fix: Restriction enzymes' sequence was not set

Also fixed builds on Linux fixing typo in font management. Series of debug messages.
GENtle-persons · Aug 29, 2024 · 17f1d45 · 17f1d45
1 parent c48bfb3
commit 17f1d45
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Showing 23 changed files with 1,056 additions and 420 deletions.
diff --git a/src/MyFrame.cpp b/src/MyFrame.cpp
@@ -191,7 +191,7 @@ void MyFrame::initme ()
 //  myapp()->sw.Start() ;
 
 #ifdef __WXGTK__
-    wxFont f ( wxFontInfo ( 8 ).Family( wxFONTFAMILY_SWISS ).Style( wxFONTSTYLE_NORMAL ).Weight( wxFONWEIGHT_NORMAL ) ) ;
+    wxFont f ( wxFontInfo ( 8 ).Family( wxFONTFAMILY_SWISS ).Style( wxFONTSTYLE_NORMAL ).Weight( wxFONTWEIGHT_NORMAL ) ) ;
     SetFont ( f ) ;
 #endif
 
@@ -2075,25 +2075,26 @@ void MyFrame::removeChild ( ChildBase *ch )
 /** \brief Activates a child (brings to front, makes visible, etc.)
  \param childno - position of child in children list, starts with 0
  */
-void MyFrame::activateChild ( const int childno )
+void MyFrame::activateChild ( const unsigned int childno )
     {
     //wxPrintf( "D: MyFrame::activateChild( %d ) - start\n" , childno) ;
     size_t numberOfChildren = children.GetCount() ;
     if ( ! numberOfChildren )
         {
-            //wxPrintf( "D: MyFrame::activateChild( %d ) - beyond number of children ( = %d), choosing NULL\n" , childno, children.GetCount() ) ;
+            wxPrintf( "D: MyFrame::activateChild( %u ) - beyond number of children ( = %lu), choosing NULL\n" , childno, children.GetCount() ) ;
             setActiveChild ( NULL ) ;
         }
     else
         {
-        if ( childno >= children.GetCount() )
+        int childtoactivate = childno ;
+        if ( childtoactivate >= children.GetCount() )
             {
-            //wxPrintf( "D: MyFrame::activateChild( %d ) - beyond number of children ( = %d), choosing first\n" , childno, children.GetCount() ) ;
-            childno = 0 ;
+            wxPrintf( "W: MyFrame::activateChild( %u ) - beyond number of children ( = %lu), choosing first\n" , childno, children.GetCount() ) ;
+            childtoactivate = 0 ; // not const
             }
-        children[childno]->Activate () ;
-        mainTree->EnsureVisible ( children[childno]->inMainTree ) ;
-        mainTree->SelectItem ( children[childno]->inMainTree ) ;
+        children[childtoactivate]->Activate () ;
+        mainTree->EnsureVisible ( children[childtoactivate]->inMainTree ) ;
+        mainTree->SelectItem ( children[childtoactivate]->inMainTree ) ;
         }
     //wxSafeYield () ;
     //wxPrintf( "D: MyFrame::activateChild( %d ) - end\n" ) ;
@@ -2167,7 +2168,7 @@ wxString MyFrame::check4update ()
     return text ;
     }
 
-wxString MyFrame::check4update_sub ( const wxString& text ) const
+wxString MyFrame::check4update_sub ( const wxString& text ) /* not const */
     {
     bool error = true ;
     if ( !text.IsEmpty() ) error = false ;
@@ -2190,7 +2191,7 @@ wxString MyFrame::check4update_sub ( const wxString& text ) const
             {
             wxString msg = it.AfterFirst ( '\n' ) ;
             msg += "\n(" + wxString ( txt("t_you_use_version") ) + myapp()->get_GENtle_version() + ")" ;
-            wxMessageDialog md ( this , msg , txt("t_new_version" ) , wxOK | wxCANCEL | wxCENTRE | wxICON_INFORMATION ) ;
+            wxMessageDialog md ( /* not const */ this , msg , txt("t_new_version" ) , wxOK | wxCANCEL | wxCENTRE | wxICON_INFORMATION ) ;
             if ( wxID_OK != md.ShowModal() )
                 {
                 return "-" ;

