X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=c578e05d66214e3a99da0ac7f905a2a574dc4980;hb=aec065f948a075773794133f102ea19eb1d59f64;hp=5d354cc082a7b4be5c45a4bbc659973b6bd0730c;hpb=56fcc7953ce4896eed89a3129d862e0aaf2d65e1;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 5d354cc..c578e05 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -34,7 +34,6 @@ import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; -import java.net.MalformedURLException; import java.net.URL; import java.util.Arrays; import java.util.Hashtable; @@ -57,14 +56,12 @@ import org.forester.util.ForesterUtil; public final class Configuration { static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; - private static final String WEB_LINK_KEY = "web_link"; private static final String DISPLAY_COLOR_KEY = "display_color"; private static final int DEPRECATED = -2; private UI _ui = UI.UNKNOWN; private boolean _use_tabbed_display = false; private boolean _hide_controls_and_menus = false; private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; - private SortedMap _weblinks = null; private SortedMap _display_colors = null; private boolean _antialias_screen = true; private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; @@ -86,7 +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_ONLY; + private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT; 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; @@ -96,8 +93,8 @@ public final class Configuration { private boolean _color_labels_same_as_parent_branch = false; private boolean _show_default_node_shapes_internal = false; private boolean _show_default_node_shapes_external = false; - private NodeShape _default_node_shape = NodeShape.CIRCLE; - private NodeFill _default_node_fill = NodeFill.GRADIENT; + private NodeShape _default_node_shape = NodeShape.RECTANGLE; + private NodeFill _default_node_fill = NodeFill.SOLID; private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private boolean _taxonomy_colorize_node_shapes = false; private int _default_bootstrap_samples = -1; @@ -244,7 +241,6 @@ public final class Configuration { else { config_filename = cf; } - setWebLinks( new TreeMap() ); setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; @@ -725,15 +721,11 @@ public final class Configuration { return _taxonomy_extraction; } - WebLink getWebLink( final String source ) { - return getWebLinks().get( source ); - } - - Map getWebLinks() { - return _weblinks; - } - boolean isAntialiasScreen() { + if ( AptxUtil.isMac() ) { + // Apple Macintosh graphics are slow, turn off anti-alias. + return false; + } return _antialias_screen; } @@ -750,10 +742,6 @@ public final class Configuration { return _editable; } - boolean isHasWebLink( final String source ) { - return getWebLinks().containsKey( source ); - } - /** * Only used by ArchaeoptryxE. * @@ -783,7 +771,7 @@ public final class Configuration { } final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) { + if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) { _ui = UI.NATIVE; } return _ui == UI.NATIVE; @@ -805,25 +793,6 @@ public final class Configuration { _taxonomy_extraction = taxonomy_extraction; } - void setWebLinks( final SortedMap weblinks ) { - _weblinks = weblinks; - } - - private void createWebLink( final String url_str, final String desc, final String source_identifier ) { - WebLink weblink = null; - boolean ex = false; - try { - weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() ); - } - catch ( final MalformedURLException e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" ); - ex = true; - } - if ( !ex && ( weblink != null ) ) { - getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink ); - } - } - private int getClickToIndex( final String name ) { int index = -1; if ( name.equals( "edit_info" ) ) { @@ -1342,10 +1311,10 @@ public final class Configuration { setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } else if ( s.equalsIgnoreCase( "yes" ) ) { - setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES ); + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } else if ( s.equalsIgnoreCase( "pfam" ) ) { - setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, @@ -1448,6 +1417,9 @@ public final class Configuration { else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC ); } + else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ); + } else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) { setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ ); } @@ -1671,17 +1643,6 @@ public final class Configuration { else if ( key.equals( DISPLAY_COLOR_KEY ) ) { putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } - else if ( key.equals( WEB_LINK_KEY ) ) { - if ( st.countTokens() == 3 ) { - createWebLink( ( String ) st.nextElement(), - ( String ) st.nextElement(), - ( String ) st.nextElement() ); - } - else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "illegal format in configuration file for key [" + key + "]" ); - } - } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename );