dna1.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

}

//-------------------------------------------------------------------//
// basefilename                                                      //
// strip path from filename & returns file name w/o path             //
//-------------------------------------------------------------------//
char* basefilename(char* pathname)
{  int k;
   int slashpos=0;
   char temp[FILENAMELENGTH];
   strcpy(temp,pathname);

   for(k=0;k<(int)strlen(temp);k++)          // find last slash or colon
       if((temp[k]=='/')||(temp[k]=='\\')||(temp[k]==':')) slashpos=k+1;   
   return(temp+slashpos);
}


//-------------------------------------------------------------------//
// printstatus                                                       //
//-------------------------------------------------------------------//
void printstatus(int state)
{
    state=state;
}


//--------------------------------------------------------------------------//
// make_2d_alias                                                            //
// usage: uint** array;                                                     //
//        uint* array_1d;                                                   //
//        array_1d = (uint*)malloc(x*y*sizeof(uint));                       //
//        array = make_2d_alias(array_1d,x,y);   // Dont mult.by sizeof uint//
//         ...                                   // compiler knows its size //
//        free(array);                                                      //
//        free(array_1d);                                                   //
// Address array using  array[y][x]  or array_1d[index]                     //
// Last parameter is first index = slowest changing index                   //
// Create a 2d alias from an array so the same data can be accessed using   //
// either [][] or [] notation. This permits interfacing with libraries      //
// requiring either type.                                                   //
//--------------------------------------------------------------------------//
int **make_2d_alias(int *b, int x, int y)
{  int k;
   int **result;
   result = (int**)malloc(y*sizeof(int *));
   for(k=0;k<y;k++) result[k] = b + k*x;
   return result;
}
uint **make_2d_alias(uint *b, int x, int y)
{  int k;
   uint **result;
   result = (uint**)malloc(y*sizeof(uint *));
   for(k=0;k<y;k++) result[k] = b + k*x;
   return result;
} 
uchar **make_2d_alias(uchar *b, int x, int y)
{  int k;
   uchar **result;
   result = (uchar**)malloc(y*sizeof(uchar *));
   for(k=0;k<y;k++) result[k] = b + k*x;
   return result;
} 
double **make_2d_alias(double *b, int x, int y)
{  int k;
   double **result;
   result = (double**)malloc(y*sizeof(double *));
   for(k=0;k<y;k++) result[k] = b + k*x;
   return result;
} 



//--------------------------------------------------------------------------//
// strupr                                                                   //
//--------------------------------------------------------------------------//
char *strupr(char *s)
{
   int k;
   for(k=0;k<(int)strlen(s);k++) s[k]=toupper(s[k]);
   return s;
}


//--------------------------------------------------------------------------//
// strlwr                                                                   //
//--------------------------------------------------------------------------//
char *strlwr(char *s)
{
   int k;
   for(k=0;k<(int)strlen(s);k++) s[k]=tolower(s[k]);
   return s;
}

  
//--------------------------------------------------------------------------//
//  filesize                                                                //
//--------------------------------------------------------------------------//
int filesize(char *filename)
{
     struct stat dstatus;
     stat(filename, &dstatus);
     return dstatus.st_size;
}
        

//-------------------------------------------------------------------//
// savesettings                                                      //
//-------------------------------------------------------------------//
void savesettings(void)
{
  FILE* fp;
  int k;
  char tempstring[FILENAMELENGTH]="";
  sprintf(tempstring,"%s/dna.ini",g.homedir);
  if((fp=fopen(tempstring, "wt"))!=NULL )
  { 
       fprintf(fp,"version %s\n",g.version);
       fprintf(fp,"rows %d\n",g.rows);
       fprintf(fp,"cols %d\n",g.cols);
       fprintf(fp,"xsize %d\n",g.main_xsize);
       fprintf(fp,"ysize %d\n",g.main_ysize);
       fprintf(fp,"print_command %s\n",g.printer_command);
       fprintf(fp,"print_name %s\n",g.printer_name);
       fprintf(fp,"print_file %s\n",g.printer_file);
       fprintf(fp,"signif_digits %d\n",g.signif);
       fprintf(fp,"save_format %d\n",g.save_format);
       fprintf(fp,"sequence_mode %d\n",g.sequence_mode);
       fprintf(fp,"nbuttons %d\n",g.nbuttons);
       for(k=0;k<g.nbuttons;k++)
          fprintf(fp,"button %s %s:%s\n",
                  g.button[k]->label, g.button[k]->activate_cmd,
                  g.button[k]->deactivate_cmd);
  }else fprintf(stderr,"Can't save settings\n");
  fclose(fp);
}
        

//-------------------------------------------------------------------//
// readsettings                                                      //
//-------------------------------------------------------------------//
void readsettings(void)
{ 
  FILE* fp;
  int gotconfig=1;
  int space=0, ret=0, but=0,k;
  char name[FILENAMELENGTH]="";
  char value[FILENAMELENGTH]="";
  char initversion[80]="";
  char tempstring[1024];
  int colon=0;

  sprintf(tempstring, "%s/dna.ini", g.homedir);
  if((fp=fopen(tempstring,"rb"))==NULL ) gotconfig=0;
  else fclose(fp);

