From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 8 Jan 2013 20:31:11 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=83f94e1775efaf3fb0bd6540ed3eba5a9da59ddd;p=jalview.git

inprogress
---

diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
index fbb52fe..ce8cb3b 100644
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file
@@ -57,7 +57,8 @@ native_ui: ?
 #     Example: 'node_label_direction: horizontal'
 #     The two possible values are: horizontal
 #                                  radial
-#  Show default node shape: 'show_default_node_shapes': values: 'yes'/'no'
+#  Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
+#  Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
 #  Default node shape size: 'default_node_size'
 #     Example: 'default_node_size: 6'
 #  Default node shape type: 'default_node_shape'
@@ -137,7 +138,8 @@ show_branch_length_values:                 no
 cladogram_type:                            ext_node_sum_dep
 phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
-show_default_node_shapes:                  no
+show_default_node_shapes_internal:         no
+show_default_node_shapes_external:         no
 default_node_size:                         6
 default_node_shape:                        circle
 default_node_fill:                         gradient
@@ -165,14 +167,6 @@ replace_underscores_in_nh_parsing:         no
 taxonomy_extraction_in_nh_parsing:         pfam
 
 
-
-#  Initial Window Size for Application and ArchaeopteryA applet
-#  ------------------------------------------------------------
-window_initial_size_x: 800
-window_initial_size_y: 800
-
-
-
 #  Checkbox Display Selection
 #  --------------------------
 #  This is used to select which checkboxes to display
@@ -207,9 +201,9 @@ show_binary_characters:         display   no
 show_binary_character_counts:   display   no
 display_internal_data:          display   yes
 dynamically_hide_data:          display   yes
-show_relation_confidence:       nodisplay no
-show_properties:                nodisplay no
-show_vector_data:               nodisplay no
+show_relation_confidence:       display   no
+show_properties:                display   no
+show_vector_data:               display   no
 
 
 
diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
index 626c83e..94d7c83 100644
--- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
+++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1
@@ -57,7 +57,8 @@ native_ui: ?
 #     Example: 'node_label_direction: horizontal'
 #     The two possible values are: horizontal
 #                                  radial
-#  Show default node shape: 'show_default_node_shapes': values: 'yes'/'no'
+#  Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
+#  Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
 #  Default node shape size: 'default_node_size'
 #     Example: 'default_node_size: 6'
 #  Default node shape type: 'default_node_shape'
@@ -123,7 +124,8 @@ show_branch_length_values:                 no
 cladogram_type:                            ext_node_sum_dep
 phylogeny_graphics_type:                   rectangular
 node_label_direction:                      horizontal
-show_default_node_shapes:                  no
+show_default_node_shapes_internal:         no
+show_default_node_shapes_external:         no
 default_node_size:                         6
 default_node_shape:                        circle
 default_node_fill:                         gradient
@@ -152,13 +154,6 @@ taxonomy_extraction_in_nh_parsing:         pfam
 
 
 
-#  Initial Window Size for Application and ArchaeopteryA applet
-#  ------------------------------------------------------------
-window_initial_size_x: 640
-window_initial_size_y: 580
-
-
-
 #  phyloXML parsing
 #  ----------------
 #  To ensure compatibility with all current and future