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;
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<String, WebLink> _weblinks = null;
private SortedMap<String, Color> _display_colors = null;
private boolean _antialias_screen = true;
private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
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;
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;
private File _path_to_local_mafft = null;
private File _path_to_local_fastme = null;
private File _path_to_local_raxml = null;
- private File _path_to_local_clustalo = null;
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
else {
config_filename = cf;
}
- setWebLinks( new TreeMap<String, WebLink>() );
setDisplayColors( new TreeMap<String, Color>() );
config_filename = config_filename.trim();
URL u = null;
return _label_for_get_ext_descendents_data;
}
- public File getPathToLocalClustalOmega() {
- return _path_to_local_clustalo;
- }
-
public File getPathToLocalFastme() {
return _path_to_local_fastme;
}
_number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
}
- public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
- _path_to_local_clustalo = path_to_local_clustalo;
- }
-
public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
_phylogeny_graphics_type = phylogeny_graphics_type;
}
return _taxonomy_extraction;
}
- WebLink getWebLink( final String source ) {
- return getWebLinks().get( source );
- }
-
- Map<String, WebLink> getWebLinks() {
- return _weblinks;
- }
-
boolean isAntialiasScreen() {
+ if ( AptxUtil.isMac() ) {
+ // Apple Macintosh graphics are slow, turn off anti-alias.
+ return false;
+ }
return _antialias_screen;
}
return _editable;
}
- boolean isHasWebLink( final String source ) {
- return getWebLinks().containsKey( source );
- }
-
/**
* Only used by ArchaeoptryxE.
*
}
final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) {
+ if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) {
_ui = UI.NATIVE;
}
return _ui == UI.NATIVE;
_taxonomy_extraction = taxonomy_extraction;
}
- void setWebLinks( final SortedMap<String, WebLink> 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" ) ) {
"value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
- else if ( key.equals( "clustalo_local" ) ) {
- final String str = ( ( String ) st.nextElement() ).trim();
- if ( !ForesterUtil.isEmpty( str ) ) {
- setPathToLocalClustalOmega( new File( str ) );
- }
- }
else if ( key.equals( "mafft_local" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
if ( !ForesterUtil.isEmpty( str ) ) {
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,
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 );
}
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 );
git://source.jalview.org / jalview.git / blobdiff