// $Id: Configuration.java,v 1.58 2010/10/04 02:24:33 cmzmasek Exp $
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// Copyright (C) 2000-2001 Washington University School of Medicine
// and Howard Hughes Medical Institute
// Copyright (C) 2003-2007 Ethalinda K.S. Cannon
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.archaeopteryx;
/**
* NOTE - The original file was obtained from SourceForge.net (Archaeopteryx Version 0.957 beta) on 2010.10.13
* and was modified by the LANL Influenza Sequence Database IT team (flu@lanl.gov)
*/
import gov.lanl.application.TPTD.applet.AppletParams;
import gov.lanl.application.treePruner.applet.KeepRemoveConfiguration;
import java.awt.Color;
import java.io.BufferedReader;
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;
import java.util.Map;
import java.util.SortedMap;
import java.util.StringTokenizer;
import java.util.TreeMap;
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.util.ForesterUtil;
//******************************************START**********************************************************//
//******************************************START CHANGED**********************************************************//
public class Configuration {
//final class Configuration { // final->public - changed
//********************************************END**********************************************************//
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 TRIPLET _native_ui = TRIPLET.FALSE;
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 String _base_font_family_name = "";
private int _base_font_size = -1;
private int _graphics_export_x = -1;
private int _graphics_export_y = -1;
private short _ov_max_width = 80;
private short _ov_max_height = 80;
private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT;
private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
private boolean _show_scale = false;
private boolean _show_branch_length_values = false;
private boolean _show_overview = true;
//******************************************START**********************************************************//
public KeepRemoveConfiguration keepRemoveConfiguration = new KeepRemoveConfiguration(this);
//********************************************END**********************************************************//
private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
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 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 _background_color_gradient = false;
private boolean _show_domain_labels = true;
private boolean _color_labels_same_as_parent_branch = false;
private int _default_bootstrap_samples = -1;
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
final static int show_annotation = 3;
final static int write_confidence_values = 4;
final static int write_events = 5;
final static int color_according_to_species = 6;
final static int color_branches = 7;
final static int width_branches = 8;
final static int show_domain_architectures = 9;
final static int show_binary_characters = 10;
final static int show_binary_character_counts = 11;
final static int show_gene_names = 12;
final static int show_sequence_acc = 13;
final static int display_internal_data = 14;
final static int dynamically_hide_data = 15;
final static int show_taxonomy_scientific_names = 16;
final static int show_taxonomy_common_names = 17;
final static int color_according_to_annotation = 18;
final static int show_property = 19;
final static int show_gene_symbols = 20;
final static int node_data_popup = 21;
final static int show_relation_confidence = 22;
// ------------------
// Click-to options
// ------------------
final static int display_node_data = 0;
final static int collapse_uncollapse = 1;
final static int reroot = 2;
final static int subtree = 3;
final static int swap = 4;
final static int color_subtree = 5;
//******************************************START CHANGED**********************************************************//
//****AC**** The numbers have been changed to make room for 6 and 7
final static int open_seq_web = 8;
final static int open_tax_web = 9;
final static int cut_subtree = 10;
final static int copy_subtree = 11;
final static int paste_subtree = 12;
final static int delete_subtree_or_node = 13;
final static int add_new_node = 14;
final static int edit_node_data = 15;
final static int blast = 16;
//********************************************END**********************************************************//
// ---------------------------
// Display options for trees
// ---------------------------
// ---------------------------------
// Pertaining to the config itself
// ---------------------------------
// Full path to config (may be URL)
String config_filename;
String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME;
final static String display_options[][] = {
{ "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
{ "Annotation", "nodisplay", "no" }, { "Confidence Value", "display", "?" }, { "Event", "display", "?" },
{ "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" },
{ "Use Branch-Width", "nodisplay", "no" }, { "Domains", "nodisplay", "no" },
{ "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
{ "Prot/Gene Name", "display", "no" }, { "Prot/Gene Acc", "display", "no" },
{ "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
{ "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
{ "Annotation Colorize", "nodisplay", "no" }, { "Property", "nodisplay", "no" },
{ "Prot/Gene Symbol", "display", "no" }, { "Rollover", "display", "yes" },
{ "Relation confidence score", "display", "no" } };
final static String clickto_options[][] = {
{ "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
{ "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
//******************************************START**********************************************************//
{"<html><b>Keep Sequences</b></br></html>", "display"}, //Display or no display depends upon the
{"<html><b>Remove/Restore Sequences</b></br></html>", "display"}, //TreePruner or TreeDecorator AppType.
