ulla 0.9.3

data/.git/COMMIT_EDITMSG

@@ -0,0 +1,13 @@
+ulla.gemspec generated
+# Please enter the commit message for your changes. Lines starting
+# with '#' will be ignored, and an empty message aborts the commit.
+# On branch master
+# Your branch is ahead of 'origin/master' by 1 commit.
+#
+# Changes to be committed:
+#   (use "git reset HEAD <file>..." to unstage)
+#
+#	modified:   Manifest.txt
+#	modified:   Rakefile
+#	new file:   ulla.gemspec
+#

data/.git/HEAD

@@ -0,0 +1 @@
+ref: refs/heads/master

data/.git/config

@@ -0,0 +1,11 @@
+[core]
+	repositoryformatversion = 0
+	filemode = true
+	bare = false
+	logallrefupdates = true
+[remote "origin"]
+	url = git@github.com:semin/ulla.git
+	fetch = +refs/heads/*:refs/remotes/origin/*
+[branch "master"]
+	remote = origin
+	merge = refs/heads/master

data/.git/description

@@ -0,0 +1 @@
+Unnamed repository; edit this file to name it for gitweb.

data/.git/hooks/applypatch-msg.sample

@@ -0,0 +1,15 @@
+#!/bin/sh
+#
+# An example hook script to check the commit log message taken by
+# applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit.  The hook is
+# allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "applypatch-msg".
+
+. git-sh-setup
+test -x "$GIT_DIR/hooks/commit-msg" &&
+	exec "$GIT_DIR/hooks/commit-msg" ${1+"$@"}
+:

data/.git/hooks/commit-msg.sample

@@ -0,0 +1,24 @@
+#!/bin/sh
+#
+# An example hook script to check the commit log message.
+# Called by git-commit with one argument, the name of the file
+# that has the commit message.  The hook should exit with non-zero
+# status after issuing an appropriate message if it wants to stop the
+# commit.  The hook is allowed to edit the commit message file.
+#
+# To enable this hook, rename this file to "commit-msg".
+
+# Uncomment the below to add a Signed-off-by line to the message.
+# Doing this in a hook is a bad idea in general, but the prepare-commit-msg
+# hook is more suited to it.
+#
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"
+
+# This example catches duplicate Signed-off-by lines.
+
+test "" = "$(grep '^Signed-off-by: ' "$1" |
+	 sort | uniq -c | sed -e '/^[ 	]*1[ 	]/d')" || {
+	echo >&2 Duplicate Signed-off-by lines.
+	exit 1
+}

data/.git/hooks/post-commit.sample

@@ -0,0 +1,8 @@
+#!/bin/sh
+#
+# An example hook script that is called after a successful
+# commit is made.
+#
+# To enable this hook, rename this file to "post-commit".
+
+: Nothing

data/.git/hooks/post-receive.sample

@@ -0,0 +1,15 @@
+#!/bin/sh
+#
+# An example hook script for the "post-receive" event.
+#
+# The "post-receive" script is run after receive-pack has accepted a pack
+# and the repository has been updated.  It is passed arguments in through
+# stdin in the form
+#  <oldrev> <newrev> <refname>
+# For example:
+#  aa453216d1b3e49e7f6f98441fa56946ddcd6a20 68f7abf4e6f922807889f52bc043ecd31b79f814 refs/heads/master
+#
+# see contrib/hooks/ for an sample, or uncomment the next line and
+# rename the file to "post-receive".
+
+#. /usr/share/doc/git-core/contrib/hooks/post-receive-email

data/.git/hooks/post-update.sample

@@ -0,0 +1,8 @@
+#!/bin/sh
+#
+# An example hook script to prepare a packed repository for use over
+# dumb transports.
+#
+# To enable this hook, rename this file to "post-update".
+
+exec git-update-server-info

