ) ;
cur->Append ( van[sel[a]] ) ;
}
}
}
void TAlignmentDialog::OnDel ( wxCommandEvent &ev )
{
wxArrayInt sel ;
unsigned int a , b , n = cur->GetSelections ( sel ) ;
for ( a = 0 ; a < n ; a++ ) vcv[sel[a]] = NULL ;
for ( a = 0 ; a < vcv.GetCount() ; a++ )
{
if ( vcv[a] == NULL )
{
for ( b = a+1 ; b < vcv.GetCount() ; b++ )
{
vcv[b-1] = vcv[b] ;
vcn[b-1] = vcn[b] ;
}
vcv.RemoveAt ( vcv.GetCount()-1 ) ;
vcn.RemoveAt ( vcn.GetCount()-1 ) ;
a-- ;
}
}
cur->Clear () ;
for ( a = 0 ; a < vcn.GetCount() ; a++ )
cur->Append ( vcn[a] ) ;
}
void TAlignmentDialog::OnUp ( wxCommandEvent &ev )
{
wxArrayInt sel ;
unsigned int a , b , n = cur->GetSelections ( sel ) ;
if ( n != 1 ) return ;
b = sel[0] ;
if ( b == 0 ) return ;
TVector *d_v = vcv[b] ; vcv[b] = vcv[b-1] ; vcv[b-1] = d_v ;
wxString d_n = vcn[b] ; vcn[b] = vcn[b-1] ; vcn[b-1] = d_n ;
cur->Clear () ;
for ( a = 0 ; a < vcn.GetCount() ; a++ )
cur->Append ( vcn[a] ) ;
cur->SetSelection ( b-1 ) ;
}
void TAlignmentDialog::OnDown ( wxCommandEvent &ev )
{
wxArrayInt sel ;
unsigned int a , b , n = cur->GetSelections ( sel ) ;
if ( n != 1 ) return ;
b = sel[0] ;
if ( b == vcv.GetCount()-1 ) return ;
TVector *d_v = vcv[b] ; vcv[b] = vcv[b+1] ; vcv[b+1] = d_v ;
wxString d_n = vcn[b] ; vcn[b] = vcn[b+1] ; vcn[b+1] = d_n ;
cur->Clear () ;
for ( a = 0 ; a < vcn.GetCount() ; a++ )
cur->Append ( vcn[a] ) ;
cur->SetSelection ( b+1 ) ;
}
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