/*
 * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
 *
 * This file is part of Bowtie 2.
 *
 * Bowtie 2 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 3 of the License, or
 * (at your option) any later version.
 *
 * Bowtie 2 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 Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef SSTRING_H_
#define SSTRING_H_

#include <string.h>
#include <iostream>
#include "assert_helpers.h"
#include "alphabet.h"
#include "random_source.h"

/**
 * Four kinds of strings defined here:
 *
 * SString:
 *   A fixed-length string using heap memory with size set at construction time
 *   or when install() member is called.
 *
 * S2bDnaString:
 *   Like SString, but stores a list uint32_t words where each word is divided
 *   into 16 2-bit slots interpreted as holding one A/C/G/T nucleotide each.
 *
 * TODO: S3bDnaString allowing N.  S4bDnaString allowing nucleotide masks.
 *
 * SStringExpandable:
 *   A string using heap memory where the size of the backing store is
 *   automatically resized as needed.  Supports operations like append, insert,
 *   erase, etc.
 *
 * SStringFixed:
 *   A fixed-length string using stack memory where size is set at compile
 *   time.
 *
 * All string classes have some extra facilities that make it easy to print the
 * string, including when the string uses an encoded alphabet.  See toZBuf()
 * and toZBufXForm().
 *
 * Global lt, eq, and gt template functions are supplied.  They are capable of
 * doing lexicographical comparisons between any of the three categories of
 * strings defined here.
 */

template<typename T>
class Class_sstr_len {
public:
	static inline size_t sstr_len(const T& s) {
		return s.length();
	}
};

template<unsigned N>
class Class_sstr_len<const char[N]> {
public:
	static inline size_t sstr_len(const char s[N]) {
		return strlen(s);
	}
};

template<>
class Class_sstr_len<const char *> {
public:
	static inline size_t sstr_len(const char *s) {
		return strlen(s);
	}
};

template<>
class Class_sstr_len<const unsigned char *> {
public:
	static inline size_t sstr_len(const unsigned char *s) {
		return strlen((const char *)s);
	}
};

template<typename T1, typename T2>
static inline bool sstr_eq(const T1& s1, const T2& s2) {
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1);
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2);
	if(len1 != len2) return false;
	for(size_t i = 0; i < len1; i++) {
		if(s1[i] != s2[i]) return false;
	}
	return true;
}

template<typename T1, typename T2>
static inline bool sstr_neq(const T1& s1, const T2& s2) {
	return !sstr_eq(s1, s2);
}

/**
 * Return true iff the given suffix of s1 is equal to the given suffix of s2 up
 * to upto characters.
 */
template<typename T1, typename T2>
static inline bool sstr_suf_upto_eq(
	const T1& s1, size_t suf1,
	const T2& s2, size_t suf2,
	size_t upto,
	bool endlt = true)
{
	assert_leq(suf1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(suf2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1) - suf1;
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2) - suf2;
	if(len1 > upto) len1 = upto;
	if(len2 > upto) len2 = upto;
	if(len1 != len2) return false;
	for(size_t i = 0; i < len1; i++) {
		if(s1[suf1+i] != s2[suf2+i]) {
			return false;
		}
	}
	return true;
}

/**
 * Return true iff the given suffix of s1 is equal to the given suffix of s2 up
 * to upto characters.
 */
template<typename T1, typename T2>
static inline bool sstr_suf_upto_neq(
	const T1& s1, size_t suf1,
	const T2& s2, size_t suf2,
	size_t upto,
	bool endlt = true)
{
	return !sstr_suf_upto_eq(s1, suf1, s2, suf2, upto, endlt);
}

/**
 * Return true iff s1 is less than s2.
 */
template<typename T1, typename T2>
static inline bool sstr_lt(const T1& s1, const T2& s2, bool endlt = true) {
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1);
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2);
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[i] < s2[i]) {
			return true;
		} else if(s1[i] > s2[i]) {
			return false;
		}
	}
	if(len1 == len2) return false;
	return (len1 < len2) == endlt;
}

/**
 * Return true iff the given suffix of s1 is less than the given suffix of s2.
 */
template<typename T1, typename T2>
static inline bool sstr_suf_lt(
	const T1& s1, size_t suf1,
	const T2& s2, size_t suf2,
	bool endlt = true)
{
	assert_leq(suf1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(suf2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1) - suf1;
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2) - suf2;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[suf1+i] < s2[suf2+i]) {
			return true;
		} else if(s1[suf1+i] > s2[suf2+i]) {
			return false;
		}
	}
	if(len1 == len2) return false;
	return (len1 < len2) == endlt;
}

/**
 * Return true iff the given suffix of s1 is less than the given suffix of s2.
 * Treat s1 and s2 as though they have lengths len1/len2.
 */
template<typename T1, typename T2>
static inline bool sstr_suf_lt(
	const T1& s1, size_t suf1, size_t len1,
	const T2& s2, size_t suf2, size_t len2,
	bool endlt = true)
{
	assert_leq(suf1, len1);
	assert_leq(suf2, len2);
	size_t left1 = len1 - suf1;
	size_t left2 = len2 - suf2;
	size_t minleft = (left1 < left2 ? left1 : left2);
	for(size_t i = 0; i < minleft; i++) {
		if(s1[suf1+i] < s2[suf2+i]) {
			return true;
		} else if(s1[suf1+i] > s2[suf2+i]) {
			return false;
		}
	}
	if(left1 == left2) return false;
	return (left1 < left2) == endlt;
}

/**
 * Return true iff the given suffix of s1 is less than the given suffix of s2
 * up to upto characters.
 */
template<typename T1, typename T2>
static inline bool sstr_suf_upto_lt(
	const T1& s1, size_t suf1,
	const T2& s2, size_t suf2,
	size_t upto,
	bool endlt = true)
{
	assert_leq(suf1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(suf2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1) - suf1;
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2) - suf2;
	if(len1 > upto) len1 = upto;
	if(len2 > upto) len2 = upto;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[suf1+i] < s2[suf2+i]) {
			return true;
		} else if(s1[suf1+i] > s2[suf2+i]) {
			return false;
		}
	}
	if(len1 == len2) return false;
	return (len1 < len2) == endlt;
}

/**
 * Return true iff the given prefix of s1 is less than the given prefix of s2.
 */
template<typename T1, typename T2>
static inline bool sstr_pre_lt(
	const T1& s1, size_t pre1,
	const T2& s2, size_t pre2,
	bool endlt = true)
{
	assert_leq(pre1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(pre2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = pre1;
	size_t len2 = pre2;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[i] < s2[i]) {
			return true;
		} else if(s1[i] > s2[i]) {
			return false;
		}
	}
	if(len1 == len2) return false;
	return (len1 < len2) == endlt;
}

/**
 * Return true iff s1 is less than or equal to s2.
 */
template<typename T1, typename T2>
static inline bool sstr_leq(const T1& s1, const T2& s2, bool endlt = true) {
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1);
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2);
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[i] < s2[i]) {
			return true;
		} else if(s1[i] > s2[i]) {
			return false;
		}
	}
	if(len1 == len2) return true;
	return (len1 < len2) == endlt;
}

/**
 * Return true iff the given suffix of s1 is less than or equal to the given
 * suffix of s2.
 */
template<typename T1, typename T2>
static inline bool sstr_suf_leq(
	const T1& s1, size_t suf1,
	const T2& s2, size_t suf2,
	bool endlt = true)
{
	assert_leq(suf1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(suf2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1) - suf1;
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2) - suf2;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[suf1+i] < s2[suf2+i]) {
			return true;
		} else if(s1[suf1+i] > s2[suf2+i]) {
			return false;
		}
	}
	if(len1 == len2) return true;
	return (len1 < len2) == endlt;
}

/**
 * Return true iff the given prefix of s1 is less than or equal to the given
 * prefix of s2.
 */
template<typename T1, typename T2>
static inline bool sstr_pre_leq(
	const T1& s1, size_t pre1,
	const T2& s2, size_t pre2,
	bool endlt = true)
{
	assert_leq(pre1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(pre2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = pre1;
	size_t len2 = pre2;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[i] < s2[i]) {
			return true;
		} else if(s1[i] > s2[i]) {
			return false;
		}
	}
	if(len1 == len2) return true;
	return (len1 < len2) == endlt;
}

/**
 * Return true iff s1 is greater than s2.
 */
template<typename T1, typename T2>
static inline bool sstr_gt(const T1& s1, const T2& s2, bool endlt = true) {
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1);
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2);
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[i] > s2[i]) {
			return true;
		} else if(s1[i] < s2[i]) {
			return false;
		}
	}
	if(len1 == len2) return false;
	return (len1 > len2) == endlt;
}

/**
 * Return true iff the given suffix of s1 is greater than the given suffix of
 * s2.
 */
template<typename T1, typename T2>
static inline bool sstr_suf_gt(
	const T1& s1, size_t suf1,
	const T2& s2, size_t suf2,
	bool endlt = true)
{
	assert_leq(suf1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(suf2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1) - suf1;
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2) - suf2;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[suf1+i] > s2[suf2+i]) {
			return true;
		} else if(s1[suf1+i] < s2[suf2+i]) {
			return false;
		}
	}
	if(len1 == len2) return false;
	return (len1 > len2) == endlt;
}

/**
 * Return true iff the given prefix of s1 is greater than the given prefix of
 * s2.
 */
template<typename T1, typename T2>
static inline bool sstr_pre_gt(
	const T1& s1, size_t pre1,
	const T2& s2, size_t pre2,
	bool endlt = true)
{
	assert_leq(pre1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(pre2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = pre1;
	size_t len2 = pre2;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[i] > s2[i]) {
			return true;
		} else if(s1[i] < s2[i]) {
			return false;
		}
	}
	if(len1 == len2) return false;
	return (len1 > len2) == endlt;
}

/**
 * Return true iff s1 is greater than or equal to s2.
 */
template<typename T1, typename T2>
static inline bool sstr_geq(const T1& s1, const T2& s2, bool endlt = true) {
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1);
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2);
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[i] > s2[i]) {
			return true;
		} else if(s1[i] < s2[i]) {
			return false;
		}
	}
	if(len1 == len2) return true;
	return (len1 > len2) == endlt;
}

/**
 * Return true iff the given suffix of s1 is greater than or equal to the given
 * suffix of s2.
 */
template<typename T1, typename T2>
static inline bool sstr_suf_geq(
	const T1& s1, size_t suf1,
	const T2& s2, size_t suf2,
	bool endlt = true)
{
	assert_leq(suf1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(suf2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = Class_sstr_len<T1>::sstr_len(s1) - suf1;
	size_t len2 = Class_sstr_len<T2>::sstr_len(s2) - suf2;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[suf1+i] > s2[suf2+i]) {
			return true;
		} else if(s1[suf1+i] < s2[suf2+i]) {
			return false;
		}
	}
	if(len1 == len2) return true;
	return (len1 > len2) == endlt;
}

