dna2.cc

unix或linux下的DNA分析软件源码 其功能如下 1. Edit up to 256 peptide or DNA sequences simultaneously. 2. Transla

  if(!g.editing) analyze();
}

//--------------------------------------------------------------------------//
// nextframe                                                                //
//--------------------------------------------------------------------------//
void nextframe(void)
{
  g.doc[g.cs].frame++;
  if(g.doc[g.cs].frame>2) g.doc[g.cs].frame=0;
  translate(0); // don't check if it's a protein
  if(!g.editing) analyze();
}


//--------------------------------------------------------------------------//
// up                                                                       //
//--------------------------------------------------------------------------//
void up(void)
{
  int cs;
  if(g.editing) cs = g.cs; else cs = g.matrix_set2;
  g.doc[cs].offset += 100;
  XClearWindow(g.display, g.draw_window);
  redrawscreen(0, 0, g.xsize, g.ysize);
}


//--------------------------------------------------------------------------//
// down                                                                     //
//--------------------------------------------------------------------------//
void down(void)
{
  int cs;
  if(g.editing) cs = g.cs; else cs = g.matrix_set2;
  g.doc[cs].offset -= 100;
  if(!g.editing) g.doc[cs].offset = max(0,g.doc[cs].offset);
  XClearWindow(g.display, g.draw_window);
  redrawscreen(0, 0, g.xsize, g.ysize);
}

//--------------------------------------------------------------------------//
// left                                                                     //
//--------------------------------------------------------------------------//
void left(void)
{
  int cs;
  if(g.editing) cs = g.cs; else cs = g.matrix_set1;
  g.doc[cs].offset += 100;
  XClearWindow(g.display, g.draw_window);
  redrawscreen(0, 0, g.xsize, g.ysize);
}


//--------------------------------------------------------------------------//
// right                                                                    //
//--------------------------------------------------------------------------//
void right(void)
{
  int cs;
  if(g.editing) cs = g.cs; else cs = g.matrix_set1;
  g.doc[cs].offset -= 100;
  if(!g.editing) g.doc[cs].offset = max(0,g.doc[cs].offset);
  XClearWindow(g.display, g.draw_window);
  redrawscreen(0, 0, g.xsize, g.ysize);
}


//--------------------------------------------------------------------------//
// toggle_sequence_mode                                                     //
//--------------------------------------------------------------------------//
void toggle_sequence_mode(void)
{
  int mode = 1 - g.sequence_mode;
  set_sequence_mode(mode);
}


//--------------------------------------------------------------------------//
// set_sequence_mode                                                        //
//--------------------------------------------------------------------------//
void set_sequence_mode(int mode)
{
  char tempstring[32];  
  int but=-1,k;
  for(k=0;k<g.nbuttons;k++) 
     if(!strcmp(g.button[k]->activate_cmd, "dna")){ but=k; break; }
  if(but<0) return;
  if(mode==PROTEIN) strcpy(tempstring, "Protein"); 
  else strcpy(tempstring, "DNA"); 
  XmString xms;
  if(but>0 && XtIsManaged(g.button[but]->widget)) 
  {   XtVaSetValues(g.button[but]->widget, XmNlabelString, 
          xms=XmStringCreateSimple(tempstring), NULL);
      XmStringFree(xms);  
  }
  g.sequence_mode = mode;
}


//--------------------------------------------------------------------------//
// edit                                                                     //
//--------------------------------------------------------------------------//
void edit(void)
{
  g.editing = 1-g.editing;
  char tempstring[32];  
  int but=-1,k;
  for(k=0;k<g.nbuttons;k++) 
     if(!strcmp(g.button[k]->activate_cmd, "edit")){ but=k; break; }

  if(g.editing) strcpy(tempstring, "Edit"); 
  else strcpy(tempstring, "Matrix plot"); 
  XmString xms;
  XtVaSetValues(g.button[but]->widget, XmNlabelString, 
      xms=XmStringCreateSimple(tempstring), NULL);
  XmStringFree(xms);  
  XClearWindow(g.display, g.draw_window);
  redrawscreen(0, 0, g.xsize, g.ysize);
}



