academic/archeopteryx: Updated for version 0.9917_beta.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

5 files changed, 515 insertions, 9 deletions

diff --git a/academic/archeopteryx/README b/academic/archeopteryx/README
index f5940b6f7f..ed8730cfab 100644
--- a/academic/archeopteryx/README
+++ b/academic/archeopteryx/README
@@ -1,8 +1,8 @@
-Archaeopteryx: visualise, analyse and edit phylogenetic trees 
+Archeopteryx: visualise, analyse and edit phylogenetic trees 
  
-Archaeopteryx is a software tool for the visualization, analysis, and
+Archeopteryx is a software tool for the visualization, analysis, and
 editing of potentially large and highly annotated phylogenetic trees.
-Archaeopteryx (the successor to ATV) is entirely written in the Java
+Archeopteryx (the successor to ATV) is entirely written in the Java
 programming language and is based on the forester libraries.
 
 Please cite:
diff --git a/academic/archeopteryx/_aptx_configuration_file.txt b/academic/archeopteryx/_aptx_configuration_file.txt
new file mode 100644
index 0000000000..a7230a4272
--- /dev/null
+++ b/academic/archeopteryx/_aptx_configuration_file.txt
@@ -0,0 +1,502 @@
+#  User Interface Look and Feel
+#  ----------------------------
+#  Possible values for 'native_ui'
+#    'yes' to use native (system) "look and feel"
+#    'no'  to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
+#    '?'   to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
+#          Archaeopteryx-style "look and feel" otherwise
+
+native_ui: ?
+
+
+
+#  Default Values for Options
+#  --------------------------
+#  Minimal confidence value to be displayed: 'min_confidence_value':
+#     Example: 'min_confidence_value: 50.0' (a commonly used 
+#     value for bootstrap support)
+#
+#  Font family name: 'font_family':
+#     Example: 'font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica'
+#     It is advisable to use more than one value for font_family (in
+#     decreasing order of preference). Font family names have to be
+#     comma separated (no spaces). Spaces in font names have to be
+#     replaced by underscores (e.g. 'Arial_Unicode_MS').
+#
+#  Font size: 'font_size':
+#     Example: 'font_size: 10'
+#
+#  Screen antialias: 'antialias_screen': values: 'yes'/'no'
+#
+#  Show Scale: 'show_scale': values: 'yes'/'no'
+#
+#  Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
+#
+#  Cladogram display type: 'cladogram_type'
+#     Example: 'cladogram_type: non_lined_up'
+#     The three possible values are: lined_up
+#                                    non_lined_up
+#
+#  Default line width for PDF export: 'pdf_export_line_wdith':
+#     Example: 'pdf_export_line_width: 0.5'
+#
+#  Show overview: 'show_overview': values: 'yes'/'no'
+#
+#  Phylogeny graphics type: 'phylogeny_graphics_type':
+#     Example: 'phylogeny_graphics_type: euro_style'
+#     The eight possible values are: rectangular
+#                                    euro_style
+#                                    rounded
+#                                    curved
+#                                    triangular
+#                                    convex
+#                                    unrooted
+#                                    circular
+#
+#  Node label direction for circular and unrooted type: 'node_label_direction':
+#     Example: 'node_label_direction: horizontal'
+#     The two possible values are: horizontal
+#                                  radial
+#
+#  Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
+#
+#  Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
+#
+#  Default node shape size: 'default_node_size'
+#     Example: 'default_node_size: 6'
+#
+#  Default node shape type: 'default_node_shape'
+#     Example: 'default_node_shape: '
+#     Possible values: circle
+#                      rectangle
+#
+#  Default node shape fill: 'default_node_fill'
+#     Example: 'default_node_fill: '
+#     Possible values: solid
+#                      gradient
+#                      none
+#
+#  To determine what data field to return by clicking on "List Node Data": 'list_node_data_field'
+#     Possible values: node_name
+#                      sequence_name
+#                      gene_name
+#                      sequence_acc
+#                      sequence_mol_seq_fasta
+#                      sequence_symbol
+#                      taxonomy_scientific_name
+#                      taxonomy_code
+#                      domains
+#                      domains_collapsed
+#                      seq_annotations
+#                      go_term_ids
+#                      user_selected
+#
+#  To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in'
+#     Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
+#     classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
+#     Possible values: window (for output to window and buffer)
+#                      console (for output to console and buffer)
+#                      buffer_only (for output to buffer only)
+#
+#  To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label'
+#     Example: 'list_node_data_custom_label: Get_Node_Data'
+# 