/**Later on change this to nodisplay if apptype is TreeDecorator from ArchaeA.java
Change Number in KeepRemoveConfiguration.java from 6 n 7 for keep and remove to higher number
if TreeDecorator demands it*/
//********************************************END**********************************************************//
{ "Open Sequence Web", "nodisplay" }, { "Open Taxonomy Web", "nodisplay" }, { "Cut Subtree", "display" },
{ "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
{ "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "display" } };
// This option is selected in the dropdown
int default_clickto = Configuration.display_node_data;
// --------------
// Color set
// --------------
TreeColorSet tree_color_set;
// -------
// Fonts
// -------
TreeFontSet tree_font_set;
// ----------------
// Species colors
// ----------------
private static Hashtable<String, Color> _species_colors;
// ----------------
// Domain colors
// ----------------
private static Hashtable<String, Color> _domain_colors;
// ----------------
// Function colors
// ----------------
private static Hashtable<String, Color> _annotation_colors;
boolean verbose = Constants.VERBOSE_DEFAULT;
private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
private TRIPLET _use_native_ui;
private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT;
private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT;
private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT;
private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT;
private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT;
private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT;
private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT;
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 static String DEFAULT_FONT_FAMILY = "";
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
DEFAULT_FONT_FAMILY = font_name;
break;
}
}
if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) {
DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ];
}
}
Configuration( final String cf, final boolean is_url, final boolean is_applet ) {
if ( ForesterUtil.isEmpty( cf ) ) {
config_filename = default_config_filename;
}
else {
config_filename = cf;
}
setWebLinks( new TreeMap<String, WebLink>() );
setDisplayColors( new TreeMap<String, Color>() );
config_filename = config_filename.trim();
URL u = null;
if ( is_url ) {
// If URL, open accordingly
try {
u = new URL( config_filename );
try {
final InputStreamReader isr = new InputStreamReader( u.openStream() );
final BufferedReader bf = new BufferedReader( isr );
readConfig( bf );
bf.close();
ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url ["
+ config_filename + "]" );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
+ config_filename + "]: " + e.getLocalizedMessage() );
}
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url ["
+ config_filename + "]" );
}
}
else {
// Otherwise, open as a file
File f = new File( config_filename );
if ( !f.exists() ) {
f = new File( config_filename + ".txt" );
}
if ( f.exists() && f.canRead() ) {
try {
final BufferedReader bf = new BufferedReader( new FileReader( f ) );
readConfig( bf );
bf.close();
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from ["
+ config_filename + "]: " + e );
}
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file ["
+ config_filename + "]" );
}
}
}
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 );
}
}
Color getGuiBackgroundColor() {
return _gui_background_color;
}
Color getGuiCheckboxTextColor() {
return _gui_checkbox_text_color;
}
Color getGuiCheckboxAndButtonActiveColor() {
return _gui_checkbox_and_button_active_color;
}
Color getGuiButtonTextColor() {
return _gui_button_text_color;
}
Color getGuiButtonBackgroundColor() {
return _gui_button_background_color;
}
//******************************************START Changed**********************************************************//
public Color getGuiMenuBackgroundColor() {
return _gui_menu_background_color;
