X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Faptx%2Faptx_configuration_files%2F_aptx_configuration_file;h=acf39bb6f4b52bc2df29599f3e8490a7d0a456b9;hb=b645b534c071c9c9e882d550eb38169190d32d30;hp=557f6225c35fa82a11414273e5e846a1a0c94d92;hpb=01a0ff8da9b487ca626059dab5f6bf9eea98ae77;p=jalview.git diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index 557f622..acf39bb 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -80,6 +80,7 @@ native_ui: ? # sequence_symbol # taxonomy_scientific_name # taxonomy_code +# taxonomy_common_name # user_selected # # To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on' @@ -107,9 +108,13 @@ 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' @@ -131,7 +136,7 @@ validate_against_phyloxml_xsd_schema: true min_confidence_value: 0.0 -font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans +font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans font_size: 10 font_size_min: 2 font_size_max: 20 @@ -162,12 +167,12 @@ confidence_value_digits: 3 background_gradient: no allow_editing: yes ext_descendents_data_to_return_on: window -ext_descendents_data_to_return: sequence_mol_seq_fasta +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: yes +taxonomy_extraction_in_nh_parsing: no # Checkbox Display Selection @@ -284,8 +289,8 @@ domain_structure_font_color: 0x909090 -# Settings Specific for Archaeopteryx Applets -# ------------------------------------------- +# Settings Specific for Archaeopteryx Applets (E and A) +# ----------------------------------------------------- # To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes' midpoint_reroot: yes @@ -312,76 +317,75 @@ fastme_local: /bin/fastme raxml_local: /bin/raxml -# Application Specific Settings -# ----------------------------- # 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 0xA0A0A0 -species_color: CAEBR 0xB0B0B0 -species_color: DROME 0x706F00 -species_color: DROPS 0x504F00 -species_color: APIME 0x7A7700 -species_color: AEDAE 0x8C5900 -species_color: TRICA 0x918E00 -species_color: NEMVE 0xAABADD -species_color: HYDAT 0x7C9BCF -species_color: LUBBA 0xF7B5CB -species_color: GEOCY 0xF5A0BD -species_color: SUBDO 0xC790B9 -species_color: MONBE 0xFC0FC0 -species_color: DICPU 0x23238E -species_color: DICDI 0x4D4DFF -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 +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: Homo_sapiens 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 0xA0A0A0 +species_color: CAEBR 0xB0B0B0 +species_color: DROME 0x706F00 +species_color: DROPS 0x504F00 +species_color: APIME 0x7A7700 +species_color: AEDAE 0x8C5900 +species_color: TRICA 0x918E00 +species_color: NEMVE 0xAABADD +species_color: HYDAT 0x7C9BCF +species_color: LUBBA 0xF7B5CB +species_color: GEOCY 0xF5A0BD +species_color: SUBDO 0xC790B9 +species_color: MONBE 0xFC0FC0 +species_color: DICPU 0x23238E +species_color: DICDI 0x4D4DFF +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