From b672af9df6c53154840bf9bc08d96b732ca737db Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 6 Dec 2012 02:14:10 +0000 Subject: [PATCH] work on taxonomy extraction for applets for aLeaves MAFFT suite --- .../_aptx_configuration_file | 24 +++++++++-------- .../_aptx_configuration_file_1 | 28 ++++++++++++-------- 2 files changed, 30 insertions(+), 22 deletions(-) diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index 5d721dd..36217a6 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -97,12 +97,15 @@ native_ui: ? # # NH/NHX/Nexus file parsing # ------------------------- -# To replace underscores with spaces during NH/NHX/Nexus file parsing (application only): -# 'replace_underscores_in_nh_parsing' -# To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694') -# during NH/NHX/Nexus file parsing (application only): 'taxonomy_extraction_in_nh_parsing' -# Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only): -# 'internal_labels_are_confidence_values' +# 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' +# +# Internal node labels are confidence values during NH/NHX/Nexus file parsing: +# 'internal_labels_are_confidence_values', possible values are 'yes', 'no' @@ -148,14 +151,13 @@ branch_length_value_digits: 3 confidence_value_digits: 3 background_gradient: no allow_editing: yes -# NH/NHX/Nexus file parsing (application only): -internal_labels_are_confidence_values: no -replace_underscores_in_nh_parsing: no -taxonomy_extraction_in_nh_parsing: pfam ext_descendents_data_to_return_on: window ext_descendents_data_to_return: user_selected #label_for_get_ext_descendents_data: Get_Node_Data - +# NH/NHX/Nexus file parsing: +internal_labels_are_confidence_values: no +replace_underscores_in_nh_parsing: no +taxonomy_extraction_in_nh_parsing: pfam # Checkbox Display Selection diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 index aafebdb..69cf370 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 @@ -94,12 +94,18 @@ native_ui: ? # Example: 'background_gradient: yes' # To allow/not allow editing (cut, copy, and paste): allow_editing # Example: 'allow_editing: yes' -# To replace underscores with spaces during NH/NHX/Nexus file parsing (application only): -# 'replace_underscores_in_nh_parsing' -# To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694') -# during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing' -# Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only): -# 'internal_labels_are_confidence_values' +# +# 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) 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' +# +# Internal node labels are confidence values during NH/NHX/Nexus file parsing: +# 'internal_labels_are_confidence_values', possible values are 'yes', 'no' @@ -131,13 +137,13 @@ branch_length_value_digits: 3 confidence_value_digits: 3 background_gradient: no allow_editing: yes -# NH/NHX/Nexus file parsing (application only): -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: node_name +ext_descendents_data_to_return: user_selected #label_for_get_ext_descendents_data: Get_Node_Data +# NH/NHX/Nexus file parsing: +internal_labels_are_confidence_values: no +replace_underscores_in_nh_parsing: no +taxonomy_extraction_in_nh_parsing: pfam -- 1.7.10.2