Enable vtkTree I/O with R and multiple inputs in vtkRCalculaterFilter.

1: Implemented the conversion between a
R phylo tree and a VTKTree.

A R "phylo" tree is a list of 5 elements, including:
edge, Nnode,edge.length, tip.label, node.label.

The indexing convension of the vertices of a tree is
different between a "phylo" tree and the vtk tree.

2: Modified the vtkRCalculaterFilter so that it can take
in multipe input data types.For example,now you could add
a table, a tree and an array to the input port 0. The filter
will convert all vtk data inputs into R variables before
running the RScripts. For now, the ouput number remains to be
one. In the future, further modifications are needed to allow
multiple outputs.

Change-Id: Iba030e0d207c204aacec1e3058fb60bc954ffea0
Fix and enhance the protein ribbon filter.

Add descriptions to vtkProteinRibbonFilter parameters.
Add a parameter to enable the small molecules visualization.
Those small molecules are now correctly represented (the atom type
fetched from the PDB file and then used was not the atom element
but was related to the atom and residue nomenclature described
in the Chemical Component Dictionary).
vtkMoleculeReader now exports the atom_type array containing the
element atomic number minus 1.
The test now uses a new PDB file.

Change-Id: I38207446635afbcdc573e3b27ca3745f885ea57a
Fix subclasses of vtkMoleculeReaderBase to work with new pipeline.

Several arrays in the output PointData were not filled, leading to
crashes in some tests.

Change-Id: Iff6e31c4dacae6f73d03b351aea8111dc54d5680
Fix bug in vtkScalarsToColorsPainter when passing attributes

This fixes a bug in the vtkScalarsToColorsPainter that would
delete the active scalars array from the input data set instead
of just unsetting it as the active scalars array.

Change-Id: I3b92683a5db28b1066480512468a43ca56721d5c
vtkImageToAMR filter to convert image to AMR.

Change-Id: I9b3a7e3f7599fd5890fedc2cf6ea97081f69f116
Merge topic 'fix-scalars-to-colors' into master

e32a2935 Fix bug in vtkScalarsToColorsPainter when passing attributes
Merge topic 'fix-glsl-shader-device-adaptor2' into pv-master

816dd16 Allow vtkShaderDeviceAdaptor2 objects to be passed via vtkInformation
751ee6c Fix bug with setting the shader program vtkGLSLShaderDeviceAdapter2
Merge topic 'update_vtk_master' into pv-master

260b45d Merge branch 'release'
293d1af Increment version to VTK 5.10.1
bf3ac65 Merge branch 'release'
d99c409 Merge branch 'netcdf_mangling_fixes_rel' into release
b895324 Merge topic 'netcdf_mangling_release_merge' into master
ed2afac Merge topic 'FixTestEmptyInput' into master
4977914 Merge topic 'CubeAxesTransparency' into master
2ffb6a7 Merge topic 'chartxyz-scene-bug' into master
1b40557 Merge topic 'fix-glsl-shader-device-adaptor2' into master
33dae29 Merge topic 'vtk_warning_fixes' into master
da39820 Merge topic 'GL2PSSyncUpstream' into master
8de5a0f really suppress linker warning
d76ba07 Merge topic 'fix-amr-windows-warnings' into master
b9a220c Merge topic 'Coverage_TimePointUtility' into master
13ddc51 Sync with svn version of gl2ps.
751913d Implement HasTranslucentPolygonalGeometry for AxisActors.
...
Merge remote branch 'pvvtk/pv-master' into HEAD

* pvvtk/pv-master:
Merge topic 'AddVTKTreeToRInterface' into master

2dc9be8e Enable vtkTree I/O with R and multiple inputs in vtkRCalculaterFilter.
Merge topic 'image-to-amr' into master

5db22a6e vtkImageToAMR filter to convert image to AMR.
Merge topic 'ChemistryFixes' into master

d34861b8 Fix subclasses of vtkMoleculeReaderBase to work with new pipeline.
fix windows-only compilation error

Change-Id: Ide66075048529982c89c878619c54652b7bb70bb
Merge topic 'fix-compiling-errors' into master

d16592e0 fix windows-only compilation error
Merge topic 'enhance-proteinribbonfilter' into master

956fecdb Fix and enhance the protein ribbon filter.
Fix hardwareSelector unsigned/signed operations

Change-Id: I712df0e28d5da6f18ed53e13d6f17917902c3dae
Merge topic 'fix_hardware_selector_warnings' into master

4b15fba7 Fix hardwareSelector unsigned/signed operations
BUG: Test failing on Windows platforms

Sloppy cut/paste error cause failures on windows platforms.

Change-Id: I014b1964638433ff16719bb4c21d073f3773b652
Merge topic 'BUG_TestXMLFileOutputWindow' into master

4d01126a BUG: Test failing on Windows platforms