/* Major problem areas */

dicknetherlands · andreasprlic · commit 68110b7bc687 · 2016-04-09T10:57:50.000-07:00
diff --git a/_wikis/BioJava3_Proposal.md b/_wikis/BioJava3_Proposal.md
@@ -171,6 +171,17 @@ Major problem areas
     exactly how BioSQL should be used, right down to details like this,
     so that all projects may be able to fully interact without knowledge
     of which tool was used to write the data to BioSQL.
+11. Gapped sequences and alignments need closer attention. Currently
+    there are two ways - a SimpleSymbolList with '-' symbols, or a
+    SimpleGappedSymbolList with proper block definitions and coordinate
+    translation and access to the ungapped sequence. The MSF alignment
+    parser uses the former which is counter-intuitive as programmers
+    reading alignments would expect simple access to the ungapped
+    sequence. There is no easy way to translate between them if you need
+    the more advanced features such as coordinate translation from
+    gapped to ungapped sequence. By allowing gap symbols directly in
+    SimpleSymbolList, it is impossible programmatically to enforce
+    whether a method accepts gapped or ungapped sequences.
 
 Categories of Improvement
 -------------------------
diff --git a/_wikis/BioJava3_Proposal.mediawiki b/_wikis/BioJava3_Proposal.mediawiki
@@ -59,6 +59,7 @@ It is suggested that development stop on the existing BioJava/BioJavaX/BioJava2
 #Equals, compareTo and hashCode methods are inconsistent and often inaccurate, e.g. customised to suit a certain behaviour pattern (e.g. the BJX extensions assume that nulls are allowable for the purposes of Hibernate, whereas really they shouldn't be and Hibernate doesn't need them either). Changing these would change the behaviour of the object model particularly when it comes to collections and maps.
 #Localisation causes mistranslation of strings from lower to upper case. For instance, in Turkish, the lower and upper case i/I do not match those in the English localisation. This causes protein sequences to be mistranslated or misrepresented. BioJava needs to be modified to take this into account.
 #BioSQL interaction is good but there are still issues - particularly to do with case conventions for naming things such as alphabets. A BioSQL mini-hackathon has been suggested as one way to nail down exactly how BioSQL should be used, right down to details like this, so that all projects may be able to fully interact without knowledge of which tool was used to write the data to BioSQL.
+#Gapped sequences and alignments need closer attention. Currently there are two ways - a SimpleSymbolList with '-' symbols, or a SimpleGappedSymbolList with proper block definitions and coordinate translation and access to the ungapped sequence. The MSF alignment parser uses the former which is counter-intuitive as programmers reading alignments would expect simple access to the ungapped sequence. There is no easy way to translate between them if you need the more advanced features such as coordinate translation from gapped to ungapped sequence. By allowing gap symbols directly in SimpleSymbolList, it is impossible programmatically to enforce whether a method accepts gapped or ungapped sequences.
 
 ==Categories of Improvement==
 
