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 (file)
--- 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 (file)
--- 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 (file)
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 (file)
index 0000000..32ed2fe
--- /dev/null
+++ b/forester/aptx/aptx_example_files/seq_colors_with_species_and_annotations.xml
@@ -0,0 +1,277 @@
+<?xml version="1.0" encoding="UTF-8"?>\r
+<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">\r
+<phylogeny rooted="true" rerootable="true">\r
+  <name>seq name colors example</name>\r
+  <clade>\r
+    <clade>\r
+      <branch_length>0.07475587</branch_length>\r
+      <clade>\r
+        <branch_length>0.10234752</branch_length>\r
+        <clade>\r
+          <name>Gnetum_gnemon_GGM15</name>\r
+          <branch_length>0.4191439</branch_length>\r
+          <taxonomy>\r
+            <id provider="uniprot">3382</id>\r
+            <code>GNEGN</code>\r
+            <scientific_name>Gnetum gnemon</scientific_name>\r
+            <common_name>Bago</common_name>\r
+            <synonym>Gnetum acutatum</synonym>\r
+            <rank>species</rank>\r
+          </taxonomy>\r
+          <sequence>\r
+            <name>Tubulin-alpha</name>\r
+            <annotation ref="subtree:A"></annotation>\r
+          </sequence>\r
+        </clade>\r
+        <clade>\r
+          <name>Picea_abies_DAL12</name>\r
+          <branch_length>0.37097505</branch_length>\r
+          <taxonomy>\r
+            <id provider="uniprot">3329</id>\r
+            <code>PICAB</code>\r
+            <scientific_name>Picea abies</scientific_name>\r
+            <common_name>Norway spruce</common_name>\r
+            <synonym>Picea excelsa</synonym>\r
+            <rank>species</rank>\r
+          </taxonomy>\r
+          <sequence>\r
+            <name>Tubulin-beta</name>\r
+            <annotation ref="subtree:A"></annotation>\r
+          </sequence>\r
+        </clade>\r
+      </clade>\r
+      <clade>\r
+        <branch_length>0.07836347</branch_length>\r
+        <clade>\r
+          <name>Gnetum_gnemon_GGM2</name>\r
+          <branch_length>0.32192346</branch_length>\r
+          <taxonomy>\r
+            <id provider="uniprot">3382</id>\r
+            <code>GNEGN</code>\r
+            <scientific_name>Gnetum gnemon</scientific_name>\r
+            <common_name>Bago</common_name>\r
+            <synonym>Gnetum acutatum</synonym>\r
+            <rank>species</rank>\r
+          </taxonomy>\r
+          <sequence>\r
+            <name>Tubulin-beta</name>\r
+            <annotation ref="subtree:A"></annotation>\r
+          </sequence>\r
+        </clade>\r
+        <clade>\r
+          <branch_length>0.13691099</branch_length>\r
+          <clade>\r
+            <name>Picea_abies_DAL13</name>\r
+            <branch_length>0.17518067</branch_length>\r
+            <taxonomy>\r
+              <id provider="uniprot">3329</id>\r
+              <code>PICAB</code>\r
+              <scientific_name>Picea abies</scientific_name>\r
+              <common_name>Norway spruce</common_name>\r
+              <synonym>Picea excelsa</synonym>\r
+              <rank>species</rank>\r
+            </taxonomy>\r
+            <sequence>\r
+              <name>Tubulin-alpha</name>\r
+              <annotation ref="subtree:A"></annotation>\r
+            </sequence>\r
+          </clade>\r
+          <clade>\r
+            <name>Picea_abies_DAL11</name>\r
+            <branch_length>0.22006623</branch_length>\r
+            <taxonomy>\r
+              <id provider="uniprot">3329</id>\r
+              <code>PICAB</code>\r
+              <scientific_name>Picea abies</scientific_name>\r
