Merge pull request #100 from smoe/optics

Optics: Mostly on indentation
GENtle-persons · Apr 30, 2024 · 979348b · 979348b
2 parents d15d404 + b6d132c
commit 979348b
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Showing 9 changed files with 46 additions and 41 deletions.
diff --git a/src/PlasmidCanvasLinear.cpp b/src/PlasmidCanvasLinear.cpp
@@ -356,6 +356,11 @@ void PlasmidCanvas::drawLinearItem ( wxDC& dc , const int _r1 , const int _r2 ,
     // Drawing polygon
     wxPoint *wp ;
     wp = (wxPoint*) malloc ( sizeof ( wxPoint ) * (pt.size()+1) ) ;
+    if (!wp)
+        {
+            wxPrintf("E: Out of memory.\n") ;
+            abort() ;
+        }
     for ( unsigned int b = 0 ; b < pt.size() ; b++ ) wp[b] = pt[b] ;
     if ( !this->p->vec->getGenomeMode() ) dc.SetPen(*wxBLACK_PEN);
     else dc.SetPen ( *MYPEN((wxColour)i->getBrush()->GetColour()) ) ;

diff --git a/src/TIMGreader.cpp b/src/TIMGreader.cpp
@@ -9,12 +9,12 @@ TIMGreader::~TIMGreader ()
     if ( buffer )
         {
         delete buffer ;
-	buffer = NULL ;
+        buffer = NULL ;
         }
     if ( output )
         {
-	free( output ) ;
-	output = NULL ;
+        free( output ) ;
+        output = NULL ;
         }
     }
 
@@ -134,12 +134,12 @@ void TIMGitem::draw ( wxDC &dc , int x1 , int y1 , int x2 , int y2 )
         }
     }
 
-int TIMGitem::xx ( int x )
+int TIMGitem::xx ( const int x ) const
     {
     return off.x + x * 19 / 24 ;
     }
 
-int TIMGitem::yy ( int y )
+int TIMGitem::yy ( const int y ) const
     {
     return off.y + y * 9 / 12 ;
     }

diff --git a/src/TIMGreader.h b/src/TIMGreader.h
@@ -14,8 +14,8 @@ class TIMGitem
     {
     public :
     void draw ( wxDC &dc , int x1 , int y1 , int x2 , int y2 ) ; ///< Draws the annotation
-    int xx ( int x ) ; ///< X-coordinate conversion
-    int yy ( int y ) ; ///< Y-coordinate conversion
+    int xx ( const int x ) const ; ///< X-coordinate conversion
+    int yy ( const int y ) const ; ///< Y-coordinate conversion
 
     int type ; ///< Annotation type
     wxPoint p1 , p2 ;

diff --git a/src/TLigationDialog.cpp b/src/TLigationDialog.cpp
@@ -87,7 +87,7 @@ void TLigationDialog::init ()
         {
         bool state = true ;
         if ( !vv[a]->hasStickyEnds() )
-           state = false ; // blunt ends are not ligated by default...
+            state = false ; // blunt ends are not ligated by default...
         l_sources->Append ( vv[a]->getName() ) ;
         l_sources->Check ( a , state ) ;
         }
@@ -98,11 +98,10 @@ void TLigationDialog::init ()
 
 void TLigationDialog::generateTargets ()
     {
-    int a ;
     int cnt = l_sources->GetCount() ;
     vector <bool> vc , used ;
     wxArrayInt vi ;
-    for ( a = 0 ; a < cnt ; a++ )
+    for ( int a = 0 ; a < cnt ; a++ )
         {
         vc.push_back ( l_sources->IsChecked ( a ) ) ;
         used.push_back ( !l_sources->IsChecked ( a ) ) ;
@@ -113,7 +112,7 @@ void TLigationDialog::generateTargets ()
     l_targets->Clear () ;
 
