New version

(Portage version: 2.0.51-r14)

6 files changed, 183 insertions, 14 deletions

diff --git a/sci-biology/elph/ChangeLog b/sci-biology/elph/ChangeLog
index 98b9ce1b0bde..b3d325f73a25 100644
--- a/sci-biology/elph/ChangeLog
+++ b/sci-biology/elph/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/elph
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/ChangeLog,v 1.2 2004/12/23 20:16:48 swegener Exp $
+# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/ChangeLog,v 1.3 2005/01/28 00:47:21 ribosome Exp $
+
+*elph-0.1.5 (27 Jan 2005)
+
+  27 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
+  +files/elph-0.1.5-usage.patch, +elph-0.1.5.ebuild:
+  New version.
 
 *elph-0.1.4 (23 Dec 2004)
 
diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest
index ee2212eddb85..ca248e57a7a4 100644
--- a/sci-biology/elph/Manifest
+++ b/sci-biology/elph/Manifest
@@ -1,15 +1,8 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
+MD5 0749629e5d0bf9ad5e76a8b930de7294 elph-0.1.5.ebuild 940
 MD5 0749629e5d0bf9ad5e76a8b930de7294 elph-0.1.4.ebuild 940
 MD5 b3f72a573aef9beb43716b0c86b3c112 ChangeLog 902
 MD5 13040a191bb49af836a11a1727f7841c metadata.xml 610
 MD5 75fe098a9b1df66ed55f16b4cfde3922 files/elph-0.1.4-usage.patch 3909
+MD5 fdc58c9dcd2752ace3fb6520676c8414 files/elph-0.1.5-usage.patch 3913
 MD5 170bc1e9213d1c70d75ae92411a3567c files/digest-elph-0.1.4 61
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v1.9.10 (GNU/Linux)
-
-iD8DBQFByye2I1lqEGTUzyQRAsUsAKCCppm0zIJdxzep/14Hp95DPn6v8ACgrKpm
-3v9rfLJ6EWezcNDsXlMjOqM=
-=lUT8
------END PGP SIGNATURE-----
+MD5 edfbe76f341ee7fc8c683b7fe0b023bd files/digest-elph-0.1.5 62
diff --git a/sci-biology/elph/elph-0.1.4.ebuild b/sci-biology/elph/elph-0.1.4.ebuild
index f3c41366b157..c74b9187477e 100644
--- a/sci-biology/elph/elph-0.1.4.ebuild
+++ b/sci-biology/elph/elph-0.1.4.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2004 Gentoo Foundation
+# Copyright 1999-2005 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/elph-0.1.4.ebuild,v 1.1 2004/12/23 18:22:19 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/elph-0.1.4.ebuild,v 1.2 2005/01/28 00:47:21 ribosome Exp $
 
 inherit eutils toolchain-funcs
 
diff --git a/sci-biology/elph/elph-0.1.5.ebuild b/sci-biology/elph/elph-0.1.5.ebuild
new file mode 100644
index 000000000000..ea8c56129428
--- /dev/null
+++ b/sci-biology/elph/elph-0.1.5.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/elph-0.1.5.ebuild,v 1.1 2005/01/28 00:47:21 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
+}
diff --git a/sci-biology/elph/files/digest-elph-0.1.5 b/sci-biology/elph/files/digest-elph-0.1.5
new file mode 100644
index 000000000000..a19bc4883e4a
--- /dev/null
+++ b/sci-biology/elph/files/digest-elph-0.1.5
@@ -0,0 +1 @@
+MD5 0c1d0bbef483e7ee46ffb6b26824682c ELPH-0.1.5.tar.gz 153150
diff --git a/sci-biology/elph/files/elph-0.1.5-usage.patch b/sci-biology/elph/files/elph-0.1.5-usage.patch
new file mode 100644
index 000000000000..139b83c1c1c6
--- /dev/null
+++ b/sci-biology/elph/files/elph-0.1.5-usage.patch
@@ -0,0 +1,133 @@
+--- 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++)