Andy -
String manipulation is nortoriously slow in Java (due to the Security model which
needs Strings to be immutable) so every manipulation reqiures a new String. If you are
dealing with a small alphabet and are going to be treating each Symbol as a String
then it may pay to create one of each String "a", "c" etc and intern them using the
String.intern() method.
I'm not sure if it will imporve performance but you might be able to avoid using
Strings and chars at all by using Edits and cross product alphabets.
see the alphabets and symbols section of http://www.biojava.org/docs/bj_in_anger/ and
also http://www.biojava.org/docs/bj_in_anger/edit.htm
Hope this helps,
Mark
-----Original Message-----
From: Andy Hammer [mailto:[EMAIL PROTECTED]
Sent: Sat 13/09/2003 12:05 p.m.
To: bio java
Cc:
Subject: [Biojava-l] Performance of SymbolList.subStr() function
This blows my mind!
In both blocks of code: seq = si.nextSequence();
//just a protein sequence
In this block of code, my system would take hours and
often crash with an out of memory error.
for(int i = 1; i <= seqLength; i++){
String seqString = seq.subStr(i,i);
char protein = seqString.charAt(0);
newSeq =
newSeq.append(newCodon(protein));//add a 3 char string
to the newSeq StringBuffer
}
I altered the above block to:
String seqString = seq.seqString();
for(int i = 0; i < seqLength; i++){
char protein = seqString.charAt(i);
newSeq = newSeq.append(newCodon(protein));
}
This program used to take 4 hours to complete. With
this simple change it is now done in 30 minutes!
Obviously, the SymbolList.subStr() function was
severly hampering my efficiency. I guess it was poor
use of the SymbolList.subStr() function. My rational
was that I didn't want to create an unneeded String
simply to represent my already existing SymbolList. I
am just trying to learn from this to become a better
programmer and would appreciate any comments on this.
Thanks!
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