monoseq is a Python library for pretty-printing DNA and protein sequences
using a monospace font. It also provides a simple command line interface.
Sequences are pretty-printed in the traditional way using blocks of letters
where each line is prefixed with the sequence position. User-specified regions
are highlighted and the output format can be HTML or plaintext with optional
styling using ANSI escape codes for use in a terminal.
The monoseq source code is hosted on GitHub. Supported Python versions for
running monoseq are 2.7, 3.2, 3.3 and PyPy (unit tests are run
automatically on these platforms using the Travis CI service). monoseq can be
installed either via the Python Package Index (PyPI) or from the source code.
By default, sequences are printed in blocks of 10 letters, 6 blocks per
line. This can be customized with the block_length and blocks_per_line
arguments:
As we’ll see in the next section, certain parts of the sequence can be
annotated for highlighting. For this to work, we need to specify another
output format than the default PlaintextFormat.
AnsiFormat adds ANSI escape codes for use in a terminal.
HtmlFormat adds HTML tags for inclusion in an HTML document.
(And if this doesn’t satisfy our needs, we can define custom output formats by
implementing Format.)
Formats are specified with the format argument of the
pprint_sequence() function. For example, this is the same example
pretty-printed with HtmlFormat:
As you can see, HtmlFormat wraps the sequence positions in <span>
tags with a class attribute value of monoseq-margin. This allows us to
add custom styling to these numbers with a CSS stylesheet.
Note
In an HTML document, include the pretty-printed sequence within
<pre> and </pre>. This preserves all whitespace and automatically
selects a monospace font.
Subsequences can be highlighted in the pretty-printed sequence by specifying
their positions. Such a specification is called an annotation. Several
annotations can be provided and each of them will be highlighted in a distinct
style (e.g., the first annotation is colored red and the second is printed in
bold).
Let’s assume our analysis shows positions 12 through 37 and 223 through 247 to
be highly conserved between species. Of course, we want to annotate our
sequence with this knowledge:
Regions are defined as in slicing notation, so zero-based and
open-ended.
Just for lack of imagination, we also want to make it clear where every 12th
nucleotide is in our sequence. We can do this by defining a second
annotation, which is printed in bold by AnsiFormat:
AnsiFormat supports up to three annotation levels and the third one
is printed underlined. So if the middle third of the sequence would be our
primary concern, we could underline it as follows:
The HtmlFormat output format supports up to 10 annotation levels, but
how to style them is up to the user. All monoseq does is add <span>
tags around annotations with class attribute values of
monoseq-annotation-{i}, where {i} is the annotation level starting
from 0.
Here are some example CSS rules for styling 4 annotation levels:
Simple pretty-printing of sequences on the command line is done with the
monoseq command. It reads one or more sequences from a file or from
standard input and pretty-prints them to standard output. The input can be a
raw sequence, or any number of sequences in FASTA format.
Subsequences can be specified for annotation with the -a argument followed
by the first and the last position of the subsequence, both one-based. For
example, to annotate the first 10 bases and the 17th base, you would add -a110-a1717.
In addition, annotation is read from the BED track specified with the -e
argument. If the input is a raw sequence, only the first chromosome is used
from the BED track. If the input is a FASTA file, chromosomes are matched with
record names.
stop (int) – End point (not included) of the range (similar to the stop
argument of the built-in range() function).
annotations (list) – For each annotation level, a list of (start, stop)
pairs defining an annotated region.
Returns:
Partitioning of the range as (start, stop, levels) tuples
defining a region with a set of annotation levels.
Return type:
list
All regions (start, stop) are defined as in slicing notation, so
zero-based and stop is not included.
The annotations argument is a list of annotations. An annotation is a
list of regions as (start, stop) tuples. The level of each annotation
is its index in annotations.
Annotation regions can overlap (overlap within one level is ignored) and
do not need to be sorted.
All regions (start, stop) are defined as in slicing notation, so
zero-based and stop is not included.
The annotations argument is a list of annotations. An annotation is a
list of regions as (start, stop) tuples. The level of each annotation
is its index in annotations.
Annotation regions can overlap (overlap within one level is ignored) and
do not need to be sorted.
