Merge pull request #76 from smoe/optics

optics: whitespace and maybe introduced const

AutoAnnotate.h

@@ -1,42 +1,42 @@
 /** \file
-	\brief Contains the AutoAnnotate class
+    \brief Contains the AutoAnnotate class
 */
 #ifndef __AUTOANNOTATE__
 #define __AUTOANNOTATE__
 
 #include "main.h"
 
 class MyChild ;
-/**	\brief The AutoAnnotate class scans database(s) for known features in the current sequence
+/** \brief The AutoAnnotate class scans database(s) for known features in the current sequence
 
-	It uses the TAutoAnnotateDialog class to display a settings dialog, then runs through one or
-	two databases (depending on the settings), extracting DNA, and matching it to the current sequence.
-	Finally, it will add all not-identified open reading frames as "unknown" features.
+    It uses the TAutoAnnotateDialog class to display a settings dialog, then runs through one or
+    two databases (depending on the settings), extracting DNA, and matching it to the current sequence.
+    Finally, it will add all not-identified open reading frames as "unknown" features.
 */
 class AutoAnnotate
-	{
-	public :
-	AutoAnnotate ( MyChild *_p = NULL ) ; ///< Constructor
-	~AutoAnnotate () {} ; ///< Destructor (empty)
+    {
+    public :
+    AutoAnnotate ( MyChild * const _p = NULL ) ; ///< Constructor
+    ~AutoAnnotate () {} ; ///< Destructor (empty)
 
-	bool SettingsDialog () ; ///< Runs the dialog; returns wether to Run or not
-	void Run () ; ///< Runs the search
-	
-	private :
-	bool ScanDatabase ( wxString database ) ; ///< Scans a database for matching features
-	bool addORFs ( TVector *v ) ; ///< Adds open reading frames as features (that could not be identified)
- 	bool MatchItem ( TVector *tv , TVectorItem &item , TVector *v , wxString &oseq ) ; ///< Compares two items to prevent double entries
- 	bool RawMatch ( TVectorItem &item , TVector *v , wxString &oseq , wxString &s ) ; ///< Tries to match the full item sequence against the current sequence
- 	void machete ( TVector *v ) ; ///< Reduces the number of identified items, so that one can actually read something in the map again :-)
- 	bool within ( TVectorItem &i1 , TVectorItem &i2 , TVector *v ) ; ///< Checks if TVectorItem i2 lies within i1 (no need to add it then)
+    bool SettingsDialog () ; ///< Runs the dialog; returns wether to Run or not
+    void Run () ; ///< Runs the search
+    
+    private :
+    bool ScanDatabase ( const wxString& database ) ; ///< Scans a database for matching features
+    bool addORFs ( TVector *v ) ; ///< Adds open reading frames as features (that could not be identified)
+    bool MatchItem ( const TVector * const tv , TVectorItem &item , TVector *v , const wxString &oseq ) ; ///< Compares two items to prevent double entries
+    bool RawMatch ( const TVectorItem &item , TVector *v , const wxString &oseq , const wxString &s ) ; ///< Tries to match the full item sequence against the current sequence
+    void machete ( TVector * const v ) ; ///< Reduces the number of identified items, so that one can actually read something in the map again :-)
+    bool within ( const TVectorItem &i1 , const TVectorItem &i2 , const TVector * const v ) ; ///< Checks if TVectorItem i2 lies within i1 (no need to add it then)
 
- 	friend class TAutoAnnotateDialog ;
- 	
- 	MyChild *p ; ///< Pointer to the calling MyChild
- 	wxArrayString alreadyin ; ///< Cache of items already added
- 	wxString commonVectorsDatabase , additionalDatabase ;
- 	bool useCommonDatabase , useAdditionalDatabase , useMachete , doAddORFs ;
+    friend class TAutoAnnotateDialog ;
+     
+    MyChild *p ; ///< Pointer to the calling MyChild
+    wxArrayString alreadyin ; ///< Cache of items already added
+    wxString commonVectorsDatabase , additionalDatabase ;
+    bool useCommonDatabase , useAdditionalDatabase , useMachete , doAddORFs ;
     wxArrayString dbname , dbfile ;
-	} ;
+    } ;
 
 #endif

MyChild.cpp

@@ -813,7 +813,7 @@ void MyChild::OnHelp(wxCommandEvent& event)
     myapp()->frame->OnHelp ( event ) ;
     }
 
-void MyChild::updateSequenceCanvas ( bool remember )
+void MyChild::updateSequenceCanvas ( const bool& remember )
     {
     myass ( cSequence , "MyChild::updateSequenceCanvas" ) ;
     TMarkMem mm ( cSequence ) ;
@@ -868,7 +868,7 @@ void MyChild::OnAA_none(wxCommandEvent& event)
     mm.remark () ;
     }
 