/**
 * Return true iff the given prefix of s1 is greater than or equal to the given
 * prefix of s2.
 */
template<typename T1, typename T2>
static inline bool sstr_pre_geq(
	const T1& s1, size_t pre1,
	const T2& s2, size_t pre2,
	bool endlt = true)
{
	assert_leq(pre1, Class_sstr_len<T1>::sstr_len(s1));
	assert_leq(pre2, Class_sstr_len<T2>::sstr_len(s2));
	size_t len1 = pre1;
	size_t len2 = pre2;
	size_t minlen = (len1 < len2 ? len1 : len2);
	for(size_t i = 0; i < minlen; i++) {
		if(s1[i] > s2[i]) {
			return true;
		} else if(s1[i] < s2[i]) {
			return false;
		}
	}
	if(len1 == len2) return true;
	return (len1 > len2) == endlt;
}

template<typename T>
static inline const char * sstr_to_cstr(const T& s) {
	return s.toZBuf();
}

template<>
inline const char * sstr_to_cstr<std::basic_string<char> >(
	const std::basic_string<char>& s)
{
	return s.c_str();
}

/**
 * Simple string class with backing memory whose size is managed by the user
 * using the constructor and install() member function.  No behind-the-scenes
 * reallocation or copying takes place.
 */
template<typename T>
class SString {
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
public:

	explicit SString() :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{ }

	explicit SString(size_t sz) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		resize(sz);
	}

	/**
	 * Create an SStringExpandable from another SStringExpandable.
	 */
	SString(const SString<T>& o) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		*this = o;
	}

	/**
	 * Create an SStringExpandable from a std::basic_string of the
	 * appropriate type.
	 */
	explicit SString(const std::basic_string<T>& str) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		install(str.c_str(), str.length());
	}

	/**
	 * Create an SStringExpandable from an array and size.
	 */
	explicit SString(const T* b, size_t sz) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		install(b, sz);
	}

	/**
	 * Create an SStringExpandable from a zero-terminated array.
	 */
	explicit SString(const T* b) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		install(b, strlen(b));
	}

	/**
	 * Destroy the expandable string object.
	 */
	virtual ~SString() {
		if(cs_ != NULL) {
			delete[] cs_;
			cs_ = NULL;
		}
		if(printcs_ != NULL) {
			delete[] printcs_;
			printcs_ = NULL;
		}
		len_ = 0;
	}

	/**
	 * Assignment to other SString.
	 */
	SString<T>& operator=(const SString<T>& o) {
		install(o.cs_, o.len_);
		return *this;
	}

	/**
	 * Assignment to other SString.
	 */
	SString<T>& operator=(const std::basic_string<T>& o) {
		install(o);
		return *this;
	}

	/**
	 * Resizes the string without preserving its contents.
	 */
	void resize(size_t sz) {
		if(cs_ != NULL) {
			delete cs_;
			cs_ = NULL;
		}
		if(printcs_ != NULL) {
			delete printcs_;
			printcs_ = NULL;
		}
		if(sz != 0) {
			cs_ = new T[sz+1];
		}
		len_ = sz;
	}

	/**
	 * Return ith character from the left of either the forward or the
	 * reverse version of the read.
	 */
	T windowGet(
		size_t i,
		bool   fw,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_lt(i, len);
		assert_leq(len, len_ - depth);
		return fw ? cs_[depth+i] : cs_[depth+len-i-1];
	}

	/**
	 * Return ith character from the left of either the forward or the
	 * reverse-complement version of the read.
	 */
	void windowGet(
		T& ret,
		bool   fw,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_leq(len, len_ - depth);
		ret.resize(len);
		for(size_t i = 0; i < len; i++) {
			ret.set(fw ? cs_[depth+i] : cs_[depth+len-i-1], i);
		}
	}

	/**
	 * Set character at index 'idx' to 'c'.
	 */
	inline void set(int c, size_t idx) {
		assert_lt(idx, len_);
		cs_[idx] = c;
	}

	/**
	 * Retrieve constant version of element i.
	 */
	inline const T& operator[](size_t i) const {
		assert_lt(i, len_);
		return cs_[i];
	}

	/**
	 * Retrieve mutable version of element i.
	 */
	inline T& operator[](size_t i) {
		assert_lt(i, len_);
		return cs_[i];
	}

	/**
	 * Retrieve constant version of element i.
	 */
	inline const T& get(size_t i) const {
		assert_lt(i, len_);
		return cs_[i];
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.  memcpy is used, not
	 * operator=.
	 */
	virtual void install(const T* b, size_t sz) {
		if(sz == 0) return;
		resize(sz);
		memcpy(cs_, b, sz * sizeof(T));
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.  memcpy is used, not
	 * operator=.
	 */
	virtual void install(const std::basic_string<T>& b) {
		size_t sz = b.length();
		if(sz == 0) return;
		resize(sz);
		memcpy(cs_, b.c_str(), sz * sizeof(T));
	}

	/**
	 * Copy all bytes from zero-terminated buffer 'b' into this string.
	 */
	void install(const T* b) {
		install(b, strlen(b));
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reversing them
	 * in the process.
	 */
	void installReverse(const char* b, size_t sz) {
		if(sz == 0) return;
		resize(sz);
		for(size_t i = 0; i < sz; i++) {
			cs_[i] = b[sz-i-1];
		}
		len_ = sz;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reversing them
	 * in the process.
	 */
	void installReverse(const SString<T>& b) {
		installReverse(b.cs_, b.len_);
	}
	
	/**
	 * Return true iff the two strings are equal.
	 */
	bool operator==(const SString<T>& o) {
		return sstr_eq(*this, o);
	}

	/**
	 * Return true iff the two strings are not equal.
	 */
	bool operator!=(const SString<T>& o) {
		return sstr_neq(*this, o);
	}

	/**
	 * Return true iff this string is less than given string.
	 */
	bool operator<(const SString<T>& o) {
		return sstr_lt(*this, o);
	}

	/**
	 * Return true iff this string is greater than given string.
	 */
	bool operator>(const SString<T>& o) {
		return sstr_gt(*this, o);
	}

	/**
	 * Return true iff this string is less than or equal to given string.
	 */
	bool operator<=(const SString<T>& o) {
		return sstr_leq(*this, o);
	}

	/**
	 * Return true iff this string is greater than or equal to given string.
	 */
	bool operator>=(const SString<T>& o) {
		return sstr_geq(*this, o);
	}

	/**
	 * Reverse the buffer in place.
	 */
	void reverse() {
		for(size_t i = 0; i < (len_ >> 1); i++) {
			T tmp = get(i);
			set(get(len_-i-1), i);
			set(tmp, len_-i-1);
		}
	}

	/**
	 * Reverse the buffer in place.
	 */
	void reverseComplement(int* rcmap) {
		size_t mid = len_ >> 1;
		for(size_t i = 0; i < (len_ >> 1); i++) {
			T tmp = get(i);
			set(rcmap[get(len_-i-1)], i);
			set(rcmap[tmp], len_-i-1);
		}
		if (len_ % 2) {
			set(rcmap[get(mid)], mid);
		}
	}

	/**
	 * Reverse a substring of the buffer in place.
	 */
	void reverseWindow(size_t off, size_t len) {
		assert_leq(off, len_);
		assert_leq(off + len, len_);
		size_t mid = len >> 1;
		for(size_t i = 0; i < mid; i++) {
			T tmp = get(off+i);
			set(get(off+len-i-1), off+i);
			set(tmp, off+len-i-1);
		}
	}

	/**
	 * Set the first len elements of the buffer to el.
	 */
	void fill(size_t len, const T& el) {
		assert_leq(len, len_);
		for(size_t i = 0; i < len; i++) {
			set(el, i);
		}
	}

	/**
	 * Set all elements of the buffer to el.
	 */
	void fill(const T& el) {
		fill(len_, el);
	}

	/**
	 * Return the length of the string.
	 */
	inline size_t length() const { return len_; }

	/**
	 * Clear the buffer.
	 */
	void clear() { len_ = 0; }

	/**
	 * Return true iff the buffer is empty.
	 */
	inline bool empty() const { return len_ == 0; }

	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	const char* toZBufXForm(const char *xform) const {
		ASSERT_ONLY(size_t xformElts = strlen(xform));
		// Lazily allocate space for print buffer
		if(printcs_ == NULL) {
			const_cast<char*&>(printcs_) = new char[len_+1];
		}
		char* printcs = const_cast<char*>(printcs_);
		assert(printcs != NULL);
		for(size_t i = 0; i < len_; i++) {
			assert_lt(cs_[i], (int)xformElts);
			printcs[i] = xform[cs_[i]];
		}
		printcs[len_] = 0;
		return printcs_;
	}

	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	virtual const T* toZBuf() const {
		const_cast<T*>(cs_)[len_] = 0;
		return cs_;
	}

	/**
	 * Return a const version of the raw buffer.
	 */
	const T* buf() const { return cs_; }

	/**
	 * Return a writeable version of the raw buffer.
	 */
	T* wbuf() { return cs_; }

protected:

	T *cs_;      // +1 so that we have the option of dropping in a terminating "\0"
	char *printcs_; // +1 so that we have the option of dropping in a terminating "\0"
	size_t len_; // # elements
};

/**
 * Simple string class with backing memory whose size is managed by the user
 * using the constructor and install() member function.  No behind-the-scenes
 * reallocation or copying takes place.
 */
class S2bDnaString {

public:

	explicit S2bDnaString() :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{ }

	explicit S2bDnaString(size_t sz) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		resize(sz);
	}

	/**
	 * Copy another object of the same class.
	 */
	S2bDnaString(const S2bDnaString& o) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		*this = o;
	}

	/**
	 * Create an SStringExpandable from a std::basic_string of the
	 * appropriate type.
	 */
	explicit S2bDnaString(
		const std::basic_string<char>& str,
		bool chars = false,
		bool colors = false) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		if(chars) {
			if(colors) {
				installColors(str.c_str(), str.length());
			} else {
				installChars(str.c_str(), str.length());
			}
		} else {
			install(str.c_str(), str.length());
		}
	}

	/**
	 * Create an SStringExpandable from an array and size.
	 */
	explicit S2bDnaString(
		const char* b,
		size_t sz,
		bool chars = false,
		bool colors = false) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		if(chars) {
			if(colors) {
				installColors(b, sz);
			} else {
				installChars(b, sz);
			}
		} else {
			install(b, sz);
		}
	}

