sci-biology/elph/files/elph-0.1.5-usage.patch

--- elph.cc.old	2005-01-11 14:17:47.000000000 -0500
+++ elph.cc	2005-01-27 19:42:30.218350552 -0500
@@ -26,11 +26,11 @@
                    period variable\n\
   -x             : print maximum positions within sequences\n\
   -g             : find significance of motif\n\
-  -t <matrix>    : test if there is significant difference between the two 
-                   input files for a given motif matrix; <matrix> is the file
+  -t <matrix>    : test if there is significant difference between the two\n\
+                   input files for a given motif matrix; <matrix> is the file\n\
                    containing the motif matrix\n\
-  -l             : compute Least Likely Consensus (LLC) for given motif 
-  -c             : in conjunction with -m option: motif is not necessarily in 
+  -l             : compute Least Likely Consensus (LLC) for given motif\n\
+  -c             : in conjunction with -m option: motif is not necessarily in\n\
                    the closest edit distance from input motif\n\
   LEN=n          : n = length of motif\n\
   ITERNO=n       : n = no of iterations to compute the global maximum;\n\
@@ -41,7 +41,7 @@
                    default = 1000\n\
  "
 
-// global variables: 
+// global variables:
 int ITER_NO=10;
 int MAX_LOOP=500;
 int printmax=0;
@@ -66,7 +66,7 @@
   seqType t;
 
   GArgs args(argc, argv, "ho:abcglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO=");
-  
+
   // == Process arguments.
 
   int e;
@@ -83,7 +83,7 @@
 
   if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files
 
-    M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);    
+    M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);
     M->twofilesignif(gdet,testfile,SignifNo,print,pattern);
 
   }
@@ -93,11 +93,11 @@
                             // given motif
 
       M = new Motif(infile,outf,t,pattern);
-      if(defLLC) { 
+      if(defLLC) {
 	double llc=M->computeLLC(pattern,print);
 	fprintf(outf,"LLC = %f\n",llc);
       }
-      
+
     }
     else {
 
@@ -108,7 +108,7 @@
     }
 
     double globAlignProb;
-    
+
     globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet);
 
 
@@ -116,13 +116,13 @@
     /*info=M->InfoPar(globAlignProb);
       fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info);
       M->printMotif();*/
-    
+
     // optimizing
     fprintf(stderr,"Optimizing...\n");
     globAlignProb=M->optimize(globAlignProb,info,closest);
     fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n");
     fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb));
-    
+
     if(runsignif) {
       M->runforsignif(SignifNo,print,gdet,pattern);
     }
@@ -134,17 +134,17 @@
 
 seqType Process_Options(GArgs* args)
 {
-    
-  if (args->startNonOpt()) { //parse the non-options arguments 
+
+  if (args->startNonOpt()) { //parse the non-options arguments
                           //(usually filenames)
         infile=args->nextNonOpt();
   }
 
-  if (infile.is_empty() || args->getOpt('h')!=NULL) 
+  if (infile.is_empty() || args->getOpt('h')!=NULL)
     GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input
 
   testfile=args->nextNonOpt();
-  
+
   GString outfile=args->getOpt('o');
   if (!outfile.is_empty()) {
     outf=fopen(outfile, "w");
@@ -156,7 +156,7 @@
   matrixfile=args->getOpt('t');
 
   GString param;
-  
+
   pattern=args->getOpt('m');
   if(pattern.is_empty()) {
     param=args->getOpt("LEN");
@@ -200,7 +200,7 @@
 
   seqType t;
   if(args->getOpt('a')!=NULL) t=aac; else t=nucl;
-  
+
   return(t);
 
 }
@@ -210,7 +210,7 @@
   Motif *M;
 
   double llcmax=-HUGE_VAL;
-  GString seed;	
+  GString seed;
   for(int i1=0;i1<4;i1++)
     for(int i2=0;i2<4;i2++)
       for(int i3=0;i3<4;i3++)