clean up

[jalview.git] / forester / java / src / org / forester / archaeopteryx / Configuration.java

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 271bdfa..5df336a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -93,7 +93,7 @@ public final class Configuration {
             { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
             { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
             { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
-            { "Branch Widths", "display", "no" }, { "Protein Domains", "display", "no" },
+            { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
             { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
             { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
             { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
@@ -220,6 +220,8 @@ public final class Configuration {
     private Color                           _vector_data_mean_color                                = Color.WHITE;
     private double                          _vector_data_height                                    = 12;
     private int                             _vector_data_width                                     = 120;
+    private boolean                         _line_up_renderable_node_data;
+    private boolean                         _right_align_domains;
     static {
         for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
             if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
@@ -1375,7 +1377,6 @@ public final class Configuration {
         else if ( key.equals( "gui_button_border_color" ) ) {
             _gui_button_border_color = Color.decode( ( String ) st.nextElement() );
         }
-      
         else if ( key.equals( "show_default_node_shapes" ) ) {
             ForesterUtil
                     .printWarningMessage( Constants.PRG_NAME,
@@ -1492,7 +1493,6 @@ public final class Configuration {
                         + "] for [ext_descendents_data_to_return_on]" );
             }
         }
-        //
         else if ( key.equals( "vector_data_min_color" ) ) {
             _vector_data_min_color = Color.decode( ( String ) st.nextElement() );
         }
@@ -1502,7 +1502,6 @@ public final class Configuration {
         else if ( key.equals( "vector_data_mean_color" ) ) {
             _vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
         }
-        //
         else if ( key.equals( "vector_data_width" ) ) {
             _vector_data_width = parseShort( ( String ) st.nextElement() );
             if ( _vector_data_width < 1 ) {
@@ -1515,7 +1514,12 @@ public final class Configuration {
                 _vector_data_height = 12;
             }
         }
-        //
+        else if ( key.equals( "line_up_renderable_data" ) ) {
+            setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
+        }
+        else if ( key.equals( "right_align_domain_architectures" ) ) {
+            setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
+        }
         else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
             // yet retrieved!
             int key_index = -1;
@@ -1747,4 +1751,20 @@ public final class Configuration {
     public int getVectorDataWidth() {
         return _vector_data_width;
     }
+
+    final public boolean isLineUpRendarableNodeData() {
+        return _line_up_renderable_node_data;
+    }
+
+    final public boolean isRightLineUpDomains() {
+        return _right_align_domains;
+    }
+
+    final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
+        _line_up_renderable_node_data = line_up_renderable_node_data;
+    }
+
+    final public void setRightLineUpDomains( final boolean right_align_domains ) {
+        _right_align_domains = right_align_domains;
+    }
 }