Added RotationAxis, which calculates (and displays) the axis of rotation for alignments.

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10018 7c6358e6-4a41-0410-a743-a5b2a554c398
Added constructor to RotationAxis

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10019 7c6358e6-4a41-0410-a743-a5b2a554c398
RotatonAxis: Handle translational alignments (<5 deg)

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10020 7c6358e6-4a41-0410-a743-a5b2a554c398
upgrading to Jmol 13.0.13

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10035 7c6358e6-4a41-0410-a743-a5b2a554c398
upgrading to Jmol 13.0.13

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10036 7c6358e6-4a41-0410-a743-a5b2a554c398
switching to latest Jmol from Maven central

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10037 7c6358e6-4a41-0410-a743-a5b2a554c398
now using a new version of forester that is for sure under lgpl

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10038 7c6358e6-4a41-0410-a743-a5b2a554c398
Small improvements to ResidueRange, AtomPosition, and ResidueNumber; added a few useful methods. No bug fixes.

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10057 7c6358e6-4a41-0410-a743-a5b2a554c398
Forgot to commit AtomPositionMap's test; adding it now.

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10058 7c6358e6-4a41-0410-a743-a5b2a554c398
new method to create jmol script

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10064 7c6358e6-4a41-0410-a743-a5b2a554c398
checking for non-existing chem comps

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10065 7c6358e6-4a41-0410-a743-a5b2a554c398
better error message

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10066 7c6358e6-4a41-0410-a743-a5b2a554c398
Made AtomCache exception messages slightly more palatable, although they still get caught and rethrown multiple times

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10067 7c6358e6-4a41-0410-a743-a5b2a554c398
Refactored RotationAxis & added documentation

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10068 7c6358e6-4a41-0410-a743-a5b2a554c398
Fixed bug in RotationAxis position

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10069 7c6358e6-4a41-0410-a743-a5b2a554c398
demo for how load secstruc assignment from pdb file

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10072 7c6358e6-4a41-0410-a743-a5b2a554c398
get pariwise alignment of protein sequences

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10073 7c6358e6-4a41-0410-a743-a5b2a554c398
Fixed a ArrayIndexOutBoundsException in CeCPMain resulting from a empty alignment and a similar issue in RotationAxis.

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10074 7c6358e6-4a41-0410-a743-a5b2a554c398
new SparseSquareMatrix implementation

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10075 7c6358e6-4a41-0410-a743-a5b2a554c398
Fixed bug with RotationAxis effecting a small fraction of 180 deg rotations

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10076 7c6358e6-4a41-0410-a743-a5b2a554c398