	/**
	 * Create an SStringFixed from a zero-terminated string.
	 */
	explicit S2bDnaString(
		const char* b,
		bool chars = false,
		bool colors = false) :
		cs_(NULL),
		printcs_(NULL),
		len_(0)
	{
		if(chars) {
			if(colors) {
				installColors(b, strlen(b));
			} else {
				installChars(b, strlen(b));
			}
		} else {
			install(b, strlen(b));
		}
	}

	/**
	 * Destroy the expandable string object.
	 */
	virtual ~S2bDnaString() {
		if(cs_ != NULL) {
			delete[] cs_;
			cs_ = NULL;
		}
		if(printcs_ != NULL) {
			delete[] printcs_;
			printcs_ = NULL;
		}
		len_ = 0;
	}

	/**
	 * Assignment to other SString.
	 */
	template<typename T>
	S2bDnaString& operator=(const T& o) {
		install(o.c_str(), o.length());
		return *this;
	}

	/**
	 * Assignment from a std::basic_string
	 */
	template<typename T>
	S2bDnaString& operator=(const std::basic_string<char>& o) {
		install(o);
		return *this;
	}

	/**
	 * Resizes the string without preserving its contents.
	 */
	void resize(size_t sz) {
		if(cs_ != NULL) {
			delete cs_;
			cs_ = NULL;
		}
		if(printcs_ != NULL) {
			delete printcs_;
			printcs_ = NULL;
		}
		len_ = sz;
		if(sz != 0) {
			cs_ = new uint32_t[nwords()];
		}
	}

	/**
	 * Return DNA character corresponding to element 'idx'.
	 */
	char toChar(size_t idx) const {
		int c = (int)get(idx);
		assert_range(0, 3, c);
		return "ACGT"[c];
	}

	/**
	 * Return color character corresponding to element 'idx'.
	 */
	char toColor(size_t idx) const {
		int c = (int)get(idx);
		assert_range(0, 3, c);
		return "0123"[c];
	}

	/**
	 * Return ith character from the left of either the forward or the
	 * reverse version of the read.
	 */
	char windowGet(
		size_t i,
		bool   fw,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_lt(i, len);
		assert_leq(len, len_ - depth);
		return fw ? get(depth+i) : get(depth+len-i-1);
	}

	/**
	 * Return ith character from the left of either the forward or the
	 * reverse-complement version of the read.
	 */
	template<typename T>
	void windowGet(
		T& ret,
		bool   fw,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_leq(len, len_ - depth);
		ret.resize(len);
		for(size_t i = 0; i < len; i++) {
			ret.set((fw ? get(depth+i) : get(depth+len-i-1)), i);
		}
	}
	
	/**
	 * Return length in 32-bit words.
	 */
	size_t nwords() const {
		return (len_ + 15) >> 4;
	}

	/**
	 * Set character at index 'idx' to 'c'.
	 */
	void set(int c, size_t idx) {
		assert_lt(idx, len_);
		assert_range(0, 3, c);
		size_t word = idx >> 4;
		size_t bpoff = (idx & 15) << 1;
		cs_[word] = cs_[word] & ~(uint32_t)(3 << bpoff);
		cs_[word] = cs_[word] |  (uint32_t)(c << bpoff);
	}

	/**
	 * Set character at index 'idx' to DNA char 'c'.
	 */
	void setChar(int c, size_t idx) {
		assert_in(toupper(c), "ACGT");
		int bp = asc2dna[c];
		set(bp, idx);
	}

	/**
	 * Set character at index 'idx' to color char 'c'.
	 */
	void setColor(int c, size_t idx) {
		assert_in(toupper(c), "0123");
		int co = asc2col[c];
		set(co, idx);
	}

	/**
	 * Set the ith 32-bit word to given word.
	 */
	void setWord(uint32_t w, size_t i) {
		assert_lt(i, nwords());
		cs_[i] = w;
	}

	/**
	 * Retrieve constant version of element i.
	 */
	char operator[](size_t i) const {
		assert_lt(i, len_);
		return get(i);
	}

	/**
	 * Retrieve constant version of element i.
	 */
	char get(size_t i) const {
		assert_lt(i, len_);
		size_t word = i >> 4;
		size_t bpoff = (i & 15) << 1;
		return (char)((cs_[word] >> bpoff) & 3);
	}

	/**
	 * Copy packed words from string 'b' into this packed string.
	 */
	void install(const uint32_t* b, size_t sz) {
		if(sz == 0) return;
		resize(sz);
		memcpy(cs_, b, sizeof(uint32_t)*nwords());
	}

	/**
	 * Copy 'sz' DNA characters encoded as integers from buffer 'b' into this
	 * packed string.
	 */
	void install(const char* b, size_t sz) {
		if(sz == 0) return;
		resize(sz);
		size_t wordi = 0;
		for(size_t i = 0; i < sz; i += 16) {
			uint32_t word = 0;
			for(int j = 0; j < 16 && (size_t)(i+j) < sz; j++) {
				uint32_t bp = (int)b[i+j];
				uint32_t shift = (uint32_t)j << 1;
				assert_range(0, 3, (int)bp);
				word |= (bp << shift);
			}
			cs_[wordi++] = word;
		}
	}

	/**
	 * Copy 'sz' DNA characters from buffer 'b' into this packed string.
	 */
	void installChars(const char* b, size_t sz) {
		if(sz == 0) return;
		resize(sz);
		size_t wordi = 0;
		for(size_t i = 0; i < sz; i += 16) {
			uint32_t word = 0;
			for(int j = 0; j < 16 && (size_t)(i+j) < sz; j++) {
				char c = b[i+j];
				assert_in(toupper(c), "ACGT");
				int bp = asc2dna[(int)c];
				assert_range(0, 3, (int)bp);
				uint32_t shift = (uint32_t)j << 1;
				word |= (bp << shift);
			}
			cs_[wordi++] = word;
		}
	}

	/**
	 * Copy 'sz' color characters from buffer 'b' into this packed string.
	 */
	void installColors(const char* b, size_t sz) {
		if(sz == 0) return;
		resize(sz);
		size_t wordi = 0;
		for(size_t i = 0; i < sz; i += 16) {
			uint32_t word = 0;
			for(int j = 0; j < 16 && (size_t)(i+j) < sz; j++) {
				char c = b[i+j];
				assert_in(c, "0123");
				int bp = asc2col[(int)c];
				assert_range(0, 3, (int)bp);
				uint32_t shift = (uint32_t)j << 1;
				word |= (bp << shift);
			}
			cs_[wordi++] = word;
		}
	}

	/**
	 * Copy 'sz' DNA characters from buffer 'b' into this packed string.
	 */
	void install(const char* b) {
		install(b, strlen(b));
	}

	/**
	 * Copy 'sz' DNA characters from buffer 'b' into this packed string.
	 */
	void installChars(const char* b) {
		installChars(b, strlen(b));
	}

	/**
	 * Copy 'sz' DNA characters from buffer 'b' into this packed string.
	 */
	void installColors(const char* b) {
		installColors(b, strlen(b));
	}

	/**
	 * Copy 'sz' DNA characters from buffer 'b' into this packed string.
	 */
	void install(const std::basic_string<char>& b) {
		install(b.c_str(), b.length());
	}

	/**
	 * Copy 'sz' DNA characters from buffer 'b' into this packed string.
	 */
	void installChars(const std::basic_string<char>& b) {
		installChars(b.c_str(), b.length());
	}

	/**
	 * Copy 'sz' DNA characters from buffer 'b' into this packed string.
	 */
	void installColors(const std::basic_string<char>& b) {
		installColors(b.c_str(), b.length());
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reversing them
	 * in the process.
	 */
	void installReverse(const char* b, size_t sz) {
		resize(sz);
		if(sz == 0) return;
		size_t wordi = 0;
		size_t bpi   = 0;
		cs_[0] = 0;
		for(size_t i =sz; i > 0; i--) {
			assert_range(0, 3, (int)b[i-1]);
			cs_[wordi] |= ((int)b[i-1] << (bpi<<1));
			if(bpi == 15) {
				wordi++;
				cs_[wordi] = 0;
				bpi = 0;
			} else bpi++;
		}
	}

	/**
	 * Copy all chars from buffer of DNA characters 'b' into this string,
	 * reversing them in the process.
	 */
	void installReverse(const char* b) {
		installReverse(b, strlen(b));
	}

	/**
	 * Copy 'sz' bytes from buffer of DNA characters 'b' into this string,
	 * reversing them in the process.
	 */
	void installReverseChars(const char* b, size_t sz) {
		resize(sz);
		if(sz == 0) return;
		size_t wordi = 0;
		size_t bpi   = 0;
		cs_[0] = 0;
		for(size_t i =sz; i > 0; i--) {
			char c = b[i-1];
			assert_in(toupper(c), "ACGT");
			int bp = asc2dna[(int)c];
			assert_range(0, 3, bp);
			cs_[wordi] |= (bp << (bpi<<1));
			if(bpi == 15) {
				wordi++;
				cs_[wordi] = 0;
				bpi = 0;
			} else bpi++;
		}
	}

	/**
	 * Copy all chars from buffer of DNA characters 'b' into this string,
	 * reversing them in the process.
	 */
	void installReverseChars(const char* b) {
		installReverseChars(b, strlen(b));
	}

	/**
	 * Copy 'sz' bytes from buffer of color characters 'b' into this string,
	 * reversing them in the process.
	 */
	void installReverseColors(const char* b, size_t sz) {
		resize(sz);
		if(sz == 0) return;
		size_t wordi = 0;
		size_t bpi   = 0;
		cs_[0] = 0;
		for(size_t i =sz; i > 0; i--) {
			char c = b[i-1];
			assert_in(c, "0123");
			int bp = asc2col[(int)c];
			assert_range(0, 3, bp);
			cs_[wordi] |= (bp << (bpi<<1));
			if(bpi == 15) {
				wordi++;
				cs_[wordi] = 0;
				bpi = 0;
			} else bpi++;
		}
	}

	/**
	 * Copy all chars from buffer of color characters 'b' into this string,
	 * reversing them in the process.
	 */
	void installReverseColors(const char* b) {
		installReverseColors(b, strlen(b));
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reversing them
	 * in the process.
	 */
	void installReverse(const S2bDnaString& b) {
		resize(b.len_);
		if(b.len_ == 0) return;
		size_t wordi = 0;
		size_t bpi   = 0;
		size_t wordb = b.nwords()-1;
		size_t bpb   = (b.len_-1) & 15;
		cs_[0] = 0;
		for(size_t i = b.len_; i > 0; i--) {
			int bbp = (int)((b[wordb] >> (bpb << 1)) & 3);
			assert_range(0, 3, bbp);
			cs_[wordi] |= (bbp << (bpi << 1));
			if(bpi == 15) {
				wordi++;
				cs_[wordi] = 0;
				bpi = 0;
			} else bpi++;
			if(bpb == 0) {
				wordb--;
				bpi = 15;
			} else bpi--;
		}
	}