diff --git a/src/MyFrame.h b/src/MyFrame.h
@@ -170,7 +170,7 @@ class MyFrame : public MyFrameType
     virtual void setActiveChild ( ChildBase * const c ) ;
     virtual wxWindow* getCommonParent() const ;
     virtual int getChildIndex ( const ChildBase * const c ) const ;
-    virtual void activateChild ( const int childno ) ;
+    virtual void activateChild ( const unsigned int childno ) ;
     virtual void lockDisplay ( const bool lock = true ) ;
     virtual bool isLocked () const ;
     virtual bool isActivating () const ;

diff --git a/src/PCR_Troubleshoot.h b/src/PCR_Troubleshoot.h
@@ -1,5 +1,5 @@
 /** \file
-    \brief Contains the FindSequenceDialog class
+    \brief Contains the PCR_troubleshoot_dialog class
 */
 #ifndef _PCRTROUBLESHOOT_H_
 #define _PCRTROUBLESHOOT_H_

diff --git a/src/PrimerDesign.cpp b/src/PrimerDesign.cpp
@@ -91,7 +91,9 @@ TPrimerDesign::TPrimerDesign(wxWindow *parent, const wxString& title, TVector *_
         }
 
     for ( int a = 0 ; a < primer.size() ; a++ )
+        {
         primer[a].getSequenceFromVector ( vec ) ;
+        }
 
     def = _T("PrimerDesign") ;
     from = -1 ;
@@ -161,8 +163,12 @@ void TPrimerDesign::OnImportPrimer ( wxCommandEvent &ev )
     wxArrayChildBase cbl ;
 
     for ( int a = 0 ; a < myapp()->frame->children.GetCount() ; a++ )
+        {
         if ( myapp()->frame->children[a] && myapp()->frame->children[a]->vec && myapp()->frame->children[a]->vec->getType() == TYPE_PRIMER )
+            {
             cbl.Add ( myapp()->frame->children[a] ) ;
+            }
+        }
 
     if ( cbl.GetCount() == 0 )
         {
@@ -172,7 +178,9 @@ void TPrimerDesign::OnImportPrimer ( wxCommandEvent &ev )
 
     wxString *sl = new wxString[cbl.GetCount()] ;
     for ( int a = 0 ; a < cbl.GetCount() ; a++ )
+        {
         sl[a] = cbl[a]->getName() ;
+        }
 
     TMyMultipleChoiceDialog scd ( this , txt("t_chose_primer_txt") , txt("t_chose_primer") , cbl.GetCount() , sl) ;
 
@@ -324,7 +332,9 @@ void TPrimerDesign::updatePrimerStats ()
         lc->SetItem ( l , 6 , wxString::Format ( _T("%d") , primer[a].from ) ) ;
         }
     for ( int a = 0 ; a <= 6 ; a++ )
+        {
         lc->SetColumnWidth ( a , wxLIST_AUTOSIZE_USEHEADER ) ;
+        }
     stat->SetValue ( _T("") ) ;
     lastPrimerActivated = -1 ;
     }
@@ -473,7 +483,9 @@ void TPrimerDesign::initme ()
     spinTextEnabeled = true ;
     sc->SetFocus() ;
     for ( int a = 0 ; a < lc->GetColumnCount() ; a++ )
+        {
         lc->SetColumnWidth ( a , wxLIST_AUTOSIZE_USEHEADER ) ;
+        }
     }
 
 void TPrimerDesign::OnEditPrimer ( wxCommandEvent &ev )
@@ -492,7 +504,9 @@ void TPrimerDesign::OnDeletePrimer ( wxCommandEvent &ev )
     if ( lastPrimerActivated == -1 ) return ;
     if ( primer.size() == 0 ) return ;
     for ( int a = lastPrimerActivated ; a + 1 < primer.size() ; a++ )
+        {
         primer[a] = primer[a+1] ;
+        }
     primer.pop_back () ;
     lastPrimerActivated = -1 ;
     showSequence () ;
@@ -540,8 +554,12 @@ void TPrimerDesign::showSequence ()
     p1->myname = _T("PRIMER_UP") ;
     p1->alternateName = txt("t_primer_up") ;
     for ( int a = 0 ; a < primer.size() ; a++ )
+        {
         if ( primer[a].upper )
+            {
             p1->addPrimer ( &primer[a] ) ;
+            }
+        }
 