}
//added public
//********************************************END**********************************************************//
//******************************************START Changed**********************************************************//
public Color getGuiMenuTextColor() {
return _gui_menu_text_color;
}
//added public
//********************************************END**********************************************************//
Color getGuiButtonBorderColor() {
return _gui_button_border_color;
}
boolean displaySequenceRelations() {
return _display_sequence_relations;
}
boolean doCheckOption( final int which ) {
return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
|| ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
}
boolean doDisplayClickToOption( final int which ) {
//******************************************START**********************************************************//
/**
* Note to programmer: Whatever happens in this method will also affect do_display_clickToOption(final int which){}
*/
if(which == 6 || which == 7){
if(AppletParams.isTreePrunerForAll() ){
clickto_options[which][1] = "display";
}
else{
clickto_options[which][1] = "nodisplay";
}
}
//********************************************END**********************************************************//
return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
}
boolean doDisplayOption( final int which ) {
return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
}
/**
* Will attempt to use the phylogeny to determine whether to check
* this or not (e.g. phylogram)
*
*/
boolean doGuessCheckOption( final int which ) {
return display_options[ which ][ 2 ].equals( "?" );
}
Map<String, Color> getAnnotationColors() {
if ( _annotation_colors == null ) {
_annotation_colors = new Hashtable<String, Color>();
}
return _annotation_colors;
}
public String getBaseFontFamilyName() {
return _base_font_family_name;
}
int getBaseFontSize() {
return _base_font_size;
}
CLADOGRAM_TYPE getCladogramType() {
return _cladogram_type;
}
private int getClickToIndex( final String name ) {
int index = -1;
if ( name.equals( "edit_info" ) ) {
index = Configuration.display_node_data;
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"configuration key [edit_info] is deprecated, use [display node data] instead" );
}
else if ( name.equals( "display_node_data" ) ) {
index = Configuration.display_node_data;
}
else if ( name.equals( "collapse_uncollapse" ) ) {
index = Configuration.collapse_uncollapse;
}
else if ( name.equals( "reroot" ) ) {
index = Configuration.reroot;
}
else if ( name.equals( "subtree" ) ) {
index = Configuration.subtree;
}
else if ( name.equals( "swap" ) ) {
index = Configuration.swap;
}
else if ( name.equals( "display_sequences" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "open_seq_web" ) ) {
index = Configuration.open_seq_web;
}
else if ( name.equals( "open_tax_web" ) ) {
index = Configuration.open_tax_web;
}
else if ( name.equals( "cut_subtree" ) ) {
index = Configuration.cut_subtree;
}
else if ( name.equals( "copy_subtree" ) ) {
index = Configuration.copy_subtree;
}
else if ( name.equals( "paste_subtree" ) ) {
index = Configuration.paste_subtree;
}
else if ( name.equals( "delete" ) ) {
index = Configuration.delete_subtree_or_node;
}
else if ( name.equals( "add_new_node" ) ) {
index = Configuration.add_new_node;
}
else if ( name.equals( "edit_node_data" ) ) {
index = Configuration.edit_node_data;
}
//******************************************START**********************************************************//
else if ( name.equals( "blast" )) {
index = Configuration.blast;
}
//********************************************END**********************************************************//
else if ( name.equals( "display_node_popup" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [display_node_popup] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "custom_option" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "color_subtree" ) ) {