+              <common_name>Norway spruce</common_name>\r
+              <synonym>Picea excelsa</synonym>\r
+              <rank>species</rank>\r
+            </taxonomy>\r
+            <sequence>\r
+              <name>Tubulin-alpha</name>\r
+              <annotation ref="subtree:A"></annotation>\r
+            </sequence>\r
+          </clade>\r
+        </clade>\r
+      </clade>\r
+    </clade>\r
+    <clade>\r
+      <branch_length>0.065986283</branch_length>\r
+      <clade>\r
+        <branch_length>0.065986283</branch_length>\r
+        <clade>\r
+          <name>Amborella_trichopoda_AmAP3</name>\r
+          <branch_length>0.16098303</branch_length>\r
+          <taxonomy>\r
+            <id provider="uniprot">13333</id>\r
+            <code>AMBTC</code>\r
+            <scientific_name>Amborella trichopoda</scientific_name>\r
+            <rank>species</rank>\r
+          </taxonomy>\r
+          <sequence>\r
+            <name>Tubulin-alpha</name>\r
+            <annotation ref="subtree:B"></annotation>\r
+          </sequence>\r
+        </clade>\r
+        <clade>\r
+          <branch_length>0.1882019</branch_length>\r
+          <clade>\r
+            <name>Nuphar_advena_Nu.ad.AP3.1</name>\r
+            <branch_length>0.076055825</branch_length>\r
+            <taxonomy>\r
+              <id provider="uniprot">77108</id>\r
+              <code>NUPAD</code>\r
+              <scientific_name>Nuphar advena</scientific_name>\r
+              <common_name>Common spatterdock</common_name>\r
+              <synonym>Nuphar lutea subsp. advena</synonym>\r
+              <rank>species</rank>\r
+            </taxonomy>\r
+            <sequence>\r
+              <name>Tubulin-alpha</name>\r
+              <annotation ref="subtree:B"></annotation>\r
+            </sequence>\r
+          </clade>\r
+          <clade>\r
+            <name>Nuphar_advena_Nu.ad.AP3.2</name>\r
+            <branch_length>0.045621026</branch_length>\r
+            <taxonomy>\r
+              <id provider="uniprot">77108</id>\r
+              <code>NUPAD</code>\r
+              <scientific_name>Nuphar advena</scientific_name>\r
+              <common_name>Common spatterdock</common_name>\r
+              <synonym>Nuphar lutea subsp. advena</synonym>\r
+              <rank>species</rank>\r
+            </taxonomy>\r
+            <sequence>\r
+              <name>Tubulin-alpha</name>\r
+              <annotation ref="subtree:B"></annotation>\r
+            </sequence>\r
+          </clade>\r
+        </clade>\r
+      </clade>\r
+      <clade>\r
+        <branch_length>0.07475587</branch_length>\r
+        <clade>\r
+          <branch_length>0.10234752</branch_length>\r
+          <clade>\r
+            <name>Gnetum_gnemon_GGM15</name>\r
+            <branch_length>0.4191439</branch_length>\r
+            <taxonomy>\r
+              <id provider="uniprot">3382</id>\r
+              <code>GNEGN</code>\r
+              <scientific_name>Gnetum gnemon</scientific_name>\r
+              <common_name>Bago</common_name>\r
+              <synonym>Gnetum acutatum</synonym>\r
+              <rank>species</rank>\r
+            </taxonomy>\r
+            <sequence>\r
+              <name>Tubulin-alpha</name>\r
+              <annotation ref="subtree:B"></annotation>\r
+            </sequence>\r
+          </clade>\r
+          <clade>\r
+            <name>Picea_abies_DAL12</name>\r
+            <branch_length>0.37097505</branch_length>\r
+            <taxonomy>\r
+              <id provider="uniprot">3329</id>\r
+              <code>PICAB</code>\r
+              <scientific_name>Picea abies</scientific_name>\r
+              <common_name>Norway spruce</common_name>\r