	/**
	 * Return true iff the two strings are equal.
	 */
	bool operator==(const S2bDnaString& o) {
		return sstr_eq(*this, o);
	}

	/**
	 * Return true iff the two strings are not equal.
	 */
	bool operator!=(const S2bDnaString& o) {
		return sstr_neq(*this, o);
	}

	/**
	 * Return true iff this string is less than given string.
	 */
	bool operator<(const S2bDnaString& o) {
		return sstr_lt(*this, o);
	}

	/**
	 * Return true iff this string is greater than given string.
	 */
	bool operator>(const S2bDnaString& o) {
		return sstr_gt(*this, o);
	}

	/**
	 * Return true iff this string is less than or equal to given string.
	 */
	bool operator<=(const S2bDnaString& o) {
		return sstr_leq(*this, o);
	}

	/**
	 * Return true iff this string is greater than or equal to given string.
	 */
	bool operator>=(const S2bDnaString& o) {
		return sstr_geq(*this, o);
	}

	/**
	 * Reverse the 2-bit encoded DNA string in-place.
	 */
	void reverse() {
		if(len_ <= 1) return;
		size_t wordf = nwords()-1;
		size_t bpf   = (len_-1) & 15;
		size_t wordi = 0;
		size_t bpi   = 0;
		while(wordf > wordi || (wordf == wordi && bpf > bpi)) {
			int f = (cs_[wordf] >> (bpf << 1)) & 3;
			int i = (cs_[wordi] >> (bpi << 1)) & 3;
			cs_[wordf] &= ~(uint32_t)(3 << (bpf << 1));
			cs_[wordi] &= ~(uint32_t)(3 << (bpi << 1));
			cs_[wordf] |=  (uint32_t)(i << (bpf << 1));
			cs_[wordi] |=  (uint32_t)(f << (bpi << 1));
			if(bpf == 0) {
				bpf = 15;
				wordf--;
			} else bpf--;
			if(bpi == 15) {
				bpi = 0;
				wordi++;
			} else bpi++;
		}
	}
	
	/**
	 * Reverse a substring of the buffer in place.
	 */
	void reverseWindow(size_t off, size_t len) {
		assert_leq(off, len_);
		assert_leq(off+len, len_);
		if(len <= 1) return;
		size_t wordf = (off+len-1) >> 4;
		size_t bpf   = (off+len-1) & 15;
		size_t wordi = (off      ) >> 4;
		size_t bpi   = (off      ) & 15;
		while(wordf > wordi || (wordf == wordi && bpf > bpi)) {
			int f = (cs_[wordf] >> (bpf << 1)) & 3;
			int i = (cs_[wordi] >> (bpi << 1)) & 3;
			cs_[wordf] &= ~(uint32_t)(3 << (bpf << 1));
			cs_[wordi] &= ~(uint32_t)(3 << (bpi << 1));
			cs_[wordf] |=  (uint32_t)(i << (bpf << 1));
			cs_[wordi] |=  (uint32_t)(f << (bpi << 1));
			if(bpf == 0) {
				bpf = 15;
				wordf--;
			} else bpf--;
			if(bpi == 15) {
				bpi = 0;
				wordi++;
			} else bpi++;
		}
	}


	/**
	 * Set the first len elements of the buffer to el.
	 */
	void fill(size_t len, char el) {
		assert_leq(len, len_);
		assert_range(0, 3, (int)el);
		size_t word = 0;
		if(len > 32) {
			// Copy el throughout block
			uint32_t bl = (uint32_t)el;
			bl |= (bl << 2);
			bl |= (bl << 4);
			bl |= (bl << 8);
			bl |= (bl << 16);
			// Fill with blocks
			size_t blen = len >> 4;
			for(; word < blen; word++) {
				cs_[word] = bl;
			}
			len = len & 15;
		}
		size_t bp = 0;
		for(size_t i = 0; i < len; i++) {
			cs_[word] &= ~(uint32_t)(3  << (bp << 1));
			cs_[word] |=  (uint32_t)(el << (bp << 1));
			if(bp == 15) {
				word++;
				bp = 0;
			} else bp++;
		}
	}

	/**
	 * Set all elements of the buffer to el.
	 */
	void fill(char el) {
		fill(len_, el);
	}

	/**
	 * Return the ith character in the window defined by fw, color, depth and
	 * len.
	 */
	char windowGetDna(
		size_t i,
		bool   fw,
		bool   color,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_lt(i, len);
		assert_leq(len, len_ - depth);
		if(fw) {
			return get(depth+i);
		} else {
			return
				color ?
					get(depth+len-i-1) :
					compDna(get(depth+len-i-1));
		}
	}

	/**
	 * Fill the given DNA buffer with the substring specified by fw,
	 * color, depth and len.
	 */
	template<typename T>
	void windowGetDna(
		T&     buf,
		bool   fw,
		bool   color,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_leq(len, len_ - depth);
		buf.resize(len);
		for(size_t i = 0; i < len; i++) {
			buf.set(
				(fw ?
					get(depth+i) :
					(color ?
						get(depth+len-i-1) :
						compDna(get(depth+len-i-1)))), i);
		}
	}

	/**
	 * Return the length of the string.
	 */
	inline size_t length() const { return len_; }

	/**
	 * Clear the buffer.
	 */
	void clear() { len_ = 0; }

	/**
	 * Return true iff the buffer is empty.
	 */
	inline bool empty() const { return len_ == 0; }

	/**
	 * Return a const version of the raw buffer.
	 */
	const uint32_t* buf() const { return cs_; }

	/**
	 * Return a writeable version of the raw buffer.
	 */
	uint32_t* wbuf() { return cs_; }

	/**
	 * Note: the size of the string once it's stored in the print buffer is 4
	 * times as large as the string as stored in compact 2-bit-per-char words.
	 */
	const char* toZBuf() const {
		if(printcs_ == NULL) {
			const_cast<char*&>(printcs_) = new char[len_+1];
		}
		char *printcs = const_cast<char*>(printcs_);
		size_t word = 0, bp = 0;
		for(size_t i = 0; i < len_; i++) {
			int c = (cs_[word] >> (bp << 1)) & 3;
			printcs[i] = "ACGT"[c];
			if(bp == 15) {
				word++;
				bp = 0;
			} else bp++;
		}
		printcs[len_] = '\0';
		return printcs_;
	}

protected:

	uint32_t *cs_; // 2-bit packed words
	char *printcs_;
	size_t len_;   // # elements
};

/**
 * Simple string class with backing memory that automatically expands as needed.
 */
template<typename T, int S = 1024, int M = 2>
class SStringExpandable {

public:

	explicit SStringExpandable() :
		cs_(NULL),
		printcs_(NULL),
		len_(0),
		sz_(0)
	{ }

	explicit SStringExpandable(size_t sz) :
		cs_(NULL),
		printcs_(NULL),
		len_(0),
		sz_(0)
	{
		expandNoCopy(sz);
	}

	/**
	 * Create an SStringExpandable from another SStringExpandable.
	 */
	SStringExpandable(const SStringExpandable<T, S>& o) :
		cs_(NULL),
		printcs_(NULL),
		len_(0),
		sz_(0)
	{
		*this = o;
	}

	/**
	 * Create an SStringExpandable from a std::basic_string of the
	 * appropriate type.
	 */
	explicit SStringExpandable(const std::basic_string<T>& str) :
		cs_(NULL),
		printcs_(NULL),
		len_(0),
		sz_(0)
	{
		install(str.c_str(), str.length());
	}

	/**
	 * Create an SStringExpandable from an array and size.
	 */
	explicit SStringExpandable(const T* b, size_t sz) :
		cs_(NULL),
		printcs_(NULL),
		len_(0),
		sz_(0)
	{
		install(b, sz);
	}

	/**
	 * Create an SStringExpandable from a zero-terminated array.
	 */
	explicit SStringExpandable(const T* b) :
		cs_(NULL),
		printcs_(NULL),
		len_(0),
		sz_(0)
	{
		install(b, strlen(b));
	}

	/**
	 * Destroy the expandable string object.
	 */
	virtual ~SStringExpandable() {
		if(cs_ != NULL) {
			delete[] cs_;
			cs_ = NULL;
		}
		if(printcs_ != NULL) {
			delete[] printcs_;
			printcs_ = NULL;
		}
		sz_ = len_ = 0;
	}

	/**
	 * Return ith character from the left of either the forward or the
	 * reverse-complement version of the read.
	 */
	T windowGet(
		size_t i,
		bool   fw,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_lt(i, len);
		assert_leq(len, len_ - depth);
		return fw ? cs_[depth+i] : cs_[depth+len-i-1];
	}

	/**
	 * Return ith character from the left of either the forward or the
	 * reverse-complement version of the read.
	 */
	void windowGet(
		T& ret,
		bool   fw,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_leq(len, len_ - depth);
		for(size_t i = 0; i < len; i++) {
			ret.append(fw ? cs_[depth+i] : cs_[depth+len-i-1]);
		}
	}

	/**
	 * Assignment to other SStringFixed.
	 */
	SStringExpandable<T,S>& operator=(const SStringExpandable<T,S>& o) {
		install(o.cs_, o.len_);
		return *this;
	}

	/**
	 * Assignment from a std::basic_string
	 */
	SStringExpandable<T,S>& operator=(const std::basic_string<T>& o) {
		install(o.c_str(), o.length());
		return *this;
	}

	/**
	 * Insert char c before position 'idx'; slide subsequent chars down.
	 */
	void insert(const T& c, size_t idx) {
		assert_lt(idx, len_);
		if(sz_ < len_ + 1) expandCopy((len_ + 1 + S) * M);
		len_++;
		// Move everyone down by 1
		// len_ is the *new* length
		for(size_t i = len_; i > idx+1; i--) {
			cs_[i-1] = cs_[i-2];
		}
		cs_[idx] = c;
	}

	/**
	 * Set character at index 'idx' to 'c'.
	 */
	void set(int c, size_t idx) {
		assert_lt(idx, len_);
		cs_[idx] = c;
	}

	/**
	 * Append char c.
	 */
	void append(const T& c) {
		if(sz_ < len_ + 1) expandCopy((len_ + 1 + S) * M);
		cs_[len_++] = c;
	}

	/**
	 * Delete char at position 'idx'; slide subsequent chars up.
	 */
	void remove(size_t idx) {
		assert_lt(idx, len_);
		assert_gt(len_, 0);
		for(size_t i = idx; i < len_-1; i++) {
			cs_[i] = cs_[i+1];
		}
		len_--;
	}

	/**
	 * Retrieve constant version of element i.
	 */
	const T& operator[](size_t i) const {
		assert_lt(i, len_);
		return cs_[i];
	}

	/**
	 * Retrieve mutable version of element i.
	 */
	T& operator[](size_t i) {
		assert_lt(i, len_);
		return cs_[i];
	}