The number of annotation levels supported depends on format.
HtmlFormat supports 10 levels, AnsiFormat supports 3
levels and annotations are ignored completely with
PlaintextFormat.
Pretty-printed sequence object that’s displayed nicely in the IPython
Notebook.
Parameters:
style (str) – Custom CSS as a format string, where a selector for the
top-level <pre> element is substituted for {selector}. See
DEFAULT_STYLE for an example.
Contributions to monoseq are very welcome! They can be feature requests,
bug reports, bug fixes, unit tests, documentation updates, or anything els you
may come up with.
A normal version number takes the form X.Y.Z where X is the major version, Y
is the minor version, and Z is the patch version. Development versions take
the form X.Y.Z.dev where X.Y.Z is the closest future release version.
Note that this scheme is not 100% compatible with SemVer which would
require X.Y.Z-dev instead of X.Y.Z.dev but compatibility with setuptools
is more important for us. Other than that, version semantics are as described
by SemVer.
Releases are published at PyPI and
available from the GitHub git repository as tags.
Make sure the section in the CHANGES file for this release is
complete and there are no uncommitted changes.
Note
Commits since release X.Y.Z can be listed with gitlogvX.Y.Z.. for
quick inspection.
Update the CHANGES file to state the current date for this release
and edit monoseq/__init__.py by updating __date__ and removing the
dev value from __version_info__.
Commit and tag the version update:
git commit -am 'Bump version to X.Y.Z'
git tag -a 'vX.Y.Z'
git push --tags
Upload the package to PyPI:
python setup.py sdist upload
Add a new entry at the top of the CHANGES file like this:
Version X.Y.Z+1
---------------
Release date to be decided.
Increment the patch version and add a dev value to __version_info__
in monoseq/__init__.py and commit these changes:
monoseq is licensed under the MIT License, meaning you can do whatever you
want with it as long as all copies include these license terms. The full
license text can be found below.
Copyright (c) 2013 by Martijn Vermaat and contributors (see AUTHORS.rst
for details).
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.
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PK -G` ` * monoseq-latest/_static/underscore-1.3.1.js// Underscore.js 1.3.1
// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore is freely distributable under the MIT license.
// Portions of Underscore are inspired or borrowed from Prototype,
// Oliver Steele's Functional, and John Resig's Micro-Templating.
// For all details and documentation:
// http://documentcloud.github.com/underscore
(function() {
// Baseline setup
// --------------
// Establish the root object, `window` in the browser, or `global` on the server.
var root = this;
// Save the previous value of the `_` variable.
var previousUnderscore = root._;
// Establish the object that gets returned to break out of a loop iteration.
var breaker = {};
// Save bytes in the minified (but not gzipped) version:
var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
// Create quick reference variables for speed access to core prototypes.
var slice = ArrayProto.slice,
unshift = ArrayProto.unshift,
toString = ObjProto.toString,
hasOwnProperty = ObjProto.hasOwnProperty;
// All **ECMAScript 5** native function implementations that we hope to use
// are declared here.
var
nativeForEach = ArrayProto.forEach,
nativeMap = ArrayProto.map,
nativeReduce = ArrayProto.reduce,
nativeReduceRight = ArrayProto.reduceRight,
nativeFilter = ArrayProto.filter,
nativeEvery = ArrayProto.every,
nativeSome = ArrayProto.some,
nativeIndexOf = ArrayProto.indexOf,
nativeLastIndexOf = ArrayProto.lastIndexOf,
nativeIsArray = Array.isArray,
nativeKeys = Object.keys,
nativeBind = FuncProto.bind;
// Create a safe reference to the Underscore object for use below.
var _ = function(obj) { return new wrapper(obj); };
// Export the Underscore object for **Node.js**, with
// backwards-compatibility for the old `require()` API. If we're in
// the browser, add `_` as a global object via a string identifier,
// for Closure Compiler "advanced" mode.
if (typeof exports !== 'undefined') {
if (typeof module !== 'undefined' && module.exports) {
exports = module.exports = _;
}
exports._ = _;
} else {
root['_'] = _;
}
// Current version.
