[med-svn] [libfastahack] 02/07: Imported Upstream version 0.0+20160702
Andreas Tille
tille at debian.org
Tue Jul 5 13:27:43 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libfastahack.
commit c222c2520cc18b82672da3f845803f16413f66e7
Author: Andreas Tille <tille at debian.org>
Date: Tue Jul 5 15:18:16 2016 +0200
Imported Upstream version 0.0+20160702
---
.gitignore | 2 -
.travis.yml | 13 --
LICENSE | 21 ++++
disorder.c | 192 -----------------------------
disorder.h | 62 ----------
libdisorder.LICENSE | 339 ----------------------------------------------------
6 files changed, 21 insertions(+), 608 deletions(-)
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 1aa62e4..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*.o
-fastahack
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index d6add9e..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-# Control file for continuous integration testing at http://travis-ci.org/
-
-language: cpp
-compiler: gcc
-sudo: required
-dist: trusty
-script: make
-os:
- - linux
- - osx
-compiler:
- - gcc
- - clang
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..38a3265
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 Erik Garrison
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/disorder.c b/disorder.c
deleted file mode 100644
index a5f7c35..0000000
--- a/disorder.c
+++ /dev/null
@@ -1,192 +0,0 @@
-/***************************************************************************
- * libdisorder: A Library for Measuring Byte Stream Entropy
- * Copyright (C) 2010 Michael E. Locasto
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 2 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the:
- * Free Software Foundation, Inc.
- * 59 Temple Place, Suite 330
- * Boston, MA 02111-1307 USA
- *
- * $Id$
- **************************************************************************/
-
-#include <math.h> //for log2()
-#include <stdio.h> //for NULL
-#include "disorder.h"
-
-#if defined(__FreeBSD__)
-#define log2(x) (log((x)) * (1./M_LN2))
-#endif
-
-/** Frequecies for each byte */
-static int m_token_freqs[LIBDO_MAX_BYTES]; //frequency of each token in sample
-static float m_token_probs[LIBDO_MAX_BYTES]; //P(each token appearing)
-static int m_num_tokens = 0; //actual number of `seen' tokens, max 256
-static float m_maxent = 0.0;
-static float m_ratio = 0.0;
-static int LIBDISORDER_INITIALIZED = 0;
-
-static void
-initialize_lib()
-{
- int i = 0;
- if(1==LIBDISORDER_INITIALIZED)
- return;
-
- m_num_tokens = 0;
-
- for(i=0;i<LIBDO_MAX_BYTES;i++)
- {
- m_token_freqs[i]=0;
- m_token_probs[i]=0.0;
- }
-
- LIBDISORDER_INITIALIZED = 1;
-}
-
-/**
- * Set m_num_tokens by iterating over m_token_freq[] and maintaining
- * a counter of each position that does not hold the value of zero.
- */
-static void
-count_num_tokens()
-{
- int i = 0;
- int counter = 0;
- for(i=0;i<LIBDO_MAX_BYTES;i++)
- {
- if(0!=m_token_freqs[i])
- {
- counter++;
- }
- }
- m_num_tokens = counter;
- return;
-}
-
-/**
- * Sum frequencies for each token (i.e., byte values 0 through 255)
- * We assume the `length' parameter is correct.
- *
- * This function is available only to functions in this file.