	/**
	 * Retrieve constant version of element i.
	 */
	const T& get(size_t i) const {
		assert_lt(i, len_);
		return cs_[i];
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.
	 */
	virtual void install(const T* b, size_t sz) {
		if(sz_ < sz) expandNoCopy((sz + S) * M);
		memcpy(cs_, b, sz * sizeof(T));
		len_ = sz;
	}


	/**
	 * Copy all bytes from zero-terminated buffer 'b' into this string.
	 */
	void install(const T* b) { install(b, strlen(b)); }

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reversing them
	 * in the process.
	 */
	void installReverse(const char* b, size_t sz) {
		if(sz_ < sz) expandNoCopy((sz + S) * M);
		for(size_t i = 0; i < sz; i++) {
			cs_[i] = b[sz-i-1];
		}
		len_ = sz;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reversing them
	 * in the process.
	 */
	void installReverse(const SStringExpandable<T, S>& b) {
		if(sz_ < b.len_) expandNoCopy((b.len_ + S) * M);
		for(size_t i = 0; i < b.len_; i++) {
			cs_[i] = b.cs_[b.len_ - i - 1];
		}
		len_ = b.len_;
	}

	/**
	 * Return true iff the two strings are equal.
	 */
	bool operator==(const SStringExpandable<T, S>& o) {
		return sstr_eq(*this, o);
	}

	/**
	 * Return true iff the two strings are not equal.
	 */
	bool operator!=(const SStringExpandable<T, S>& o) {
		return sstr_neq(*this, o);
	}

	/**
	 * Return true iff this string is less than given string.
	 */
	bool operator<(const SStringExpandable<T, S>& o) {
		return sstr_lt(*this, o);
	}

	/**
	 * Return true iff this string is greater than given string.
	 */
	bool operator>(const SStringExpandable<T, S>& o) {
		return sstr_gt(*this, o);
	}

	/**
	 * Return true iff this string is less than or equal to given string.
	 */
	bool operator<=(const SStringExpandable<T, S>& o) {
		return sstr_leq(*this, o);
	}

	/**
	 * Return true iff this string is greater than or equal to given string.
	 */
	bool operator>=(const SStringExpandable<T, S>& o) {
		return sstr_geq(*this, o);
	}

	/**
	 * Reverse the buffer in place.
	 */
	void reverse() {
		for(size_t i = 0; i < (len_ >> 1); i++) {
			T tmp = get(i);
			set(get(len_-i-1), i);
			set(tmp, len_-i-1);
		}
	}

	/**
	 * Reverse a substring of the buffer in place.
	 */
	void reverseWindow(size_t off, size_t len) {
		assert_leq(off, len_);
		assert_leq(off + len, len_);
		size_t mid = len >> 1;
		for(size_t i = 0; i < mid; i++) {
			T tmp = get(off+i);
			set(get(off+len-i-1), off+i);
			set(tmp, off+len-i-1);
		}
	}

	/**
	 * Simply resize the buffer.  If the buffer is resized to be
	 * longer, the newly-added elements will contain garbage and should
	 * be initialized immediately.
	 */
	void resize(size_t len) {
		if(sz_ < len) expandCopy((len + S) * M);
		len_ = len;
	}

	/**
	 * Simply resize the buffer.  If the buffer is resized to be
	 * longer, new elements will be initialized with 'el'.
	 */
	void resize(size_t len, const T& el) {
		if(sz_ < len) expandCopy((len + S) * M);
		if(len > len_) {
			for(size_t i = len_; i < len; i++) {
				cs_[i] = el;
			}
		}
		len_ = len;
	}

	/**
	 * Set the first len elements of the buffer to el.
	 */
	void fill(size_t len, const T& el) {
		assert_leq(len, len_);
		for(size_t i = 0; i < len; i++) {
			cs_[i] = el;
		}
	}

	/**
	 * Set all elements of the buffer to el.
	 */
	void fill(const T& el) {
		fill(len_, el);
	}

	/**
	 * Trim len characters from the beginning of the string.
	 */
	void trimBegin(size_t len) {
		assert_leq(len, len_);
		if(len == len_) {
			len_ = 0; return;
		}
		for(size_t i = 0; i < len_-len; i++) {
			cs_[i] = cs_[i+len];
		}
		len_ -= len;
	}

	/**
	 * Trim len characters from the end of the string.
	 */
	void trimEnd(size_t len) {
		if(len >= len_) len_ = 0;
		else len_ -= len;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.
	 */
	void append(const T* b, size_t sz) {
		if(sz_ < len_ + sz) expandCopy((len_ + sz + S) * M);
		memcpy(cs_ + len_, b, sz * sizeof(T));
		len_ += sz;
	}

	/**
	 * Copy bytes from zero-terminated buffer 'b' into this string.
	 */
	void append(const T* b) {
		append(b, strlen(b));
	}

	/**
	 * Return the length of the string.
	 */
	size_t length() const { return len_; }

	/**
	 * Clear the buffer.
	 */
	void clear() { len_ = 0; }

	/**
	 * Return true iff the buffer is empty.
	 */
	bool empty() const { return len_ == 0; }

	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	const char* toZBufXForm(const char *xform) const {
		ASSERT_ONLY(size_t xformElts = strlen(xform));
		if(empty()) {
			const_cast<char&>(zero_) = 0;
			return &zero_;
		}
		char* printcs = const_cast<char*>(printcs_);
		// Lazily allocate space for print buffer
		for(size_t i = 0; i < len_; i++) {
			assert_lt(cs_[i], (int)xformElts);
			printcs[i] = xform[(int)cs_[i]];
		}
		printcs[len_] = 0;
		return printcs_;
	}

	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	virtual const T* toZBuf() const {
		if(empty()) {
			const_cast<T&>(zeroT_) = 0;
			return &zeroT_;
		}
		assert_leq(len_, sz_);
		const_cast<T*>(cs_)[len_] = 0;
		return cs_;
	}

	/**
	 * Return true iff this DNA string matches the given nucleotide
	 * character string.
	 */
	bool eq(const char *str) const {
		const char *self = toZBuf();
		return strcmp(str, self) == 0;
	}

	/**
	 * Return a const version of the raw buffer.
	 */
	const T* buf() const { return cs_; }

	/**
	 * Return a writeable version of the raw buffer.
	 */
	T* wbuf() { return cs_; }

protected:
	/**
	 * Allocate new, bigger buffer and copy old contents into it.  If
	 * requested size can be accommodated by current buffer, do nothing.
	 */
	void expandCopy(size_t sz) {
		if(sz_ >= sz) return; // done!
		T *tmp  = new T[sz + 1];
		char *ptmp = new char[sz + 1];
		if(cs_ != NULL) {
			memcpy(tmp, cs_, sizeof(T)*len_);
			delete[] cs_;
		}
		if(printcs_ != NULL) {
			memcpy(ptmp, printcs_, sizeof(char)*len_);
			delete[] printcs_;
		}
		cs_ = tmp;
		printcs_ = ptmp;
		sz_ = sz;
	}

	/**
	 * Allocate new, bigger buffer.  If requested size can be
	 * accommodated by current buffer, do nothing.
	 */
	void expandNoCopy(size_t sz) {
		if(sz_ >= sz) return; // done!
		if(cs_      != NULL) delete[] cs_;
		if(printcs_ != NULL) delete[] printcs_;
		cs_ = new T[sz + 1];
		printcs_ = new char[sz + 1];
		sz_ = sz;
	}

	T *cs_;      // +1 so that we have the option of dropping in a terminating "\0"
	char *printcs_; // +1 so that we have the option of dropping in a terminating "\0"
	char zero_;  // 0 terminator for empty string
	T zeroT_;    // 0 terminator for empty string
	size_t len_; // # filled-in elements
	size_t sz_;  // size capacity of cs_
};

/**
 * Simple string class with in-object storage.
 *
 * All copies induced by, e.g., operator=, the copy constructor,
 * install() and append(), are shallow (using memcpy/sizeof).  If deep
 * copies are needed, use a different class.
 *
 * Reading from an uninitialized element results in an assert as long
 * as NDEBUG is not defined.  If NDEBUG is defined, the result is
 * undefined.
 */
template<typename T, int S>
class SStringFixed {
public:
	explicit SStringFixed() : len_(0) { }

	/**
	 * Create an SStringFixed from another SStringFixed.
	 */
	SStringFixed(const SStringFixed<T, S>& o) {
		*this = o;
	}

	/**
	 * Create an SStringFixed from another SStringFixed.
	 */
	explicit SStringFixed(const std::basic_string<T>& str) {
		install(str.c_str(), str.length());
	}

	/**
	 * Create an SStringFixed from an array and size.
	 */
	explicit SStringFixed(const T* b, size_t sz) {
		install(b, sz);
	}

	/**
	 * Create an SStringFixed from a zero-terminated string.
	 */
	explicit SStringFixed(const T* b) {
		install(b, strlen(b));
	}

	virtual ~SStringFixed() { } // C++ needs this

	/**
	 * Retrieve constant version of element i.
	 */
	inline const T& operator[](size_t i) const {
		return get(i);
	}

	/**
	 * Retrieve mutable version of element i.
	 */
	inline T& operator[](size_t i) {
		return get(i);
	}

	/**
	 * Retrieve constant version of element i.
	 */
	inline const T& get(size_t i) const {
		assert_lt(i, len_);
		return cs_[i];
	}

	/**
	 * Retrieve mutable version of element i.
	 */
	inline T& get(size_t i) {
		assert_lt(i, len_);
		return cs_[i];
	}

	/**
	 * Return ith character from the left of either the forward or the
	 * reverse-complement version of the read.
	 */
	T windowGet(
		size_t i,
		bool   fw,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_lt(i, len);
		assert_leq(len, len_ - depth);
		return fw ? cs_[depth+i] : cs_[depth+len-i-1];
	}

	/**
	 * Return ith character from the left of either the forward or the
	 * reverse-complement version of the read.
	 */
	void windowGet(
		T& ret,
		bool   fw,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = len_;
		assert_leq(len, len_ - depth);
		for(size_t i = 0; i < len; i++) {
			ret.append(fw ? cs_[depth+i] : cs_[depth+len-i-1]);
		}
	}

	/**
	 * Assignment to other SStringFixed.
	 */
	SStringFixed<T,S>& operator=(const SStringFixed<T,S>& o) {
		install(o.cs_, o.len_);
		return *this;
	}

	/**
	 * Assignment from a std::basic_string
	 */
	SStringFixed<T,S>& operator=(const std::basic_string<T>& o) {
		install(o);
		return *this;
	}