//--------------------------------------------------------------------------//
// undo                                                                     //
//--------------------------------------------------------------------------//
void undo(void)
{
  g.doc[g.cs].n = g.doc[g.cs].on;
  memcpy(g.doc[g.cs].text, g.doc[g.cs].otext, g.doc[g.cs].n);
  memcpy(g.doc[g.cs].dtext, g.doc[g.cs].otext, g.doc[g.cs].n);
  g.doc[g.cs].type = g.doc[g.cs].otype;
  g.doc[g.cs].frame = 0;
  g.doc[g.cs].offset = 0;
  g.doc[g.cs].touched = 0;  
  XClearWindow(g.display, g.draw_window);
  redrawscreen(0, 0, g.xsize, g.ysize);
}


//---------------------------------------------------------------//
// dna2protein                                                   //
//---------------------------------------------------------------//
int dna2protein(char *code)
{ 
   int k;
   char c[8];
   for(k=0; k<3; k++){ if(code[k]=='T') c[k]='U'; else c[k]=code[k]; }
   c[3] = 0;
   if(!(strcmp(c,"UUU"))) return 'F';
   if(!(strcmp(c,"UUC"))) return 'F';
   if(!(strcmp(c,"UUA"))) return 'L';
   if(!(strcmp(c,"UUG"))) return 'L';

   if(!(strcmp(c,"UCU"))) return 'S';
   if(!(strcmp(c,"UCC"))) return 'S';
   if(!(strcmp(c,"UCA"))) return 'S';
   if(!(strcmp(c,"UCG"))) return 'S';
   if(!(strcmp(c,"UCN"))) return 'S';

   if(!(strcmp(c,"UAU"))) return 'Y';
   if(!(strcmp(c,"UAC"))) return 'Y';
   if(!(strcmp(c,"UAA"))) return 'x';
   if(!(strcmp(c,"UAG"))) return 'x';
   if(!(strcmp(c,"UAN"))) return 'Y';

   if(!(strcmp(c,"UGU"))) return 'C';
   if(!(strcmp(c,"UGC"))) return 'C';
   if(!(strcmp(c,"UGA"))) return 'x';
   if(!(strcmp(c,"UGG"))) return 'W';


   if(!(strcmp(c,"CUU"))) return 'L';
   if(!(strcmp(c,"CUC"))) return 'L';
   if(!(strcmp(c,"CUA"))) return 'L';
   if(!(strcmp(c,"CUG"))) return 'L';
   if(!(strcmp(c,"CUN"))) return 'L';

   if(!(strcmp(c,"CCU"))) return 'P';
   if(!(strcmp(c,"CCC"))) return 'P';
   if(!(strcmp(c,"CCA"))) return 'P';
   if(!(strcmp(c,"CCG"))) return 'P';
   if(!(strcmp(c,"CCN"))) return 'P';

   if(!(strcmp(c,"CAU"))) return 'H';
   if(!(strcmp(c,"CAC"))) return 'H';
   if(!(strcmp(c,"CAA"))) return 'Q';
   if(!(strcmp(c,"CAG"))) return 'Q';

   if(!(strcmp(c,"CGU"))) return 'R';
   if(!(strcmp(c,"CGC"))) return 'R';
   if(!(strcmp(c,"CGA"))) return 'R';
   if(!(strcmp(c,"CGG"))) return 'R';
   if(!(strcmp(c,"CGN"))) return 'R';


   if(!(strcmp(c,"AUU"))) return 'I';
   if(!(strcmp(c,"AUC"))) return 'I';
   if(!(strcmp(c,"AUA"))) return 'I';
   if(!(strcmp(c,"AUG"))) return 'M';

   if(!(strcmp(c,"ACU"))) return 'T';
   if(!(strcmp(c,"ACC"))) return 'T';
   if(!(strcmp(c,"ACA"))) return 'T';
   if(!(strcmp(c,"ACG"))) return 'T';
   if(!(strcmp(c,"ACN"))) return 'T';

   if(!(strcmp(c,"AAU"))) return 'N';
   if(!(strcmp(c,"AAC"))) return 'N';
   if(!(strcmp(c,"AAA"))) return 'K';
   if(!(strcmp(c,"AAG"))) return 'K';

   if(!(strcmp(c,"AGU"))) return 'S';
   if(!(strcmp(c,"AGC"))) return 'S';
   if(!(strcmp(c,"AGA"))) return 'R';
   if(!(strcmp(c,"AGG"))) return 'R';

   if(!(strcmp(c,"GUU"))) return 'V';
   if(!(strcmp(c,"GUC"))) return 'V';
   if(!(strcmp(c,"GUA"))) return 'V';
   if(!(strcmp(c,"GUG"))) return 'V';
   if(!(strcmp(c,"GUN"))) return 'V';

