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work on data buffer for aLeaves MAFFT suite + 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 1591e63..deaaec8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -47,6 +47,7 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.phylogeny.data.NodeData.NODE_DATA;
 import org.forester.phylogeny.data.NodeVisualization;
 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
@@ -56,7 +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";
@@ -86,7 +87,7 @@ public final class Configuration {
     private short                           _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
     private boolean                         _editable                                              = true;
     private boolean                         _nh_parsing_replace_underscores                        = false;
-    private boolean                         _nh_parsing_extract_pfam_taxonomy_codes                = false;
+    private TAXONOMY_EXTRACTION             _taxonomy_extraction                                   = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
     private boolean                         _internal_number_are_confidence_for_nh_parsing         = false;
     private boolean                         _display_sequence_relations                            = false;
     private boolean                         _validate_against_phyloxml_xsd_schema                  = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT;
@@ -150,6 +151,7 @@ public final class Configuration {
     final static int                        edit_node_data                                         = 14;
     final static int                        sort_descendents                                       = 15;
     final static int                        get_ext_desc_data                                      = 16;
+    final static int                        select_nodes                                           = 17;
     // ---------------------------
     // Display options for trees
     // ---------------------------
@@ -162,7 +164,7 @@ public final class Configuration {
     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" },
+            { "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" }, { "Prot/Gene Name", "display", "yes" },
@@ -178,7 +180,7 @@ public final class Configuration {
             { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
             { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
             { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
-            { "Sort Descendants", "display" }, { "Return", "display" }                            };
+            { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } };
     // This option is selected in the dropdown
     int                                     default_clickto                                        = Configuration.display_node_data;
     // --------------
@@ -213,7 +215,7 @@ public final class Configuration {
     private Color                           _gui_button_border_color                               = Constants.BUTTON_BORDER_COLOR_DEFAULT;
     private Color                           _domain_structure_font_color                           = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
     private Color                           _domain_structure_base_color                           = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
-    private NODE_DATA                       _ext_desc_data_to_return                               = NODE_DATA.NODE_NAME;
+    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 static String                   DEFAULT_FONT_FAMILY                                    = "";
@@ -415,6 +417,9 @@ public final class Configuration {
         else if ( name.equals( "edit_node_data" ) ) {
             index = Configuration.edit_node_data;
         }
+        else if ( name.equals( "select_nodes" ) ) {
+            index = Configuration.select_nodes;
+        }
         else if ( name.equals( "display_node_popup" ) ) {
             ForesterUtil.printWarningMessage( Constants.PRG_NAME,
                                               "configuration key [display_node_popup] is deprecated" );
@@ -625,8 +630,8 @@ public final class Configuration {
         return _editable;
     }
 
-    boolean isExtractPfamTaxonomyCodesInNhParsing() {
-        return _nh_parsing_extract_pfam_taxonomy_codes;
+    final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+        return _taxonomy_extraction;
     }
 
     boolean isHasWebLink( final String source ) {
@@ -920,8 +925,8 @@ public final class Configuration {
         _editable = editable;
     }
 
-    public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
-        _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
+    final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+        _taxonomy_extraction = taxonomy_extraction;
     }
 
     private void setGraphicsExportX( final int graphics_export_x ) {
@@ -1200,7 +1205,7 @@ public final class Configuration {
         }
         else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
             final boolean r = parseBoolean( ( String ) st.nextElement() );
-            if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
+            if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
                 ForesterUtil
                         .printWarningMessage( Constants.PRG_NAME,
                                               "attempt to extract taxonomies and replace underscores at the same time" );
@@ -1209,16 +1214,26 @@ public final class Configuration {
                 setReplaceUnderscoresInNhParsing( r );
             }
         }
-        else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
-            final boolean e = parseBoolean( ( String ) st.nextElement() );
-            if ( e && isReplaceUnderscoresInNhParsing() ) {
+        else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) {
+            final String s = ( String ) st.nextElement();
+            if ( s.equalsIgnoreCase( "no" ) ) {
+                setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+            }
+            else if ( s.equalsIgnoreCase( "yes" ) ) {
+                setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+            }
+            else if ( s.equalsIgnoreCase( "pfam" ) ) {
+                setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+            }
+            else {
+                ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+                                                  "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
+            }
+            if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
                 ForesterUtil
                         .printWarningMessage( Constants.PRG_NAME,
                                               "attempt to extract taxonomies and replace underscores at the same time" );
             }
-            else {
-                setExtractPfamTaxonomyCodesInNhParsing( e );
-            }
         }
         else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
             setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) );
@@ -1315,6 +1330,9 @@ public final class Configuration {
             else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
                 setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
             }
+            else if ( s.equalsIgnoreCase( "user_selected" ) ) {
+                setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
+            }
             else {
                 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
                         + "] for [ext_descendents_data_to_return]" );
@@ -1338,6 +1356,9 @@ 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]" );