-void MyChild::OnAA_setit(int mode)
+void MyChild::OnAA_setit(const int mode)
     {
     bool wasZero = aa_state == AA_NONE ;
     int oldscrollpos , dummy , oldmarkfrom , oldmarkto , oldmarkwhat ;
@@ -995,7 +995,7 @@ void MyChild::OnPrintRestrictionList(wxCommandEvent& event)
     vector <wxString> c_name , c_pos ;
     for ( int a = 0 ; a < vec->rc.size() ; a++ )
         {
-	int b;
+        int b;
         for ( b = 0 ; b < c_name.size() && c_name[b] != vec->rc[a].e->getName() ; b++ ) ;
         if ( b == c_name.size() )
             {
@@ -1083,7 +1083,7 @@ void MyChild::OnMarkAll(wxCommandEvent& event)
     Refresh () ;
     }
 
-wxString MyChild::doExtractAA ( bool coding )
+wxString MyChild::doExtractAA ( const bool& coding )
     {
     if ( aa_state == AA_NONE || aa_state == AA_ALL )
         {
@@ -1396,19 +1396,19 @@ void MyChild::OnPrintReport(wxCommandEvent& event)
         {
         y += ch ;
         pdc->DrawText ( vec->items[a].name , x0 , y ) ;
-//        sprintf ( t , "%d" , vec->items[a].from ) ; pdc->DrawText ( t , x1 , y ) ;
-//        sprintf ( t , "%d" , vec->items[a].to ) ; pdc->DrawText ( t , x2 , y ) ;
+//      sprintf ( t , "%d" , vec->items[a].from ) ; pdc->DrawText ( t , x1 , y ) ;
+//      sprintf ( t , "%d" , vec->items[a].to ) ; pdc->DrawText ( t , x2 , y ) ;
 
-          pdc->DrawText ( wxString::Format ( _T("%d") , vec->items[a].from ) , x1 , y ) ;
-          pdc->DrawText ( wxString::Format ( _T("%d") , vec->items[a].to ) , x2 , y ) ;
+        pdc->DrawText ( wxString::Format ( _T("%d") , vec->items[a].from ) , x1 , y ) ;
+        pdc->DrawText ( wxString::Format ( _T("%d") , vec->items[a].to ) , x2 , y ) ;
 
         int len = vec->items[a].to - vec->items[a].from + 1 ;
         if ( vec->items[a].to < vec->items[a].from )
            len += vec->getSequenceLength() ;
-//        sprintf ( t , "%d" , len ) ; pdc->DrawText ( t , x3 , y ) ;
+//      sprintf ( t , "%d" , len ) ; pdc->DrawText ( t , x3 , y ) ;
         pdc->DrawText ( wxString::Format ( _T("%d") , len ) , x3 , y ) ;
 
-//        sprintf ( t , "itemtype%d" , vec->items[a].type ) ;
+//      sprintf ( t , "itemtype%d" , vec->items[a].type ) ;
         pdc->DrawText ( txt(wxString::Format( _T("itemtype%d") , vec->items[a].type)) , x4 , y ) ;
         if ( vec->items[a].direction > 0 ) pdc->DrawText ( txt("cw") , x5 , y ) ;
         else pdc->DrawText ( txt("ccw") , x5 , y ) ;
@@ -1670,7 +1670,7 @@ void MyChild::add_siRNA ( const int item )
    vec->updateDisplay () ;
    }
 
-int MyChild::add_siRNA_sub ( wxString s , int pos )
+int MyChild::add_siRNA_sub ( const wxString& s , const int pos )
    {
    int score = 0 ;
    if ( s.GetChar ( 2 ) != 'A' ) return 0 ;

MyChild.h

@@ -51,7 +51,7 @@ class MyChild: public ChildBase
     virtual void OnAA_three_M1(wxCommandEvent& event); ///< "Display amino acids, reading frame -1" event handler
     virtual void OnAA_three_M2(wxCommandEvent& event); ///< "Display amino acids, reading frame -2" event handler
     virtual void OnAA_three_M3(wxCommandEvent& event); ///< "Display amino acids, reading frame -3" event handler
-    virtual void OnAA_setit(int mode); ///< Sets the amino acid display mode (called by the OnAA_ event handlers)
+    virtual void OnAA_setit(const int mode); ///< Sets the amino acid display mode (called by the OnAA_ event handlers)
 
     virtual void OnActivate(wxActivateEvent& event); ///< Activation event handler
     virtual void Undo(wxCommandEvent& event); ///< Undo event handler
@@ -99,8 +99,8 @@ class MyChild: public ChildBase
     virtual void initPanels () ; ///< Initializes the panels
     virtual wxString getName () const ; ///< Returns the module name
     virtual void EnforceRefesh () ; ///< Force display refresh
-    virtual void updateSequenceCanvas ( bool remember = false ) ; ///< Refresh the sequence display
-    virtual wxString doExtractAA ( bool coding = true ) ; ///< Extract amino acid sequence from DNA
+    virtual void updateSequenceCanvas ( const bool& remember = false ) ; ///< Refresh the sequence display
+    virtual wxString doExtractAA ( const bool& coding = true ) ; ///< Extract amino acid sequence from DNA
     virtual bool runRestriction ( const wxString& s ) ; ///< Run the restriction
     virtual void addFragmentsToGel ( const wxString& title , wxArrayInt &cuts , TVirtualGel * const gel , const TRestrictionEditor& ed , const bool partial ) const ; ///< Add restriction fragments to gel
     virtual MyChild *doTransformSequence ( const bool inNewVector , const bool complement , const bool invers ) ; ///< Transform the sequence
@@ -121,7 +121,7 @@ class MyChild: public ChildBase
     virtual void initMenus () ; ///< Initialize the menus
 
     void add_siRNA ( const int item ) ;
-    int add_siRNA_sub ( wxString s , int pos ) ;
+    int add_siRNA_sub ( const wxString& s , const int pos ) ;
 
     wxChoice *fontsize ;
 