   if(!(strcmp(c,"GCU"))) return 'A';
   if(!(strcmp(c,"GCC"))) return 'A';
   if(!(strcmp(c,"GCA"))) return 'A';
   if(!(strcmp(c,"GCG"))) return 'A';
   if(!(strcmp(c,"GCN"))) return 'A';

   if(!(strcmp(c,"GAU"))) return 'D';
   if(!(strcmp(c,"GAC"))) return 'D';
   if(!(strcmp(c,"GAA"))) return 'E';
   if(!(strcmp(c,"GAG"))) return 'E';

   if(!(strcmp(c,"GGU"))) return 'G';
   if(!(strcmp(c,"GGC"))) return 'G';
   if(!(strcmp(c,"GGA"))) return 'G';
   if(!(strcmp(c,"GGG"))) return 'G';
   if(!(strcmp(c,"GGN"))) return 'G';

   return 'x';
}

//--------------------------------------------------------------------------//
// compare                                                                  //
//--------------------------------------------------------------------------//
void compare(void)
{
 message("Compare not implemented");
}


//--------------------------------------------------------------------------//
// statistics                                                               //
//--------------------------------------------------------------------------//
void statistics(void)
{
   int k,n,cs=g.cs;
   int listcount = -1, selection;
   char listtitle[100] = "Sequence statistics";                  
   char **info;                                    
   int *count = new int[32];
   info = new char*[MAXCOMMENTS];
   if(!g.doc[cs].n) return;

   count_bases(cs, count, n);

   info[++listcount] = new char[128]; 
   sprintf(info[listcount], "Length %d", n);

   info[++listcount] = new char[128]; 
   sprintf(info[listcount], "Mol. wt %g", molecular_weight(cs));

   info[++listcount] = new char[128]; 
   sprintf(info[listcount], "Expected frequency %g", peptide_frequency(cs));

   info[++listcount] = new char[128]; 
   sprintf(info[listcount],     "AA     Total    Pct.");

   for(k=0; k<=26; k++)
   if(count[k])
   {  info[++listcount] = new char[128]; 
      sprintf(info[listcount], " %c     %3d       %2.3g",
          k+'A', count[k], 100.0*(double)count[k]/(double)n);   
   }

   selection = 0;
   listinfo l;
   l.title = listtitle;
   l.info  = info;
   l.size  = listcount+1;
   l.itemstoshow = listcount-1;
   l.firstitem   = 1;
   l.wantsort    = 0;
   l.wantsave    = 0;
   l.helptopic   = 0;
   l.allowedit   = 0;
   l.selection   = &selection;
   l.width       = 0;
   l.transient   = 0;
   l.wantfunction = 0;
   l.autoupdate   = 0;
   l.clearbutton  = 0;
   l.highest_erased = 0;

   list(&l);

   for(k=0;k<=listcount;k++) delete[] info[k];              
   delete[] info;
   delete[] count;
   g.getout=0;
}


//--------------------------------------------------------------------------//
// molecular weight                                                         //
//--------------------------------------------------------------------------//
double molecular_weight(int cs)
{
  double mw = 0;
  int k;
  for(k=0;k<g.doc[cs].n;k++)
  if(g.doc[cs].type==DNA)
  switch(g.doc[cs].text[k])  
  {   case 'A': mw +=313.23; break;
      case 'G': mw +=329.23; break;
      case 'C': mw +=289.20; break;
      case 'T': mw +=304.21; break;
      case 'U': mw +=290.19; break;     
  }else
  switch(g.doc[cs].text[k])  
  {   case 'A': mw += 71.09; break;
      case 'C': mw +=103.15; break;
      case 'D': mw +=115.09; break;
      case 'E': mw +=129.12; break;
      case 'F': mw +=147.18; break;
      case 'G': mw += 57.05; break;
      case 'H': mw +=137.14; break;
      case 'I': mw +=113.16; break;
      case 'K': mw +=128.17; break;
      case 'L': mw +=113.16; break;
      case 'M': mw +=131.19; break;
      case 'N': mw +=114.11; break;
      case 'P': mw += 97.12; break;
      case 'Q': mw +=128.14; break;
      case 'R': mw +=156.19; break;
      case 'S': mw += 87.08; break;
      case 'T': mw +=101.11; break;
      case 'V': mw += 99.14; break;
      case 'W': mw +=186.21; break;
      case 'Y': mw +=163.18; break;