+#  Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
+#
+#  Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
+#
+#  Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
+#
+#  Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no'
+#
+#  Number of fraction digits for branch length values: 'branch_length_value_digits'
+#
+#  Number of fraction digits for confidence values: 'confidence_value_digits'
+#
+#  To turn on/off background color gradient: background_gradient
+#     Example: 'background_gradient: yes'
+#
+#  To allow/not allow editing (cut, copy, and paste): allow_editing
+#     Example: 'allow_editing: yes'
+#
+#  To allow/not allow thicker strokes for very small trees: allow_thick_strokes
+#     Example: 'allow_thick_strokes: yes'
+#
+#  NH/NHX/Nexus file parsing
+#  -------------------------
+#  To replace underscores with spaces during NH/NHX/Nexus file parsing:
+#     'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
+#
+#  To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
+#  from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
+#     possible values are:
+#     'no'
+#     'pfam_strict'  (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
+#     'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
+#     'aggressive'   (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
+#
+#  Internal node labels are confidence values during NH/NHX/Nexus file parsing:
+#     'internal_labels_are_confidence_values', possible values are 'yes', 'no'
+#
+#  phyloXML parsing
+#  ----------------
+#  To ensure compatibility with all current and future 
+#  phyloXML applications and to detect malformatted and
+#  possibly erroneous data, it is strongly recommended
+#  to enable validation of all phyloXML files
+#  against the XSD Schema (see: http://www.phyloxml.org/),
+#  with:
+#  'validate_against_phyloxml_xsd_schema: true'
+
+
+min_confidence_value:                      0.0
+font_family:                               Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
+font_size:                                 10
+font_size_min:                             2
+font_size_max:                             20
+antialias_screen:                          yes
+show_scale:                                yes
+cladogram_type:                            non_lined_up
+phylogeny_graphics_type:                   rectangular
+node_label_direction:                      horizontal
+show_default_node_shapes_internal:         no
+show_default_node_shapes_external:         no
+show_node_shapes_for_nodes_with_vis_data:  yes 
+default_node_size:                         4
+default_node_shape:                        rectangle
+default_node_fill:                         solid
+pdf_export_line_width:                     0.5
+show_overview:                             yes
+overview_width:                            120
+overview_height:                           120
+overview_placement_type:                   upper_left
+color_labels_same_as_branch_length_values: no
+display_sequence_relations:                no
+show_domain_labels:                        yes
+line_up_renderable_data:                   yes
+right_align_domain_architectures:          no
+show_seq_annotation_ref_sources:           yes
+branch_length_value_digits:                3
+confidence_value_digits:                   2
+background_gradient:                       no
+allow_editing:                             yes
+allow_thick_strokes:                       no
+list_node_data_in:                         window
+list_node_data_field:                      user_selected
+list_node_data_custom_label:         
+#  NH/NHX/Nexus file parsing:
+internal_labels_are_confidence_values:     no
+replace_underscores_in_nh_parsing:         no
+taxonomy_extraction_in_nh_parsing:         no
+#  phyloXML parsing:
+validate_against_phyloxml_xsd_schema:      true
+
+
+#  Checkbox Display Selection
+#  --------------------------
+#  This is used to select which checkboxes to display
+#  and what their initial values should be.
+#  Format: 'name: display|nodisplay yes|no'
+#  Note: if an option is not displayed, it will not be enabled
+#
+#  For the following use '?' to let Archaeopteryx decide (depending on tree):
+#  - 'phylogram'
+#  - 'write_confidence_values'
+#  - 'write_events'
+
+phylogram:                      display   ?
+rollover:                       display   yes
+color_according_to_sequence:    display   no
+color_according_to_species:     display   no
+color_according_to_annotation:  display   no
+show_node_names:                display   yes
+show_seq_names:                 display   yes
+show_seq_symbols:               display   yes
+show_seq_acc:                   display   no
+show_gene_names:                display   yes
+show_taxonomy_code:             display   yes
+show_taxonomy_scientific_names: display   yes
+show_taxonomy_rank:             display   no
+show_taxonomy_common_names:     display   no
+show_taxonomy_images:           display   no
+show_annotations:               display   no
+write_confidence_values:        display   ?
+write_branch_length_values:     display   no
+write_events:                   display   ?
