[Biojava-l] SCF Parser issues with gaps and unread peak values ?

[Ashika Umanga Umagiliya]

Greetings all,

Please refer to image at:  http://i43.tinypic.com/sfdjs6.png

As shown in Figure1 , I am drawing bases using Phrap ACE file and 
drawing chromatographs using
Biojava 'ChromatoGraphics' . I use .SCF file generated by phrep.

As can be seen in Figure 1 , the alignment breaks from the 'Magenta 
callbase-box'.The reason is may be the 'SCF parser' has ignored one of 
the peaks which should be a 'T'.


Figure 2 : Shows what need to be happen.If somehow if I can fill it with 
a T (or may be sometimes a Gap) I can save the alignment between sequences.

Figure 3 : Shows the same Chromatograph using ChromasPro , It has 
identified the peak as a T.

I went throught the biojavas SCF  parser , I noticed that it finally 
creates a 'SimpleAlignment'.Can I utilize 'GappedSymbolList' and fix this?
Is there a way to read the gaps (or incases like this , the correct base 
T) and make these two align.

Thanks in advance,
Umanga