     // Using each selected item as a starter
-    for ( a = 0 ; a < cnt ; a++ )
+    for ( int a = 0 ; a < cnt ; a++ )
         {
         if ( vc[a] )
            {
@@ -129,7 +128,7 @@ void TLigationDialog::generateTargets ()
            }
         }
 
-    for ( a = 0 ; a < vt.GetCount() ; a++ )
+    for ( int a = 0 ; a < vt.GetCount() ; a++ )
         {
         l_targets->Append ( vt[a] ) ;
         l_targets->Check ( a , true ) ;
@@ -191,15 +190,15 @@ void TLigationDialog::curseTargets ( vector <bool> &vc , vector <bool> &used , w
         myass ( a >= 0 && a < vc.size() , "TLigationDialog::curseTargets:4b" ) ;
         myass ( a >= 0 && a < used.size() , "TLigationDialog::curseTargets:4c" ) ;
         if ( vc[a] && !used[a] && doMatch ( vi[cnt-1] , a , true ) ) // Turned around
-           {
-           used[a] = true ;
-           vi.Add ( a ) ;
-           orientation.push_back ( true ) ;
-           curseTargets ( vc , used , vi ) ;
-           orientation.pop_back () ;
-           vi.RemoveAt ( vi.GetCount() - 1 ) ;
-           used[a] = false ;
-           }
+            {
+            used[a] = true ;
+            vi.Add ( a ) ;
+            orientation.push_back ( true ) ;
+            curseTargets ( vc , used , vi ) ;
+            orientation.pop_back () ;
+            vi.RemoveAt ( vi.GetCount() - 1 ) ;
+            used[a] = false ;
+            }
         }
     }
 
@@ -210,7 +209,7 @@ wxString TLigationDialog::invert ( const wxString& s ) const
     return t ;
     }
 
-bool TLigationDialog::doMatch ( int l , int r , bool invertSecond )
+bool TLigationDialog::doMatch ( const int& l , const int& r , const bool& invertSecond ) const
     {
     wxString s1 , s2 ;
 
@@ -219,15 +218,15 @@ bool TLigationDialog::doMatch ( int l , int r , bool invertSecond )
     myass ( r >= 0 && r < vv.GetCount() , "TLigationDialog::doMatch:3" ) ;
     myass ( vv[r] , "TLigationDialog::doMatch:4" ) ;
     if ( invertSecond )
-       {
-       s1 = vv[l]->getStickyEnd(false,true) + invert ( vv[r]->getStickyEnd(false,false) ) ;
-       s2 = vv[l]->getStickyEnd(false,false) + invert ( vv[r]->getStickyEnd(false,true) ) ;
-       }
+        {
+        s1 = vv[l]->getStickyEnd(false,true) + invert ( vv[r]->getStickyEnd(false,false) ) ;
+        s2 = vv[l]->getStickyEnd(false,false) + invert ( vv[r]->getStickyEnd(false,true) ) ;
+        }
     else
-       {
-       s1 = vv[l]->getStickyEnd(false,true) + vv[r]->getStickyEnd(true,true) ;
-       s2 = vv[l]->getStickyEnd(false,false) + vv[r]->getStickyEnd(true,false) ;
-       }
+        {
+        s1 = vv[l]->getStickyEnd(false,true) + vv[r]->getStickyEnd(true,true) ;
+        s2 = vv[l]->getStickyEnd(false,false) + vv[r]->getStickyEnd(true,false) ;
+        }
 
