From: cmzmasek@gmail.com Date: Mon, 23 Jun 2014 21:25:43 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dd8e6f3ab54507a5e4f1e66b3270eb6946cee5d7;p=jalview.git in progress --- diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index 7388b82..1c417bb 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -211,6 +211,7 @@ 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: display no show_node_names: display yes @@ -346,6 +347,13 @@ 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 @@ -448,9 +456,10 @@ 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 @@ -463,15 +472,12 @@ 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 @@ -481,9 +487,9 @@ domain_color: hGDE_amylase 0x0000EE domain_color: hDGE_amylase 0x0000EE + # Annotation colors # ----------------- - annotation_color: dehydrogenase 0x0000FF annotation_color: kinase 0xFF00FF annotation_color: protease 0x009900 diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 index 34e7723..8b41305 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 @@ -186,6 +186,7 @@ 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 @@ -298,6 +299,13 @@ 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 @@ -400,4 +408,44 @@ 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 diff --git a/forester/aptx/aptx_example_files/demo_colors.nhx b/forester/aptx/aptx_example_files/demo_colors.nhx deleted file mode 100644 index 700c8cf..0000000 --- a/forester/aptx/aptx_example_files/demo_colors.nhx +++ /dev/null @@ -1,6 +0,0 @@ -((red1:12[&&NHX:C=200.0.0],red2:12[&&NHX:C=155.0.0],red3:12[&&NHX:C=55.0.0],red4:12[&&NHX:C=30.0.0])red:12[&&NHX:C=255.0.0], - (jean1:12[&&NHX:C=100.50.0],jean2:12[&&NHX:C=100.0.40])jean:12[&&NHX:C=100.100.100], - (bred:12[&&NHX:C=255.0.0],bgreen:12[&&NHX:C=0.255.0])black:12[&&NHX:C=0.0.0], - (green1:12[&&NHX:C=0.50.0],green2:12[&&NHX:C=0.150.0])green:12[&&NHX:C=0.255.0], - (purp1:12[&&NHX:C=200.0.200],purp2:12[&&NHX:C=155.0.155])purp:12[&&NHX:C=255.0.255], - (yello1:12[&&NHX:C=200.150.0],yello2:12[&&NHX:C=155.100.0])yello:12[&&NHX:C=255.255.0])root:12[&&NHX:C=0.255.255]; diff --git a/forester/aptx/aptx_example_files/seq_colors_with_species_and_annotations.xml b/forester/aptx/aptx_example_files/seq_colors_with_species_and_annotations.xml new file mode 100644 index 0000000..32ed2fe --- /dev/null +++ b/forester/aptx/aptx_example_files/seq_colors_with_species_and_annotations.xml @@ -0,0 +1,277 @@ + + + + seq name colors example + + + 0.07475587 + + 0.10234752 + + Gnetum_gnemon_GGM15 + 0.4191439 + + 3382 + GNEGN + Gnetum gnemon + Bago + Gnetum acutatum + species + + + Tubulin-alpha + + + + + Picea_abies_DAL12 + 0.37097505 + + 3329 + PICAB + Picea abies + Norway spruce + Picea excelsa + species + + + Tubulin-beta + + + + + + 0.07836347 + + Gnetum_gnemon_GGM2 + 0.32192346 + + 3382 + GNEGN + Gnetum gnemon + Bago + Gnetum acutatum + species + + + Tubulin-beta + + + + + 0.13691099 + + Picea_abies_DAL13 + 0.17518067 + + 3329 + PICAB + Picea abies + Norway spruce + Picea excelsa + species + + + Tubulin-alpha + + + + + Picea_abies_DAL11 + 0.22006623 + + 3329 + PICAB + Picea abies + Norway spruce + Picea excelsa + species + + + Tubulin-alpha + + + + + + + + 0.065986283 + + 0.065986283 + + Amborella_trichopoda_AmAP3 + 0.16098303 + + 13333 + AMBTC + Amborella trichopoda + species + + + Tubulin-alpha + + + + + 0.1882019 + + Nuphar_advena_Nu.ad.AP3.1 + 0.076055825 + + 77108 + NUPAD + Nuphar advena + Common spatterdock + Nuphar lutea subsp. advena + species + + + Tubulin-alpha + + + + + Nuphar_advena_Nu.ad.AP3.2 + 0.045621026 + + 77108 + NUPAD + Nuphar advena + Common spatterdock + Nuphar lutea subsp. advena + species + + + Tubulin-alpha + + + + + + + 0.07475587 + + 0.10234752 + + Gnetum_gnemon_GGM15 + 0.4191439 + + 3382 + GNEGN + Gnetum gnemon + Bago + Gnetum acutatum + species + + + Tubulin-alpha + + + + + Picea_abies_DAL12 + 0.37097505 + + 3329 + PICAB + Picea abies + Norway spruce + Picea excelsa + species + + + Tubulin-beta + + + + + + 0.07836347 + + Gnetum_gnemon_GGM2 + 0.32192346 + + 3382 + GNEGN + Gnetum gnemon + Bago + Gnetum acutatum + species + + + Tubulin-beta + + + + + 0.13691099 + + Picea_abies_DAL13 + 0.17518067 + + 3329 + PICAB + Picea abies + Norway spruce + Picea excelsa + species + + + Tubulin-delta + + + + + Picea_abies_DAL11 + 0.22006623 + + 3329 + PICAB + Picea abies + Norway spruce + Picea excelsa + species + + + Tubulin-delta + + + + + + + + + 0.13691099 + + Picea_abies_DAL13 + 0.17518067 + + 3329 + PICAB + Picea abies + Norway spruce + Picea excelsa + species + + + Tubulin-epsilon + + + + Picea_abies_DAL11 + 0.22006623 + + 3329 + PICAB + Picea abies + Norway spruce + Picea excelsa + species + + + + + + \ No newline at end of file