in progress

[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 95281c4..72b1b5f 100644 (file)
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -69,6 +69,22 @@ native_ui: ?
 #     Possible values: solid
 #                      gradient
 #                      none
+#
+#  To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return'
+#     Possible values: node_name
+#                      sequence_name
+#                      sequence_acc
+#                      sequence_mol_seq
+#                      sequence_symbol
+#                      taxonomy_scientific_name
+#                      taxonomy_code
+#                      user_selected
+#  To determine where to return data by clicking on "Return ...": 'ext_descendents_data_to_return_on'
+#     Possible values: window
+#                      console
+#  To override label for menu item to return data of external nodes (default ""Return ..."): 'label_for_get_ext_descendents_data'
+#     Example: 'label_for_get_ext_descendents_data: 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'
@@ -86,6 +102,7 @@ native_ui: ?
 #     'internal_labels_are_confidence_values'
 
 
+
 min_confidence_value:                      0.0
 font_family:                               Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
 font_size:                                 10
@@ -118,6 +135,9 @@ allow_editing:                             yes
 internal_labels_are_confidence_values:     no
 replace_underscores_in_nh_parsing:         no
 extract_taxonomy_codes_in_nh_parsing:      yes
+ext_descendents_data_to_return_on:         window
+ext_descendents_data_to_return:            user_selected
+#label_for_get_ext_descendents_data:        Get_Node_Data         
 
 
 
@@ -174,23 +194,28 @@ 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: reroot               display
-click_to: subtree              display
-click_to: swap                 display
-click_to: color_subtree        display
-click_to: open_seq_web         display
-click_to: open_tax_web         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: display_node_data        display
+click_to: collapse_uncollapse      display
+click_to: reroot                   display
+click_to: subtree                  display
+click_to: swap                     display
+click_to: sort_descendants         display
+click_to: color_subtree            display
+click_to: open_seq_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
@@ -236,6 +261,7 @@ gui_menu_text_color:                  0xFFFFFF
 gui_button_border_color:              0x000000
 
 
+
 #  Domain Structure Display Colors
 #  -------------------------------
 domain_structure_base_color:          0x202020
@@ -283,7 +309,10 @@ use_tabbed_display:      yes
 #  EXPERIMENTAL: DO NOT USE!!
 
 default_number_of_bootstrap_resamples: 100
-
+mafft_local:                            /bin/mafft
+clustalo_local:                         C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe
+fastme_local:                           /bin/fastme
+raxml_local:                            /bin/raxml
 
 
 #  Application Specific Settings
@@ -405,43 +434,7 @@ domain_color: PAAD_DAPIN    0x9999CC
 domain_color: NB-ARC        0x500050
 domain_color: WD40          0x888888
 domain_color: RVT_1         0x999900
-domain_color: NOPS          0x505000
-domain_color: RRM_1         0x004400
-domain_color: fn3           0xFFCC00
-domain_color: Ank           0xCC33FF
-domain_color: Pkinase       0x339900
-domain_color: Pkinase_Tyr   0x336600
-domain_color: ig            0x660066
-domain_color: zf-C3HC4      0x6699FF
-domain_color: zf-CCHC       0x6699EE
-domain_color: zf-C2H2       0x6699CC
-domain_color: zf-B_box      0x6699DD
-domain_color: PDZ           0x66FFCC
-domain_color: SH3_2         0x996600
-domain_color: MIRO          0xCCFF00
-domain_color: Myb_DNA-binding 0xDDDDDD
-domain_color: NHL           0x336666
-domain_color: PKD_channel   0x336666
-domain_color: Ion_trans     0x996666
-domain_color: CAP_GLY       0xCC9900
-domain_color: LRR_1         0xFFFF99
-domain_color: LRR_2         0xFFFF66
-domain_color: LRR_3         0xFFFF33
-domain_color: LRR_adjacent  0xFFFF00
-domain_color: LRRCT         0xFFCC99
-domain_color: LRRNT         0xFFCC66
-domain_color: LRRNT_2       0xFFCC33
-domain_color: Ank           0x990099
-domain_color: Sushi         0x004400
-domain_color: ZU5           0xFF9999
-domain_color: V-set         0x3399FF
-domain_color: TPR_1         0xFF1493
-domain_color: TPR_2         0xFF69B4
-domain_color: TPR_3         0xCD6090
-domain_color: TPR_4         0xFF6A6A
-domain_color: TPR_MLP1_2    0x33FF00
-domain_color: Collagen      0xFF7F00
-domain_color: MIF           0xADD8E6
+
 
 
 #  Annotation colors