MyFrame.cpp

@@ -2785,7 +2785,7 @@ bool MyFrameDropTarget::OnDropFiles(wxCoord x, wxCoord y, const wxArrayString& f
     for ( int a = 0 ; a < filenames.GetCount() ; a++ )
         {
         wxString path = filenames[a] ;
-	int b ;
+        int b ;
         for ( b = path.length() - 1 ; path.GetChar(b) != '\\' && path.GetChar(b) != '/' ; b-- ) ;
         wxString file = path.substr ( b+1 ) ;
         myapp()->frame->importFile ( file , path , -1 ) ;
@@ -2802,6 +2802,6 @@ TProject::TProject ()
     enzyme_rules = NULL ;
     }
 
-TEnzymeRules *TProject::getEnzymeRules () { return enzyme_rules ; }
-void TProject::setEnzymeRules ( TEnzymeRules *er ) { enzyme_rules = er ; }
+TEnzymeRules *TProject::getEnzymeRules () const { return enzyme_rules ; }
+void TProject::setEnzymeRules ( TEnzymeRules * const er ) { enzyme_rules = er ; }
 

MyFrame.h

@@ -72,7 +72,7 @@ class TProject
  	TProject () ; ///< Constructor
 	virtual ~TProject () {} ; ///< Dummy destructor
 
-    virtual TEnzymeRules *getEnzymeRules () ; ///< Returns the restriction enzyme display rules for the project
+    virtual TEnzymeRules *getEnzymeRules () const ; ///< Returns the restriction enzyme display rules for the project
     virtual void setEnzymeRules ( TEnzymeRules *er ) ; ///< Sets the restriction enzyme display rules for the project
 
     wxString name ;  ///< \brief The project name

TPrimerDialog.cpp

@@ -76,7 +76,7 @@ wxSpinCtrl *TPrimerDialog::addSpinCtrl ( const int id , const wxString& title ,
     return n ;
     }
 
-void TPrimerDialog::initme ( TPrimer * const _p , TPrimerDesign * const _pd )
+void TPrimerDialog::initme ( TPrimer * const _p , const TPrimerDesign * const _pd )
     {
     p = _p ;
     pd = _pd ;
@@ -183,9 +183,9 @@ void TPrimerDialog::updateList ()
         t = pd->vec->getSequence() ;
         s = t ;
         for ( int a = 0 ; a < p->sequence.length() ; a++ )
-	    {
+            {
             s.SetChar( a+p->from-1 , p->sequence.GetChar(a) ) ;
-	    }
+            }
         l1 = p->from - 1 - l5->GetValue() ;
         l2 = p->from - 1 + r5->GetValue() ;
         r1 = p->to - 1 - l3->GetValue() ;
@@ -196,9 +196,9 @@ void TPrimerDialog::updateList ()
         t = pd->inverse_template_vector->getSequence() ;
         s = t ;
         for ( int a = 0 ; a < p->sequence.length() ; a++ )
-	    {
+            {
             s.SetChar ( a+p->from-1 , p->sequence.GetChar(a) ) ;
-	    }
+            }
         l1 = p->from - 1 - l3->GetValue() ;
         l2 = p->from - 1 + r3->GetValue() ;
         r1 = p->to - 1 - l5->GetValue() ;

TPrimerDialog.h

@@ -22,7 +22,7 @@ class TPrimerDialog : public wxDialog
     public:
     TPrimerDialog(wxWindow *parent , const wxString& title ) ; ///< Constructor
     ~TPrimerDialog() ; ///< Destructor
-    void initme ( TPrimer * const _p , TPrimerDesign * const _pd ) ; ///< Initialize
+    void initme ( TPrimer * const _p , const TPrimerDesign * const _pd ) ; ///< Initialize
     wxSpinCtrl *addSpinCtrl ( const int id , const wxString& title , const int x , const int y , const int def ) ; ///< Create a new wxSpinCtrl (this dialog has so many of them...)
 
     TPrimer *p , *cp ;
@@ -41,7 +41,7 @@ class TPrimerDialog : public wxDialog
     void ShowLC () ; ///< Refreshes the potential primer list
 
     private :
-    TPrimerDesign *pd ;
+    const TPrimerDesign *pd ;
     vector <TPrimer> pl ; ///< The list of potential primers
 
     wxSpinCtrl *l3 , *l5 , *r3 , *r5 , *lmin , *lmax , *tmin , *tmax ;