index = Configuration.color_subtree;
}
else if ( name.equals( "go_to_swiss_prot" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
return DEPRECATED;
}
//******************************************START**********************************************************//
else{
if(AppletParams.isTreePrunerForAll() ){
index = keepRemoveConfiguration.getClickToIndex(name,index);
}
}
//********************************************END**********************************************************//
return index;
}
int getClickToOptionsCount() {
return clickto_options.length;
}
String getClickToTitle( final int which ) {
return clickto_options[ which ][ 0 ];
}
int getDefaultDisplayClicktoOption() {
return default_clickto;
}
SortedMap<String, Color> getDisplayColors() {
return _display_colors;
}
String getDisplayTitle( final int which ) {
return display_options[ which ][ 0 ];
}
Map<String, Color> getDomainColors() {
if ( _domain_colors == null ) {
_domain_colors = new Hashtable<String, Color>();
}
return _domain_colors;
}
int getGraphicsExportX() {
return _graphics_export_x;
}
int getGraphicsExportY() {
return _graphics_export_y;
}
int getDefaultBootstrapSamples() {
return _default_bootstrap_samples;
}
double getMinConfidenceValue() {
return _min_confidence_value;
}
NODE_LABEL_DIRECTION getNodeLabelDirection() {
return _node_label_direction;
}
short getNumberOfDigitsAfterCommaForBranchLengthValues() {
return _number_of_digits_after_comma_for_branch_length_values;
}
short getNumberOfDigitsAfterCommaForConfidenceValues() {
return _number_of_digits_after_comma_for_confidence_values;
}
short getOvMaxHeight() {
return _ov_max_height;
}
short getOvMaxWidth() {
return _ov_max_width;
}
OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
return _ov_placement;
}
PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
return _phylogeny_graphics_type;
}
float getPrintLineWidth() {
return _print_line_width;
}
Hashtable<String, Color> getSpeciesColors() {
if ( _species_colors == null ) {
_species_colors = new Hashtable<String, Color>();
}
return _species_colors;
}
TreeColorSet getTreeColorSet() {
return null;
}
TreeFontSet getTreeFontSet() {
return null;
}
WebLink getWebLink( final String source ) {
return getWebLinks().get( source );
}
Map<String, WebLink> getWebLinks() {
return _weblinks;
}
boolean isAntialiasScreen() {
return _antialias_screen;
}
public boolean isBackgroundColorGradient() {
return _background_color_gradient;
}
/**
* Convenience method.
*
* @return true if value in configuration file was 'yes'
*/
boolean isDrawAsPhylogram() {
return doCheckOption( display_as_phylogram );
}
boolean isEditable() {
return _editable;
}
boolean isExtractPfamTaxonomyCodesInNhParsing() {
return _nh_parsing_extract_pfam_taxonomy_codes;
}
boolean isHasWebLink( final String source ) {
return getWebLinks().containsKey( source );
}
/**
* Only used by ArchaeoptryxE.
*
*/
boolean isHideControlPanelAndMenubar() {
return _hide_controls_and_menus;
}
boolean isInternalNumberAreConfidenceForNhParsing() {
return _internal_number_are_confidence_for_nh_parsing;
}
boolean isReplaceUnderscoresInNhParsing() {
return _nh_parsing_replace_underscores;
}
boolean isShowBranchLengthValues() {
return _show_branch_length_values;
}
boolean isShowOverview() {
return _show_overview;
}
boolean isShowScale() {
return _show_scale;
}
//******************************************START Changed**********************************************************//
public final boolean isUseNativeUI() { //added public
//********************************************END**********************************************************//
if ( ( _use_native_ui == null ) || ( _use_native_ui == TRIPLET.UNKNOWN ) ) {
if ( ( _native_ui == TRIPLET.UNKNOWN ) && Util.isMac() && Util.isJava15() ) {
_use_native_ui = TRIPLET.TRUE;
}
else if ( _native_ui == TRIPLET.TRUE ) {
_use_native_ui = TRIPLET.TRUE;
}
else {
_use_native_ui = TRIPLET.FALSE;
}
}
return _use_native_ui == TRIPLET.TRUE;
}
/**
* Only used by ArchaeoptryxE.