data/.git/hooks/pre-applypatch.sample

@@ -0,0 +1,14 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed
+# by applypatch from an e-mail message.
+#
+# The hook should exit with non-zero status after issuing an
+# appropriate message if it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-applypatch".
+
+. git-sh-setup
+test -x "$GIT_DIR/hooks/pre-commit" &&
+	exec "$GIT_DIR/hooks/pre-commit" ${1+"$@"}
+:

data/.git/hooks/pre-commit.sample

@@ -0,0 +1,18 @@
+#!/bin/sh
+#
+# An example hook script to verify what is about to be committed.
+# Called by git-commit with no arguments.  The hook should
+# exit with non-zero status after issuing an appropriate message if
+# it wants to stop the commit.
+#
+# To enable this hook, rename this file to "pre-commit".
+
+if git-rev-parse --verify HEAD 2>/dev/null
+then
+	against=HEAD
+else
+	# Initial commit: diff against an empty tree object
+	against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
+fi
+
+exec git diff-index --check --cached $against --

data/.git/hooks/pre-rebase.sample

@@ -0,0 +1,169 @@
+#!/bin/sh
+#
+# Copyright (c) 2006, 2008 Junio C Hamano
+#
+# The "pre-rebase" hook is run just before "git-rebase" starts doing
+# its job, and can prevent the command from running by exiting with
+# non-zero status.
+#
+# The hook is called with the following parameters:
+#
+# $1 -- the upstream the series was forked from.
+# $2 -- the branch being rebased (or empty when rebasing the current branch).
+#
+# This sample shows how to prevent topic branches that are already
+# merged to 'next' branch from getting rebased, because allowing it
+# would result in rebasing already published history.
+
+publish=next
+basebranch="$1"
+if test "$#" = 2
+then
+	topic="refs/heads/$2"
+else
+	topic=`git symbolic-ref HEAD` ||
+	exit 0 ;# we do not interrupt rebasing detached HEAD
+fi
+
+case "$topic" in
+refs/heads/??/*)
+	;;
+*)
+	exit 0 ;# we do not interrupt others.
+	;;
+esac
+
+# Now we are dealing with a topic branch being rebased
+# on top of master.  Is it OK to rebase it?
+
+# Does the topic really exist?
+git show-ref -q "$topic" || {
+	echo >&2 "No such branch $topic"
+	exit 1
+}
+
+# Is topic fully merged to master?
+not_in_master=`git-rev-list --pretty=oneline ^master "$topic"`
+if test -z "$not_in_master"
+then
+	echo >&2 "$topic is fully merged to master; better remove it."
+	exit 1 ;# we could allow it, but there is no point.
+fi
+
+# Is topic ever merged to next?  If so you should not be rebasing it.
+only_next_1=`git-rev-list ^master "^$topic" ${publish} | sort`
+only_next_2=`git-rev-list ^master           ${publish} | sort`
+if test "$only_next_1" = "$only_next_2"
+then
+	not_in_topic=`git-rev-list "^$topic" master`
+	if test -z "$not_in_topic"
+	then
+		echo >&2 "$topic is already up-to-date with master"
+		exit 1 ;# we could allow it, but there is no point.
+	else
+		exit 0
+	fi
+else
+	not_in_next=`git-rev-list --pretty=oneline ^${publish} "$topic"`
+	perl -e '
+		my $topic = $ARGV[0];
+		my $msg = "* $topic has commits already merged to public branch:\n";
+		my (%not_in_next) = map {