     // Upper template sequence
     SeqDNA *s1 = new SeqDNA ( sc ) ;

diff --git a/src/ProgramOptionsDialog.cpp b/src/ProgramOptionsDialog.cpp
@@ -23,6 +23,7 @@ END_EVENT_TABLE()
 
 TEnzymeSettingsTab::TEnzymeSettingsTab ( wxWindow *parent , const int _mode ) : wxPanel ( parent )
     {
+    wxPrintf( "D: TEnzymeSettingsTab::TEnzymeSettingsTab - start\n" ) ;
     myapp()->frame->push_help ( _T("GENtle:Options") ) ;
     mode = _mode ;
     int w , h ;
@@ -129,6 +130,8 @@ TEnzymeSettingsTab::TEnzymeSettingsTab ( wxWindow *parent , const int _mode ) :
     this->Show () ;
     updateGlobalEnzymes () ;
     vs->Fit ( this ) ;
+
+    wxPrintf( "D: TEnzymeSettingsTab::TEnzymeSettingsTab - end\n" ) ;
     }
 
 ProgramOptionsDialog::~ProgramOptionsDialog ()
@@ -138,6 +141,7 @@ ProgramOptionsDialog::~ProgramOptionsDialog ()
 
 void TEnzymeSettingsTab::updateGlobalEnzymes ()
     {
+    wxPrintf( "D: TEnzymeSettingsTab::updateGlobalEnzymes - start\n" ) ;
     bool use = useSettings->GetValue() ;
     useMinCutoff->Enable ( use ) ;
     useMaxCutoff->Enable ( use ) ;
@@ -159,6 +163,7 @@ void TEnzymeSettingsTab::updateGlobalEnzymes ()
     updateColorButton ( bcol1 , col1 ) ;
     updateColorButton ( bcol2 , col2 ) ;
     updateColorButton ( bcol3 , col3 ) ;
+    wxPrintf( "D: TEnzymeSettingsTab::updateGlobalEnzymes - end - useMaxCutoff:%d\n" , useMaxCutoff ) ;
     }
 
 void TEnzymeSettingsTab::updateColorButton ( wxButton *b , const wxColour &c )
@@ -202,14 +207,19 @@ void TEnzymeSettingsTab::OnButton3 ( wxCommandEvent &event )
 
 void TEnzymeSettingsTab::updateColor ( wxColour &c )
     {
-    wxPrintf("D: TEnzymeSettingsTab::updateColor(%s)\n",c.GetAsString()) ;
+    wxPrintf("D: TEnzymeSettingsTab::updateColor(%s) - start\n",c.GetAsString()) ;
 
     wxColour c2 = wxGetColourFromUser ( this , c ) ;
-    wxPrintf("D: TEnzymeSettingsTab  wxGetColourFromUser -> %s\n",c2.GetAsString()) ;
+    wxPrintf("D: TEnzymeSettingsTab::updateColor(%s)  wxGetColourFromUser -> %s\n" , c.GetAsString() , c2.GetAsString()) ;
 
-    if ( !c2.Ok() ) return ;
+    if ( !c2.Ok() )
+        {
+        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()) ;
     }
 
 
@@ -449,9 +459,11 @@ void TEnzymeRules::init () // Default settings
 
 void TEnzymeRules::load_global_settings () /* not const */
     {
+    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" ) ;
     }
 
 void TEnzymeRules::save_global_settings () const
@@ -543,8 +555,9 @@ wxString TEnzymeRules::to_string () const
     return ret ;
     }
 