*
*/
boolean isUseTabbedDisplay() {
return _use_tabbed_display;
}
boolean isValidatePhyloXmlAgainstSchema() {
return _validate_against_phyloxml_xsd_schema;
}
private boolean parseBoolean( final String str ) {
final String my_str = str.trim().toLowerCase();
if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
return true;
}
else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
return false;
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
return false;
}
}
private double parseDouble( final String str ) {
double d = 0.0;
try {
d = Double.parseDouble( str );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
d = 0.0;
}
return d;
}
private float parseFloat( final String str ) {
float f = 0.0f;
try {
f = Float.parseFloat( str );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
f = 0.0f;
}
return f;
}
private int parseInt( final String str ) {
int i = -1;
try {
i = Integer.parseInt( str );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
i = -1;
}
return i;
}
private short parseShort( final String str ) {
short i = -1;
try {
i = Short.parseShort( str );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
i = -1;
}
return i;
}
private void processFontFamily( final StringTokenizer st ) {
setBaseFontFamilyName( "" );
final String font_str = ( ( String ) st.nextElement() ).trim();
final String[] fonts = font_str.split( ",+" );
for( String font : fonts ) {
font = font.replace( '_', ' ' ).trim();
if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
setBaseFontFamilyName( font );
break;
}
}
}
/**
* read each line of config file, process non-comment lines
* @throws IOException
*/
private void readConfig( final BufferedReader conf_in ) throws IOException {
String line;
do {
line = conf_in.readLine();
if ( line != null ) {
line = line.trim();
// skip comments and blank lines
if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
// convert runs of spaces to tabs
line = line.replaceAll( "\\s+", "\t" );
final StringTokenizer st = new StringTokenizer( line, "\t" );
setKeyValue( st );
}
}
} while ( line != null );
}
private void setAntialiasScreen( final boolean antialias_screen ) {
_antialias_screen = antialias_screen;
}
public void setBackgroundColorGradient( final boolean background_color_gradient ) {
_background_color_gradient = background_color_gradient;
}
private void setBaseFontFamilyName( final String base_font_family_name ) {
_base_font_family_name = base_font_family_name;
}
private void setBaseFontSize( final int base_font_size ) {
_base_font_size = base_font_size;
}
private void setShowDomainLabels( final boolean show_domain_labels ) {
_show_domain_labels = show_domain_labels;
}
private void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
_color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
}
private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
_cladogram_type = cladogram_type;
}
void setDisplayColors( final SortedMap<String, Color> display_colors ) {
_display_colors = display_colors;
}
private void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
_display_sequence_relations = display_sequence_relations;
}
private void setEditable( final boolean editable ) {
_editable = editable;
}
private void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) {
_nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes;
}
private void setGraphicsExportX( final int graphics_export_x ) {
_graphics_export_x = graphics_export_x;
}
private void setGraphicsExportY( final int graphics_export_y ) {
_graphics_export_y = graphics_export_y;
}
private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
_default_bootstrap_samples = default_bootstrap_samples;
}
private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
_internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
}
/**
* Set a key-value(s) tuple
*/
private void setKeyValue( final StringTokenizer st ) {
String key = ( String ) st.nextElement();
key = key.replace( ':', ' ' );
key = key.trim();
key = key.toLowerCase();
// Handle single value settings first:
if ( key.equals( "default_click_to" ) ) {
final String clickto_name = ( String ) st.nextElement();
default_clickto = getClickToIndex( clickto_name );
if ( default_clickto == -1 ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
+ "] for [default_click_to]" );
default_clickto = 0;
}
else if ( default_clickto == DEPRECATED ) {
// Deprecated.
