JAL-2805 bunch of needed methods/constants made public

[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 b4a4398..43bc6ad 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -135,7 +135,7 @@ public final class Configuration {
         { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
         { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
         { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" }
-        , { "Taxonomy Rank", "display", "no" }};
+        , { "Taxonomy Rank", "display", "no" }, { "Show External Data", "display", "yes" }};
     final static int                        display_as_phylogram                                   = 0;
     final static int                        show_node_names                                        = 1;
     final static int                        show_tax_code                                          = 2;
@@ -166,6 +166,7 @@ public final class Configuration {
     final static int                        show_mol_seqs                                          = 27;
     final static int                        write_branch_length_values                             = 28;
     final static int                        show_tax_rank                                          = 29;
+    final static int                        display_external_data                                  = 30;
     
     static final String                     VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA                   = "validate_against_phyloxml_xsd_schema";
     private static Hashtable<String, Color> _sequence_colors;
@@ -526,6 +527,10 @@ public final class Configuration {
     public void setDisplayInternalData( final boolean b ) {
         display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
     }
+    
+    public void setDisplayExternalData( final boolean b ) {
+        display_options[ display_external_data ][ 2 ] = b ? "yes" : "no";
+    }
 
     public void setDisplayMultipleSequenceAlignment( final boolean b ) {
         display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
@@ -988,20 +993,6 @@ public final class Configuration {
                 setMaxBaseFontSize( i );
             }
         }
-        else if ( key.equals( "graphics_export_x" ) ) {
-           // final String str = ( ( String ) st.nextElement() ).trim();
-           // final int i = parseInt( str );
-           // if ( i > 0 ) {
-           //     setGraphicsExportX( i );
-           // }
-        }
-        else if ( key.equals( "graphics_export_y" ) ) {
-            //final String str = ( ( String ) st.nextElement() ).trim();
-           // final int i = parseInt( str );
-            //if ( i > 0 ) {
-            //    setGraphicsExportY( i );
-            //}
-        }
         else if ( key.equals( "pdf_export_line_width" ) ) {
             final String str = ( ( String ) st.nextElement() ).trim();
             final float f = parseFloat( str );
@@ -1083,22 +1074,14 @@ public final class Configuration {
             if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
                 setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
             }
-            else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
-                setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
-            }
-            else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
-                setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
+            else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.LINED_UP.toString() ) ) {
+                setCladogramType( Options.CLADOGRAM_TYPE.LINED_UP );
             }
             else {
                 ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str
                                                   + "] for [cladogram_type]" );
             }
         }
-        else if ( key.equals( "non_lined_up_cladogram" ) ) {
-            ForesterUtil
-            .printWarningMessage( AptxConstants.PRG_NAME,
-                                  "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
-        }
         else if ( key.equals( "hide_controls_and_menus" ) ) {
             _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
         }
@@ -1456,6 +1439,9 @@ public final class Configuration {
             else if ( key.equals( "display_internal_data" ) ) {
                 key_index = Configuration.display_internal_data;
             }
+            else if ( key.equals( "display_external_data" ) ) {
+                key_index = Configuration.display_external_data;
+            }
             else if ( key.equals( "dynamically_hide_data" ) ) {
                 key_index = Configuration.dynamically_hide_data;
             }
@@ -1687,6 +1673,10 @@ public final class Configuration {
         return _gui_menu_text_color;
     }
 
+    static int getGuiFontSize() {
+        return 11;
+    }
+    
     int getMaxBaseFontSize() {
         return _max_base_font_size;
     }
@@ -1745,7 +1735,7 @@ public final class Configuration {
         return _species_colors;
     }
 
-    final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+    public final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
         return _taxonomy_extraction;
     }
 
@@ -1774,11 +1764,11 @@ public final class Configuration {
         return _hide_controls_and_menus;
     }
 
-    boolean isInternalNumberAreConfidenceForNhParsing() {
+    public boolean isInternalNumberAreConfidenceForNhParsing() {
         return _internal_number_are_confidence_for_nh_parsing;
     }
 
-    boolean isReplaceUnderscoresInNhParsing() {
+    public boolean isReplaceUnderscoresInNhParsing() {
         return _nh_parsing_replace_underscores;
     }
 
@@ -1805,7 +1795,7 @@ public final class Configuration {
         return _use_tabbed_display;
     }
 
-    boolean isValidatePhyloXmlAgainstSchema() {
+   public boolean isValidatePhyloXmlAgainstSchema() {
         return _validate_against_phyloxml_xsd_schema;
     }