_.VERSION = '1.3.1';
// Collection Functions
// --------------------
// The cornerstone, an `each` implementation, aka `forEach`.
// Handles objects with the built-in `forEach`, arrays, and raw objects.
// Delegates to **ECMAScript 5**'s native `forEach` if available.
var each = _.each = _.forEach = function(obj, iterator, context) {
if (obj == null) return;
if (nativeForEach && obj.forEach === nativeForEach) {
obj.forEach(iterator, context);
} else if (obj.length === +obj.length) {
for (var i = 0, l = obj.length; i < l; i++) {
if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
}
} else {
for (var key in obj) {
if (_.has(obj, key)) {
if (iterator.call(context, obj[key], key, obj) === breaker) return;
}
}
}
};
// Return the results of applying the iterator to each element.
// Delegates to **ECMAScript 5**'s native `map` if available.
_.map = _.collect = function(obj, iterator, context) {
var results = [];
if (obj == null) return results;
if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
each(obj, function(value, index, list) {
results[results.length] = iterator.call(context, value, index, list);
});
if (obj.length === +obj.length) results.length = obj.length;
return results;
};
// **Reduce** builds up a single result from a list of values, aka `inject`,
// or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
_.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
var initial = arguments.length > 2;
if (obj == null) obj = [];
if (nativeReduce && obj.reduce === nativeReduce) {
if (context) iterator = _.bind(iterator, context);
return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
}
each(obj, function(value, index, list) {
if (!initial) {
memo = value;
initial = true;
} else {
memo = iterator.call(context, memo, value, index, list);
}
});
if (!initial) throw new TypeError('Reduce of empty array with no initial value');
return memo;
};
// The right-associative version of reduce, also known as `foldr`.
// Delegates to **ECMAScript 5**'s native `reduceRight` if available.
_.reduceRight = _.foldr = function(obj, iterator, memo, context) {
var initial = arguments.length > 2;
if (obj == null) obj = [];
if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
if (context) iterator = _.bind(iterator, context);
return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
}
var reversed = _.toArray(obj).reverse();
if (context && !initial) iterator = _.bind(iterator, context);
return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
};
// Return the first value which passes a truth test. Aliased as `detect`.
_.find = _.detect = function(obj, iterator, context) {
var result;
any(obj, function(value, index, list) {
if (iterator.call(context, value, index, list)) {
result = value;
return true;
}
});
return result;
};
// Return all the elements that pass a truth test.
// Delegates to **ECMAScript 5**'s native `filter` if available.
// Aliased as `select`.
_.filter = _.select = function(obj, iterator, context) {
var results = [];
if (obj == null) return results;
if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
each(obj, function(value, index, list) {
if (iterator.call(context, value, index, list)) results[results.length] = value;
});
return results;
};
// Return all the elements for which a truth test fails.
_.reject = function(obj, iterator, context) {
var results = [];
if (obj == null) return results;
each(obj, function(value, index, list) {
if (!iterator.call(context, value, index, list)) results[results.length] = value;
});
return results;
};
// Determine whether all of the elements match a truth test.
// Delegates to **ECMAScript 5**'s native `every` if available.
// Aliased as `all`.
_.every = _.all = function(obj, iterator, context) {
var result = true;
if (obj == null) return result;
if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
each(obj, function(value, index, list) {
if (!(result = result && iterator.call(context, value, index, list))) return breaker;
});
return result;
};
// Determine if at least one element in the object matches a truth test.
// Delegates to **ECMAScript 5**'s native `some` if available.
// Aliased as `any`.
var any = _.some = _.any = function(obj, iterator, context) {
iterator || (iterator = _.identity);
var result = false;
if (obj == null) return result;
if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
each(obj, function(value, index, list) {
if (result || (result = iterator.call(context, value, index, list))) return breaker;
});
return !!result;
};
// Determine if a given value is included in the array or object using `===`.
// Aliased as `contains`.
_.include = _.contains = function(obj, target) {
var found = false;
if (obj == null) return found;
if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
found = any(obj, function(value) {
return value === target;
});
return found;
};
// Invoke a method (with arguments) on every item in a collection.
_.invoke = function(obj, method) {
var args = slice.call(arguments, 2);
return _.map(obj, function(value) {
return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
});
};
// Convenience version of a common use case of `map`: fetching a property.
