[Biojava-l] please do respond

2002-10-11 Thread Abdul Dagogo
Dear friend, I will like to solicit your help in a business preposition, which is by nature very confidential and a Top Secret. I know that a transaction of this magnitude will make any one worried and apprehensive but I am assuring you not to worry, as all will be well at the end of this

Re: [Biojava-l] equals() method for SymbolList

2002-10-11 Thread Matthew Pocock
Hi Lachlan, SymbolList should be behaving like a string over its symbols. It is silly if it doesn't do this. Hash codes should realy be calculated in a different (but sequence-dependant) way to avoid scanning the whole of very large sequences just to do a hash lookup. Anyone got any ideas? If yo

Re: [Biojava-l] equals() method for SymbolList

2002-10-11 Thread Phillip Lord
> "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes: Matthew> SymbolList should be behaving like a string over its Matthew> symbols. It is silly if it doesn't do this. Hash codes Matthew> should realy be calculated in a different (but Matthew> sequence-dependant) way to avoid sc

Re: [Biojava-l] equals() method for SymbolList

2002-10-11 Thread Keith James
> "Phillip" == Phillip Lord <[EMAIL PROTECTED]> writes: > "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes: Matthew> SymbolList should be behaving like a string over its Matthew> symbols. It is silly if it doesn't do this. Hash codes Matthew> should realy be calculated

RE: [Biojava-l] GCG format...

2002-10-11 Thread Wiepert, Mathieu
Hi, Have you considered doing a system call to seqret (from emboss)? Is that a possibility for you? Not sure what system you are running on, etc. May be a hack, but it would work. Or else system calls to GCG, which will also do some formatting for you. Again a hack, but workable... -Mat

Re: [Biojava-l] equals() method for SymbolList

2002-10-11 Thread Phillip Lord
> "Keith" == Keith James <[EMAIL PROTECTED]> writes: > "Phillip" == Phillip Lord <[EMAIL PROTECTED]> writes: > "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes: Matthew> SymbolList should be behaving like a string over its Matthew> symbols. It is silly if it doesn't do thi

[Biojava-l] Set-up on True64

2002-10-11 Thread Warth,Rainer,LAUSANNE,NRC/BS
Dear all, I am new to biojava. I am currently setting it up on a Compaq True 64 v.5.1 server. I managed to get things going on my Windows and Linux box ( although this was not very hard). Now I encounter this problem in the Compa machine and I do not really know what to do. Best, Rainer I d

[Biojava-l] Swissprot parsing

2002-10-11 Thread satyanarayana pasupuleti
Hello all: I am trying to extract information from a Swissprot file using the below code. SequenceIterator seqIter = SeqIOTools.readSwissprot(br); while (seqIter.hasNext()) { Sequence sequence = seqIter.nextSequence(); Annotation seqAn = sequence.getAnnotation(); Set set = seqAn.keys();

[Biojava-l] equals() method for SymbolList

2002-10-11 Thread Lachlan Coin
Hi, I think this was raised a while back, but the equals() methods are not overridden in SymbolList classes, hence to compare equality you must do: sl1.toList().equals(sl2.toList()). I was just wondering if it were possible to change this, so that two SymbolLists are equal if they contain the sam