making access methods public

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8708 7c6358e6-4a41-0410-a743-a5b2a554c398
fixing typo

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8709 7c6358e6-4a41-0410-a743-a5b2a554c398
Added fix for rare cases when there are more than 18 chains in a COMPND and chains after 72 character limit are omitted form the structure. Entries such as 3mk3 will no longer throw a StructureException due to being unable to find a chain when  LinkChains2Compound() calls StructureImpl.findChain(). Test and test file included in commit.

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8710 7c6358e6-4a41-0410-a743-a5b2a554c398
Bug fixes plus new feature: sanity check for sequence to program matching. For example, blasting a ProteinSequence with blastn will return an Exception.

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8711 7c6358e6-4a41-0410-a743-a5b2a554c398
adding check for max-size

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8714 7c6358e6-4a41-0410-a743-a5b2a554c398
fix for structures with more than 6 domains

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8715 7c6358e6-4a41-0410-a743-a5b2a554c398
removing dependency on old biojava-core

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8716 7c6358e6-4a41-0410-a743-a5b2a554c398
More info added for location of available databases to the URLAPI interface

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8717 7c6358e6-4a41-0410-a743-a5b2a554c398
More info added for location of available databases to the URLAPI interface

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8718 7c6358e6-4a41-0410-a743-a5b2a554c398
More info added for location of available databases to the URLAPI interface

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8719 7c6358e6-4a41-0410-a743-a5b2a554c398
biojava3-protmod: only merge modifications of the same type and with undefined category

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8726 7c6358e6-4a41-0410-a743-a5b2a554c398
catching some inconsistencies with some custom site records

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8727 7c6358e6-4a41-0410-a743-a5b2a554c398
now allowing to call scaleablematrixpanel for debugging

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8730 7c6358e6-4a41-0410-a743-a5b2a554c398
now also setting SITE records in reduced Structures

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8733 7c6358e6-4a41-0410-a743-a5b2a554c398
Fix for http://bugzilla.open-bio.org/show_bug.cgi?id=3174

Multi-line REF sub-sections in the JRNL section are now correctly parsed to extract the full date, volume, etc and include the full-length journal name.


git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8734 7c6358e6-4a41-0410-a743-a5b2a554c398
making Sites comparable

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8738 7c6358e6-4a41-0410-a743-a5b2a554c398
slightly different toString

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8739 7c6358e6-4a41-0410-a743-a5b2a554c398
making comparable

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8740 7c6358e6-4a41-0410-a743-a5b2a554c398
cleanup, removing desription internal variable, since not used

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8741 7c6358e6-4a41-0410-a743-a5b2a554c398
Added exception handling for when the JournalParser tries to convert a date in the PDB JRNL REF subsection from a string to an int. This will now warn the user that there is an incorrect datatype instead of falling over. 

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@8742 7c6358e6-4a41-0410-a743-a5b2a554c398