_.pluck = function(obj, key) {
return _.map(obj, function(value){ return value[key]; });
};
// Return the maximum element or (element-based computation).
_.max = function(obj, iterator, context) {
if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
if (!iterator && _.isEmpty(obj)) return -Infinity;
var result = {computed : -Infinity};
each(obj, function(value, index, list) {
var computed = iterator ? iterator.call(context, value, index, list) : value;
computed >= result.computed && (result = {value : value, computed : computed});
});
return result.value;
};
// Return the minimum element (or element-based computation).
_.min = function(obj, iterator, context) {
if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
if (!iterator && _.isEmpty(obj)) return Infinity;
var result = {computed : Infinity};
each(obj, function(value, index, list) {
var computed = iterator ? iterator.call(context, value, index, list) : value;
computed < result.computed && (result = {value : value, computed : computed});
});
return result.value;
};
// Shuffle an array.
_.shuffle = function(obj) {
var shuffled = [], rand;
each(obj, function(value, index, list) {
if (index == 0) {
shuffled[0] = value;
} else {
rand = Math.floor(Math.random() * (index + 1));
shuffled[index] = shuffled[rand];
shuffled[rand] = value;
}
});
return shuffled;
};
// Sort the object's values by a criterion produced by an iterator.
_.sortBy = function(obj, iterator, context) {
return _.pluck(_.map(obj, function(value, index, list) {
return {
value : value,
criteria : iterator.call(context, value, index, list)
};
}).sort(function(left, right) {
var a = left.criteria, b = right.criteria;
return a < b ? -1 : a > b ? 1 : 0;
}), 'value');
};
// Groups the object's values by a criterion. Pass either a string attribute
// to group by, or a function that returns the criterion.
_.groupBy = function(obj, val) {
var result = {};
var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
each(obj, function(value, index) {
var key = iterator(value, index);
(result[key] || (result[key] = [])).push(value);
});
return result;
};
// Use a comparator function to figure out at what index an object should
// be inserted so as to maintain order. Uses binary search.
_.sortedIndex = function(array, obj, iterator) {
iterator || (iterator = _.identity);
var low = 0, high = array.length;
while (low < high) {
var mid = (low + high) >> 1;
iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
}
return low;
};
// Safely convert anything iterable into a real, live array.
_.toArray = function(iterable) {
if (!iterable) return [];
if (iterable.toArray) return iterable.toArray();
if (_.isArray(iterable)) return slice.call(iterable);
if (_.isArguments(iterable)) return slice.call(iterable);
return _.values(iterable);
};
// Return the number of elements in an object.
_.size = function(obj) {
return _.toArray(obj).length;
};
// Array Functions
// ---------------
// Get the first element of an array. Passing **n** will return the first N
// values in the array. Aliased as `head`. The **guard** check allows it to work
// with `_.map`.
_.first = _.head = function(array, n, guard) {
return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
};
// Returns everything but the last entry of the array. Especcialy useful on
// the arguments object. Passing **n** will return all the values in
// the array, excluding the last N. The **guard** check allows it to work with
// `_.map`.
_.initial = function(array, n, guard) {
return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
};
// Get the last element of an array. Passing **n** will return the last N
// values in the array. The **guard** check allows it to work with `_.map`.
_.last = function(array, n, guard) {
if ((n != null) && !guard) {
return slice.call(array, Math.max(array.length - n, 0));
} else {
return array[array.length - 1];
}
};
// Returns everything but the first entry of the array. Aliased as `tail`.
// Especially useful on the arguments object. Passing an **index** will return
// the rest of the values in the array from that index onward. The **guard**
// check allows it to work with `_.map`.
_.rest = _.tail = function(array, index, guard) {
return slice.call(array, (index == null) || guard ? 1 : index);
};
// Trim out all falsy values from an array.
_.compact = function(array) {
return _.filter(array, function(value){ return !!value; });
};
// Return a completely flattened version of an array.
_.flatten = function(array, shallow) {
return _.reduce(array, function(memo, value) {
if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
memo[memo.length] = value;
return memo;
}, []);
};
// Return a version of the array that does not contain the specified value(s).