+use_visual_styles:              display   no
+width_branches:                 display   no
+show_domain_architectures:      display   no
+show_msa:                       display   no
+show_binary_characters:         display   no
+show_binary_character_counts:   display   no
+display_internal_data:          display   yes
+dynamically_hide_data:          display   yes
+show_relation_confidence:       display   no
+show_properties:                display   no
+show_vector_data:               display   no
+
+
+
+#  Combo-box Display Selection
+#  ---------------------------
+#  Format: 'name: display/nodisplay'
+click_to: display_node_data        display
+click_to: collapse_uncollapse      display
+click_to: uncollapse_all           display
+click_to: reroot                   display
+click_to: subtree                  display
+click_to: swap                     display
+click_to: order_subtree            display
+click_to: sort_descendants         display
+click_to: color_subtree            display
+click_to: change_node_font         display
+click_to: color_node_font          display
+click_to: open_seq_web             display
+click_to: open_pdb_web             display
+click_to: open_tax_web             display
+click_to: blast                    display
+click_to: cut_subtree              display
+click_to: copy_subtree             display
+click_to: paste_subtree            display
+click_to: delete                   display
+click_to: add_new_node             display
+click_to: edit_node_data           display
+click_to: select_nodes             display
+click_to: get_ext_descendents_data display
+
+#   Default click-to option (any of the above if set to "display")
+default_click_to: display_node_data
+
+
+
+#  Default Tree Display Colors
+#  ---------------------------
+
+display_color: background                 0x000000
+display_color: background_gradient_bottom 0x0000FF
+display_color: sequence                   0xE6E6E6
+display_color: taxonomy                   0xB4B4B4
+display_color: confidence                 0xB4B4B4
+display_color: branch_length              0x8C8C8C
+display_color: branch                     0xFFFFFF
+display_color: node_box                   0xFFFFFF
+display_color: collapsed                  0xFFFFFF
+display_color: matching_a                 0x00FF00
+display_color: matching_b                 0xFF0000
+display_color: matching_a_and_b           0xFFFF00
+display_color: duplication                0xFF0000
+display_color: speciation                 0x00FF00
+display_color: duplication_or_specation   0xFFFF00
+display_color: domain_label               0xE6E6E6
+display_color: domain_base                0x646464
+display_color: binary_domain_combinations 0x4169FF
+display_color: annotation                 0xADFF2F
+display_color: overview                   0x828282
+
+
+
+#  GUI (graphical user interface) Colors
+#  -------------------------------------
+#
+#  These are ignored if native (system) "look and feel"
+#  is being used ('native_ui: yes').
+
+gui_background_color:                 0x202020
+gui_checkbox_text_color:              0xDCDCDC
+gui_checkbox_and_button_active_color: 0xFF0000
+gui_button_text_color:                0xFFFFFF
+gui_button_background_color:          0x404040
+gui_menu_background_color:            0x000000
+gui_menu_text_color:                  0xFFFFFF
+gui_button_border_color:              0x000000
+
+
+#  Vector Data Display Colors and Sizes
+#  ------------------------------------
+vector_data_min_color:                0x0000FF
+vector_data_max_color:                0xFFFF00
+vector_data_mean_color:               0x000000
+vector_data_width:                    120
+vector_data_height:                   12
+
+
+#  Settings Specific for Archaeopteryx Applets (E and A)
+#  -----------------------------------------------------
+#  To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
+
+midpoint_reroot: yes
+
+
+
+#  Settings Specific for ArchaeopteryxE Applets
+#  --------------------------------------------
+#  To hide controls and menus: 'hide_controls_and_menus: yes'
+#  To use tabbed display     : 'use_tabbed_display: yes'
+
+hide_controls_and_menus: no
+use_tabbed_display:      yes
+
+
+
+#  Settings For Phylogenetic Inference
+#  -----------------------------------
+#  EXPERIMENTAL: DO NOT USE!!
