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moved to: https://sites.google.com/site/cmzmasek/home/software/forester
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
Options.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/Options.java
b/forester/java/src/org/forester/archaeopteryx/Options.java
index
abbc7c7
..
43b8fec
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/
forester/java/src/org/forester/archaeopteryx/Options.java
@@
-21,12
+21,13
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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;
import java.awt.Font;
package org.forester.archaeopteryx;
import java.awt.Font;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.NodeData;
import org.forester.phylogeny.data.NodeData.NODE_DATA;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.NodeData;
import org.forester.phylogeny.data.NodeData.NODE_DATA;
@@
-67,7
+68,7
@@
final public class Options {
private short _number_of_digits_after_comma_for_confidence_values;
private short _number_of_digits_after_comma_for_branch_length_values;
private boolean _nh_parsing_replace_underscores;
private short _number_of_digits_after_comma_for_confidence_values;
private short _number_of_digits_after_comma_for_branch_length_values;
private boolean _nh_parsing_replace_underscores;
- private boolean _nh_parsing_extract_pfam_taxonomy_codes;
+ private TAXONOMY_EXTRACTION _taxonomy_extraction;
private boolean _editable;
private boolean _background_color_gradient;
private boolean _show_domain_labels;
private boolean _editable;
private boolean _background_color_gradient;
private boolean _show_domain_labels;
@@
-185,7
+186,7
@@
final public class Options {
_number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
_number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
_nh_parsing_replace_underscores = false;
_number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
_number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
_nh_parsing_replace_underscores = false;
- _nh_parsing_extract_pfam_taxonomy_codes = false;
+ _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY;
_cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
_show_domain_labels = true;
setAbbreviateScientificTaxonNames( false );
_cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
_show_domain_labels = true;
setAbbreviateScientificTaxonNames( false );
@@
-239,8
+240,8
@@
final public class Options {
return _editable;
}
return _editable;
}
- final boolean isExtractPfamTaxonomyCodesInNhParsing() {
- return _nh_parsing_extract_pfam_taxonomy_codes;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
final boolean isGraphicsExportUsingActualSize() {
}
final boolean isGraphicsExportUsingActualSize() {
@@
-343,8
+344,8
@@
final public class Options {
_editable = editable;
}
_editable = editable;
}
- final void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
- _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
+ final void setTaxonomyExtractio( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
}
final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
}
final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) {
@@
-481,7
+482,7
@@
final public class Options {
instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
.getNumberOfDigitsAfterCommaForConfidenceValues() );
}
instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
.getNumberOfDigitsAfterCommaForConfidenceValues() );
}
- instance.setExtractPfamTaxonomyCodesInNhParsing( configuration.isExtractPfamTaxonomyCodesInNhParsing() );
+ instance.setTaxonomyExtractio( configuration.getTaxonomyExtraction() );
instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
instance.setInternalNumberAreConfidenceForNhParsing( configuration
.isInternalNumberAreConfidenceForNhParsing() );
instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
instance.setInternalNumberAreConfidenceForNhParsing( configuration
.isInternalNumberAreConfidenceForNhParsing() );