_.without = function(array) {
return _.difference(array, slice.call(arguments, 1));
};
// Produce a duplicate-free version of the array. If the array has already
// been sorted, you have the option of using a faster algorithm.
// Aliased as `unique`.
_.uniq = _.unique = function(array, isSorted, iterator) {
var initial = iterator ? _.map(array, iterator) : array;
var result = [];
_.reduce(initial, function(memo, el, i) {
if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
memo[memo.length] = el;
result[result.length] = array[i];
}
return memo;
}, []);
return result;
};
// Produce an array that contains the union: each distinct element from all of
// the passed-in arrays.
_.union = function() {
return _.uniq(_.flatten(arguments, true));
};
// Produce an array that contains every item shared between all the
// passed-in arrays. (Aliased as "intersect" for back-compat.)
_.intersection = _.intersect = function(array) {
var rest = slice.call(arguments, 1);
return _.filter(_.uniq(array), function(item) {
return _.every(rest, function(other) {
return _.indexOf(other, item) >= 0;
});
});
};
// Take the difference between one array and a number of other arrays.
// Only the elements present in just the first array will remain.
_.difference = function(array) {
var rest = _.flatten(slice.call(arguments, 1));
return _.filter(array, function(value){ return !_.include(rest, value); });
};
// Zip together multiple lists into a single array -- elements that share
// an index go together.
_.zip = function() {
var args = slice.call(arguments);
var length = _.max(_.pluck(args, 'length'));
var results = new Array(length);
for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
return results;
};
// If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
// we need this function. Return the position of the first occurrence of an
// item in an array, or -1 if the item is not included in the array.
// Delegates to **ECMAScript 5**'s native `indexOf` if available.
// If the array is large and already in sort order, pass `true`
// for **isSorted** to use binary search.
_.indexOf = function(array, item, isSorted) {
if (array == null) return -1;
var i, l;
if (isSorted) {
i = _.sortedIndex(array, item);
return array[i] === item ? i : -1;
}
if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
return -1;
};
// Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
_.lastIndexOf = function(array, item) {
if (array == null) return -1;
if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
var i = array.length;
while (i--) if (i in array && array[i] === item) return i;
return -1;
};
// Generate an integer Array containing an arithmetic progression. A port of
// the native Python `range()` function. See
// [the Python documentation](http://docs.python.org/library/functions.html#range).
_.range = function(start, stop, step) {
if (arguments.length <= 1) {
stop = start || 0;
start = 0;
}
step = arguments[2] || 1;
var len = Math.max(Math.ceil((stop - start) / step), 0);
var idx = 0;
var range = new Array(len);
while(idx < len) {
range[idx++] = start;
start += step;
}
return range;
};
// Function (ahem) Functions
// ------------------
// Reusable constructor function for prototype setting.
var ctor = function(){};
// Create a function bound to a given object (assigning `this`, and arguments,
// optionally). Binding with arguments is also known as `curry`.
// Delegates to **ECMAScript 5**'s native `Function.bind` if available.
// We check for `func.bind` first, to fail fast when `func` is undefined.
_.bind = function bind(func, context) {
var bound, args;
if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
if (!_.isFunction(func)) throw new TypeError;
args = slice.call(arguments, 2);
return bound = function() {
if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
ctor.prototype = func.prototype;
var self = new ctor;
var result = func.apply(self, args.concat(slice.call(arguments)));
if (Object(result) === result) return result;
return self;
};
};
// Bind all of an object's methods to that object. Useful for ensuring that
// all callbacks defined on an object belong to it.
_.bindAll = function(obj) {
var funcs = slice.call(arguments, 1);
if (funcs.length == 0) funcs = _.functions(obj);
each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
return obj;
};
// Memoize an expensive function by storing its results.
_.memoize = function(func, hasher) {
var memo = {};
hasher || (hasher = _.identity);
return function() {
var key = hasher.apply(this, arguments);
return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
};
};
// Delays a function for the given number of milliseconds, and then calls
// it with the arguments supplied.
