wrong branch, big sorry

This reverts commit e77d08a6.

Fixes BZDNG-416

the internal representation of a transformation for EntityImpl was changed from Mat4 to Transform
in preparation for adding transformations to entity views; this impacts quite a few higher-level routines
that used the transformation matrix, which now can use the more elegant Transform::Apply method instead;

GetTransformationMatrix and IsTransformationIdentity methods in the EntityHandle interface are marked
as deprecated; use GetTransform and HasTransform instead. In addition, there is a ClearTransform method
which ensures that the internal has_transform flag gets set to false

geom::Transform was extended to offer ApplyInverse, and matrix inversion exceptions are handled internally

constructing a Vec3 from a Vec4 no longer throws a DivideByZero error when w is close to zero, instead it
is silently assumed that this is not a true homogeneous coordinate conversion

as an additional comment (and note to self), atom->GetPos always returns transformed positions; however,
GetAltPos returns original positions, and original positions are also stored in the AtomGroup on the
Impl level. Both the mol unit test as well as the PDB writer expect this behavior; the PDB writer applies
the transform after calling GetAltPos. Commented code is in place now to change this behavior, i.e. have
GetAltPos return transformed positions, making it consistent with GetPos, should this be desired.

behaviour in GaussianSmooth function in table class

to the editor. still messy and no unit tests...

to check for breaking of the in_sequence property.
Added an SetInSequence() function to the ChainHandle to check and update
the in_sequence property

Previously we were returning the wrong index for residues
in chains that contained a certain residue number more
than once. We were always returning the index of the first
residue. Among other things, this fixes BZDNG-229.

Previously we were returning the wrong index for residues
in chains that contained a certain residue number more
than once. We were always returning the index of the first
residue. Among other things, this fixes BZDNG-229.

added QueryFlags handling to mol::QueryViewWrapper
fixed empty pov output (caused by multiple renderer problem in gfx::Entity impl)
removed GLEW_VERSION_2_0 tokens
various tiny gfx tweaks
added stereo toggling key to gui ('=')
added residue reordering to mol::EntityEditor

GetGeometricStart()/GetGeometricEnd() has been deprecated and
will be removed sooner or later.

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2501 5a81b35b-ba03-0410-adc8-b2c5c5119f08

The old signatures are still available in Python, but produce
a deprecation warning. After some time, we will remove the
long signatures completely.

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2113 5a81b35b-ba03-0410-adc8-b2c5c5119f08

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1742 5a81b35b-ba03-0410-adc8-b2c5c5119f08