HI! I am writing some small app that uses GappedSymbolList and i see some wierd behaviour.
The first "problem" is when i have a GappedSymbolList and i insert a gap into the View sequence ( the one that shows gaps ). As long as i insert a gap/ gaps at a positin where there isnt any gap, all is fine. On the other hand, if i inserta gap at a position where there is a gap, the gap gets inserted into the NEXT block of gaps, and if there isnt any next block of gaps, the gap gets appended at the end of the sequence. A simple text example will describe this much better. the example basicly just inserts a gap at position 3 in the view, a couple of time, and then prints the output, and it looks like this: aattggcc Initial sequence aa-ttggcc 1 gap inserted at position 3 aa-ttggcc- 1 additional gap inserted at position 3 aa-ttggcc-- 1 additional gap inserted at position 3 aa-ttggcc--- 1 additional gap inserted at position 3 for me, this is not the way i think anyone would expect it to work. I think most people would just expect that gap insertion should work the same, irrespectively of what symbol is at the position where the gap gets inserted. And that the end result should look like this. aa----ttggcc The second ting i am having some thoughts about is the viewToSource function, if you try to convert from view to source coordinates, and the view coordinate contains a gap, you get a return value of -1. The JavaDoc dont mention anything about what happens when you try to go from view to source coordinates and the view coordinate contains a gap, but it returns a -1 and that is ok i guess. But, this gives me lots of problems, as i have users graphicly specify an intervall on the GapedSequenceList, and i then want the source coordinates. If the user chooses one endpoint that is a gap, i will have to start scaning symbol for symbol, in the View coordinates, and then use the first non gap symbol.So would it be wrong, to change the viewToSource method to not return -1, but to actualy return the source position where the gap is inserted, multiplied by -1 ? This would most likely dont break any code that just checks if viewToSource returns -1 as most people will have done it like if( x < 0 ) and not like if( x == -1 ). And then you can get a meaningfull conversoin from view to source, and if you dont care, you can only chec if the return value is negaitve. to clarify what i mean, i will give a short eample here aswell. aa---ttggcc as it is now, viewToSoruce( 4 ) will return -1, i would propose that it should return -3 instead, because it is at position three in the source sequence, the gaps are inserted. And the value shold be negative, to indicate that there is no direct link between the view position and the source, as the view is a gap. I do understand that there might be things this little proposal does to other parts, that are not wanted, and therefore, this should only be seen as a little question / proposal, and nothing more, if there is a reason to only return -1 and nothing else, i will just do the dirty solution of walking along the view sequence until i find a non gap symbol. Anyway, i have tested this on linux ( jdk 1.3.1 from sun ) and windows ( jdk 1.4.0b3 ), using both the binary biojava-20010920.jar release aswell as one of the older releases, and the behaviour is the same in all combinations. to finnish this off, i would just like to say thanks to all who have contributed to biojava as it simplifies many nasty tasks a lot. Sincerely, Kalle Näslund _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
