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  #1  
Old 03-26-2008, 02:44 AM
Tolnaftate2004 Tolnaftate2004 is offline
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Programming Exercise #3

In a string of N characters, calculate the frequencies of repeated patterns, e.g., given "AUGCCCGTAUACGTA", one would get CGTA:2, CGT:2, GTA:2, CG:2, GT:2, TA:2, AU:2, CC:2. You do not need to display the information, only get the data in a format from which it can be extracted (hopefully in a pattern that is of order less than the algorithm). You may assume that only the letters A-Z will be used to make the given string.

It may help to review Programming Exercises #1 and #2.

Remember, the goal is to make this as efficient as possible with graal script.
Your algorithm will be ranked first by big-O notation, then by runtime speed.
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Last edited by Tolnaftate2004; 03-27-2008 at 05:49 AM..
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  #2  
Old 03-26-2008, 02:52 AM
cbk1994 cbk1994 is offline
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Do we need to find every pattern possible, or just ones specified?

For example,

findAllPatterns( n )

or something like

findNumber( n, pattern )
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Old 03-26-2008, 03:25 AM
DrakilorP2P DrakilorP2P is offline
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Assuming that the algorithm should find the number of occurrences of a string in another string. Which it shouldn't.

PHP Code:
function findFrequencyOfPattern(haystackneedle)
{
  
temp.occurrences 0;
  for (
temp.i=0temp.i<haystack.length() - needle.length() + 1temp.i++) {
    if (
haystack.substring(temp.ineedle.length()) == needletemp.occurrences++;
  }
  return 
temp.occurrences;

PHP Code:
temp.haystack "AUGCCCGTAUACGTA";
temp.needles = {"CGTA""CGT""GTA""CG""GT""TA""AU""CC"};
sendrpgmessage(temp.haystack);
for (
temp.needletemp.needles) {
  
sendrpgmessage(temp.needle ": " findFrequencyOfPattern(temp.haystacktemp.needle));

Outputs:
PHP Code:
AUGCCCGTAUACGTA
CGTA
2
CGT
2
GTA
2
CG
2
GT
2
TA
2
AU
2
CC


Last edited by DrakilorP2P; 03-26-2008 at 09:57 AM..
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Old 03-26-2008, 05:05 AM
cbk1994 cbk1994 is offline
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Okay, I have mine finished. It takes about 5 seconds to run (go figure!) but it gets the right answer, at least from what I have seen.

PHP Code:
StringAUOccurances2
String
CCOccurances2
String
CGOccurances2
String
CGTOccurances2
String
CGTAOccurances2
String
GTOccurances2
String
GTAOccurances2
String
TAOccurances
This is what it outputs in RC.

The script is very inefficient and slow, but it works ...

NOTE: You will need to change the [] in the format to a percent sign, it won't let me post without giving me a bad request error. Look for this line:
echo( format( "String: []s, Occurances: []s", rc[0], rc[1] ) );

PHP Code:
function onCreated()
{
  
temp.includeSingle false// Include ones that only appear once?
  
  
temp."AUGCCCGTAUACGTA";
  
temp.na stringToArrayList);
    
  
temp.occ = {};
  
  for ( 
temp.na )
  {
    
temp.fr findFrequencyn);
    if ( 
temp.fr == && includeSingle == false )
    {
      continue;
    }
    
occ.add( { rtemp.fr } );
  }
  
  for ( 
temp.rc occ )
  {
    echo( 
format"String: []s, Occurances: []s"rc[0], rc[1] ) );
  }
}
function 
stringToArrayListstr )
{
  
temp.= {};
  for ( 
temp.char 0char str.length(); char ++ )
  {
    for ( 
temp.charlen 2charlen str.length() +  charcharlen ++ )
    {
      
temp.count ++;
      
temp.newText str.substringcharcharlen );
      if ( 
newText != str && p.index( @ newText ) == -)
      {
        
p.addnewText );
      }
      if ( 
count >= 100 )
      {
        
sleep.05 );
        
count 0;
      }
    }
  }
  return 
p;
}
function 
findFrequencystrphrase )
{
  
temp.0;
  for ( 
temp.char 0char str.length(); char ++ )
  {
    for ( 
temp.charlen 1charlen str.length() +  charcharlen ++ )
    {
      
temp.count ++;
      
temp.newText str.substringcharcharlen );
      if ( 
newText != str )
      {
        if ( 
newText == phrase )
        {
          
++;
        }
      }
      if ( 
count >= 100 )
      {
        
sleep.05 );
        
count 0;
      }
    }
  }
  return 
o;

This looks for all possible combinations, then finds how often they occur.

Also, if a mod wants to delete my last post in this thread they can, it won't let me edit it or delete it anymore for some reason, gives a Bad Request error.
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  #5  
Old 03-26-2008, 07:34 AM
Tolnaftate2004 Tolnaftate2004 is offline
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Quote:
Originally Posted by DrakilorP2P View Post
Assuming that the algorithm should find the number of occurrences of a string in another string.
Nooooooot quite.