     TVector v ;
     v.setSequence ( s1 ) ;

diff --git a/src/TLigationDialog.h b/src/TLigationDialog.h
@@ -25,7 +25,7 @@ class TLigationDialog : public wxDialog
     virtual void init () ; ///< Initialize
     virtual void generateTargets () ; ///< Generate the target list
     virtual void curseTargets ( vector <bool> &vc , vector <bool> &used , wxArrayInt &vi ) ; ///< Recurse through targets
-    virtual bool doMatch ( int l , int r , bool invertSecond = false ) ; ///< Do these match?
+    virtual bool doMatch ( const int& l , const int& r , const bool& invertSecond = false ) const ; ///< Do these match?
     virtual wxString getVIName ( const wxArrayInt &vi ) const ; ///< Generate a name
     virtual void addVTname ( const wxString& name , wxArrayInt &vi , const bool circular ) ; ///< Add this one
 

diff --git a/src/TPrimer.cpp b/src/TPrimer.cpp
@@ -236,9 +236,8 @@ void TPrimer::OligoCount () /* not const */
 
     for ( int i = 1 ; i < seq.length() ; i++ ) //first base can not be IUpacbase
         {
-        wxString base , base0 ;
-        base0 += seq.GetChar(i-1) ;
-        base += seq.GetChar(i) ;
+        wxString base0 = seq.GetChar(i-1) ;
+        wxString base = seq.GetChar(i) ;
         double *temp ;
 
         temp=CalcIUpair(base0, base, i, false );

diff --git a/src/TSilmutDialog.cpp b/src/TSilmutDialog.cpp
@@ -178,8 +178,8 @@ void TSilmutDialog::OnCancel ( wxCommandEvent &ev )
 
 void TSilmutDialog::OnSpin ( wxSpinEvent &event )
     {
- wxCommandEvent event2 ;
- OnSpin2 ( event2 ) ;
+    wxCommandEvent event2 ;
+    OnSpin2 ( event2 ) ;
     }
 
 void TSilmutDialog::OnSpin2 ( wxCommandEvent &event )

diff --git a/src/ureadseq.c b/src/ureadseq.c
@@ -1124,7 +1124,7 @@ char *readSeq(
 
 
 char *listSeqs(
-      const char  *filename_,   /* file name */
+      const char  * const filename_,   /* file name */
       const size_t skiplines_,
       const short format_,      /* sequence file format */
       size_t *nseq_,       /* number of seqs in file, for listSeqs() */
@@ -1345,17 +1345,18 @@ short seqFileFormatFp(
   if (format == kPhylip) {
     /* check for interleaved or sequential -- really messy */
     int tname, tseq;
-    size_t i, j, nspp= 0, nlen= 0, ilen, leaf= 0, seq= 0;
+    size_t j, nspp= 0, nlen= 0, ilen, leaf= 0, seq= 0;
     char  *ps;
 
     rewind(fseq);
-    for (i=0; i < *skiplines; i++) ReadOneLine(sp);
+    for (size_t i=0; i < *skiplines; i++) ReadOneLine(sp);
     nlines= 0;
     ReadOneLine(sp);
     sscanf( sp, "%ld%ld", &nspp, &nlen);
     ReadOneLine(sp); /* 1st seq line */
     for (ps= sp+10, ilen=0; *ps!=0; ps++) if (isprint(*ps)) ilen++;
 
+    size_t i;
     for (i= 1; i<nspp; i++) {
       ReadOneLine(sp);
 
@@ -1379,6 +1380,8 @@ short seqFileFormatFp(
         ilen= 0;
         }
       }
+
+    // value of i reused here, which should be nspp
     for ( nspp *= 2 ; i<nspp; i++) {  /* this should be only bases if interleaf */
       ReadOneLine(sp);
 

diff --git a/src/ureadseq.h b/src/ureadseq.h
@@ -126,8 +126,7 @@ extern "C" {
 extern short seqFileFormat(const char *filename, size_t *skiplines, short *error );
 extern short seqFileFormatFp(FILE *fseq, size_t  *skiplines, short *error );
 
-extern char *listSeqs(const char *filename, const size_t skiplines,
-                       const short format, size_t *nseq, short *error );
+extern char *listSeqs(const char * const filename, const size_t skiplines, const short format, size_t *nseq, short *error );
 
 extern char *readSeq(const size_t whichEntry, const char *filename,
                       const size_t skiplines, const short format,