From 9d40a4782e72d69e82f593bbcf3656d7b8672e7a Mon Sep 17 00:00:00 2001
From: Christian Iseli <c4chris@fedoraproject.org>
Date: Feb 22 2007 16:22:31 +0000
Subject: Import elph.spec elph-chris.patch.


---

diff --git a/.cvsignore b/.cvsignore
index e69de29..ed4c607 100644
--- a/.cvsignore
+++ b/.cvsignore
@@ -0,0 +1 @@
+ELPH-1.0.1.tar.gz
diff --git a/elph-chris.patch b/elph-chris.patch
new file mode 100644
index 0000000..d35de48
--- /dev/null
+++ b/elph-chris.patch
@@ -0,0 +1,37 @@
+--- ELPH/sources/elph.cc.chris	2007-02-09 23:29:11.000000000 +0100
++++ ELPH/sources/elph.cc	2007-02-09 23:29:26.000000000 +0100
+@@ -43,7 +43,7 @@
+                    default = 500\n\
+   SGFNO=n        : n = no of iterations to compute significance of motif;\n\
+                    default = 1000\n\
+- "
++"
+ 
+ /* I am eliminating the following option from help file because it has no effect because I am never shuffling the file
+   -z             : when using the makov chain file generation, don't exhaust\n\
+--- ELPH/sources/GBase.h.chris	2006-09-28 19:07:25.000000000 +0200
++++ ELPH/sources/GBase.h	2007-02-09 23:21:52.000000000 +0100
+@@ -61,13 +61,16 @@
+ typedef void GFreeProc(pointer item); //usually just delete,
+       //but may also support structures with embedded dynamic members
+ 
+-#define GMALLOC(ptr,size)  if (!GMalloc((pointer*)(&ptr),size)) \
+-                                     GError(ERR_ALLOC)
+-#define GCALLOC(ptr,size)  if (!GCalloc((pointer*)(&ptr),size)) \
+-                                     GError(ERR_ALLOC)
+-#define GREALLOC(ptr,size) if (!GRealloc((pointer*)(&ptr),size)) \
+-                                     GError(ERR_ALLOC)
+-#define GFREE(ptr)       GFree((pointer*)(&ptr))
++#define GMALLOC(ptr,size) \
++  if ((ptr = static_cast<typeof(ptr)>(malloc(size))) == NULL) \
++    GError(ERR_ALLOC)
++#define GCALLOC(ptr,size) \
++  if ((ptr = static_cast<typeof(ptr)>(calloc(size, 1))) == NULL) \
++    GError(ERR_ALLOC)
++#define GREALLOC(ptr,size) \
++  if ((ptr = static_cast<typeof(ptr)>(realloc(ptr,size))) == NULL && size != 0) \
++    GError(ERR_ALLOC)
++#define GFREE(ptr)       free(ptr)
+ 
+ 
+ 
diff --git a/elph.spec b/elph.spec
new file mode 100644
index 0000000..cfd7919
--- /dev/null
+++ b/elph.spec
@@ -0,0 +1,55 @@
+Name:           elph
+Version:        1.0.1
+Release:        1%{?dist}
+Summary:        Tool to find motifs in a set of DNA or protein sequences
+
+Group:          Applications/Engineering
+License:        Artistic
+URL:            http://www.cbcb.umd.edu/software/ELPH/
+Source0:        ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-1.0.1.tar.gz
+Patch0:         %{name}-chris.patch
+BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+
+%description
+ELPH is a general-purpose Gibbs sampler for finding motifs in a set of
+DNA or protein sequences. The program takes as input a set containing
+anywhere from a few dozen to thousands of sequences, and searches
+through them for the most common motif, assuming that each sequence
+contains one copy of the motif.
+
+
+%prep
+%setup -q -n ELPH
+%patch0 -p 1 -b .chris
+
+
+%build
+make -C sources %{?_smp_mflags} \
+  CFLAGS="$RPM_OPT_FLAGS -fno-exceptions -fno-rtti -D_REENTRANT"
+
+
+%check
+
+
+%install
+rm -rf $RPM_BUILD_ROOT
+mkdir -p $RPM_BUILD_ROOT%{_bindir}
+install -m 755 sources/elph $RPM_BUILD_ROOT/%{_bindir}
+
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+
+%files
+%defattr(-,root,root,-)
+%doc COPYRIGHT LICENSE README Readme.ELPH VERSION
+%{_bindir}/elph
+
+
+%changelog
+* Thu Feb 22 2007 Christian Iseli <Christian.Iseli@licr.org> 1.0.1-1
+ - Import in FC-6.
+
+* Fri Feb  9 2007 Christian Iseli <Christian.Iseli@licr.org> 1.0.1-0
+ - Create spec file.
diff --git a/sources b/sources
index e69de29..6439180 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+eb96b4dde3ab12ba1f31a4230a829ff3  ELPH-1.0.1.tar.gz