From 9b8fed885e8d0687ac000a8d26ea4bb9bd45c6bf Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 3 Apr 2013 20:15:14 +0000 Subject: [PATCH] bugfix --- forester/java/src/org/forester/archaeopteryx/Configuration.java | 2 +- forester/java/src/org/forester/archaeopteryx/Constants.java | 2 +- forester/java/src/org/forester/archaeopteryx/MainFrame.java | 2 +- .../java/src/org/forester/archaeopteryx/MainFrameApplication.java | 3 +++ forester/java/src/org/forester/archaeopteryx/Options.java | 2 +- 5 files changed, 7 insertions(+), 4 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 3839128..a1c16c2 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -83,7 +83,7 @@ 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 TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT; + private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; 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; diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 8dd077f..6beacfa 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -43,7 +43,7 @@ public final class Constants { public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; final static String VERSION = "0.9812 A1ST"; - final static String PRG_DATE = "130401"; + final static String PRG_DATE = "130403"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica", "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index e4bd6f1..c353213 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -1318,7 +1318,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) { - options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE ); + options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) { options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 53ca7cb..977bcbb 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -547,6 +547,9 @@ public final class MainFrameApplication extends MainFrame { } updateOptions( getOptions() ); } + else if ( o == _extract_taxonomy_no_rbmi ) { + updateOptions( getOptions() ); + } else if ( o == _inference_from_msa_item ) { executePhyleneticInference( false ); } diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index e90ae20..f8aa376 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -458,7 +458,7 @@ 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; - _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT; + _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; _show_domain_labels = true; setAbbreviateScientificTaxonNames( false ); -- 1.7.10.2