}
}
else if ( key.equals( "native_ui" ) ) {
final String my_str = ( ( String ) st.nextElement() ).trim().toLowerCase();
if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
_native_ui = TRIPLET.TRUE;
}
else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
_native_ui = TRIPLET.FALSE;
}
else if ( my_str.equals( "?" ) ) {
_native_ui = TRIPLET.UNKNOWN;
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
+ "]" );
_native_ui = TRIPLET.FALSE;
}
}
else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "antialias_screen" ) ) {
setAntialiasScreen( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "phylogeny_graphics_type" ) ) {
final String type_str = ( ( String ) st.nextElement() ).trim();
if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CONVEX.toString() ) ) {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
}
else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CURVED.toString() ) ) {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
}
else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE.toString() ) ) {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
}
else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.ROUNDED.toString() ) ) {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
}
else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR.toString() ) ) {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR.toString() ) ) {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
}
else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.UNROOTED.toString() ) ) {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
else if ( type_str.equalsIgnoreCase( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR.toString() ) ) {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
}
else {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
+ "] for [phylogeny_graphics_type]" );
}
}
else if ( key.equals( "min_confidence_value" ) ) {
final String mcv_str = ( ( String ) st.nextElement() ).trim();
final double d = parseDouble( mcv_str );
setMinConfidenceValue( d );
}
else if ( key.equals( "font_family" ) ) {
processFontFamily( st );
}
else if ( key.equals( "font_size" ) ) {
final String size_str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( size_str );
setBaseFontSize( i );
}
else if ( key.equals( "graphics_export_x" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
setGraphicsExportX( i );
}
else if ( key.equals( "graphics_export_y" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
setGraphicsExportY( i );
}
else if ( key.equals( "pdf_export_line_width" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final float f = parseFloat( str );
if ( f > 0 ) {
setPrintLineWidth( f );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"value for [pdf_export_line_width] cannot be zero or negative" );
}
}
else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) {
final String str = ( ( String ) st.nextElement() ).trim();
final int i = parseInt( str );
if ( i >= 0 ) {
setDefaultBootstrapSamples( i );
}
else {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
else if ( key.equals( "show_scale" ) ) {
setShowScale( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "show_overview" ) ) {
setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "show_branch_length_values" ) ) {
setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "background_gradient" ) ) {
setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "color_labels_same_as_branch_length_values" ) ) {
setColorLabelsSameAsParentBranch( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "show_domain_labels" ) ) {
setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "cladogram_type" ) ) {
final String type_str = ( ( String ) st.nextElement() ).trim();
if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) {
setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP );
}
else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) {
setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
}
else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) {
setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
+ "] for [cladogram_type]" );
}
}
else if ( key.equals( "non_lined_up_cladogram" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
}
else if ( key.equals( "hide_controls_and_menus" ) ) {
_hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
}
else if ( key.equals( "use_tabbed_display" ) ) {
_use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
}
else if ( key.equals( "overview_width" ) ) {
final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
setOvMaxWidth( i );
}
else if ( key.equals( "overview_height" ) ) {
final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
setOvMaxHeight( i );
}
else if ( key.equals( "overview_placement_type" ) ) {
final String type_str = ( ( String ) st.nextElement() ).trim();
if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT.toTag() ) ) {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
}
else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT.toTag() ) ) {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
}
else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT.toTag() ) ) {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
}
else if ( type_str.equalsIgnoreCase( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT.toTag() ) ) {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
}
else {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
+ "] for [overview_placement_type]" );
}
}
else if ( key.equals( "node_label_direction" ) ) {
final String type_str = ( ( String ) st.nextElement() ).trim();
if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.HORIZONTAL.toString() ) ) {
setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
}
else if ( type_str.equalsIgnoreCase( NODE_LABEL_DIRECTION.RADIAL.toString() ) ) {
setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
}
else {
setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
+ "] for [node_label_direction]" );
}
}
else if ( key.equals( "branch_length_value_digits" ) ) {
final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
if ( i >= 0 ) {
setNumberOfDigitsAfterCommaForBranchLengthValue( i );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
+ "] for [branch_length_value_digits]" );
}
}
else if ( key.equals( "confidence_value_digits" ) ) {
final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
if ( i >= 0 ) {
setNumberOfDigitsAfterCommaForConfidenceValues( i );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
+ "] for [confidence_value_digits]" );
}
}
else if ( key.equals( "allow_editing" ) ) {
setEditable( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "display_sequence_relations" ) ) {
setDisplaySequenceRelations( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) {
final boolean r = parseBoolean( ( String ) st.nextElement() );
if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"attempt to extract taxonomies and replace underscores at the same time" );
}
else {
setReplaceUnderscoresInNhParsing( r );
}
}
else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) {
final boolean e = parseBoolean( ( String ) st.nextElement() );
if ( e && 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() ) );
}
else if ( key.equals( "glyph_type" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [glyph_type] is deprecated" );
}
else if ( key.equals( "gui_background_color" ) ) {
_gui_background_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "gui_checkbox_text_color" ) ) {
_gui_checkbox_text_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "gui_checkbox_and_button_active_color" ) ) {
_gui_checkbox_and_button_active_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "gui_button_text_color" ) ) {
_gui_button_text_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "gui_button_background_color" ) ) {
_gui_button_background_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "gui_menu_background_color" ) ) {
_gui_menu_background_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "gui_menu_text_color" ) ) {
_gui_menu_text_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "gui_button_border_color" ) ) {
_gui_button_border_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "domain_structure_font_color" ) ) {
_domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "domain_structure_base_color" ) ) {
_domain_structure_base_color = Color.decode( ( String ) st.nextElement() );
}
else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
// yet retrieved!
