[Biojava-dev] Greedy SymbolList.subStr()!

[Rainer Pudimat]

Hello,

I am debugging a search algorithm because it breaks
with an OutOfMemoryException after a long time
whereas I would expect constant memory demands.

After running a profiler for several parts of the
programme, I found out that the biojava method

SymbolList.subStr(int,int) (biojava 1.3)

is the greedy piece of code.
For instance, consider the following two loops which
do the same:

1.
int r =....;
int l =....;
int length=0;
Sequence seq= .....;
while(true)
{
    length = seq.subStr(l,r).length();
}

This programm stops with OutOfMemoryException.

2.
int r =....;
int l =....;
int length=0;
Sequence seq= .....;
while(true)
{
    length = seq.seqString().subString(l-1,r-1).length();
}

This programm never ends.

Bye,
Rainer Pudimat