+			/^([0-9a-f]+) /;
+			($1 => 1);
+		} split(/\n/, $ARGV[1]);
+		for my $elem (map {
+				/^([0-9a-f]+) (.*)$/;
+				[$1 => $2];
+			} split(/\n/, $ARGV[2])) {
+			if (!exists $not_in_next{$elem->[0]}) {
+				if ($msg) {
+					print STDERR $msg;
+					undef $msg;
+				}
+				print STDERR " $elem->[1]\n";
+			}
+		}
+	' "$topic" "$not_in_next" "$not_in_master"
+	exit 1
+fi
+
+exit 0
+
+################################################################
+
+This sample hook safeguards topic branches that have been
+published from being rewound.
+
+The workflow assumed here is:
+
+ * Once a topic branch forks from "master", "master" is never
+   merged into it again (either directly or indirectly).
+
+ * Once a topic branch is fully cooked and merged into "master",
+   it is deleted.  If you need to build on top of it to correct
+   earlier mistakes, a new topic branch is created by forking at
+   the tip of the "master".  This is not strictly necessary, but
+   it makes it easier to keep your history simple.
+
+ * Whenever you need to test or publish your changes to topic
+   branches, merge them into "next" branch.
+
+The script, being an example, hardcodes the publish branch name
+to be "next", but it is trivial to make it configurable via
+$GIT_DIR/config mechanism.
+
+With this workflow, you would want to know:
+
+(1) ... if a topic branch has ever been merged to "next".  Young
+    topic branches can have stupid mistakes you would rather
+    clean up before publishing, and things that have not been
+    merged into other branches can be easily rebased without
+    affecting other people.  But once it is published, you would
+    not want to rewind it.
+
+(2) ... if a topic branch has been fully merged to "master".
+    Then you can delete it.  More importantly, you should not
+    build on top of it -- other people may already want to
+    change things related to the topic as patches against your
+    "master", so if you need further changes, it is better to
+    fork the topic (perhaps with the same name) afresh from the
+    tip of "master".
+
+Let's look at this example:
+
+		   o---o---o---o---o---o---o---o---o---o "next"
+		  /       /           /           /
+		 /   a---a---b A     /           /
+		/   /               /           /
+	       /   /   c---c---c---c B         /
+	      /   /   /             \         /
+	     /   /   /   b---b C     \       /
+	    /   /   /   /             \     /
+    ---o---o---o---o---o---o---o---o---o---o---o "master"
+
+
+A, B and C are topic branches.
+
+ * A has one fix since it was merged up to "next".
+
+ * B has finished.  It has been fully merged up to "master" and "next",
+   and is ready to be deleted.
+
+ * C has not merged to "next" at all.
+
+We would want to allow C to be rebased, refuse A, and encourage
+B to be deleted.
+
+To compute (1):
+
+	git-rev-list ^master ^topic next
+	git-rev-list ^master        next
+
+	if these match, topic has not merged in next at all.
+
+To compute (2):
+
+	git-rev-list master..topic
+
+	if this is empty, it is fully merged to "master".