_.delay = function(func, wait) {
var args = slice.call(arguments, 2);
return setTimeout(function(){ return func.apply(func, args); }, wait);
};
// Defers a function, scheduling it to run after the current call stack has
// cleared.
_.defer = function(func) {
return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
};
// Returns a function, that, when invoked, will only be triggered at most once
// during a given window of time.
_.throttle = function(func, wait) {
var context, args, timeout, throttling, more;
var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
return function() {
context = this; args = arguments;
var later = function() {
timeout = null;
if (more) func.apply(context, args);
whenDone();
};
if (!timeout) timeout = setTimeout(later, wait);
if (throttling) {
more = true;
} else {
func.apply(context, args);
}
whenDone();
throttling = true;
};
};
// Returns a function, that, as long as it continues to be invoked, will not
// be triggered. The function will be called after it stops being called for
// N milliseconds.
_.debounce = function(func, wait) {
var timeout;
return function() {
var context = this, args = arguments;
var later = function() {
timeout = null;
func.apply(context, args);
};
clearTimeout(timeout);
timeout = setTimeout(later, wait);
};
};
// Returns a function that will be executed at most one time, no matter how
// often you call it. Useful for lazy initialization.
_.once = function(func) {
var ran = false, memo;
return function() {
if (ran) return memo;
ran = true;
return memo = func.apply(this, arguments);
};
};
// Returns the first function passed as an argument to the second,
// allowing you to adjust arguments, run code before and after, and
// conditionally execute the original function.
_.wrap = function(func, wrapper) {
return function() {
var args = [func].concat(slice.call(arguments, 0));
return wrapper.apply(this, args);
};
};
// Returns a function that is the composition of a list of functions, each
// consuming the return value of the function that follows.
_.compose = function() {
var funcs = arguments;
return function() {
var args = arguments;
for (var i = funcs.length - 1; i >= 0; i--) {
args = [funcs[i].apply(this, args)];
}
return args[0];
};
};
// Returns a function that will only be executed after being called N times.
_.after = function(times, func) {
if (times <= 0) return func();
return function() {
if (--times < 1) { return func.apply(this, arguments); }
};
};
// Object Functions
// ----------------
// Retrieve the names of an object's properties.
// Delegates to **ECMAScript 5**'s native `Object.keys`
_.keys = nativeKeys || function(obj) {
if (obj !== Object(obj)) throw new TypeError('Invalid object');
var keys = [];
for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
return keys;
};
// Retrieve the values of an object's properties.
_.values = function(obj) {
return _.map(obj, _.identity);
};
// Return a sorted list of the function names available on the object.
// Aliased as `methods`
_.functions = _.methods = function(obj) {
var names = [];
for (var key in obj) {
if (_.isFunction(obj[key])) names.push(key);
}
return names.sort();
};
// Extend a given object with all the properties in passed-in object(s).
_.extend = function(obj) {
each(slice.call(arguments, 1), function(source) {
for (var prop in source) {
obj[prop] = source[prop];
}
});
return obj;
};
// Fill in a given object with default properties.
_.defaults = function(obj) {
each(slice.call(arguments, 1), function(source) {
for (var prop in source) {
if (obj[prop] == null) obj[prop] = source[prop];
}
});
return obj;
};
// Create a (shallow-cloned) duplicate of an object.
_.clone = function(obj) {
if (!_.isObject(obj)) return obj;
return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
};
// Invokes interceptor with the obj, and then returns obj.
// The primary purpose of this method is to "tap into" a method chain, in
// order to perform operations on intermediate results within the chain.
_.tap = function(obj, interceptor) {
interceptor(obj);
return obj;
};
// Internal recursive comparison function.
function eq(a, b, stack) {
// Identical objects are equal. `0 === -0`, but they aren't identical.