  initversion[0]=0;
  if(gotconfig)
  {  fp=fopen(tempstring,"rt");
     while(!feof(fp))
     { 
       fgets(name, 80, fp);
       if(feof(fp))break;
       space = strcspn(name," ");                // Position of 1st space
       ret = (int)index(name, '\n') - (int)name; // Position of final \n
       name[space]=0;
       name[ret]=0;
       strcpy(value, 1+name+space);
       if(strcmp(name,"version")==SAME) strcpy(initversion,value); 
       if(strcmp(name,"button")==SAME) 
       {   if(but>=g.nbuttons)
               fprintf(stderr,"tnimage.ini: Error: button count mismatch, ignoring user button\n");
           else
           {   
               space = strcspn(value," ");           // Position of 1st space
               colon = strcspn(value,":");           // Position of 1st colon
               strncpy(g.button[but]->label, value, space);
               g.button[but]->label[space]=0;
               strncpy(g.button[but]->activate_cmd, value+space+1, colon-space-1);
               g.button[but]->activate_cmd[colon-space-1]=0;
               if(colon<(int)strlen(value))
                  strncpy(g.button[but]->deactivate_cmd, value+colon+1, COMMAND_LENGTH);
               else
                  strcpy(g.button[but]->deactivate_cmd, "null");
               but++;
           }
       }
       if(strcmp(name,"nbuttons")==SAME) 
       {   g.nbuttons = max(0,atoi(value));
           g.button = new ButtonStruct*[g.nbuttons];
           for(k=0;k<g.nbuttons;k++)
           {   g.button[k] = new ButtonStruct;
               g.button[k]->button = 0;
               g.button[k]->state  = OFF;
               g.button[k]->widget = 0;
               g.button[k]->label  = new char[LABEL_LENGTH];
               g.button[k]->activate_cmd = new char[COMMAND_LENGTH];
               g.button[k]->deactivate_cmd = new char[COMMAND_LENGTH];
           }
       }
       if(strcmp(name,"rows")==SAME) g.rows=atoi(value);
       if(strcmp(name,"cols")==SAME) g.cols=atoi(value);
       if(strcmp(name,"xsize")==SAME) g.main_xsize=atoi(value);
       if(strcmp(name,"ysize")==SAME) g.main_ysize=atoi(value);
       g.xsize = g.main_xsize - 154 - 16;
       g.ysize = g.main_ysize - 24 - 16;
       if(strcmp(name,"print_command")==SAME) strcpy(g.printer_command,value);
       if(strcmp(name,"print_name")==SAME) strcpy(g.printer_name,value);
       if(strcmp(name,"print_file")==SAME) strcpy(g.printer_file,value);
       if(strcmp(name,"signif_digits")==SAME) g.signif=atoi(value);
       if(strcmp(name,"save_format")==SAME) g.save_format=atoi(value);
       if(strcmp(name,"sequence_mode")==SAME) g.sequence_mode=atoi(value);
     }
     fclose(fp);
  }
  if(!gotconfig)
  {
       const int NBUTTONS=24;
       g.nbuttons=NBUTTONS;
       char buttonname[NBUTTONS][20]= { 
                                        "Open",       "Save",  
                                        "Config",     "Close",
                                        "Compare",    "Align",
                                        "Reverse",    "Translate",
                                        "Edit",       "Statistics",
                                        "Print",      "Comments",
                                        "Offset#1",   "Offset#2",
                                        "Prev.frame", "Next攆rame",
                                        "Up",         "Down",
                                        "Left",       "Right",
                                        "Undo",       "Select",
                                        "DNA",        "Quit",
                                      };

       //// Non-null commands here will be activated when button is pushed.
       char activatecmd[NBUTTONS][20] = { 
                                        "read",       "save",  
                                        "config",     "close",  
                                        "compare",    "align",
                                        "reverse",    "translate",
                                        "edit",       "statistics",
                                        "print",      "comments",
                                        "offset1",    "offset2",
                                        "prevframe",  "nextframe",
                                        "up",         "down",
                                        "left",       "right",
                                        "undo",       "select",
                                        "dna",        "quit",
                                      };


       //// Non-null commands here will cause button to stay pushed, and
       //// the command activated when button is un-pushed.
       char deactivatecmd[NBUTTONS][20] = { 
                                        "null",       "null",  
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                        "null",       "null",
                                      };

       g.button = new ButtonStruct*[NBUTTONS];
       for(k=0;k<NBUTTONS;k++) 
       {   g.button[k] = new ButtonStruct;
           g.button[k]->button = 0;
           g.button[k]->state  = OFF;
           g.button[k]->widget = 0;
           g.button[k]->label = new char[LABEL_LENGTH];
           g.button[k]->activate_cmd = new char[COMMAND_LENGTH];
           g.button[k]->deactivate_cmd = new char[COMMAND_LENGTH];
           strcpy(g.button[k]->label, buttonname[k]);
           strcpy(g.button[k]->activate_cmd, activatecmd[k]);
           strcpy(g.button[k]->deactivate_cmd, deactivatecmd[k]);
       }
  }
}        


//-------------------------------------------------------------------//
// abouttheprogram                                                   //
//-------------------------------------------------------------------//
void abouttheprogram(void)
{
   char *tempstring = new char[1024];
   sprintf(tempstring, "dna version %s\nCompiled on %s %s\nCopyright (C) 1999 by T. Nelson",
      g.version, __DATE__, __TIME__);
   message(tempstring);
   delete[] tempstring;
}

//-------------------------------------------------------------------//
// help                                                              //
//-------------------------------------------------------------------//
void help(int helptopic)
{
   char *tempstring = new char[1024];
   message("The programmer forgot to add \na help system!!!",ERROR);
   delete[] tempstring;
}