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

  }
  return mw + 18.0;
}



//--------------------------------------------------------------------------//
// peptide_frequency                                                        //
//--------------------------------------------------------------------------//
double peptide_frequency(int cs)
{
  double p = 1.0;
  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': p *=0.25; break;
      case 'G': p *=0.25; break;
      case 'C': p *=0.25; break;
      case 'T': p *=0.25; break;
      case 'U': p *=0.25; break;     
  }else
  switch(g.doc[cs].text[k])  
  {   case 'A': p *=0.083; break;
      case 'C': p *=0.017; break;
      case 'D': p *=0.053; break;
      case 'E': p *=0.062; break;
      case 'F': p *=0.039; break;
      case 'G': p *=0.072; break;
      case 'H': p *=0.022; break;
      case 'I': p *=0.052; break;
      case 'K': p *=0.057; break;
      case 'L': p *=0.090; break;
      case 'M': p *=0.024; break;
      case 'N': p *=0.044; break;
      case 'P': p *=0.051; break;
      case 'Q': p *=0.040; break;
      case 'R': p *=0.057; break;
      case 'S': p *=0.069; break;
      case 'T': p *=0.058; break;
      case 'V': p *=0.066; break;
      case 'W': p *=0.013; break;
      case 'Y': p *=0.032; break;
  }
  return p;
}



//--------------------------------------------------------------------------//
// count_bases                                                              //
//--------------------------------------------------------------------------//
void count_bases(int cs, int *count, int &n)
{
  int ii, k, len=g.doc[cs].n;
  for(k=0; k<=26; k++) count[k]=0;
  for(k=0; k<len; k++) 
  {   ii = g.doc[cs].text[k]-'A';
      if(between(ii,0,26)) count[ii]++;
  }
  n = 0;
  for(k=0; k<=26; k++) n += count[k];
}


//--------------------------------------------------------------------------//
// close                                                                    //
//--------------------------------------------------------------------------//
void close(void)
{
  g.noofsequences--;
  init_editor(g.cs);
  XClearWindow(g.display, g.draw_window);
  redrawscreen(0, 0, g.xsize, g.ysize);
}


//--------------------------------------------------------------------------//
// set_offset                                                               //
//--------------------------------------------------------------------------//
void set_offset(int cs)
{
  char tempstring[128];
  sprintf(tempstring, "Offset for sequence #%d", cs+1);
  g.doc[cs].offset = clickbox(tempstring, g.doc[cs].offset, 0, g.doc[cs].n, null, 0);
  XClearWindow(g.display, g.draw_window);
  redrawscreen(0, 0, g.xsize, g.ysize);
}


//--------------------------------------------------------------------------//
//  configure                                                               //
//--------------------------------------------------------------------------//
void configure(void)
{
   int j,k;
   Dialog dialog;
   dialog.needrepeat=0;
   strcpy(dialog.title,"Configuration");

   strcpy(dialog.radio[0][0],"Save file format");             
   strcpy(dialog.radio[0][1],"Screen");
   strcpy(dialog.radio[0][2],"Highlight format");

   dialog.radioset[0] = g.save_format;

   strcpy(dialog.boxes[0],"Matrix Data");
   strcpy(dialog.boxes[1],"1st sequence");
   strcpy(dialog.boxes[2],"2nd sequence");

   sprintf(dialog.answer[1], "%d ", g.matrix_set1+1);
   sprintf(dialog.answer[2], "%d ", g.matrix_set2+1);

   dialog.boxtype[0]=LABEL;
   dialog.boxtype[1]=INTCLICKBOX; dialog.boxmin[1]=1; dialog.boxmax[1]=MAXSEQUENCES;
   dialog.boxtype[2]=INTCLICKBOX; dialog.boxmin[2]=1; dialog.boxmax[2]=MAXSEQUENCES;

   dialog.noofboxes=3;
   dialog.noofradios=1;
   dialog.radiono[0]=3;
   dialog.helptopic=0;

   for(j=0;j<10;j++) for(k=0;k<20;k++) dialog.radiotype[j][k]=RADIO;
   dialog.keep=0;
   dialog.want_changecicb = 0;
   dialog.f1 = null;
   dialog.transient = 1;
   strcpy(dialog.path,".");

