Moved from app-sci/elph to sci-biology/elph.

2 files changed, 134 insertions, 0 deletions

diff --git a/sci-biology/elph/files/digest-elph-0.1.4 b/sci-biology/elph/files/digest-elph-0.1.4
new file mode 100644
index 000000000000..623e842d2d74
--- /dev/null
+++ b/sci-biology/elph/files/digest-elph-0.1.4
@@ -0,0 +1 @@
+MD5 5065b4d6062d8654fae5337cf0ea0e01 ELPH-0.1.4.tar.gz 40181
diff --git a/sci-biology/elph/files/elph-0.1.4-usage.patch b/sci-biology/elph/files/elph-0.1.4-usage.patch
new file mode 100644
index 000000000000..be49e2d1ebb8
--- /dev/null
+++ b/sci-biology/elph/files/elph-0.1.4-usage.patch
@@ -0,0 +1,133 @@
+--- elph.cc~	2003-06-03 14:45:22.000000000 -0400
++++ elph.cc	2004-10-30 10:14:49.220415168 -0400
+@@ -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:abglvdxt: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++)