+              <synonym>Picea excelsa</synonym>\r
+              <rank>species</rank>\r
+            </taxonomy>\r
+            <sequence>\r
+              <name>Tubulin-beta</name>\r
+              <annotation ref="subtree:B"></annotation>\r
+            </sequence>\r
+          </clade>\r
+        </clade>\r
+        <clade>\r
+          <branch_length>0.07836347</branch_length>\r
+          <clade>\r
+            <name>Gnetum_gnemon_GGM2</name>\r
+            <branch_length>0.32192346</branch_length>\r
+            <taxonomy>\r
+              <id provider="uniprot">3382</id>\r
+              <code>GNEGN</code>\r
+              <scientific_name>Gnetum gnemon</scientific_name>\r
+              <common_name>Bago</common_name>\r
+              <synonym>Gnetum acutatum</synonym>\r
+              <rank>species</rank>\r
+            </taxonomy>\r
+            <sequence>\r
+              <name>Tubulin-beta</name>\r
+              <annotation ref="subtree:B"></annotation>\r
+            </sequence>\r
+          </clade>\r
+          <clade>\r
+            <branch_length>0.13691099</branch_length>\r
+            <clade>\r
+              <name>Picea_abies_DAL13</name>\r
+              <branch_length>0.17518067</branch_length>\r
+              <taxonomy>\r
+                <id provider="uniprot">3329</id>\r
+                <code>PICAB</code>\r
+                <scientific_name>Picea abies</scientific_name>\r
+                <common_name>Norway spruce</common_name>\r
+                <synonym>Picea excelsa</synonym>\r
+                <rank>species</rank>\r
+              </taxonomy>\r
+              <sequence>\r
+                <name>Tubulin-delta</name>\r
+                <annotation ref="subtree:B"></annotation>\r
+              </sequence>\r
+            </clade>\r
+            <clade>\r
+              <name>Picea_abies_DAL11</name>\r
+              <branch_length>0.22006623</branch_length>\r
+              <taxonomy>\r
+                <id provider="uniprot">3329</id>\r
+                <code>PICAB</code>\r
+                <scientific_name>Picea abies</scientific_name>\r
+                <common_name>Norway spruce</common_name>\r
+                <synonym>Picea excelsa</synonym>\r
+                <rank>species</rank>\r
+              </taxonomy>\r
+              <sequence>\r
+                <name>Tubulin-delta</name>\r
+                <annotation ref="subtree:B"></annotation>\r
+              </sequence>\r
+            </clade>\r
+          </clade>\r
+        </clade>\r
+      </clade>\r
+    </clade>\r
+    <clade>\r
+      <branch_length>0.13691099</branch_length>\r
+      <clade>\r
+        <name>Picea_abies_DAL13</name>\r
+        <branch_length>0.17518067</branch_length>\r
+        <taxonomy>\r
+          <id provider="uniprot">3329</id>\r
+          <code>PICAB</code>\r
+          <scientific_name>Picea abies</scientific_name>\r
+          <common_name>Norway spruce</common_name>\r
+          <synonym>Picea excelsa</synonym>\r
+          <rank>species</rank>\r
+        </taxonomy>\r
+        <sequence>\r
+          <name>Tubulin-epsilon</name>\r
+        </sequence>\r
+      </clade>\r
+      <clade>\r
+        <name>Picea_abies_DAL11</name>\r
+        <branch_length>0.22006623</branch_length>\r
+        <taxonomy>\r
+          <id provider="uniprot">3329</id>\r
+          <code>PICAB</code>\r
+          <scientific_name>Picea abies</scientific_name>\r
+          <common_name>Norway spruce</common_name>\r
+          <synonym>Picea excelsa</synonym>\r
+          <rank>species</rank>\r
+        </taxonomy>\r
+      </clade>\r
+    </clade>\r
+  </clade>\r
+</phylogeny>\r
+</phyloxml>
\ No newline at end of file