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[jalview.git] / forester / aptx / aptx_configuration_files / _aptx_configuration_file
diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
index 0ff3dc7..47e84d0 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -163,7 +163,6 @@ font_size_min:                             2
 font_size_max:                             20
 antialias_screen:                          yes
 show_scale:                                yes
-show_branch_length_values:                 no
 cladogram_type:                            ext_node_sum_dep
 phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
@@ -172,7 +171,6 @@ show_default_node_shapes_external:         no
 default_node_size:                         4
 default_node_shape:                        rectangle
 default_node_fill:                         solid
-taxonomy_colorize_node_shapes:             no
 #graphics_export_x:                         595
 #graphics_export_y:                         792
 pdf_export_line_width:                     0.5
@@ -183,6 +181,8 @@ 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:                   no
+right_align_domain_architectures:          no
 show_seq_annotation_ref_sources:           yes
 branch_length_value_digits:                3
 confidence_value_digits:                   3
@@ -212,7 +212,8 @@ validate_against_phyloxml_xsd_schema:      true
 
 phylogram:                      display   ?
 rollover:                       display   yes
-color_according_to_species:     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
@@ -222,13 +223,15 @@ show_gene_names:                display   yes
 show_taxonomy_code:             display   yes
 show_taxonomy_scientific_names: display   yes
 show_taxonomy_common_names:     display   no
-show_taxonomy_images:           display   yes
+show_taxonomy_images:           display   no
 show_annotations:               display   no
 write_confidence_values:        display   ?
+write_branch_length_values:     display   no
 write_events:                   display   ?
-color_branches:                 display   no
+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
@@ -249,7 +252,10 @@ click_to: subtree                  display
 click_to: swap                     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
@@ -271,18 +277,21 @@ default_click_to: display_node_data
 
 display_color: background                 0x000000
 display_color: background_gradient_bottom 0x0000FF
-display_color: sequence                   0xDCDCDC
+display_color: sequence                   0xE6E6E6
 display_color: taxonomy                   0xB4B4B4
-display_color: confidence                 0x38B0DE
+display_color: confidence                 0xB4B4B4
 display_color: branch_length              0x8C8C8C
 display_color: branch                     0xFFFFFF
 display_color: node_box                   0xFFFFFF
-display_color: collapsed                  0xFFFF00
-display_color: matching_nodes             0x00FF00
+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: domains                    0x7B68EE
+display_color: domain_label               0xE6E6E6
+display_color: domain_base                0x646464
 display_color: binary_domain_combinations 0x4169FF
 display_color: annotation                 0xADFF2F
 display_color: overview                   0x828282
@@ -305,12 +314,13 @@ gui_menu_text_color:                  0xFFFFFF
 gui_button_border_color:              0x000000
 
 
-
-#  Domain Structure Display Colors
-#  -------------------------------
-domain_structure_base_color:          0x202020
-domain_structure_font_color:          0x909090
-
+#  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)
@@ -342,6 +352,13 @@ 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
@@ -444,27 +461,40 @@ 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: 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