From 7a172acb8e93cf85a11ddd1fdc4170ce9b5ba785 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Wed, 8 Mar 2017 22:35:39 +0100
Subject: sci-biology/elph: Remove old

Package-Manager: Portage-2.3.4, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/4165
---
 sci-biology/elph/files/elph-0.1.5-usage.patch | 133 --------------------------
 1 file changed, 133 deletions(-)
 delete mode 100644 sci-biology/elph/files/elph-0.1.5-usage.patch

(limited to 'sci-biology/elph/files/elph-0.1.5-usage.patch')

diff --git a/sci-biology/elph/files/elph-0.1.5-usage.patch b/sci-biology/elph/files/elph-0.1.5-usage.patch
deleted file mode 100644
index 139b83c1c1c6..000000000000
--- a/sci-biology/elph/files/elph-0.1.5-usage.patch
+++ /dev/null
@@ -1,133 +0,0 @@
---- 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++)
-- 
cgit v1.2.3-65-gdbad