int key_index = -1;
if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) {
key_index = Configuration.display_as_phylogram;
if ( key.equals( "use_real_br_lengths" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" );
}
}
else if ( key.equals( "rollover" ) ) {
key_index = Configuration.node_data_popup;
}
else if ( key.equals( "color_according_to_species" ) ) {
key_index = Configuration.color_according_to_species;
}
else if ( key.equals( "show_node_names" ) ) {
key_index = Configuration.show_node_names;
}
else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) {
key_index = Configuration.show_tax_code;
if ( key.equals( "show_taxonomy" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" );
}
}
else if ( key.equals( "write_br_length_values" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [write_br_length_values] is deprecated" );
key_index = DEPRECATED;
}
else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) {
key_index = Configuration.write_confidence_values;
if ( key.equals( "write_bootstrap_values" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" );
}
}
else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) {
key_index = Configuration.write_events;
if ( key.equals( "write_dup_spec" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME,
"configuration key [write_dup_spec] is deprecated, use [write_events] instead" );
}
}
else if ( key.equals( "color_branches" ) ) {
key_index = Configuration.color_branches;
}
else if ( key.equals( "width_branches" ) ) {
key_index = Configuration.width_branches;
}
else if ( key.equals( "color_orthologous" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [color_orthologous] is deprecated" );
}
else if ( key.equals( "color_subtree_neighbors" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [color_subtree_neighbors] is deprecated" );
}
else if ( key.equals( "color_super_orthologous" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [color_super_orthologous] is deprecated" );
}
else if ( key.equals( "mark_nodes_with_box" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [mark_nodes_with_box] is deprecated" );
key_index = DEPRECATED;
}
else if ( key.equals( "show_domain_architectures" ) ) {
key_index = Configuration.show_domain_architectures;
}
else if ( key.equals( "show_annotations" ) ) {
key_index = Configuration.show_annotation;
}
else if ( key.equals( "show_binary_characters" ) ) {
key_index = Configuration.show_binary_characters;
}
else if ( key.equals( "show_binary_character_counts" ) ) {
key_index = Configuration.show_binary_character_counts;
}
else if ( key.equals( "show_gene_names" ) ) {
key_index = Configuration.show_gene_names;
}
else if ( key.equals( "show_gene_symbols" ) ) {
key_index = Configuration.show_gene_symbols;
}
else if ( key.equals( "show_sequence_acc" ) ) {
key_index = Configuration.show_sequence_acc;
}
else if ( key.equals( "show_node_ids" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" );
key_index = DEPRECATED;
}
else if ( key.equals( "display_internal_data" ) ) {
key_index = Configuration.display_internal_data;
}
else if ( key.equals( "dynamically_hide_data" ) ) {
key_index = Configuration.dynamically_hide_data;
}
else if ( key.equals( "show_taxonomy_names" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [show_taxonomy_names] is deprecated" );
key_index = DEPRECATED;
}
else if ( key.equals( "show_taxonomy_scientific_names" ) ) {
key_index = Configuration.show_taxonomy_scientific_names;
}
else if ( key.equals( "show_taxonomy_common_names" ) ) {
key_index = Configuration.show_taxonomy_common_names;
}
else if ( key.equals( "color_according_to_annotation" ) ) {
key_index = Configuration.color_according_to_annotation;
}
else if ( key.equals( "show_property" ) ) {
key_index = Configuration.show_property;
}
else if ( key.equals( "show_relation_confidence" ) ) {
key_index = Configuration.show_relation_confidence;
}
// If we've found the key, set the values
if ( key_index >= 0 ) {
display_options[ key_index ][ 1 ] = ( String ) st.nextElement();
display_options[ key_index ][ 2 ] = ( String ) st.nextElement();
// otherwise, keep looking
}
else {
if ( key_index == DEPRECATED ) {
// Deprecated.
