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Top Forums Programming Improve the performance of my C++ code Post 302931903 by Corona688 on Friday 16th of January 2015 10:01:08 AM
Old 01-16-2015
Quote:
Originally Posted by yifangt
My problem is the implementation. I want to step to "my second stage" of programming by using those available libraries.
"hash table" isn't exactly a library, it's different enough from other data structures it's often hand-rolled. Generalizing it too much would run the risk of poor performance, you need to pick the right algorithms for your application. It has a lot of restrictions as well (hard to iterate, deletion can cause something like fragmentation, and it can't be sorted). I've seen a few attempts at building a library for it, but nothing I ever liked very much.

In the end it's not that complicated. It's a big array with strict rules about what data gets put in what element. I'd suggest "open chaining" for your table -- basically an array full of lists -- with an index that's not really hashed at all, just converted from ACGT into boolean. Four letters would be 8 bits, for an array 256 long for example. Then you could just look up the first four letters of your sequence, find that list, and speedily check every possible thing which might contain your sequence without having to brute-force it.

Last edited by Corona688; 01-16-2015 at 11:24 AM..
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PERLREFTUT(1)						 Perl Programmers Reference Guide					     PERLREFTUT(1)

NAME
perlreftut - Mark's very short tutorial about references DESCRIPTION
One of the most important new features in Perl 5 was the capability to manage complicated data structures like multidimensional arrays and nested hashes. To enable these, Perl 5 introduced a feature called `references', and using references is the key to managing complicated, structured data in Perl. Unfortunately, there's a lot of funny syntax to learn, and the main manual page can be hard to follow. The man- ual is quite complete, and sometimes people find that a problem, because it can be hard to tell what is important and what isn't. Fortunately, you only need to know 10% of what's in the main page to get 90% of the benefit. This page will show you that 10%. Who Needs Complicated Data Structures? One problem that came up all the time in Perl 4 was how to represent a hash whose values were lists. Perl 4 had hashes, of course, but the values had to be scalars; they couldn't be lists. Why would you want a hash of lists? Let's take a simple example: You have a file of city and country names, like this: Chicago, USA Frankfurt, Germany Berlin, Germany Washington, USA Helsinki, Finland New York, USA and you want to produce an output like this, with each country mentioned once, and then an alphabetical list of the cities in that country: Finland: Helsinki. Germany: Berlin, Frankfurt. USA: Chicago, New York, Washington. The natural way to do this is to have a hash whose keys are country names. Associated with each country name key is a list of the cities in that country. Each time you read a line of input, split it into a country and a city, look up the list of cities already known to be in that country, and append the new city to the list. When you're done reading the input, iterate over the hash as usual, sorting each list of cities before you print it out. If hash values can't be lists, you lose. In Perl 4, hash values can't be lists; they can only be strings. You lose. You'd probably have to combine all the cities into a single string somehow, and then when time came to write the output, you'd have to break the string into a list, sort the list, and turn it back into a string. This is messy and error-prone. And it's frustrating, because Perl already has per- fectly good lists that would solve the problem if only you could use them. The Solution By the time Perl 5 rolled around, we were already stuck with this design: Hash values must be scalars. The solution to this is references. A reference is a scalar value that refers to an entire array or an entire hash (or to just about anything else). Names are one kind of reference that you're already familiar with. Think of the President of the United States: a messy, inconvenient bag of blood and bones. But to talk about him, or to represent him in a computer program, all you need is the easy, convenient scalar string "George Bush". References in Perl are like names for arrays and hashes. They're Perl's private, internal names, so you can be sure they're unambiguous. Unlike "George Bush", a reference only refers to one thing, and you always know what it refers to. If you have a reference to an array, you can recover the entire array from it. If you have a reference to a hash, you can recover the entire hash. But the reference is still an easy, compact scalar value. You can't have a hash whose values are arrays; hash values can only be scalars. We're stuck with that. But a single reference can refer to an entire array, and references are scalars, so you can have a hash of references to arrays, and it'll act a lot like a hash of arrays, and it'll be just as useful as a hash of arrays. We'll come back to this