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feature: Removing debug warnings/comments #117

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Aug 31, 2024
Merged

feature: Removing debug warnings/comments #117

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36 changes: 18 additions & 18 deletions src/ProgramOptionsDialog.cpp
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ END_EVENT_TABLE()

TEnzymeSettingsTab::TEnzymeSettingsTab ( wxWindow *parent , const int _mode ) : wxPanel ( parent )
{
wxPrintf( "D: TEnzymeSettingsTab::TEnzymeSettingsTab - start\n" ) ;
//wxPrintf( "D: TEnzymeSettingsTab::TEnzymeSettingsTab - start\n" ) ;
myapp()->frame->push_help ( _T("GENtle:Options") ) ;
mode = _mode ;
int w , h ;
Expand Down Expand Up @@ -131,7 +131,7 @@ TEnzymeSettingsTab::TEnzymeSettingsTab ( wxWindow *parent , const int _mode ) :
updateGlobalEnzymes () ;
vs->Fit ( this ) ;

wxPrintf( "D: TEnzymeSettingsTab::TEnzymeSettingsTab - end\n" ) ;
//wxPrintf( "D: TEnzymeSettingsTab::TEnzymeSettingsTab - end\n" ) ;
}

ProgramOptionsDialog::~ProgramOptionsDialog ()
Expand All @@ -141,7 +141,7 @@ ProgramOptionsDialog::~ProgramOptionsDialog ()

void TEnzymeSettingsTab::updateGlobalEnzymes ()
{
wxPrintf( "D: TEnzymeSettingsTab::updateGlobalEnzymes - start\n" ) ;
//wxPrintf( "D: TEnzymeSettingsTab::updateGlobalEnzymes - start\n" ) ;
bool use = useSettings->GetValue() ;
useMinCutoff->Enable ( use ) ;
useMaxCutoff->Enable ( use ) ;
Expand All @@ -163,7 +163,7 @@ void TEnzymeSettingsTab::updateGlobalEnzymes ()
updateColorButton ( bcol1 , col1 ) ;
updateColorButton ( bcol2 , col2 ) ;
updateColorButton ( bcol3 , col3 ) ;
wxPrintf( "D: TEnzymeSettingsTab::updateGlobalEnzymes - end - useMaxCutoff:%d\n" , useMaxCutoff ) ;
//wxPrintf( "D: TEnzymeSettingsTab::updateGlobalEnzymes - end - useMaxCutoff:%d\n" , useMaxCutoff ) ;
}

void TEnzymeSettingsTab::updateColorButton ( wxButton *b , const wxColour &c )
Expand Down Expand Up @@ -207,19 +207,19 @@ void TEnzymeSettingsTab::OnButton3 ( wxCommandEvent &event )

void TEnzymeSettingsTab::updateColor ( wxColour &c )
{
wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) - start\n",c.GetAsString()) ;
//wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) - start\n",c.GetAsString()) ;

wxColour c2 = wxGetColourFromUser ( this , c ) ;
wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) wxGetColourFromUser -> %s\n" , c.GetAsString() , c2.GetAsString()) ;
//wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) wxGetColourFromUser -> %s\n" , c.GetAsString() , c2.GetAsString()) ;

if ( !c2.Ok() )
{
wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) -> ret !c2.Ok()" ,c.GetAsString() , c2.GetAsString()) ;
//wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) -> ret !c2.Ok()" ,c.GetAsString() , c2.GetAsString()) ;
return ;
}
c = c2 ;
updateGlobalEnzymes () ;
wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) - end\n",c.GetAsString()) ;
//wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) - end\n",c.GetAsString()) ;
}


Expand Down Expand Up @@ -459,11 +459,11 @@ void TEnzymeRules::init () // Default settings

void TEnzymeRules::load_global_settings () /* not const */
{
wxPrintf( "D: TEnzymeRules::load_global_settings - start\n" ) ;
//wxPrintf( "D: TEnzymeRules::load_global_settings - start\n" ) ;
init () ;
wxString s = myapp()->frame->LS->getOption ( _T("GLOBALENZYMESETTINGS") , _T("") ) ;
from_string ( s ) ;
wxPrintf( "D: TEnzymeRules::load_global_settings - end\n" ) ;
//wxPrintf( "D: TEnzymeRules::load_global_settings - end\n" ) ;
}

void TEnzymeRules::save_global_settings () const
Expand Down Expand Up @@ -557,7 +557,7 @@ wxString TEnzymeRules::to_string () const