// See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
if (a === b) return a !== 0 || 1 / a == 1 / b;
// A strict comparison is necessary because `null == undefined`.
if (a == null || b == null) return a === b;
// Unwrap any wrapped objects.
if (a._chain) a = a._wrapped;
if (b._chain) b = b._wrapped;
// Invoke a custom `isEqual` method if one is provided.
if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
// Compare `[[Class]]` names.
var className = toString.call(a);
if (className != toString.call(b)) return false;
switch (className) {
// Strings, numbers, dates, and booleans are compared by value.
case '[object String]':
// Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
// equivalent to `new String("5")`.
return a == String(b);
case '[object Number]':
// `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
// other numeric values.
return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
case '[object Date]':
case '[object Boolean]':
// Coerce dates and booleans to numeric primitive values. Dates are compared by their
// millisecond representations. Note that invalid dates with millisecond representations
// of `NaN` are not equivalent.
return +a == +b;
// RegExps are compared by their source patterns and flags.
case '[object RegExp]':
return a.source == b.source &&
a.global == b.global &&
a.multiline == b.multiline &&
a.ignoreCase == b.ignoreCase;
}
if (typeof a != 'object' || typeof b != 'object') return false;
// Assume equality for cyclic structures. The algorithm for detecting cyclic
// structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
var length = stack.length;
while (length--) {
// Linear search. Performance is inversely proportional to the number of
// unique nested structures.
if (stack[length] == a) return true;
}
// Add the first object to the stack of traversed objects.
stack.push(a);
var size = 0, result = true;
// Recursively compare objects and arrays.
if (className == '[object Array]') {
// Compare array lengths to determine if a deep comparison is necessary.
size = a.length;
result = size == b.length;
if (result) {
// Deep compare the contents, ignoring non-numeric properties.
while (size--) {
// Ensure commutative equality for sparse arrays.
if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
}
}
} else {
// Objects with different constructors are not equivalent.
if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
// Deep compare objects.
for (var key in a) {
if (_.has(a, key)) {
// Count the expected number of properties.
size++;
// Deep compare each member.
if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
}
}
// Ensure that both objects contain the same number of properties.
if (result) {
for (key in b) {
if (_.has(b, key) && !(size--)) break;
}
result = !size;
}
}
// Remove the first object from the stack of traversed objects.
stack.pop();
return result;
}
// Perform a deep comparison to check if two objects are equal.
_.isEqual = function(a, b) {
return eq(a, b, []);
};
// Is a given array, string, or object empty?
// An "empty" object has no enumerable own-properties.
_.isEmpty = function(obj) {
if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
for (var key in obj) if (_.has(obj, key)) return false;
return true;
};
// Is a given value a DOM element?
_.isElement = function(obj) {
return !!(obj && obj.nodeType == 1);
};
// Is a given value an array?
// Delegates to ECMA5's native Array.isArray
_.isArray = nativeIsArray || function(obj) {
return toString.call(obj) == '[object Array]';
};
// Is a given variable an object?
_.isObject = function(obj) {
return obj === Object(obj);
};
// Is a given variable an arguments object?
_.isArguments = function(obj) {
return toString.call(obj) == '[object Arguments]';
};
if (!_.isArguments(arguments)) {
_.isArguments = function(obj) {
return !!(obj && _.has(obj, 'callee'));
};
}
// Is a given value a function?
_.isFunction = function(obj) {
return toString.call(obj) == '[object Function]';
};
// Is a given value a string?
_.isString = function(obj) {
return toString.call(obj) == '[object String]';
};
// Is a given value a number?
_.isNumber = function(obj) {
return toString.call(obj) == '[object Number]';
};
// Is the given value `NaN`?
_.isNaN = function(obj) {
// `NaN` is the only value for which `===` is not reflexive.
return obj !== obj;
};
// Is a given value a boolean?
_.isBoolean = function(obj) {
return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
};
// Is a given value a date?
_.isDate = function(obj) {
return toString.call(obj) == '[object Date]';
};
// Is the given value a regular expression?
_.isRegExp = function(obj) {
return toString.call(obj) == '[object RegExp]';
};
// Is a given value equal to null?
_.isNull = function(obj) {
return obj === null;
};
// Is a given variable undefined?
_.isUndefined = function(obj) {
return obj === void 0;
};
// Has own property?
_.has = function(obj, key) {
return hasOwnProperty.call(obj, key);
};
// Utility Functions
// -----------------
// Run Underscore.js in *noConflict* mode, returning the `_` variable to its
// previous owner. Returns a reference to the Underscore object.
_.noConflict = function() {
root._ = previousUnderscore;
return this;
};
// Keep the identity function around for default iterators.