data/.git/hooks/prepare-commit-msg.sample

@@ -0,0 +1,36 @@
+#!/bin/sh
+#
+# An example hook script to prepare the commit log message.
+# Called by git-commit with the name of the file that has the
+# commit message, followed by the description of the commit
+# message's source.  The hook's purpose is to edit the commit
+# message file.  If the hook fails with a non-zero status,
+# the commit is aborted.
+#
+# To enable this hook, rename this file to "prepare-commit-msg".
+
+# This hook includes three examples.  The first comments out the
+# "Conflicts:" part of a merge commit.
+#
+# The second includes the output of "git diff --name-status -r"
+# into the message, just before the "git status" output.  It is
+# commented because it doesn't cope with --amend or with squashed
+# commits.
+#
+# The third example adds a Signed-off-by line to the message, that can
+# still be edited.  This is rarely a good idea.
+
+case "$2,$3" in
+  merge,)
+    perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;;
+
+# ,|template,)
+#   perl -i.bak -pe '
+#      print "\n" . `git diff --cached --name-status -r`
+#	 if /^#/ && $first++ == 0' "$1" ;;
+
+  *) ;;
+esac
+
+# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
+# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"

data/.git/hooks/update.sample

@@ -0,0 +1,107 @@
+#!/bin/sh
+#
+# An example hook script to blocks unannotated tags from entering.
+# Called by git-receive-pack with arguments: refname sha1-old sha1-new
+#
+# To enable this hook, rename this file to "update".
+#
+# Config
+# ------
+# hooks.allowunannotated
+#   This boolean sets whether unannotated tags will be allowed into the
+#   repository.  By default they won't be.
+# hooks.allowdeletetag
+#   This boolean sets whether deleting tags will be allowed in the
+#   repository.  By default they won't be.
+# hooks.allowdeletebranch
+#   This boolean sets whether deleting branches will be allowed in the
+#   repository.  By default they won't be.
+#
+
+# --- Command line
+refname="$1"
+oldrev="$2"
+newrev="$3"
+
+# --- Safety check
+if [ -z "$GIT_DIR" ]; then
+	echo "Don't run this script from the command line." >&2
+	echo " (if you want, you could supply GIT_DIR then run" >&2
+	echo "  $0 <ref> <oldrev> <newrev>)" >&2
+	exit 1
+fi
+
+if [ -z "$refname" -o -z "$oldrev" -o -z "$newrev" ]; then
+	echo "Usage: $0 <ref> <oldrev> <newrev>" >&2
+	exit 1
+fi
+
+# --- Config
+allowunannotated=$(git config --bool hooks.allowunannotated)
+allowdeletebranch=$(git config --bool hooks.allowdeletebranch)
+allowdeletetag=$(git config --bool hooks.allowdeletetag)
+
+# check for no description
+projectdesc=$(sed -e '1q' "$GIT_DIR/description")
+if [ -z "$projectdesc" -o "$projectdesc" = "Unnamed repository; edit this file to name it for gitweb." ]; then
+	echo "*** Project description file hasn't been set" >&2
+	exit 1
+fi
+
+# --- Check types
+# if $newrev is 0000...0000, it's a commit to delete a ref.
+if [ "$newrev" = "0000000000000000000000000000000000000000" ]; then
+	newrev_type=delete
+else
+	newrev_type=$(git-cat-file -t $newrev)
+fi
+
+case "$refname","$newrev_type" in
+	refs/tags/*,commit)
+		# un-annotated tag
+		short_refname=${refname##refs/tags/}
+		if [ "$allowunannotated" != "true" ]; then
+			echo "*** The un-annotated tag, $short_refname, is not allowed in this repository" >&2
+			echo "*** Use 'git tag [ -a | -s ]' for tags you want to propagate." >&2
+			exit 1
+		fi
+		;;
+	refs/tags/*,delete)
+		# delete tag
+		if [ "$allowdeletetag" != "true" ]; then
+			echo "*** Deleting a tag is not allowed in this repository" >&2
+			exit 1
+		fi
+		;;
+	refs/tags/*,tag)
+		# annotated tag
+		;;
+	refs/heads/*,commit)
+		# branch
+		;;
+	refs/heads/*,delete)
+		# delete branch
+		if [ "$allowdeletebranch" != "true" ]; then
+			echo "*** Deleting a branch is not allowed in this repository" >&2
+			exit 1
+		fi
+		;;
+	refs/remotes/*,commit)
+		# tracking branch
+		;;
+	refs/remotes/*,delete)
+		# delete tracking branch
+		if [ "$allowdeletebranch" != "true" ]; then
+			echo "*** Deleting a tracking branch is not allowed in this repository" >&2
+			exit 1
+		fi
+		;;
+	*)
+		# Anything else (is there anything else?)
+		echo "*** Update hook: unknown type of update to ref $refname of type $newrev_type" >&2
+		exit 1
+		;;
+esac
+
+# --- Finished
+exit 0

data/.git/info/exclude

@@ -0,0 +1,6 @@
+# git-ls-files --others --exclude-from=.git/info/exclude
+# Lines that start with '#' are comments.
+# For a project mostly in C, the following would be a good set of
+# exclude patterns (uncomment them if you want to use them):
+# *.[oa]
+# *~