	/**
	 * Insert char c before position 'idx'; slide subsequent chars down.
	 */
	void insert(const T& c, size_t idx) {
		assert_lt(len_, S);
		assert_lt(idx, len_);
		// Move everyone down by 1
		for(int i = len_; i > idx; i--) {
			cs_[i] = cs_[i-1];
		}
		cs_[idx] = c;
		len_++;
	}

	/**
	 * Set character at index 'idx' to 'c'.
	 */
	void set(int c, size_t idx) {
		assert_lt(idx, len_);
		cs_[idx] = c;
	}

	/**
	 * Append char c.
	 */
	void append(const T& c) {
		assert_lt(len_, S);
		cs_[len_++] = c;
	}

	/**
	 * Delete char at position 'idx'; slide subsequent chars up.
	 */
	void remove(size_t idx) {
		assert_lt(idx, len_);
		assert_gt(len_, 0);
		for(size_t i = idx; i < len_-1; i++) {
			cs_[i] = cs_[i+1];
		}
		len_--;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.
	 */
	virtual void install(const T* b, size_t sz) {
		assert_leq(sz, S);
		memcpy(cs_, b, sz * sizeof(T));
		len_ = sz;
	}

	/**
	 * Copy all bytes from zero-terminated buffer 'b' into this string.
	 */
	void install(const T* b) { install(b, strlen(b)); }

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reversing them
	 * in the process.
	 */
	void installReverse(const char* b, size_t sz) {
		assert_leq(sz, S);
		for(size_t i = 0; i < sz; i++) {
			cs_[i] = b[sz-i-1];
		}
		len_ = sz;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reversing them
	 * in the process.
	 */
	void installReverse(const SStringFixed<T, S>& b) {
		assert_leq(b.len_, S);
		for(size_t i = 0; i < b.len_; i++) {
			cs_[i] = b.cs_[b.len_ - i - 1];
		}
		len_ = b.len_;
	}

	/**
	 * Return true iff the two strings are equal.
	 */
	bool operator==(const SStringFixed<T, S>& o) {
		return sstr_eq(*this, o);
	}

	/**
	 * Return true iff the two strings are not equal.
	 */
	bool operator!=(const SStringFixed<T, S>& o) {
		return sstr_neq(*this, o);
	}

	/**
	 * Return true iff this string is less than given string.
	 */
	bool operator<(const SStringFixed<T, S>& o) {
		return sstr_lt(*this, o);
	}

	/**
	 * Return true iff this string is greater than given string.
	 */
	bool operator>(const SStringFixed<T, S>& o) {
		return sstr_gt(*this, o);
	}

	/**
	 * Return true iff this string is less than or equal to given string.
	 */
	bool operator<=(const SStringFixed<T, S>& o) {
		return sstr_leq(*this, o);
	}

	/**
	 * Return true iff this string is greater than or equal to given string.
	 */
	bool operator>=(const SStringFixed<T, S>& o) {
		return sstr_geq(*this, o);
	}

	/**
	 * Reverse the buffer in place.
	 */
	void reverse() {
		for(size_t i = 0; i < (len_ >> 1); i++) {
			T tmp = get(i);
			set(get(len_-i-1), i);
			set(tmp, len_-i-1);
		}
	}

	/**
	 * Reverse a substring of the buffer in place.
	 */
	void reverseWindow(size_t off, size_t len) {
		assert_leq(off, len_);
		assert_leq(off + len, len_);
		size_t mid = len >> 1;
		for(size_t i = 0; i < mid; i++) {
			T tmp = get(off+i);
			set(get(off+len-i-1), off+i);
			set(tmp, off+len-i-1);
		}
	}

	/**
	 * Simply resize the buffer.  If the buffer is resized to be
	 * longer, the newly-added elements will contain garbage and should
	 * be initialized immediately.
	 */
	void resize(size_t len) {
		assert_lt(len, S);
		len_ = len;
	}

	/**
	 * Simply resize the buffer.  If the buffer is resized to be
	 * longer, new elements will be initialized with 'el'.
	 */
	void resize(size_t len, const T& el) {
		assert_lt(len, S);
		if(len > len_) {
			for(size_t i = len_; i < len; i++) {
				cs_[i] = el;
			}
		}
		len_ = len;
	}

	/**
	 * Set the first len elements of the buffer to el.
	 */
	void fill(size_t len, const T& el) {
		assert_leq(len, len_);
		for(size_t i = 0; i < len; i++) {
			cs_[i] = el;
		}
	}

	/**
	 * Set all elements of the buffer to el.
	 */
	void fill(const T& el) {
		fill(len_, el);
	}

	/**
	 * Trim len characters from the beginning of the string.
	 */
	void trimBegin(size_t len) {
		assert_leq(len, len_);
		if(len == len_) {
			len_ = 0; return;
		}
		for(size_t i = 0; i < len_-len; i++) {
			cs_[i] = cs_[i+len];
		}
		len_ -= len;
	}

	/**
	 * Trim len characters from the end of the string.
	 */
	void trimEnd(size_t len) {
		if(len >= len_) len_ = 0;
		else len_ -= len;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.
	 */
	void append(const T* b, size_t sz) {
		assert_leq(sz + len_, S);
		memcpy(cs_ + len_, b, sz * sizeof(T));
		len_ += sz;
	}

	/**
	 * Copy bytes from zero-terminated buffer 'b' into this string.
	 */
	void append(const T* b) {
		append(b, strlen(b));
	}

	/**
	 * Return the length of the string.
	 */
	size_t length() const { return len_; }

	/**
	 * Clear the buffer.
	 */
	void clear() { len_ = 0; }

	/**
	 * Return true iff the buffer is empty.
	 */
	bool empty() const { return len_ == 0; }

	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	virtual const T* toZBuf() const {
		const_cast<T*>(cs_)[len_] = 0;
		return cs_;
	}

	/**
	 * Return true iff this DNA string matches the given nucleotide
	 * character string.
	 */
	bool eq(const char *str) const {
		const char *self = toZBuf();
		return strcmp(str, self) == 0;
	}
	
	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	const char* toZBufXForm(const char *xform) const {
		ASSERT_ONLY(size_t xformElts = strlen(xform));
		char* printcs = const_cast<char*>(printcs_);
		for(size_t i = 0; i < len_; i++) {
			assert_lt(cs_[i], (int)xformElts);
			printcs[i] = xform[cs_[i]];
		}
		printcs[len_] = 0;
		return printcs_;
	}

	/**
	 * Return a const version of the raw buffer.
	 */
	const T* buf() const { return cs_; }

	/**
	 * Return a writeable version of the raw buffer.
	 */
	T* wbuf() { return cs_; }

protected:
	T cs_[S+1]; // +1 so that we have the option of dropping in a terminating "\0"
	char printcs_[S+1]; // +1 so that we have the option of dropping in a terminating "\0"
	size_t len_;
};

//
// Stream put operators
//

template <typename T, int S, int M>
std::ostream& operator<< (std::ostream& os, const SStringExpandable<T, S, M>& str) {
	os << str.toZBuf();
	return os;
}

template <typename T, int S>
std::ostream& operator<< (std::ostream& os, const SStringFixed<T, S>& str) {
	os << str.toZBuf();
	return os;
}

extern uint8_t asc2dna[];
extern uint8_t asc2col[];

extern uint8_t asc2dna_3N[2][256];



/**
 * Encapsulates a fixed-length DNA string with characters encoded as
 * chars.  Only capable of encoding A, C, G, T and N.  The length is
 * specified via the template parameter S.
 */
template<int S>
class SDnaStringFixed : public SStringFixed<char, S> {
public:

	explicit SDnaStringFixed() : SStringFixed<char, S>() { }

	/**
	 * Create an SStringFixed from another SStringFixed.
	 */
	SDnaStringFixed(const SDnaStringFixed<S>& o) :
		SStringFixed<char, S>(o) { }

	/**
	 * Create an SStringFixed from a C++ basic_string.
	 */
	explicit SDnaStringFixed(const std::basic_string<char>& str) :
		SStringFixed<char, S>(str) { }

	/**
	 * Create an SStringFixed from an array and size.
	 */
	explicit SDnaStringFixed(const char* b, size_t sz) :
		SStringFixed<char, S>(b, sz) { }

	/**
	 * Create an SStringFixed from a zero-terminated string.
	 */
	explicit SDnaStringFixed(
		const char* b,
		bool chars = false,
		bool colors = false) :
		SStringFixed<char, S>()
	{
		if(chars) {
			if(colors) {
				installColors(b, strlen(b));
			} else {
				installChars(b, strlen(b));
			}
		} else {
			install(b, strlen(b));
		}
	}

	virtual ~SDnaStringFixed() { } // C++ needs this

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reverse-
	 * complementing them in the process, assuming an encoding where
	 * 0=A, 1=C, 2=G, 3=T, 4=N.
	 */
	void installReverseComp(const char* b, size_t sz) {
		assert_leq(sz, S);
		for(size_t i = 0; i < sz; i++) {
			this->cs_[i] = (b[sz-i-1] == 4 ? 4 : b[sz-i-1] ^ 3);
		}
		this->len_ = sz;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reverse-
	 * complementing them in the process, assuming an encoding where
	 * 0=A, 1=C, 2=G, 3=T, 4=N.
	 */
	void installReverseComp(const SDnaStringFixed<S>& b) {
		assert_leq(b.len_, S);
		for(size_t i = 0; i < b.len_; i++) {
			this->cs_[i] = (b.cs_[b.len_-i-1] == 4 ? 4 : b.cs_[b.len_-i-1] ^ 3);
		}
		this->len_ = b.len_;
	}

	/**
	 * Either reverse or reverse-complement (depending on "color") this
	 * DNA buffer in-place.
	 */
	void reverseComp(bool color = false) {
		if(color) {
			this->reverse();
		} else {
			for(size_t i = 0; i < (this->len_ >> 1); i++) {
				char tmp1 = (this->cs_[i] == 4 ? 4 : this->cs_[i] ^ 3);
				char tmp2 = (this->cs_[this->len_-i-1] == 4 ? 4 : this->cs_[this->len_-i-1] ^ 3);
				this->cs_[i] = tmp2;
				this->cs_[this->len_-i-1] = tmp1;
			}
			// Do middle element iff there are an odd number
			if((this->len_ & 1) != 0) {
				char tmp = this->cs_[this->len_ >> 1];
				tmp = (tmp == 4 ? 4 : tmp ^ 3);
				this->cs_[this->len_ >> 1] = tmp;
			}
		}
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.
	 */
	virtual void install(const char* b, size_t sz) {
		assert_leq(sz, S);
		memcpy(this->cs_, b, sz);
#ifndef NDEBUG
		for(size_t i = 0; i < sz; i++) {
			assert_leq(this->cs_[i], 4);
			assert_geq(this->cs_[i], 0);
		}
#endif
		this->len_ = sz;
	}

