Various bug fixes and features for genomic alignments including a table of overlapping alignments and alternating shades for blocks.

Bio/EnsEMBL/GlyphSet.pm => Removed scaling constraint from draw_cigar_feature method.
Bio/EnsEMBL/GlyphSet/_alignment_multiple.pm => Added alternating shades to GenomicAlignBlock objects to distinguish separate blocks. Define a zmenu for the Region and individual Blocks for GenomicAlignBlock objects (not ConstrainedElements). Group together elements from low coverage species. Added cigar string to enable the display of cigar glyphs.
Bio/EnsEMBL/GlyphSet/_alignment_pairwise.pm => Added full target_species alignment parameters to align variable
EnsEMBL/Web/Component.pm => Split check_for_align_errors into 2 methods: check_for_align_in_database and check_for_missing_species.
EnsEMBL/Web/Component/Compara_Alignments.pm => Parse the align parameter to extract the target species and target slice. Group the alignments according to group_id and dbID. Draw a table to select overlapping alignments.
EnsEMBL/Web/ZMenu/MultipleAlignment.pm => Added full target_species alignment parameters to align variable. Added This region and This block entries to the zmenu
EnsEMBL/Web/ZMenu/PairwiseAlignment.pm => Added full target_species alignment parameters to align variable
Merge branch 'master' of https://github.com/Ensembl/ensembl-webcode
Merge pull request #25 from kathryn-beal/master

Master