city-country problem later, after we've seen some syntax for managing references. Syntax There are just two ways to make a reference, and just two ways to use it once you have it. Making References Make Rule 1 If you put a "" in front of a variable, you get a reference to that variable. $aref = @array; # $aref now holds a reference to @array $href = \%hash; # $href now holds a reference to %hash Once the reference is stored in a variable like $aref or $href, you can copy it or store it just the same as any other scalar value: $xy = $aref; # $xy now holds a reference to @array $p[3] = $href; # $p[3] now holds a reference to %hash $z = $p[3]; # $z now holds a reference to %hash These examples show how to make references to variables with names. Sometimes you want to make an array or a hash that doesn't have a name. This is analogous to the way you like to be able to use the string " " or the number 80 without having to store it in a named vari- able first. Make Rule 2 "[ ITEMS ]" makes a new, anonymous array, and returns a reference to that array. "{ ITEMS }" makes a new, anonymous hash. and returns a reference to that hash. $aref = [ 1, "foo", undef, 13 ]; # $aref now holds a reference to an array $href = { APR => 4, AUG => 8 }; # $href now holds a reference to a hash The references you get from rule 2 are the same kind of references that you get from rule 1: # This: $aref = [ 1, 2, 3 ]; # Does the same as this: @array = (1, 2, 3); $aref = @array; The first line is an abbreviation for the following two lines, except that it doesn't create the superfluous array variable @array. Using References What can you do with a reference once you have it? It's a scalar value, and we've seen that you can store it as a scalar and get it back again just like any scalar. There are just two more ways to use it: Use Rule 1 If $aref contains a reference to an array, then you can put "{$aref}" anywhere you would normally put the name of an array. For example, "@{$aref}" instead of @array. Here are some examples of that: Arrays: @a @{$aref} An array reverse @a reverse @{$aref} Reverse the array $a[3] ${$aref}[3] An element of the array $a[3] = 17; ${$aref}[3] = 17 Assigning an element On each line are two expressions that do the same thing. The left-hand versions operate on the array @a, and the right-hand versions oper- ate on the array that is referred to by $aref, but once they find the array they're operating on, they do the same things to the arrays. Using a hash reference is exactly the same: %h %{$href} A hash keys %h keys %{$href} Get the keys from the hash $h{'red'} ${$href}{'red'} An element of the hash $h{'red'} = 17 ${$href}{'red'} = 17 Assigning an element Use Rule 2 "${$aref}[3]" is too hard to read, so you can write "$aref->[3]" instead. "${$href}{red}" is too hard to read, so you can write "$href->{red}" instead. Most often, when you have an array or a hash, you want to get or set a single element from it. "${$aref}[3]" and "${$href}{'red'}" have too much punctuation, and Perl lets you abbreviate. If $aref holds a reference to an array, then "$aref->[3]" is the fourth element of the array. Don't confuse this with $aref[3], which is the fourth element of a totally different array, one deceptively named @aref. $aref and @aref are unrelated the same way that $item and @item are. Similarly, "$href->{'red'}" is part of the hash referred to by the scalar variable $href, perhaps even one with no name. $href{'red'} is part of the deceptively named %href hash. It's easy to forget to leave out the "->", and if you do, you'll get bizarre results when your program gets array and hash elements out of totally unexpected hashes and arrays that weren't the ones you wanted to use. An Example Let's see a quick example of how all this is useful. First, remember that "[1, 2, 3]" makes an anonymous array containing "(1, 2, 3)", and gives you a reference to that array. Now think about @a = ( [1, 2, 3], [4, 5, 6], [7, 8, 9] ); @a is an array with three elements, and each one is a reference to another array. $a[1] is one of these references. It refers to an array, the array containing "(4, 5, 6)", and because it is a reference to an array, USE RULE 2 says that we can write $a[1]->[2] to get the third element from that array. $a[1]->[2] is the 6. Similarly, $a[0]->[1] is the 2. What we have here is like a two-dimensional array; you can write $a[ROW]->[COLUMN] to get or set the element in any row and any column of the array. The notation still looks a little cumbersome, so there's one more abbreviation: Arrow Rule In between two subscripts, the arrow is optional. Instead of $a[1]->[2], we can write $a[1][2]; it means the same thing. Instead of $a[0]->[1], we can write $a[0][1]; it means the same thing. Now it really looks like two-dimensional arrays! You can see why the arrows are important. Without them, we would have had to write "${$a[1]}[2]" instead of $a[1][2]. For three-dimen- sional arrays, they let us write $x[2][3][5] instead of the unreadable "${${$x[2]}[3]}[5]". Solution Here's the answer to the problem I posed earlier, of reformatting a file of city and country names. 