}
else if ( key.equals( "click_to" ) ) {
final String click_to_name = ( String ) st.nextElement();
key_index = getClickToIndex( click_to_name );
if ( key_index >= 0 ) {
clickto_options[ key_index ][ 1 ] = ( String ) st.nextElement();
}
else if ( key_index == DEPRECATED ) {
// Deprecated.
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: "
+ click_to_name );
}
}
else if ( key.equals( "species_color" ) ) {
getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "domain_color" ) ) {
getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "annotation_color" ) ) {
getAnnotationColors()
.put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "function_color" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [function_color] is deprecated" );
}
else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
getDisplayColors().put( ( 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 );
}
}
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
+ config_filename );
}
}
private void setMinConfidenceValue( final double min_confidence_value ) {
_min_confidence_value = min_confidence_value;
}
void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
_node_label_direction = node_label_direction;
}
private void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
}
private void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
}
private void setOvMaxHeight( final short ov_max_height ) {
_ov_max_height = ov_max_height;
}
private void setOvMaxWidth( final short ov_max_width ) {
_ov_max_width = ov_max_width;
}
private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
_ov_placement = ov_placement;
}
void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
_phylogeny_graphics_type = phylogeny_graphics_type;
}
private void setPrintLineWidth( final float print_line_width ) {
_print_line_width = print_line_width;
}
private void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
_nh_parsing_replace_underscores = nh_parsing_replace_underscores;
}
private void setShowBranchLengthValues( final boolean show_branch_length_values ) {
_show_branch_length_values = show_branch_length_values;
}
private void setShowOverview( final boolean show_overview ) {
_show_overview = show_overview;
}
private void setShowScale( final boolean show_scale ) {
_show_scale = show_scale;
}
private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
_validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
}
void setWebLinks( final SortedMap<String, WebLink> weblinks ) {
_weblinks = weblinks;
}
static String getDefaultFontFamilyName() {
return DEFAULT_FONT_FAMILY;
}
//******************************************START**********************************************************//
public boolean do_display_clickToOption( final int which ) {
/**
* Note to programmer: Whatever happens in this method will also affect doDisplayClickToOption(final int which){}
*/
if(which == 6 || which == 7){
if(AppletParams.isTreePrunerForAll() ){
clickto_options[which][1] = "display";
}
else{
clickto_options[which][1] = "nodisplay";
}
}
return clickto_options[ which ][ 1 ].equals( "display" );
}
public String get_click_toTitle( final int which ) {
return clickto_options[ which ][ 0 ];
}
//********************************************END**********************************************************//
static enum TRIPLET {
TRUE, FALSE, UNKNOWN
}
public Color getDomainStructureFontColor() {
return _domain_structure_font_color;
}
public Color getDomainStructureBaseColor() {
return _domain_structure_base_color;
}
public boolean isColorLabelsSameAsParentBranch() {
return _color_labels_same_as_parent_branch;
}
public boolean isShowDomainLabels() {
return _show_domain_labels;
}
}