Quote:
Originally Posted by cbkbud View Post
Okay, I have mine finished. It takes about 5 seconds to run (go figure!) but it gets the right answer, at least from what I have seen.
This is closer (), but no doubt we can do better. ~O(n³)
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Old 03-26-2008, 05:26 PM
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Quote:
Originally Posted by cbkbud View Post
NOTE: You will need to change the [] in the format to a percent sign, it won't let me post without giving me a bad request error. Look for this line:
echo( format( "String: []s, Occurances: []s", rc[0], rc[1] ) );
Tiny tip: If you post a "normal" post without any % signs, you can just edit it with quick edit afterwards and add them. Won't give an error.
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Old 03-26-2008, 08:16 AM
Inverness Inverness is offline
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PHP Code:
function findpatterns(str) {
  
temp.outc = {};
  
temp.out = {};
  
temp.sub "";
  
temp.0;
  
temp.0;
  
temp.0;

  for (
2str.length(); ++) {
    for (
0str.length(); ++) {
      if (
str.length() - 1) {
        continue;
      }
      
sub str.substring(ei);
      
str.positions(sub);
      if (
p.size() > 1) {
        if (
outc.index(sub) < 0) {
          
outc.add(sub);
          
out.add({subp.size()});
        }
      }
    }
  }
  return 
out;

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Old 03-26-2008, 09:13 AM
Tolnaftate2004 Tolnaftate2004 is offline
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I have updated the guidelines slightly.
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Killa Be: when i got that locker in 6th grade the only thing in it was a picture of a midget useing a firehose :/
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  #9  
Old 03-26-2008, 09:59 AM
DrakilorP2P DrakilorP2P is offline
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Quote:
Originally Posted by Tolnaftate2004 View Post
I have updated the guidelines slightly.
Why isn't strings of length one considered valid patterns?
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Old 03-26-2008, 12:11 PM
Tolnaftate2004 Tolnaftate2004 is offline
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Quote:
Originally Posted by DrakilorP2P View Post
Why isn't strings of length one considered valid patterns?
A solid color does not a pattern make.
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Old 03-26-2008, 01:28 PM
Inverness Inverness is offline
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No comment on what I posted?

You've irritated me.
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Old 03-26-2008, 07:26 PM
Tolnaftate2004 Tolnaftate2004 is offline
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Quote:
Originally Posted by Inverness View Post
No comment on what I posted?

You've irritated me.
Yours is still O(n³).

e: The new standard set by DrakilorP2P, O(n²)
@Ziro: Will keep that in mind.
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Killa Be: when i got that locker in 6th grade the only thing in it was a picture of a midget useing a firehose :/

Last edited by Tolnaftate2004; 03-26-2008 at 07:57 PM..
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Old 03-26-2008, 09:40 PM
Inverness Inverness is offline
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Quote:
Originally Posted by Tolnaftate2004 View Post
Yours is still O(n³).

e: The new standard set by DrakilorP2P, O(n²)
What the hell are you talking about?

Increased speed of script:
PHP Code:
function findpatterns(str) {
  
temp.time timevar2;
  
temp.outc = {};
  
temp.out = {};
  for (
temp.2temp.temp.str.length(); temp.++) {
    for (
temp.0temp.temp.str.length(); temp.++) {
      if (
temp.temp.temp.str.length() - 1) {
        continue;
      }
      
temp.sub temp.str.substring(temp.etemp.i);
      
temp.temp.str.positions(temp.sub);
      if (
temp.p.size() > 1) {
        if (
temp.outc.index(temp.sub) < 0) {
          
temp.outc.add(temp.sub);
          
temp.out.add(temp.sub ":" temp.p.size());
        }
      }
    }
  }
  echo(
"Time: " timevar2 temp.time);
  return 
temp.out;

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Old 03-26-2008, 09:49 PM
Tolnaftate2004 Tolnaftate2004 is offline
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Quote:
Originally Posted by Inverness View Post
What the hell are you talking about?
This is big O notation, it is how we measure the efficiency of algorithms, without being hardware-specific. The O stands for order, which can take 2 meanings:
  1. In mathematics, O(f) is for all terms order f and above. f is usually a function where the parameter is much less than 1 (error terms).
  2. In computer science O(f) is the major factor in determining algorithm efficiency. f is a function of n, which is a whole number.

For example, the quicksort algorithm is O(n log n) [for every item to sort, it takes log base 2 of n loops to find its place].
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Killa Be: when i got that locker in 6th grade the only thing in it was a picture of a midget useing a firehose :/

Last edited by Tolnaftate2004; 03-26-2008 at 10:04 PM..
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Old 03-27-2008, 10:25 PM
napo_p2p napo_p2p is offline
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PHP Code:
function findpatterns(str) {
  
temp.loc 0;
  
temp.temp.str.length();
  
temp.results = new[0];
  
  while (
temp.loc temp.l) {
    
temp.len 2;
    while (
temp.len <= (temp.temp.loc)) {
      
temp.seq temp.str.substring(temp.loctemp.len);
      
temp.("count_" temp.seq)++;
      if (
temp.("count_" temp.seq) == 2) {
        
temp.results.add(temp.seq);
      }
      
temp.len++;
    }
    
temp.loc++;
  }

  for (
temp.rtemp.results) {
    echo(
temp.": " temp.("count_" temp.r));
  }

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Last edited by napo_p2p; 03-27-2008 at 10:27 PM.. Reason: .
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