data/.git/logs/HEAD

@@ -0,0 +1,3 @@
+0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000	clone: from git@github.com:semin/ulla.git
+c87d9b5b7bf5161f25e71698f85f8fac2602ed5d c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 Semin Lee <seminlee@gmail.com> 1235419011 +0000	commit: egor has been renamed to ulla
+c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 956112dd5ba2da60f043f4152a846c6922474bd4 Semin Lee <seminlee@gmail.com> 1235419394 +0000	commit: ulla.gemspec generated

data/.git/logs/refs/heads/master

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+0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000	clone: from git@github.com:semin/ulla.git
+c87d9b5b7bf5161f25e71698f85f8fac2602ed5d c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 Semin Lee <seminlee@gmail.com> 1235419011 +0000	commit: egor has been renamed to ulla
+c4a0553ca0e3c4628e688ecb5e3304a8a8ac0c28 956112dd5ba2da60f043f4152a846c6922474bd4 Semin Lee <seminlee@gmail.com> 1235419394 +0000	commit: ulla.gemspec generated

data/.git/logs/refs/remotes/origin/HEAD

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+0000000000000000000000000000000000000000 c87d9b5b7bf5161f25e71698f85f8fac2602ed5d Semin Lee <seminlee@gmail.com> 1235418356 +0000	clone: from git@github.com:semin/ulla.git

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data/.git/packed-refs

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+# pack-refs with: peeled 
+dfa502c200e3bedb9574f484264a898c2aed09cb refs/tags/REL-0.9.3
+dfa502c200e3bedb9574f484264a898c2aed09cb refs/tags/REL-0.9.0
+b20ce7072cbf7801ab72bd464bb77a0154aafbdf refs/tags/REL-0.0.5
+31ee2a6788abc7036e30175fc8c96ae808725feb refs/tags/REL-0.0.4
+f617333d5f3bda259d927074fe5ff4332db99412 refs/tags/REL-0.0.3
+18609e3b5637c7b102c0d7bdec44a1dcedc4c2e3 refs/tags/REL-0.0.2
+c87d9b5b7bf5161f25e71698f85f8fac2602ed5d refs/remotes/origin/master

data/.git/refs/heads/master

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+956112dd5ba2da60f043f4152a846c6922474bd4

data/.git/refs/remotes/origin/HEAD

@@ -0,0 +1 @@
+ref: refs/remotes/origin/master

data/.gitignore

@@ -0,0 +1,8 @@
+pkg
+doc
+.DS_Store
+tmp
+data
+*.log
+*.swp
+*~

data/History.txt

@@ -0,0 +1,42 @@
+== 0.9.3 23/2/2009
+
+* Egor has been renamed to Ulla!
+
+== 0.9.0 13/2/2009
+
+* Added --heatmap option for heat map generation from substitution tables
+* Added --heatmap-format option for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
+* Added --heatmap-stem option to set a file name of total heat maps figure when --heatmap 1 or 2 is set
+* Added --heatmap-columns option to set the number of tables in a row when --heatmap 1 or 2 is set
+* Added --heatmap-values option to print values in the cells of heat maps
+* Renamed --noround option to --noroundoff
+* 'simple_memoize' RubyGem package is no longer required
+
+== 0.0.5 23/1/2009
+
+* Warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
+* Added --augosigma option to avoid excessive influence of background frequencies
+* Added --noround option was added to get original log odds ratios
+* Added --p1smooth option was added to enable p1 probability smoothing when partial smoothing
+* Fixed a bug in p2 probability calculation of the partial smoothing procedure
+* Fixed a bug in total probability/log odds ratio calculation
+* Changed default verbosity from ERROR to WARN
+* Refactored codes to be more human readable and DRY
+
+== 0.0.4 15/12/2008
+
+* Fixed a bug to generated log-odds ratio matrices with --nosmooth option
+* Copes with no observations or mutations
+
+== 0.0.3 09/12/2008
+
+* Added --cys (-j) 2 not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
+* Fixed a bug to make masking works for target amino acid, too
+
+== 0.0.2 13/11/2008
+
+* Supports user provided constrained environment features are properly handled
+
+== 0.0.1 07/11/2008
+
+* Initial release