removed view as NHX

[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 f506905..7b440a8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -24,7 +24,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -57,7 +57,7 @@ import org.forester.util.ForesterUtil;
 public final class Configuration {
 
     public enum EXT_NODE_DATA_RETURN_ON {
-        CONSOLE, WINODW;
+        CONSOLE, WINODW, BUFFER_ONLY;
     }
     static final String                     VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA                   = "validate_against_phyloxml_xsd_schema";
     private static final String             WEB_LINK_KEY                                           = "web_link";
@@ -163,17 +163,18 @@ public final class Configuration {
     String                                  default_config_filename                                = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
     final static String                     display_options[][]                                    = {
             { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
-            { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" },
-            { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" },
-            { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" },
-            { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
-            { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
-            { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
-            { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
-            { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
-            { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
-            { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
-            { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" }             };
+            { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
+            { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
+            { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" },
+            { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" },
+            { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
+            { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" },
+            { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
+            { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
+            { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
+            { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
+            { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
+            { "Properties", "nodisplay", "no" }                                                   };
     final static String                     clickto_options[][]                                    = {
             { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
             { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
@@ -218,6 +219,8 @@ public final class Configuration {
     private NODE_DATA                       _ext_desc_data_to_return                               = NODE_DATA.UNKNOWN;
     private String                          _label_for_get_ext_descendents_data                    = "";
     private EXT_NODE_DATA_RETURN_ON         _ext_node_data_return_on                               = EXT_NODE_DATA_RETURN_ON.WINODW;
+    private int                             _frame_x_size;
+    private int                             _frame_y_size;
     private static String                   DEFAULT_FONT_FAMILY                                    = "";
     static {
         for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
@@ -1028,17 +1031,23 @@ public final class Configuration {
         else if ( key.equals( "font_size" ) ) {
             final String size_str = ( ( String ) st.nextElement() ).trim();
             final int i = parseInt( size_str );
-            setBaseFontSize( i );
+            if ( i > 0 ) {
+                setBaseFontSize( i );
+            }
         }
         else if ( key.equals( "graphics_export_x" ) ) {
             final String str = ( ( String ) st.nextElement() ).trim();
             final int i = parseInt( str );
-            setGraphicsExportX( i );
+            if ( i > 0 ) {
+                setGraphicsExportX( i );
+            }
         }
         else if ( key.equals( "graphics_export_y" ) ) {
             final String str = ( ( String ) st.nextElement() ).trim();
             final int i = parseInt( str );
-            setGraphicsExportY( i );
+            if ( i > 0 ) {
+                setGraphicsExportY( i );
+            }
         }
         else if ( key.equals( "pdf_export_line_width" ) ) {
             final String str = ( ( String ) st.nextElement() ).trim();
@@ -1051,6 +1060,20 @@ public final class Configuration {
                                                   "value for [pdf_export_line_width] cannot be zero or negative" );
             }
         }
+        else if ( key.equals( "window_initial_size_x" ) ) {
+            final String str = ( ( String ) st.nextElement() ).trim();
+            final int i = parseInt( str );
+            if ( i > 0 ) {
+                setFrameXSize( i );
+            }
+        }
+        else if ( key.equals( "window_initial_size_y" ) ) {
+            final String str = ( ( String ) st.nextElement() ).trim();
+            final int i = parseInt( str );
+            if ( i > 0 ) {
+                setFrameYSize( i );
+            }
+        }
         else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
             final String str = ( ( String ) st.nextElement() ).trim();
             final int i = parseInt( str );
@@ -1222,7 +1245,7 @@ public final class Configuration {
             else if ( s.equalsIgnoreCase( "yes" ) ) {
                 setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
             }
-            else if ( s.equalsIgnoreCase( "pfam_only" ) ) {
+            else if ( s.equalsIgnoreCase( "pfam" ) ) {
                 setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
             }
             else {
@@ -1356,6 +1379,9 @@ public final class Configuration {
             else if ( s.equals( "window" ) ) {
                 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
             }
+            else if ( s.equals( "buffer_only" ) ) {
+                setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
+            }
             else {
                 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
                         + "] for [ext_descendents_data_to_return_on]" );
@@ -1673,4 +1699,20 @@ public final class Configuration {
     private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
         _ext_node_data_return_on = ext_node_data_return_on;
     }
+
+    public int getFrameXSize() {
+        return _frame_x_size;
+    }
+
+    public int getFrameYSize() {
+        return _frame_y_size;
+    }
+
+    public void setFrameXSize( final int frame_x_size ) {
+        _frame_x_size = frame_x_size;
+    }
+
+    public void setFrameYSize( final int frame_y_size ) {
+        _frame_y_size = frame_y_size;
+    }
 }