   ///////////////////
   dialogbox(dialog); 
   ///////////////////

   g.save_format = dialog.radioset[0];
   g.matrix_set1 = atoi(dialog.answer[1])-1;
   g.matrix_set2 = atoi(dialog.answer[2])-1;
   return;
}


//--------------------------------------------------------------------------//
// save                                                                     //
//--------------------------------------------------------------------------//
void save(int needfilename)
{
  int j,k;
  char title[128];
  FILE *fp;
  static char filename[FILENAMELENGTH] = "Untitled";
  if(needfilename)
  {    strcpy(filename, getfilename(filename));
       if(cant_overwrite_file(filename)) return;
  }else  // for printing
       strcpy(filename, "/tmp/dna.print");
  if((fp=fopen(filename,"w"))==NULL) 
  {   message("Can't open file");
      return;
  }
  
  if(g.editing)
  {  if(g.save_format==SCREEN)
     {   save_screen_text(fp); 
     }else if(g.save_format==HIGHLIGHT)
     {   fprintf(fp, "TITLE Alignment\n");
         fprintf(fp, "#These are comments \n");
         fprintf(fp, "#Boxes are specified by x1 x2 y1 y2, for example:\n");
         fprintf(fp, "#BOX 40 54 1 2\n");
         fprintf(fp, "#LABEL 41 0 Labels can be placed using x y coordinates\n");
         fprintf(fp, "#TEXT 0 This text would be placed at row 0\n");
         fprintf(fp, "SEQUENCES\n");
         for(k=0; k<g.noofsequences; k++)
         {   strncpy(title, basefilename(g.doc[k].filename), 20);
             for(j=strlen(title); j<20; j++) title[j] = ' ';
             title[20] = 0;
             fprintf(fp, "%s | %s\n", title, g.doc[k].text);
         }
         fprintf(fp, "END\n");
     }
  }else
  {  save_screen_image(fp);
  }
  fclose(fp);   
  g.touched = 0;
}


//--------------------------------------------------------------------------//
// save_screen_text                                                         //
//--------------------------------------------------------------------------//
void save_screen_text(FILE *fp)
{
  int seq,k,longest=0,pos=0,width;
  int charsperline = g.xsize / g.doc[0].charwidth; 
  int negoff[g.noofsequences];
  char *s1;
  char *s2;
        
  for(k=0; k<g.noofsequences; k++) 
  {   if(g.doc[k].n > longest) longest = g.doc[k].n;
      if(g.doc[k].offset < 0) negoff[k] = -g.doc[k].offset;
      else negoff[k] = 0;
  }
  while(pos < longest)
  {   for(seq=0; seq<g.noofsequences; seq++)
      {   s1 = pos + g.doc[seq].text + g.doc[seq].offset;
          width = charsperline;
          for(k=0; k<width; k++)
          {   if(s1+k < g.doc[seq].text) fputc(' ', fp);
              else if(s1[k]) fputc(s1[k], fp);
          }
          fputc('\n', fp);
          if(seq+1<g.noofsequences && g.doc[seq+1].n)
          {   s2 = pos + g.doc[seq+1].text + g.doc[seq+1].offset;          
              for(k=0; k<width; k++) 
              {   if(matchable_base(s1[k], g.doc[seq].type) && 
                     matchable_base(s2[k], g.doc[seq+1].type))
                  {  if(toupper(s1[k]) == toupper(s2[k])) 
                       fputc('|', fp);
                     else  fputc(' ', fp);
                  }
              }
              fputc('\n', fp);
          }
      }
      fputs("\n\n", fp);
      pos += charsperline;
  }
}


//--------------------------------------------------------------------------//
// save_screen_image                                                        //
//--------------------------------------------------------------------------//
void save_screen_image(FILE *fp)
{
  int k,x,v,y;
  int set1 = g.matrix_set1;
  int set2 = g.matrix_set2;
  char *s1 = g.doc[set1].text;
  char *s2 = g.doc[set2].text;
  int n1 = 8 * ((g.doc[set1].n + 7) / 8);
  int n2 = g.doc[set2].n;
        
  fprintf(fp, "P4 %d %d\n", n1, n2);
  for(y=0;y<n2;y++)  
  for(x=0;x<n1;x+=8)  
  {   v = 0;
      for(k=0;k<8;k++)
      if(x+k < g.doc[set1].n) v |= ((s1[x+k]==s2[y])<<(7-k));
      fwrite(&v,1,1,fp);
  }
}


