git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
in progress
[jalview.git] / forester / aptx / aptx_configuration_files / _aptx_configuration_file_1
diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
index 432efba..1c1da51 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
@@ -107,9 +107,13 @@ native_ui: ?
 #  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) from node names during NH/NHX/Nexus file parsing:
-#     'taxonomy_extraction_in_nh_parsing',
-#     possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), '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'
@@ -121,7 +125,6 @@ font_family:                               Arial,Helvetica,Verdana,Tahoma,Dialog
 font_size:                                 10
 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
@@ -130,7 +133,6 @@ 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
@@ -141,8 +143,10 @@ 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
 branch_length_value_digits:                3
-confidence_value_digits:                   3
+confidence_value_digits:                   2
 background_gradient:                       no
 allow_editing:                             yes
 ext_descendents_data_to_return_on:         window
@@ -151,7 +155,7 @@ ext_descendents_data_to_return:            user_selected
 #  NH/NHX/Nexus file parsing:
 internal_labels_are_confidence_values:     no
 replace_underscores_in_nh_parsing:         no
-taxonomy_extraction_in_nh_parsing:         pfam    
+taxonomy_extraction_in_nh_parsing:         pfam_relaxed    
 
 
 
@@ -183,6 +187,7 @@ validate_against_phyloxml_xsd_schema: true
 
 phylogram:                      display   ?
 rollover:                       display   yes
+color_according_to_sequence:    display   no
 color_according_to_species:     display   no
 color_according_to_annotation:  nodisplay no
 show_node_names:                display   yes
@@ -195,10 +200,12 @@ show_taxonomy_common_names:     nodisplay no
 show_taxonomy_images:           nodisplay no
 show_annotations:               nodisplay no
 write_confidence_values:        display   ?
+write_branch_length_values:     display   no
 write_events:                   nodisplay no
-color_branches:                 display   no
+use_visual_styles:              display   no
 width_branches:                 display   no
 show_domain_architectures:      nodisplay no
+show_msa:                       nodisplay no
 show_binary_characters:         nodisplay no
 show_binary_character_counts:   nodisplay no
 display_internal_data:          display   yes
@@ -219,6 +226,7 @@ click_to: swap                     display
 click_to: sort_descendants         display
 click_to: color_subtree            display
 click_to: open_seq_web             nodisplay
+click_to: open_pdb_web             nodisplay
 click_to: open_tax_web             nodisplay
 click_to: blast                    nodisplay
 click_to: cut_subtree              nodisplay
@@ -239,18 +247,21 @@ 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
@@ -292,6 +303,13 @@ use_tabbed_display:      yes
 
 
 
+#  Sequence colors
+#  ---------------
+#  Format: species_color: sequencename hexcolor
+sequence_color: Tubulin-alpha        0xEE0000
+sequence_color: Tubulin-beta         0x00EE00
+
+
 #  Species colors
 #  --------------
 #  Format: species_color: speciesname hexcolor
@@ -394,4 +412,44 @@ 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
\ No newline at end of file