	/**
	 * Copy buffer 'b' of ASCII DNA characters into normal DNA
	 * characters.
	 */
	virtual void installChars(const char* b, size_t sz) {
		assert_leq(sz, S);
		for(size_t i = 0; i < sz; i++) {
			assert_in(toupper(b[i]), "ACGTN-");
			this->cs_[i] = asc2dna[(int)b[i]];
			assert_geq(this->cs_[i], 0);
			assert_leq(this->cs_[i], 4);
		}
		this->len_ = sz;
	}

	/**
	 * Copy buffer 'b' of ASCII color characters into normal DNA
	 * characters.
	 */
	virtual void installColors(const char* b, size_t sz) {
		assert_leq(sz, S);
		for(size_t i = 0; i < sz; i++) {
			assert_in(b[i], "0123.");
			this->cs_[i] = asc2col[(int)b[i]];
			assert_geq(this->cs_[i], 0);
			assert_leq(this->cs_[i], 4);
		}
		this->len_ = sz;
	}

	/**
	 * Copy C++ string of ASCII DNA characters into normal DNA
	 * characters.
	 */
	virtual void installChars(const std::basic_string<char>& str) {
		installChars(str.c_str(), str.length());
	}

	/**
	 * Copy C++ string of ASCII color characters into normal DNA
	 * characters.
	 */
	virtual void installColors(const std::basic_string<char>& str) {
		installColors(str.c_str(), str.length());
	}

	/**
	 * Set DNA character at index 'idx' to 'c'.
	 */
	void set(int c, size_t idx) {
		assert_lt(idx, this->len_);
		assert_leq(c, 4);
		assert_geq(c, 0);
		this->cs_[idx] = c;
	}

	/**
	 * Append DNA char c.
	 */
	void append(const char& c) {
		assert_lt(this->len_, S);
		assert_leq(c, 4);
		assert_geq(c, 0);
		this->cs_[this->len_++] = c;
	}

	/**
	 * Set DNA character at index 'idx' to 'c'.
	 */
	void setChar(char c, size_t idx) {
		assert_lt(idx, this->len_);
		assert_in(toupper(c), "ACGTN");
		this->cs_[idx] = asc2dna[(int)c];
	}

	/**
	 * Append DNA character.
	 */
	void appendChar(char c) {
		assert_lt(this->len_, S);
		assert_in(toupper(c), "ACGTN");
		this->cs_[this->len_++] = asc2dna[(int)c];
	}

	/**
	 * Return DNA character corresponding to element 'idx'.
	 */
	char toChar(size_t idx) const {
		assert_geq((int)this->cs_[idx], 0);
		assert_leq((int)this->cs_[idx], 4);
		return "ACGTN"[(int)this->cs_[idx]];
	}

	/**
	 * Retrieve constant version of element i.
	 */
	const char& operator[](size_t i) const {
		return this->get(i);
	}

	/**
	 * Retrieve constant version of element i.
	 */
	const char& get(size_t i) const {
		assert_lt(i, this->len_);
		assert_leq(this->cs_[i], 4);
		assert_geq(this->cs_[i], 0);
		return this->cs_[i];
	}

	/**
	 * Return the ith character in the window defined by fw, color,
	 * depth and len.
	 */
	char windowGetDna(
		size_t i,
		bool   fw,
		bool   color,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = this->len_;
		assert_lt(i, len);
		assert_leq(len, this->len_ - depth);
		if(fw) return this->cs_[depth+i];
		else   return color ? this->cs_[depth+len-i-1] :
		                      compDna(this->cs_[depth+len-i-1]);
	}

	/**
	 * Fill the given DNA buffer with the substring specified by fw,
	 * color, depth and len.
	 */
	void windowGetDna(
		SDnaStringFixed<S>& buf,
		bool   fw,
		bool   color,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = this->len_;
		assert_leq(len, this->len_ - depth);
		for(size_t i = 0; i < len; i++) {
			buf.append(fw ? this->cs_[depth+i] :
			                (color ? this->cs_[depth+len-i-1] :
			                         compDna(this->cs_[depth+len-i-1])));
		}
	}

	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	virtual const char* toZBuf() const { return this->toZBufXForm("ACGTN"); }
};

/**
 * Encapsulates a fixed-length DNA string with characters encoded as
 * chars.  Only capable of encoding A, C, G, T and N.  The length is
 * specified via the template parameter S.
 */

template<int S = 1024, int M = 2>
class SDnaStringExpandable : public SStringExpandable<char, S, M> {
public:

	explicit SDnaStringExpandable() : SStringExpandable<char, S, M>() { }

	/**
	 * Create an SStringFixed from another SStringFixed.
	 */
	SDnaStringExpandable(const SDnaStringExpandable<S, M>& o) :
		SStringExpandable<char, S, M>(o) { }

	/**
	 * Create an SStringFixed from a C++ basic_string.
	 */
	explicit SDnaStringExpandable(
		const std::basic_string<char>& str,
		bool chars = false,
		bool colors = false) :
		SStringExpandable<char, S, M>()
	{
		if(chars) {
			if(colors) {
				installColors(str);
			} else {
				installChars(str);
			}
		} else {
			install(str);
		}
	}

	/**
	 * Create an SStringFixed from an array and size.
	 */
	explicit SDnaStringExpandable(
		const char* b,
		size_t sz,
		bool chars = false,
		bool colors = false) :
		SStringExpandable<char, S, M>()
	{
		if(chars) {
			if(colors) {
				installColors(b, sz);
			} else {
				installChars(b, sz);
			}
		} else {
			install(b, sz);
		}
	}

	/**
	 * Create an SStringFixed from a zero-terminated string.
	 */
	explicit SDnaStringExpandable(
		const char* b,
		bool chars = false,
		bool colors = false) :
		SStringExpandable<char, S, M>()
	{
		install(b, chars, colors);
	}

	virtual ~SDnaStringExpandable() { } // C++ needs this

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reverse-
	 * complementing them in the process, assuming an encoding where
	 * 0=A, 1=C, 2=G, 3=T, 4=N.
	 */
	void installReverseComp(const char* b, size_t sz) {
		if(this->sz_ < sz) this->expandCopy((sz + S) * M);
		for(size_t i = 0; i < sz; i++) {
			this->cs_[i] = (b[sz-i-1] == 4 ? 4 : b[sz-i-1] ^ 3);
		}
		this->len_ = sz;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reverse-
	 * complementing them in the process, assuming an encoding where
	 * 0=A, 1=C, 2=G, 3=T, 4=N.
	 */
	void installReverseComp(const SDnaStringExpandable<S, M>& b) {
		if(this->sz_ < b.len_) this->expandCopy((b.len_ + S) * M);
		for(size_t i = 0; i < b.len_; i++) {
			this->cs_[i] = (b.cs_[b.len_-i-1] == 4 ? 4 : b.cs_[b.len_-i-1] ^ 3);
		}
		this->len_ = b.len_;
	}

	/**
	 * Either reverse or reverse-complement (depending on "color") this
	 * DNA buffer in-place.
	 */
	void reverseComp(bool color = false) {
		if(color) {
			this->reverse();
		} else {
			for(size_t i = 0; i < (this->len_ >> 1); i++) {
				char tmp1 = (this->cs_[i] == 4 ? 4 : this->cs_[i] ^ 3);
				char tmp2 = (this->cs_[this->len_-i-1] == 4 ? 4 : this->cs_[this->len_-i-1] ^ 3);
				this->cs_[i] = tmp2;
				this->cs_[this->len_-i-1] = tmp1;
			}
			// Do middle element iff there are an odd number
			if((this->len_ & 1) != 0) {
				char tmp = this->cs_[this->len_ >> 1];
				tmp = (tmp == 4 ? 4 : tmp ^ 3);
				this->cs_[this->len_ >> 1] = tmp;
			}
		}
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.
	 */
	virtual void install(
		const char* b,
		bool chars = false,
		bool colors = false)
	{
		if(chars) {
			if(colors) {
				installColors(b, strlen(b));
			} else {
				installChars(b, strlen(b));
			}
		} else {
			install(b, strlen(b));
		}
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.
	 */
	virtual void install(const char* b, size_t sz) {
		if(this->sz_ < sz) this->expandCopy((sz + S) * M);
		memcpy(this->cs_, b, sz);
#ifndef NDEBUG
		for(size_t i = 0; i < sz; i++) {
			assert_range(0, 4, (int)this->cs_[i]);
		}
#endif
		this->len_ = sz;
	}

	/**
	 * Copy buffer 'b' of ASCII DNA characters into normal DNA
	 * characters.
	 */
	virtual void installChars(const char* b, size_t sz) {
		if(this->sz_ < sz) this->expandCopy((sz + S) * M);
		for(size_t i = 0; i < sz; i++) {
			assert_in(toupper(b[i]), "ACGTN-");
			this->cs_[i] = asc2dna[(int)b[i]];
			assert_range(0, 4, (int)this->cs_[i]);
		}
		this->len_ = sz;
	}

	/**
	 * Copy buffer 'b' of ASCII color characters into normal DNA
	 * characters.
	 */
	virtual void installColors(const char* b, size_t sz) {
		if(this->sz_ < sz) this->expandCopy((sz + S) * M);
		for(size_t i = 0; i < sz; i++) {
			assert_in(b[i], "0123.");
			this->cs_[i] = asc2col[(int)b[i]];
			assert_range(0, 4, (int)this->cs_[i]);
		}
		this->len_ = sz;
	}

	/**
	 * Copy C++ string of ASCII DNA characters into normal DNA
	 * characters.
	 */
	virtual void installChars(const std::basic_string<char>& str) {
		installChars(str.c_str(), str.length());
	}

	/**
	 * Copy C++ string of ASCII color characters into normal DNA
	 * characters.
	 */
	virtual void installColors(const std::basic_string<char>& str) {
		installColors(str.c_str(), str.length());
	}

	/**
	 * Set DNA character at index 'idx' to 'c'.
	 */
	void set(int c, size_t idx) {
		assert_lt(idx, this->len_);
		assert_range(0, 4, c);
		this->cs_[idx] = c;
	}

	/**
	 * Append DNA char c.
	 */
	void append(const char& c) {
		if(this->sz_ < this->len_ + 1) {
			this->expandCopy((this->len_ + 1 + S) * M);
		}
		assert_range(0, 4, (int)c);
		this->cs_[this->len_++] = c;
	}

	/**
	 * Set DNA character at index 'idx' to 'c'.
	 */
	void setChar(char c, size_t idx) {
		assert_lt(idx, this->len_);
		assert_in(toupper(c), "ACGTN");
		this->cs_[idx] = asc2dna[(int)c];
	}

	/**
	 * Append DNA character.
	 */
	void appendChar(char c) {
		if(this->sz_ < this->len_ + 1) {
			this->expandCopy((this->len_ + 1 + S) * M);
		}
		assert_in(toupper(c), "ACGTN");
		this->cs_[this->len_++] = asc2dna[(int)c];
	}