//--------------------------------------------------------------------------//
// printsequence                                                            //
//--------------------------------------------------------------------------//
void printsequence(void)
{
  char tempstring[FILENAMELENGTH];
  int j, k;
  Dialog dialog;
  dialog.needrepeat=0;
  strcpy(dialog.title,"Print");

  strcpy(dialog.boxes[0],"Print Parameters");
  strcpy(dialog.boxes[1],"Printer command");
  strcpy(dialog.boxes[2],"Printer device");
  strcpy(dialog.boxes[3],"Print to file");

  for(k=1;k<=3;k++) if(g.printer_device==k) dialog.boxset[k]=1; else dialog.boxset[k]=0;
  strcpy(dialog.answer[1], g.printer_command);
  strcpy(dialog.answer[2], g.printer_name);
  strcpy(dialog.answer[3], g.printer_file);
  dialog.boxtype[0]=LABEL; 
  dialog.boxtype[1]=TOGGLESTRING; 
  dialog.boxtype[2]=TOGGLESTRING;
  dialog.boxtype[3]=TOGGLESTRING;

  dialog.noofboxes=4;
  dialog.noofradios=0;
  dialog.radiono[0]=0;
  dialog.helptopic=0;

  for(j=0;j<10;j++) for(k=0;k<20;k++) dialog.radiotype[j][k]=RADIO;
  dialog.keep=0;
  dialog.want_changecicb = 0;
  dialog.f1 = printcheck;
  dialog.transient = 1;
  strcpy(dialog.path,".");

  ///////////////////
  dialogbox(dialog); 
  ///////////////////

  if(g.getout) return;
  for(k=1;k<=3;k++) if(dialog.boxset[k]) g.printer_device = k;
  strcpy(g.printer_command, dialog.answer[1]);
  strcpy(g.printer_name, dialog.answer[2]);
  strcpy(g.printer_file, dialog.answer[3]);

  save(0); // save in /tmp/dna.print
  if(!g.editing)
  {   sprintf(tempstring, "pnmtops /tmp/dna.print > /tmp/dna.ps");
      printf("%s\n", tempstring);
      system(tempstring);
  }
  switch(g.printer_device)
  {
     case 1:      // printer command
         if(g.editing) sprintf(tempstring, "%s /tmp/dna.print", g.printer_command);
         else sprintf(tempstring, "%s /tmp/dna.ps", g.printer_command);
         printf("%s\n", tempstring);
         system(tempstring);
         break;
     case 2:      // printer name
         if(g.editing) sprintf(tempstring, "cat /tmp/dna.print > %s", g.printer_name);
         else sprintf(tempstring, "cat /tmp/dna.ps > %s", g.printer_name);
         printf("%s\n", tempstring);
         system(tempstring);
         break;
     case 3:      // file name
         if(g.editing) sprintf(tempstring, "cp /tmp/dna.print %s", g.printer_file);
         else sprintf(tempstring, "cp /tmp/dna.ps %s", g.printer_file);
         printf("%s\n", tempstring);
         system(tempstring);
         break;
  }
  unlink("/tmp/dna.print");
  if(!g.editing) unlink("/tmp/dna.ps");
  
}


//--------------------------------------------------------------------------//
//  printcheck                                                              //
//--------------------------------------------------------------------------//
void printcheck(dialoginfo *a, int radio, int box, int boxbutton)
{
  int k;
  if(boxbutton==0 && between(box,1,3))                  // Printer device
  {  for(k=1;k<=3;k++) a->boxset[k]=False;
     for(k=1;k<=3;k++) if(k==box) a->boxset[k]=True;  
     for(k=1;k<=3;k++) if(k!=box)
         XmToggleButtonSetState(a->boxwidget[k][0],a->boxset[k],False);
  }
}