+
+default_number_of_bootstrap_resamples: 100
+mafft_local:                            /bin/mafft
+fastme_local:                           /bin/fastme
+raxml_local:                            /bin/raxml
+
+
+
+#  Sequence colors
+#  ---------------
+#  Format: species_color: sequencename hexcolor
+sequence_color: Tubulin-alpha        0xEE0000
+sequence_color: Tubulin-beta         0x00EE00
+
+
+#  Species colors
+#  --------------
+#  Format: species_color: speciesname hexcolor
+species_color: BRAFL        0x00FFFF
+species_color: SPHGR        0x9620F0
+species_color: STRPU        0x9620F0
+species_color: CIOIN        0xFF1CAE
+species_color: CIOSA        0xFF2CAE
+species_color: BOVIN        0x5C3317
+species_color: CANFA        0x8B2323
+species_color: HUMAN        0xFF2400
+species_color: PANTR        0xCC2400
+species_color: MOUSE        0xFF7F00
+species_color: RAT          0xFFEF00
+species_color: MONDO        0xEE9A49
+species_color: ORNAN        0xCD853F
+species_color: XENLA        0x6BAA23
+species_color: XENTR        0x6BAA23
+species_color: CHICK        0xFFC125
+species_color: FUGRU        0x0000FF
+species_color: BRARE        0x0000DD
+species_color: DANRE        0x0000BB
+species_color: TETNG        0x0000AA
+species_color: ORYLA        0x000088
+species_color: GASAC        0x000066
+species_color: CAEEL        0x666699
+species_color: CAEBR        0xB0B0B0
+species_color: DROME        0x663366
+species_color: DROPS        0x996699
+species_color: APIME        0x7A7700
+species_color: AEDAE        0x8C5900
+species_color: TRICA        0x918E00
+species_color: NEMVE        0x0066CC
+species_color: HYDAT        0x3399FF
+species_color: HYDVU        0x3399FF
+species_color: LUBBA        0xF7B5CB
+species_color: GEOCY        0xF5A0BD
+species_color: AMPQE        0x009966
+species_color: SUBDO        0xC790B9
+species_color: MONBE        0xFC0FC0
+species_color: DICPU        0xFFCC33
+species_color: DICDI        0xFFCC00
+species_color: ENTHI        0x5959AB
+species_color: ARATH        0x00FF00
+species_color: POPTR        0x006400
+species_color: VITVI        0x00CD00
+species_color: GLYMA        0x00FF7F
+species_color: ORYSA        0x008B00
+species_color: ORYSJ        0x008C00
+species_color: SORBI        0x00EE76
+species_color: SELMO        0x238E23
+species_color: PHYPA        0x09F911
+species_color: OSTLU        0x7FFF00
+species_color: OSTTA        0x7FFF00
+species_color: OSTRC        0x7FFF00
+species_color: MICPU        0x66CD00
+species_color: MIC99        0x66CD00
+species_color: CHLRE        0xB3EE3A
+species_color: VOLCA        0xC0FF3E
+species_color: CHLSP        0x6B8E23
+species_color: CYAME        0xD02090
+species_color: YEAST        0xAAAAAA
+species_color: BACFR        0xFF0000
+species_color: BACTN        0xFFFF00
+species_color: MYXXD        0x0000FF
+species_color: STIAU        0x00FFFF
+species_color: BACOV        0x8C5900
+species_color: BACUN        0x66CD00
+species_color: PORGI        0x918E00
+# rank: Class
+species_color: Mammalia       0xFF0000
+species_color: mammals        0xFF0000
+# rank: Phylum
+species_color: Chordata       0x8470FF
+species_color: Echinodermata  0x6495ED
+species_color: Hemichordata   0x7EC0EE
+species_color: Arthropoda     0x7AC5CD
+species_color: Nematoda       0x7171C6
+species_color: Tardigrada     0x388E8E
+species_color: Annelida       0xC67171
+species_color: Mollusca       0x00F5FF
+species_color: Ctenophora     0xBBFFFF
+species_color: Cnidaria       0xFF83FA
+species_color: Placozoa       0xEED2EE
+species_color: Porifera       0xFF3E96
+species_color: Microsporidia  0x8B8378
+species_color: Ascomycota     0xFF6347
+species_color: Basidiomycota  0xFFD700
+species_color: Chlorophyta    0x00C78C
+species_color: Streptophyta   0x00C957
+# rank: Kingdom
+species_color: Viridiplantae  0x00FF00
+species_color: plants         0x00FF00
+species_color: Metazoa        0x0000FF
+species_color: animals        0x0000FF
