[Biojava-l] leader and trailer in Renderers

I've been going thru' the SequencePanel code to document it a bit more and I am puzzled over the intent behind the leader and trailer allocations in this code. If I understand the SequencePanel source correctly, each renderer tells SequencePanel thru' getMinimumLeader and getMinimumTrailer the nu

Re: [Biojava-l] leader and trailer in Renderers

The leading and trailing space is requested per renderer. This is because some glyphs (e.g. numbers) are scale-invarient and will be clipped off if the rendering is clipped exactly. I think the container of the sequence renderers loops over these and finds the maximum one. Then, it individualy

[Biojava-l] mutating subsequence

Hi, Is there a way I can change the content of a SubSequence object? In the constructor I give it the parent sequence, the start and end index of that sequence. But what if I want to change it later? I want to reset the start and/or the end, and thereby changing the length of the subsequenc

[Biojava-l] pdb parser example

Hi. I've tried to run the PDB parser example, but hit a snag. C:\stuff\biojava\biojava-live\demos>java eventbasedparsing.Pdb2XML files\pdb\hgh_ori.pdb WARNING: ignoring attempt to set illegal combination of parser features no protocol: files\pdb\hgh_ori.pdb Couldn't open file Am I being stupi

Re: [Biojava-l] pdb parser example

Matthew Pocock wrote: > Hi. > > I've tried to run the PDB parser example, but hit a snag. > > C:\stuff\biojava\biojava-live\demos>java eventbasedparsing.Pdb2XML > files\pdb\hgh_ori.pdb > WARNING: ignoring attempt to set illegal combination of parser features > > no protocol: files\pdb\hgh_ori.

Re: [Biojava-l] pdb parser example

I don't think my last mail was completel clear (i.e. correct!) it needs to be: file:// followed by the full path to the file i.e. you'll have 3 slashes... e.g. file:///usr/local/people/matt/stuff/biojava/you/get/the/idea/... S. -- Simon M. Brocklehurst, Ph.D. Head of Bioinformatics & Advanced

Re: [Biojava-l] pdb parser example

OK - using a fully quailfied FILE url worked. Also, I got rid of the capabilities message by ading sax/ to the capability names in Pdb2XMLConverter lines 97/98 oParser.setFeature("http://xml.org/sax/features/namespaces",true); oParser.setFeature("http://xml.org/sax/featu

Re: [Biojava-l] mutating subsequence

On Mon, Mar 04, 2002 at 11:19:31AM -0500, Guoneng Zhong wrote: > Hi, > Is there a way I can change the content of a SubSequence object? In the > constructor I give it the parent sequence, the start and end index of > that sequence. But what if I want to change it later? I want to reset > the

[Biojava-l] BufferedReader and FastaFormat

Hi - When working with small FASTA libraries (in terms of the number of entries) the following snippet of code works fine, try{ SequenceIterator i = SeqIOTools.readFastaDNA(new BufferedReader(new FileReader(f))); while(i.hasNext()){ Sequence s = i.nextSeque

Re: [Biojava-l] leader and trailer in Renderers

On Mon, 4 Mar 2002, Matthew Pocock wrote: > The leading and trailing space is requested per renderer. This is > because some glyphs (e.g. numbers) are scale-invarient and will be > clipped off if the rendering is clipped exactly. I think the container > of the sequence renderers loops over the

Re: [Biojava-l] BufferedReader and FastaFormat

On Tue, Mar 05, 2002 at 10:07:11AM +1300, Schreiber, Mark wrote: > > java.io.IOException: Mark invalid > at java.io.BufferedReader.reset(BufferedReader.java:467) > at > org.biojava.bio.seq.io.FastaFormat.readSequenceData(FastaFormat.java:164 > ) > at > org.biojava.bio.seq.io.Fas