domain + go output work begins

[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 8629845..2d09a77 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -238,6 +238,7 @@ public final class Configuration {
     private float                           _print_line_width                                      = Constants.PDF_LINE_WIDTH_DEFAULT;
     private boolean                         _show_annotation_ref_source                            = true;
     private boolean                         _show_default_node_shapes_external                     = false;
+    private boolean                         _show_default_node_shapes_for_marked_nodes             = false;
     private boolean                         _show_default_node_shapes_internal                     = false;
     private boolean                         _show_domain_labels                                    = true;
     private boolean                         _show_overview                                         = true;
@@ -251,8 +252,9 @@ 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;
+    private boolean                         _line_up_renderable_node_data                          = true;
+    private boolean                         _right_align_domains                                   = false;
+    private boolean                         _allow_thick_strokes                                   = false;
     static {
         for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
             if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
@@ -353,7 +355,7 @@ public final class Configuration {
     /**
      * Will attempt to use the phylogeny to determine whether to check
      * this or not (e.g. phylogram)
-     * 
+     *
      */
     boolean doGuessCheckOption( final int which ) {
         return display_options[ which ][ 2 ].equals( "?" );
@@ -699,7 +701,7 @@ public final class Configuration {
 
     /**
      * Convenience method.
-     * 
+     *
      * @return true if value in configuration file was 'yes'
      */
     boolean isDrawAsPhylogram() {
@@ -746,6 +748,10 @@ public final class Configuration {
         return _show_default_node_shapes_external;
     }
 
+    public boolean isShowDefaultNodeShapesForMarkedNodes() {
+        return _show_default_node_shapes_for_marked_nodes;
+    }
+
     public boolean isShowDefaultNodeShapesInternal() {
         return _show_default_node_shapes_internal;
     }
@@ -862,7 +868,7 @@ public final class Configuration {
 
     /**
      * read each line of config file, process non-comment lines
-     * @throws IOException 
+     * @throws IOException
      */
     private void readConfig( final BufferedReader conf_in ) throws IOException {
         String line;
@@ -1380,20 +1386,15 @@ 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,
-                                          "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
-            final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
-            setShowDefaultNodeShapesInternal( b );
-            setShowDefaultNodeShapesExternal( b );
-        }
         else if ( key.equals( "show_default_node_shapes_internal" ) ) {
             setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
         }
         else if ( key.equals( "show_default_node_shapes_external" ) ) {
             setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
         }
+        else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) {
+            setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+        }
         else if ( key.equals( "default_node_size" ) ) {
             final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
             setDefaultNodeShapeSize( i );
@@ -1523,6 +1524,9 @@ public final class Configuration {
         else if ( key.equals( "right_align_domain_architectures" ) ) {
             setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
         }
+        else if ( key.equals( "allow_thick_strokes" ) ) {
+            _allow_thick_strokes = parseBoolean( ( String ) st.nextElement() );
+        }
         else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
             // yet retrieved!
             int key_index = -1;
@@ -1761,6 +1765,10 @@ public final class Configuration {
         _show_default_node_shapes_external = show_default_node_shapes_external;
     }
 
+    public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
+        _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
+    }
+
     public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
         _show_default_node_shapes_internal = show_default_node_shapes_internal;
     }
@@ -1788,4 +1796,8 @@ public final class Configuration {
     private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
         _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
     }
+
+    public boolean isAllowThickStrokes() {
+        return _allow_thick_strokes;
+    }
 }