+species_color: Fungi          0xFF9912
+# rank: Superkingdom
+species_color: Viruses        0xFFD700
+species_color: Bacteria       0x00FF00
+species_color: Archaea        0x0000FF
+species_color: Eukaryota      0xFF0000
+species_color: eukaryotes     0xFF0000
+
+
+
+#  Domain colors
+#  -------------
+domain_color: Cofilin_ADF     0xFC0FC0
+domain_color: TIR             0x900000
+domain_color: NACHT           0x202020
+domain_color: CARD            0xFF0000
+domain_color: Peptidase_C14   0x00FF00
+domain_color: Death           0x0000FF
+domain_color: DED             0x00FFFF
+domain_color: BIR             0xCCFF33
+domain_color: PAAD_DAPIN      0x9999CC
+domain_color: NB-ARC          0x500050
+domain_color: WD40            0x888888
+domain_color: RVT_1           0x999900
+domain_color: CBM_48          0xFF0000
+domain_color: Alpha-amylase   0x0000FF
+domain_color: Alpha-amylase_C 0x0080FF
+domain_color: CBM_48          0xFF0000
+domain_color: Alpha-amylase   0x0000FF
+domain_color: Alpha-amylase_C 0x0080FF
+domain_color: GDE_N           0x009000
+domain_color: GDE_C           0x00FF00
+domain_color: hGDE_N          0x990099
+domain_color: GDE_N_bis       0x007000
+domain_color: hGDE_central    0xFF8000
+domain_color: hGDE_amylase    0x0000EE
+domain_color: hDGE_amylase    0x0000EE
+
+
+
+#  Annotation colors
+#  -----------------
+annotation_color: dehydrogenase 0x0000FF
+annotation_color: kinase        0xFF00FF
+annotation_color: protease      0x009900
+annotation_color: transcription 0xAAAA00
+
+
+# END
diff --git a/academic/archeopteryx/archeopteryx.SlackBuild b/academic/archeopteryx/archeopteryx.SlackBuild
index bc74f234cd..c7041a1f24 100644
--- a/academic/archeopteryx/archeopteryx.SlackBuild
+++ b/academic/archeopteryx/archeopteryx.SlackBuild
@@ -23,12 +23,12 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=archeopteryx
-VERSION=${VERSION:-0.9901_beta}
+VERSION=${VERSION:-0.9917_beta}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 SRCNAM=forester
-SRCVER=1038
+SRCVER=1044
 ARCH=noarch
 
 CWD=$(pwd)
@@ -47,6 +47,10 @@ install -D -m755 $CWD/${SRCNAM}_${SRCVER}.jar $PKG/usr/bin/$PRGNAM.jar
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 
+# Include the example configuration file in the package. Copy it in your $HOME.
+mkdir -p $PKG/usr/share/$PRGNAM
+cp $CWD/_aptx_configuration_file.txt $PKG/usr/share/$PRGNAM
+
 # I did not find an icon, so I quickly modified some picture of an archeopteryx...
 mkdir -p $PKG/usr/share/{applications,pixmaps}
 cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
diff --git a/academic/archeopteryx/archeopteryx.info b/academic/archeopteryx/archeopteryx.info
index 6c45f20adc..61071b1cd4 100644
--- a/academic/archeopteryx/archeopteryx.info
+++ b/academic/archeopteryx/archeopteryx.info
@@ -1,8 +1,8 @@
 PRGNAM="archeopteryx"
-VERSION="0.9901_beta"
+VERSION="0.9917_beta"
 HOMEPAGE="https://sites.google.com/site/cmzmasek/home/software/archaeopteryx"
-DOWNLOAD="https://googledrive.com/host/0BxMokdxOh-JRM1d2azFoRnF3bGM/download/forester_1038.jar"
-MD5SUM="e101cba9a22f6df63e9bcd8fa199c029"
+DOWNLOAD="https://dl.dropboxusercontent.com/u/14456265/forester/download/forester_1044.jar"
+MD5SUM="1e55a5eee563e39e0a66b836faf09897"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="jdk"
diff --git a/academic/archeopteryx/slack-desc b/academic/archeopteryx/slack-desc
index 387deab9c7..84df0deffa 100644
--- a/academic/archeopteryx/slack-desc
+++ b/academic/archeopteryx/slack-desc
@@ -8,7 +8,7 @@
             |-----handy-ruler------------------------------------------------------|
 archeopteryx: archeopteryx (Visualise, analyse and edit phylogenetic trees)
 archeopteryx:
-archeopteryx: Archaeopteryx is a software tool for the visualization, analysis,
+archeopteryx: Archeopteryx is a software tool for the visualization, analysis,
 archeopteryx: and editing of potentially large and highly annotated phylogenetic
 archeopteryx: trees.
 archeopteryx: