+++ /dev/null
-# ChangeLog for app-sci/elph
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/elph/ChangeLog,v 1.4 2004/11/07 20:36:06 ribosome Exp $
-
- 07 Nov 2004; Olivier Fisette <ribosome@gentoo.org> metadata.xml,
- -elph-0.1.2.ebuild, elph-0.1.4.ebuild:
- Removed buggy version (0.1.2). Added 0.1.4 to x86. Set myself as
- maintainer. Added long description.
-
- 30 Oct 2004; Olivier Fisette <ribosome@gentoo.org> +elph-0.1.4.ebuild
- +files/elph-0.1.4-usage.patch :
- New version.
-
-*elph-0.1.2 (22 May 2003)
-
- 22 May 2003; Jon Portnoy <avenj@gentoo.org> elph-0.1.2.ebuild :
- Initial import. Ebuild submitted by Stephen Diener in bug
- #21308.
+++ /dev/null
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/elph/elph-0.1.4.ebuild,v 1.2 2004/11/07 20:36:06 ribosome Exp $
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program"
-HOMEPAGE="http://www.tigr.org/software/ELPH/index.shtml"
-SRC_URI="ftp://ftp.tigr.org/pub/software/ELPH/ELPH-${PV}.tar.gz"
-LICENSE="Artistic"
-
-SLOT="0"
-KEYWORDS="x86"
-IUSE=""
-
-S="${WORKDIR}/ELPH/sources"
-
-src_unpack() {
- unpack ${A}
- cd ${S}
- epatch ${FILESDIR}/${P}-usage.patch
- sed -i -e "s/CC := g++/CC := $(tc-getCXX)/" Makefile
- sed -i -e "s/-fno-exceptions -fno-rtti -D_REENTRANT -g/${CXXFLAGS}/" Makefile
- sed -i -e "s/LINKER := g++/LINKER := $(tc-getCXX)/" Makefile
-}
-
-src_compile() {
- make || die
-}
-
-src_install() {
- dobin elph
- cd ${WORKDIR}/ELPH
- dodoc VERSION
- newdoc Readme.ELPH README
-}
+++ /dev/null
---- 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++)
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