-void TEnzymeRules::from_string ( const wxString &s )
+void TEnzymeRules::from_string ( const wxString& s )
     {
+    wxPrintf( "D: TEnzymeRules::from_string - start\n" ) ;
     init () ;
     wxArrayString as ;
     explode ( _T("\r") , s , as ) ;
@@ -576,6 +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" ) ;
     }
 
 wxColour TEnzymeRules::scan_color ( const wxString& s ) const
@@ -600,9 +614,26 @@ 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() ) ;
     for ( int a = 0 ; a < v->re.GetCount() ; a++ )
+        {
+        if ( NULL == v->re[a] )
+            {
+            wxPrintf( "E: Found first restriction enzyme re[%d] that is NULL.\n" , a ) ;
+            abort() ;
+            }
+        if ( v->re[a]->getSequence().IsEmpty() )
+            {
+            wxPrintf( "E: Found first restriction enzyme (%s) with empty sequence.\n" , v->re[a]->getName() ) ;
+            abort() ;
+            }
         v->getCuts ( v->re[a] , /* not const */ v->rc , false ) ;
-    if ( !useit ) return ;
+        }
+    if ( !useit )
+        {
+        wxPrintf( "D: TEnzymeRules::getVectorCuts - ret !useit ( on %s )\n" , v->getName() ) ;
+        return ;
+        }
 
     // Getting the default list of enzymes
     wxArrayTRestrictionEnzyme ve ;
@@ -640,17 +671,31 @@ void TEnzymeRules::getVectorCuts ( /* not const */ TVector * const v ) const
 
     // Add what has the correct number of cuts
     v->re2.Clear () ; // The list of used enzymes that were *not* added manually
-    int max = 10000000 ; // Ridiculously high number
+    int max = 500 ; // Upper limit of what GENtle can display as it seems
     if ( use_max_cutoff ) max = max_cutoff ;
     for ( int a = 0 ; a < ve.GetCount() ; a++ )
         {
         vector <TRestrictionCut> vc ;
         v->getCuts ( ve[a] , vc , false , max ) ;
-        if ( ( !use_min_cutoff || min_cutoff <= vc.size() ) && ( !use_max_cutoff || max_cutoff >= vc.size() ) )
+        if ( use_min_cutoff &&  min_cutoff <= vc.size() )
             {
+            wxPrintf( "D: TEnzymeRules::getVectorCuts - min cutoff - enzyme:%s vc.size():%lu\n" , ve[a]->getName() , vc.size() ) ;
+            }
+        else if ( use_max_cutoff && max_cutoff >= vc.size() )
+            {
+            wxPrintf( "D: TEnzymeRules::getVectorCuts - max cutoff - enzyme:%s vc.size():%lu\n" , ve[a]->getName() , vc.size() ) ;
+            }
+        else
+            {
+            wxPrintf( "D: TEnzymeRules::getVectorCuts - 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++ ) v->rc.push_back ( vc[b] ) ;
+            for ( int b = 0 ; b < vc.size() ; b++ )
+                {
+                v->rc.push_back ( vc[b] ) ;
+                }
             }
         }
+
+    wxPrintf( "D: TEnzymeRules::getVectorCuts - end - (for %s, v->re2.GetCount(): %lu)\n" , v->getName(), v->re2.GetCount() ) ;
     }
 
diff --git a/src/ProgramOptionsDialog.h b/src/ProgramOptionsDialog.h
@@ -106,8 +106,10 @@ class TEnzymeRules
     virtual wxColour *getColor ( const int cuts ) ; ///< Returns a pointer to a wxColour structure with the correct color for the given number of cuts
 
     bool useit ;
-    int min_cutoff , max_cutoff ;
-    bool use_min_cutoff , use_max_cutoff ;
+    int min_cutoff ;
+    int max_cutoff ; ///< limits the maximal number of cuts for an enzyme on a single sequence to be accepted
+    bool use_min_cutoff ;
+    bool use_max_cutoff ; ///< flag to enforce maximal number of cuts for an enzyme on a single sequence
     bool recog4 , recog5 , recog6 , recog_longer ;
     bool pattern3 , pattern5 , pattern_blunt ;
     bool showgc ;