_.identity = function(value) {
return value;
};
// Run a function **n** times.
_.times = function (n, iterator, context) {
for (var i = 0; i < n; i++) iterator.call(context, i);
};
// Escape a string for HTML interpolation.
_.escape = function(string) {
return (''+string).replace(/&/g, '&').replace(//g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/');
};
// Add your own custom functions to the Underscore object, ensuring that
// they're correctly added to the OOP wrapper as well.
_.mixin = function(obj) {
each(_.functions(obj), function(name){
addToWrapper(name, _[name] = obj[name]);
});
};
// Generate a unique integer id (unique within the entire client session).
// Useful for temporary DOM ids.
var idCounter = 0;
_.uniqueId = function(prefix) {
var id = idCounter++;
return prefix ? prefix + id : id;
};
// By default, Underscore uses ERB-style template delimiters, change the
// following template settings to use alternative delimiters.
_.templateSettings = {
evaluate : /<%([\s\S]+?)%>/g,
interpolate : /<%=([\s\S]+?)%>/g,
escape : /<%-([\s\S]+?)%>/g
};
// When customizing `templateSettings`, if you don't want to define an
// interpolation, evaluation or escaping regex, we need one that is
// guaranteed not to match.
var noMatch = /.^/;
// Within an interpolation, evaluation, or escaping, remove HTML escaping
// that had been previously added.
var unescape = function(code) {
return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'");
};
// JavaScript micro-templating, similar to John Resig's implementation.
// Underscore templating handles arbitrary delimiters, preserves whitespace,
// and correctly escapes quotes within interpolated code.
_.template = function(str, data) {
var c = _.templateSettings;
var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' +
'with(obj||{}){__p.push(\'' +
str.replace(/\\/g, '\\\\')
.replace(/'/g, "\\'")
.replace(c.escape || noMatch, function(match, code) {
return "',_.escape(" + unescape(code) + "),'";
})
.replace(c.interpolate || noMatch, function(match, code) {
return "'," + unescape(code) + ",'";
})
.replace(c.evaluate || noMatch, function(match, code) {
return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('";
})
.replace(/\r/g, '\\r')
.replace(/\n/g, '\\n')
.replace(/\t/g, '\\t')
+ "');}return __p.join('');";
var func = new Function('obj', '_', tmpl);
if (data) return func(data, _);
return function(data) {
return func.call(this, data, _);
};
};
// Add a "chain" function, which will delegate to the wrapper.
_.chain = function(obj) {
return _(obj).chain();
};
// The OOP Wrapper
// ---------------
// If Underscore is called as a function, it returns a wrapped object that
// can be used OO-style. This wrapper holds altered versions of all the
// underscore functions. Wrapped objects may be chained.
var wrapper = function(obj) { this._wrapped = obj; };
// Expose `wrapper.prototype` as `_.prototype`
_.prototype = wrapper.prototype;
// Helper function to continue chaining intermediate results.
var result = function(obj, chain) {
return chain ? _(obj).chain() : obj;
};
// A method to easily add functions to the OOP wrapper.
var addToWrapper = function(name, func) {
wrapper.prototype[name] = function() {
var args = slice.call(arguments);
unshift.call(args, this._wrapped);
return result(func.apply(_, args), this._chain);
};
};
// Add all of the Underscore functions to the wrapper object.
_.mixin(_);
// Add all mutator Array functions to the wrapper.
each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
var method = ArrayProto[name];
wrapper.prototype[name] = function() {
var wrapped = this._wrapped;
method.apply(wrapped, arguments);
var length = wrapped.length;
if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0];
return result(wrapped, this._chain);
};
});
// Add all accessor Array functions to the wrapper.
each(['concat', 'join', 'slice'], function(name) {
var method = ArrayProto[name];
wrapper.prototype[name] = function() {
return result(method.apply(this._wrapped, arguments), this._chain);
};
});
// Start chaining a wrapped Underscore object.
wrapper.prototype.chain = function() {
this._chain = true;
return this;
};
// Extracts the result from a wrapped and chained object.
wrapper.prototype.value = function() {
return this._wrapped;
};
}).call(this);
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