void TEnzymeRules::from_string ( const wxString& s )
{
wxPrintf( "D: TEnzymeRules::from_string - start\n" ) ;
//wxPrintf( "D: TEnzymeRules::from_string - start\n" ) ;
init () ;
wxArrayString as ;
explode ( _T("\r") , s , as ) ;
Expand Down Expand Up @@ -589,7 +589,7 @@ void TEnzymeRules::from_string ( const wxString& s )
else if ( key == _T("methylation") ) methylation = l ;
else if ( key == _T("showgc") ) showgc = l ;
}
wxPrintf( "D: TEnzymeRules::from_string - end\n" ) ;
//wxPrintf( "D: TEnzymeRules::from_string - end\n" ) ;
}

wxColour TEnzymeRules::scan_color ( const wxString& s ) const
Expand All @@ -614,7 +614,7 @@ wxColour *TEnzymeRules::getColor ( const int cuts )

void TEnzymeRules::getVectorCuts ( /* not const */ TVector * const v ) const
{
wxPrintf( "D: TEnzymeRules::getVectorCuts - start ( on %s )\n" , v->getName() ) ;
//wxPrintf( "D: TEnzymeRules::getVectorCuts - start ( on %s )\n" , v->getName() ) ;
for ( int a = 0 ; a < v->re.GetCount() ; a++ )
{
if ( NULL == v->re[a] )
Expand All @@ -638,7 +638,7 @@ void TEnzymeRules::getVectorCuts ( /* not const */ TVector * const v ) const
// Getting the default list of enzymes
wxArrayTRestrictionEnzyme ve ;
wxArrayString vs ;
wxPrintf( "D: TEnzymeRules::getVectorCuts - requesting Enzymes for default group '%s'\n" , default_group ) ;
//wxPrintf( "D: TEnzymeRules::getVectorCuts - requesting Enzymes for default group '%s'\n" , default_group ) ;
myapp()->frame->LS->getEnzymesInGroup ( default_group , vs ) ;
ve.Alloc ( vs.GetCount() ) ;

Expand Down Expand Up @@ -680,15 +680,15 @@ void TEnzymeRules::getVectorCuts ( /* not const */ TVector * const v ) const
v->getCuts ( ve[a] , vc , false , max ) ;
if ( use_min_cutoff && min_cutoff > vc.size() )
{
wxPrintf( "D: TEnzymeRules::getVectorCuts - min cutoff: %d - skipping enzyme:%s - too few cuts - vc.size():%lu\n" , min_cutoff, ve[a]->getName() , vc.size() ) ;
//wxPrintf( "D: TEnzymeRules::getVectorCuts - min cutoff: %d - skipping enzyme:%s - too few cuts - vc.size():%lu\n" , min_cutoff, ve[a]->getName() , vc.size() ) ;
}
else if ( use_max_cutoff && max_cutoff < vc.size() )
{
wxPrintf( "D: TEnzymeRules::getVectorCuts - max cutoff: %d - skipping enzyme:%s - too many cuts - vc.size():%lu\n" , max_cutoff, ve[a]->getName() , vc.size() ) ;
//wxPrintf( "D: TEnzymeRules::getVectorCuts - max cutoff: %d - skipping enzyme:%s - too many cuts - vc.size():%lu\n" , max_cutoff, ve[a]->getName() , vc.size() ) ;
}
else
{
wxPrintf( "D: TEnzymeRules::getVectorCuts - accepting - accepting enzyme:%s vc.size():%lu\n" , ve[a]->getName() , vc.size() ) ;
//wxPrintf( "D: TEnzymeRules::getVectorCuts - accepting - accepting enzyme:%s vc.size():%lu\n" , ve[a]->getName() , vc.size() ) ;
v->re2.Add ( ve[a] ) ;
for ( int b = 0 ; b < vc.size() ; b++ )
{
Expand All @@ -697,6 +697,6 @@ void TEnzymeRules::getVectorCuts ( /* not const */ TVector * const v ) const
}
}

wxPrintf( "D: TEnzymeRules::getVectorCuts - end - (for %s, v->re2.GetCount(): %lu)\n" , v->getName(), v->re2.GetCount() ) ;
//wxPrintf( "D: TEnzymeRules::getVectorCuts - end - (for %s, v->re2.GetCount(): %lu)\n" , v->getName(), v->re2.GetCount() ) ;
}