	/**
	 * Return DNA character corresponding to element 'idx'.
	 */
	char toChar(size_t idx) const {
		assert_range(0, 4, (int)this->cs_[idx]);
		return "ACGTN"[(int)this->cs_[idx]];
	}

	/**
	 * Retrieve constant version of element i.
	 */
	inline const char& operator[](size_t i) const {
		return this->get(i);
	}

	/**
	 * Retrieve constant version of element i.
	 */
	inline const char& get(size_t i) const {
		assert_lt(i, this->len_);
		assert_range(0, 4, (int)this->cs_[i]);
		return this->cs_[i];
	}

	/**
	 * Return the ith character in the window defined by fw, color,
	 * depth and len.
	 */
	char windowGetDna(
		size_t i,
		bool   fw,
		bool   color,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = this->len_;
		assert_lt(i, len);
		assert_leq(len, this->len_ - depth);
		if(fw) return this->cs_[depth+i];
		else   return color ? this->cs_[depth+len-i-1] :
		                      compDna(this->cs_[depth+len-i-1]);
	}

	/**
	 * Fill the given DNA buffer with the substring specified by fw,
	 * color, depth and len.
	 */
	void windowGetDna(
		SDnaStringExpandable<S, M>& buf,
		bool   fw,
		bool   color,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = this->len_;
		assert_leq(len, this->len_ - depth);
		for(size_t i = 0; i < len; i++) {
			buf.append(fw ? this->cs_[depth+i] :
			                (color ? this->cs_[depth+len-i-1] :
			                         compDna(this->cs_[depth+len-i-1])));
		}
	}

	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	virtual const char* toZBuf() const { return this->toZBufXForm("ACGTN"); }
};

/**
 * Encapsulates an expandable DNA string with characters encoded as
 * char-sized masks.  Encodes A, C, G, T, and all IUPAC, as well as the
 * empty mask indicating "matches nothing."
 */
template<int S = 16, int M = 2>
class SDnaMaskString : public SStringExpandable<char, S, M> {
public:

	explicit SDnaMaskString() : SStringExpandable<char, S, M>() { }

	/**
	 * Create an SStringFixed from another SStringFixed.
	 */
	SDnaMaskString(const SDnaMaskString<S, M>& o) :
		SStringExpandable<char, S, M>(o) { }

	/**
	 * Create an SStringFixed from a C++ basic_string.
	 */
	explicit SDnaMaskString(const std::basic_string<char>& str) :
		SStringExpandable<char, S, M>(str) { }

	/**
	 * Create an SStringFixed from an array and size.
	 */
	explicit SDnaMaskString(const char* b, size_t sz) :
		SStringExpandable<char, S, M>(b, sz) { }

	/**
	 * Create an SStringFixed from a zero-terminated string.
	 */
	explicit SDnaMaskString(const char* b, bool chars = false) :
		SStringExpandable<char, S, M>()
	{
		if(chars) {
			installChars(b, strlen(b));
		} else {
			install(b, strlen(b));
		}
	}

	virtual ~SDnaMaskString() { } // C++ needs this

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reverse-
	 * complementing them in the process, assuming an encoding where
	 * 0=A, 1=C, 2=G, 3=T, 4=N.
	 */
	void installReverseComp(const char* b, size_t sz) {
		while(this->sz_ < sz) {
			this->expandNoCopy((sz + S) * M);
		}
		for(size_t i = 0; i < sz; i++) {
			this->cs_[i] = maskcomp[(int)b[sz-i-1]];
		}
		this->len_ = sz;
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string, reverse-
	 * complementing them in the process, assuming an encoding where
	 * 0=A, 1=C, 2=G, 3=T, 4=N.
	 */
	void installReverseComp(const SDnaMaskString<S, M>& b) {
		while(this->sz_ < b.len_) {
			this->expandNoCopy((b.len_ + S) * M);
		}
		for(size_t i = 0; i < b.len_; i++) {
			this->cs_[i] = maskcomp[(int)b.cs_[b.len_-i-1]];
		}
		this->len_ = b.len_;
	}

	/**
	 * Either reverse or reverse-complement (depending on "color") this
	 * DNA buffer in-place.
	 */
	void reverseComp(bool color = false) {
		if(color) {
			this->reverse();
		} else {
			for(size_t i = 0; i < (this->len_ >> 1); i++) {
				char tmp1 = maskcomp[(int)this->cs_[i]];
				char tmp2 = maskcomp[(int)this->cs_[this->len_-i-1]];
				this->cs_[i] = tmp2;
				this->cs_[this->len_-i-1] = tmp1;
			}
			// Do middle element iff there are an odd number
			if((this->len_ & 1) != 0) {
				char tmp = this->cs_[this->len_ >> 1];
				tmp = maskcomp[(int)tmp];
				this->cs_[this->len_ >> 1] = tmp;
			}
		}
	}

	/**
	 * Copy 'sz' bytes from buffer 'b' into this string.
	 */
	virtual void install(const char* b, size_t sz) {
		while(this->sz_ < sz) {
			this->expandNoCopy((sz + S) * M);
		}
		memcpy(this->cs_, b, sz);
#ifndef NDEBUG
		for(size_t i = 0; i < sz; i++) {
			assert_range((int)this->cs_[i], 0, 15);
		}
#endif
		this->len_ = sz;
	}

	/**
	 * Copy buffer 'b' of ASCII DNA characters into DNA masks.
	 */
	virtual void installChars(const char* b, size_t sz) {
		while(this->sz_ < sz) {
			this->expandNoCopy((sz + S) * M);
		}
		for(size_t i = 0; i < sz; i++) {
			assert_in(b[i], iupacs);
			this->cs_[i] = asc2dnamask[(int)b[i]];
			assert_range((int)this->cs_[i], 0, 15);
		}
		this->len_ = sz;
	}

	/**
	 * Copy C++ string of ASCII DNA characters into normal DNA
	 * characters.
	 */
	virtual void installChars(const std::basic_string<char>& str) {
		installChars(str.c_str(), str.length());
	}

	/**
	 * Set DNA character at index 'idx' to 'c'.
	 */
	void set(int c, size_t idx) {
		assert_lt(idx, this->len_);
		assert_range(c, 0, 15);
		this->cs_[idx] = c;
	}

	/**
	 * Append DNA char c.
	 */
	void append(const char& c) {
		while(this->sz_ < this->len_+1) {
			this->expandNoCopy((this->len_ + 1 + S) * M);
		}
		assert_range((int)c, 0, 15);
		this->cs_[this->len_++] = c;
	}

	/**
	 * Set DNA character at index 'idx' to 'c'.
	 */
	void setChar(char c, size_t idx) {
		assert_lt(idx, this->len_);
		assert_in(toupper(c), iupacs);
		this->cs_[idx] = asc2dnamask[(int)c];
	}

	/**
	 * Append DNA character.
	 */
	void appendChar(char c) {
		while(this->sz_ < this->len_+1) {
			expandNoCopy((this->len_ + 1 + S) * M);
		}
		assert_in(toupper(c), iupacs);
		this->cs_[this->len_++] = asc2dnamask[(int)c];
	}

	/**
	 * Return DNA character corresponding to element 'idx'.
	 */
	char toChar(size_t idx) const {
		assert_range((int)this->cs_[idx], 0, 15);
		return mask2iupac[(int)this->cs_[idx]];
	}

	/**
	 * Retrieve constant version of element i.
	 */
	const char& operator[](size_t i) const {
		return this->get(i);
	}

	/**
	 * Retrieve mutable version of element i.
	 */
	char& operator[](size_t i) {
		return this->get(i);
	}

	/**
	 * Retrieve constant version of element i.
	 */
	const char& get(size_t i) const {
		assert_lt(i, this->len_);
		assert_range((int)this->cs_[i], 0, 15);
		return this->cs_[i];
	}

	/**
	 * Retrieve mutable version of element i.
	 */
	char& get(size_t i) {
		assert_lt(i, this->len_);
		assert_range((int)this->cs_[i], 0, 15);
		return this->cs_[i];
	}

	/**
	 * Return the ith character in the window defined by fw, color,
	 * depth and len.
	 */
	char windowGetDna(
		size_t i,
		bool   fw,
		bool   color,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = this->len_;
		assert_lt(i, len);
		assert_leq(len, this->len_ - depth);
		if(fw) return this->cs_[depth+i];
		else   return color ? this->cs_[depth+len-i-1] :
		                      maskcomp[this->cs_[depth+len-i-1]];
	}

	/**
	 * Fill the given DNA buffer with the substring specified by fw,
	 * color, depth and len.
	 */
	void windowGetDna(
		SDnaStringFixed<S>& buf,
		bool   fw,
		bool   color,
		size_t depth = 0,
		size_t len = 0) const
	{
		if(len == 0) len = this->len_;
		assert_leq(len, this->len_ - depth);
		for(size_t i = 0; i < len; i++) {
			buf.append(fw ? this->cs_[depth+i] :
			                (color ? this->cs_[depth+len-i-1] :
			                         maskcomp[this->cs_[depth+len-i-1]]));
		}
	}

	/**
	 * Sample a random substring of the given length from this DNA
	 * string and install the result in 'dst'.
	 */
	template<typename T>
	void randSubstr(
		RandomSource& rnd,  // pseudo-random generator
		T& dst,             // put sampled substring here
		size_t len,         // length of substring to extract
		bool watson = true, // true -> possibly extract from Watson strand
		bool crick = true)  // true -> possibly extract from Crick strand
	{
		assert(watson || crick);
		assert_geq(this->len_, len);
		size_t poss = this->len_ - len + 1;
		assert_gt(poss, 0);
		uint32_t rndoff = (uint32_t)(rnd.nextU32() % poss);
		bool fw;
		if     (watson && !crick) fw = true;
		else if(!watson && crick) fw = false;
		else {
			fw = rnd.nextBool();
		}
		if(fw) {
			// Install Watson substring
			for(size_t i = 0; i < len; i++) {
				dst[i] = this->cs_[i + rndoff];
			}
		} else {
			// Install Crick substring
			for(size_t i = 0; i < len; i++) {
				dst[i] = maskcomp[(int)this->cs_[i + rndoff + (len - i - 1)]];
			}
		}
	}

	/**
	 * Put a terminator in the 'len_'th element and then return a
	 * pointer to the buffer.  Useful for printing.
	 */
	virtual const char* toZBuf() const { return this->toZBufXForm(iupacs); }
};

typedef SStringExpandable<char, 1024, 2> BTString;
typedef SDnaStringExpandable<1024, 2>    BTDnaString;
typedef SDnaMaskString<32, 2>            BTDnaMask;

#endif /* SSTRING_H_ */