1 while (<>) { 2 chomp; 3 my ($city, $country) = split /, /; 4 push @{$table{$country}}, $city; 5 } 6 7 foreach $country (sort keys %table) { 8 print "$country: "; 9 my @cities = @{$table{$country}}; 10 print join ', ', sort @cities; 11 print ". "; 12 } The program has two pieces: Lines 1--5 read the input and build a data structure, and lines 7--12 analyze the data and print out the report. In the first part, line 4 is the important one. We're going to have a hash, %table, whose keys are country names, and whose values are (references to) arrays of city names. After acquiring a city and country name, the program looks up $table{$country}, which holds (a ref- erence to) the list of cities seen in that country so far. Line 4 is totally analogous to push @array, $city; except that the name "array" has been replaced by the reference "{$table{$country}}". The "push" adds a city name to the end of the referred-to array. In the second part, line 9 is the important one. Again, $table{$country} is (a reference to) the list of cities in the country, so we can recover the original list, and copy it into the array @cities, by using "@{$table{$country}}". Line 9 is totally analogous to @cities = @array; except that the name "array" has been replaced by the reference "{$table{$country}}". The "@" tells Perl to get the entire array. The rest of the program is just familiar uses of "chomp", "split", "sort", "print", and doesn't involve references at all. There's one fine point I skipped. Suppose the program has just read the first line in its input that happens to mention Greece. Control is at line 4, $country is 'Greece', and $city is 'Athens'. Since this is the first city in Greece, $table{$country} is undefined---in fact there isn't an 'Greece' key in %table at all. What does line 4 do here? 4 push @{$table{$country}}, $city; This is Perl, so it does the exact right thing. It sees that you want to push "Athens" onto an array that doesn't exist, so it helpfully makes a new, empty, anonymous array for you, installs it in the table, and then pushes "Athens" onto it. This is called `autovivifica- tion'. The Rest I promised to give you 90% of the benefit with 10% of the details, and that means I left out 90% of the details. Now that you have an overview of the important parts, it should be easier to read the perlref manual page, which discusses 100% of the details. Some of the highlights of perlref: o You can make references to anything, including scalars, functions, and other references. o In USE RULE 1, you can omit the curly brackets whenever the thing inside them is an atomic scalar variable like $aref. For example, @$aref is the same as "@{$aref}", and $$aref[1] is the same as "${$aref}[1]". If you're just starting out, you may want to adopt the habit of always including the curly brackets. o To see if a variable contains a reference, use the `ref' function. It returns true if its argument is a reference. Actually it's a little better than that: It returns HASH for hash references and ARRAY for array references. o If you try to use a reference like a string, you get strings like ARRAY(0x80f5dec) or HASH(0x826afc0) If you ever see a string that looks like this, you'll know you printed out a reference by mistake. A side effect of this representation is that you can use "eq" to see if two references refer to the same thing. (But you should usu- ally use "==" instead because it's much faster.) o You can use a string as if it were a reference. If you use the string "foo" as an array reference, it's taken to be a reference to the array @foo. This is called a soft reference or symbolic reference. You might prefer to go on to perllol instead of perlref; it discusses lists of lists and multidimensional arrays in detail. After that, you should move on to perldsc; it's a Data Structure Cookbook that shows recipes for using and printing out arrays of hashes, hashes of arrays, and other kinds of data. Summary Everyone needs compound data structures, and in Perl the way you get them is with references. There are four important rules for managing references: Two for making references and two for using them. Once you know these rules you can do most of the important things you need to do with references. Credits Author: Mark-Jason Dominus, Plover Systems ("mjd-perl-ref+@plover.com") This article originally appeared in The Perl Journal ( http://www.tpj.com/ ) volume 3, #2. Reprinted with permission. The original title was Understand References Today. Distribution Conditions Copyright 1998 The Perl Journal. When included as part of the Standard Version of Perl, or as part of its complete documentation whether printed or otherwise, this work may be distributed only under the terms of Perl's Artistic License. Any distribution of this file or derivatives thereof outside of that pack- age require that special arrangements be made with copyright holder. Irrespective of its distribution, all code examples in these files are hereby placed into the public domain. You are permitted and encour- aged to use this code in your own programs for fun or for profit as you see fit. A simple comment in the code giving credit would be cour- teous but is not required. perl v5.8.0 2003-02-18 PERLREFTUT(1)
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