28 changes: 14 additions & 14 deletions src/SequenceTypeAA.cpp
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -163,47 +163,47 @@ void SeqAA::fixOffsets ( TVector * const v )

void SeqAA::initFromTVector ( const TVector * const v )
{
wxPrintf( "D: SeqAA::initFromTVector - start\n" ) ;
//wxPrintf( "D: SeqAA::initFromTVector - start\n" ) ;

if ( ! v )
{
wxPrintf ( " SeqAA::initFromTVector ( NULL ) - abort\n" ) ;
wxPrintf ( "E: SeqAA::initFromTVector ( NULL ) - abort\n" ) ;
abort() ;
}

wxPrintf( "D: SeqAA::initFromTVector( %s ) - start\n" , v->getName() ) ;
//wxPrintf( "D: SeqAA::initFromTVector( %s ) - start\n" , v->getName() ) ;

showNumbers = true ;
if ( ! vec )
{
wxPrintf ( "D: SeqAA::initFromTVector: allocating new vector.\n" ) ;
//wxPrintf ( "D: SeqAA::initFromTVector: allocating new vector.\n" ) ;
vec = new TVector ( ) ;
}
else
{
wxPrintf ( "D: SeqAA::initFromTVector: reusing existing vector - why?\n" ) ;
//wxPrintf ( "D: SeqAA::initFromTVector: reusing existing vector - why?\n" ) ;
}
wxPrintf ( "D: SeqAA::initFromTVector: pre vec->copy()\n" ) ;
//wxPrintf ( "D: SeqAA::initFromTVector: pre vec->copy()\n" ) ;
vec->copy ( *v ) ;
wxPrintf ( "D: SeqAA::initFromTVector: post vec->copy()\n" ) ;
//wxPrintf ( "D: SeqAA::initFromTVector: post vec->copy()\n" ) ;

bool truncateEditSequence = false ;
if ( can && can->getEditMode() && vec->getSequenceLength() && vec->getSequenceChar(vec->getSequenceLength()-1) == ' ' )
{
wxPrintf ( "D: SeqAA::initFromTVector: can && can->getEditMode() && vec->getSequenceLength() && vec->getSequenceChar(vec->getSequenceLength()-1) == ' '\n" ) ;
//wxPrintf ( "D: SeqAA::initFromTVector: can && can->getEditMode() && vec->getSequenceLength() && vec->getSequenceChar(vec->getSequenceLength()-1) == ' '\n" ) ;
vec->eraseSequence ( vec->getSequenceLength()-1 , 1 ) ;
truncateEditSequence = true ;
}

wxString t = vec->getSequence() ;
if (0 >= t.length())
{
wxPrintf("D: SeqAA::initFromTVector: Assigned the empty string with t=%ld.\n" , t.length() ) ;
//wxPrintf("D: SeqAA::initFromTVector: Assigned the empty string with t=%ld.\n" , t.length() ) ;
s="";
}
else
{
wxPrintf("D: SeqAA::initFromTVector: Assigning blanks of length %ld\n", t.length() ) ;
//wxPrintf("D: SeqAA::initFromTVector: Assigning blanks of length %ld\n", t.length() ) ;
wxString empty(' ', t.length() ) ;
s = empty ;
}
Expand Down Expand Up @@ -296,7 +296,7 @@ void SeqAA::initFromTVector ( const TVector * const v )
}
if ( truncateEditSequence )
{
wxPrintf ( "D; SeqAA::initFromTVector: truncateEditSequence\n" ) ;
//wxPrintf ( "D; SeqAA::initFromTVector: truncateEditSequence\n" ) ;
vec->addToSequence ( _T(" ") ) ;
s += _T(" ") ;
}
Expand All @@ -308,7 +308,7 @@ void SeqAA::initFromTVector ( const TVector * const v )
// mem += sizeof ( wxArrayTProteaseCut ) + sizeof ( wxArrayTProtease ) + sizeof ( wxArrayTVectorItem ) ;
mylog ( "AA_mem" , wxString::Format ( "%d" , mem ) ) ;

wxPrintf( "D: SeqAA::initFromTVector - end\n" ) ;
//wxPrintf( "D: SeqAA::initFromTVector - end\n" ) ;
}

// direct
Expand Down Expand Up @@ -341,7 +341,7 @@ int SeqAA::arrange_direct ( const int n ) /* not const */

void SeqAA::show_direct ( wxDC& dc )
{
wxPrintf("D: SeqAA::show_direct - start\n" ) ;
//wxPrintf("D: SeqAA::show_direct - start\n" ) ;
myass ( itemsperline , "AA:show_direct_ipl" ) ;
if ( !itemsperline ) return ;
mylog ( "SeqAA::show_direct" , "0" ) ;
Expand Down Expand Up @@ -506,7 +506,7 @@ void SeqAA::show_direct ( wxDC& dc )
dc.SetBackgroundMode ( bm ) ;
dc.SetTextBackground ( tbg ) ;
dc.SetTextForeground ( tfg ) ;
wxPrintf("D: SeqAA::show_direct - end\n" ) ;
//wxPrintf("D: SeqAA::show_direct - end\n" ) ;
}

int SeqAA::getLine ( const int _y ) const
Expand Down
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