- */
-static void
-get_token_frequencies(char* buf,
- long long length)
-{
- int i=0;
- char* itr=NULL;
- unsigned char c=0;
-
- itr = buf;
-
- //reset number of tokens
- m_num_tokens = 0;
-
- //make sure freqency and probability arrays are cleared
- for(i=0;i<LIBDO_MAX_BYTES;i++)
- {
- m_token_freqs[i] = 0;
- m_token_probs[i] = 0.0;
- }
-
- for(i=0;i<length;i++)
- {
- c = (unsigned char)*itr;
- //assert(0<=c<LIBDO_MAX_BYTES);
- m_token_freqs[c]++;
- itr++;
- }
-}
-
-/**
- * Return entropy (in bits) of this buffer of bytes. We assume that the
- * `length' parameter is correct. This implementation is a translation
- * of the PHP code found here:
- *
- * http://onlamp.com/pub/a/php/2005/01/06/entropy.html
- *
- * with a helpful hint on the `foreach' statement from here:
- *
- * http://php.net/manual/en/control-structures.foreach.php
- */
-float
-shannon_H(char* buf,
- long long length)
-{
- int i = 0;
- float bits = 0.0;
- char* itr=NULL; //values of itr should be zero to 255
- unsigned char token;
- int num_events = 0; //`length' parameter
- float freq = 0.0; //loop variable for holding freq from m_token_freq[]
- float entropy = 0.0; //running entropy sum
-
- if(NULL==buf || 0==length)
- return 0.0;
-
- if(0==LIBDISORDER_INITIALIZED)
- initialize_lib();
-
- itr = buf;
- m_maxent = 0.0;
- m_ratio = 0.0;
- num_events = length;
- get_token_frequencies(itr, num_events); //modifies m_token_freqs[]
- //set m_num_tokens by counting unique m_token_freqs entries
- count_num_tokens();
-
- if(m_num_tokens>LIBDO_MAX_BYTES)
- {
- //report error somehow?
- return 0.0;
- }
-
- //iterate through whole m_token_freq array, but only count
- //spots that have a registered token (i.e., freq>0)
- for(i=0;i<LIBDO_MAX_BYTES;i++)
- {
- if(0!=m_token_freqs[i])
- {
- token = i;
- freq = ((float)m_token_freqs[token]);
- m_token_probs[token] = (freq / ((float)num_events));
- entropy += m_token_probs[token] * log2(m_token_probs[token]);
- }
- }
-
- bits = -1.0 * entropy;
- m_maxent = log2(m_num_tokens);
- m_ratio = bits / m_maxent;
-
- return bits;
-}
-
-int
-get_num_tokens()
-{
- return m_num_tokens;
-}
-
-float
-get_max_entropy()
-{
- return m_maxent;
-}
-
-float
-get_entropy_ratio()
-{
- return m_ratio;
-}
diff --git a/disorder.h b/disorder.h
deleted file mode 100644
index 3458774..0000000
--- a/disorder.h
+++ /dev/null
@@ -1,62 +0,0 @@
-/***************************************************************************
- * libdisorder: A Library for Measuring Byte Stream Entropy
- * Copyright (C) 2010 Michael E. Locasto
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 2 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the:
- * Free Software Foundation, Inc.
- * 59 Temple Place, Suite 330
- * Boston, MA 02111-1307 USA
- *
- * $Id$
- **************************************************************************/
-
-#ifndef __DISORDER_H_
-#define __DISORDER_H_
-
-/** Max number of bytes (i.e., tokens) */
-#define LIBDO_MAX_BYTES 256
-
-/** A convienance value for clients of this library. Feel free to change
- * if you plan to use a larger buffer. You can also safely ignore it, as
- * libdisorder does not use this value internally; it relies on the
- * client-supplied `length' parameter.
- *
- * NB: Might become deprecated because it is potentially misleading and
- * has zero relationship to any library internal state.
- */
-#define LIBDO_BUFFER_LEN 16384
-
-/**
- * Given a pointer to an array of bytes, return a float indicating the
- * level of entropy in bits (a number between zero and eight),
- * assuming a space of 256 possible byte values. The second argument
- * indicates the number of bytes in the sequence. If this sequence
- * runs into unallocated memory, this function should fail with a
- * SIGSEGV.
- */
-float shannon_H(char*, long long);
-
-/** Report the number of (unique) tokens seen. This is _not_ the
- number of individual events seen. For example, if the library sees
- the string `aaab', the number of events is 4 and the number of
- tokens is 2. */
-int get_num_tokens(void);
-
-/** Returns maximum entropy for byte distributions log2(256)=8 bits*/
-float get_max_entropy(void);
-
-/** Returns the ratio of entropy to maxentropy */
-float get_entropy_ratio(void);
-
-#endif
diff --git a/libdisorder.LICENSE b/libdisorder.LICENSE
deleted file mode 100644
index 8bbcff9..0000000
--- a/libdisorder.LICENSE
+++ /dev/null
@@ -1,339 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 2, June 1991
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-consider it more useful to permit linking proprietary applications with the
-library. If this is what you want to do, use the GNU Library General
-Public License instead of this License.
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