X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=d232fdde92ee8b080b32333ec7a52fa4937054a3;hb=a07102813fbac79ba1a534dc9954a8500dc5e5ff;hp=72c57532368fb438aa87314d75f38bb37526e93d;hpb=5958d8c92c06f76da04a466ef7636e93a640b6a3;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 72c5753..d232fdd 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -47,6 +47,7 @@ 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.phylogeny.data.NodeData.NODE_DATA; import org.forester.phylogeny.data.NodeVisualization; import org.forester.phylogeny.data.NodeVisualization.NodeFill; import org.forester.phylogeny.data.NodeVisualization.NodeShape; @@ -54,6 +55,9 @@ import org.forester.util.ForesterUtil; public final class Configuration { + public enum EXT_NODE_DATA_RETURN_ON { + CONSOLE, WINODW; + } 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"; @@ -90,12 +94,16 @@ public final class Configuration { private boolean _show_domain_labels = true; private boolean _abbreviate_scientific_names = false; private boolean _color_labels_same_as_parent_branch = false; - private int _default_bootstrap_samples = -1; private boolean _show_default_node_shapes = false; private NodeShape _default_node_shape = NodeShape.CIRCLE; private NodeFill _default_node_fill = NodeFill.GRADIENT; 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; @@ -133,13 +141,15 @@ public final class Configuration { final static int color_subtree = 5; final static int open_seq_web = 6; final static int open_tax_web = 7; - final static int cut_subtree = 8; - final static int copy_subtree = 9; - final static int paste_subtree = 10; - final static int delete_subtree_or_node = 11; - final static int add_new_node = 12; - final static int edit_node_data = 13; - final static int blast = 14; + final static int blast = 8; + final static int cut_subtree = 9; + final static int copy_subtree = 10; + final static int paste_subtree = 11; + final static int delete_subtree_or_node = 12; + final static int add_new_node = 13; + final static int edit_node_data = 14; + final static int sort_descendents = 15; + final static int get_ext_desc_data = 16; // --------------------------- // Display options for trees // --------------------------- @@ -151,7 +161,7 @@ public final class Configuration { 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", "?" }, + { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" }, { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, @@ -165,9 +175,10 @@ public final class Configuration { 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" }, - { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Cut Subtree", "display" }, - { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, - { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" } }; + { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" }, + { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, + { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" }, + { "Sort Descendants", "display" }, { "Return", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -202,6 +213,9 @@ public final class Configuration { 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 NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN; + private String _label_for_get_ext_descendents_data = ""; + private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW; private static String DEFAULT_FONT_FAMILY = ""; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { @@ -363,6 +377,12 @@ public final class Configuration { else if ( name.equals( "swap" ) ) { index = Configuration.swap; } + else if ( name.equals( "sort_descendants" ) ) { + index = Configuration.sort_descendents; + } + else if ( name.equals( "get_ext_descendents_data" ) ) { + index = Configuration.get_ext_desc_data; + } else if ( name.equals( "display_sequences" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); @@ -374,6 +394,9 @@ public final class Configuration { else if ( name.equals( "open_tax_web" ) ) { index = Configuration.open_tax_web; } + else if ( name.equals( "blast" ) ) { + index = Configuration.blast; + } else if ( name.equals( "cut_subtree" ) ) { index = Configuration.cut_subtree; } @@ -423,6 +446,18 @@ public final class Configuration { return _default_bootstrap_samples; } + public File getpathToLocalMafft() { + return _path_to_local_mafft; + } + + public File getPathToLocalFastme() { + return _path_to_local_fastme; + } + + public File getPathToLocalRaxml() { + return _path_to_local_raxml; + } + int getDefaultDisplayClicktoOption() { return default_clickto; } @@ -674,7 +709,7 @@ public final class Configuration { private double parseDouble( final String str ) { double d = 0.0; try { - d = Double.parseDouble( str ); + d = Double.parseDouble( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); @@ -686,7 +721,7 @@ public final class Configuration { private float parseFloat( final String str ) { float f = 0.0f; try { - f = Float.parseFloat( str ); + f = Float.parseFloat( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); @@ -698,7 +733,7 @@ public final class Configuration { private int parseInt( final String str ) { int i = -1; try { - i = Integer.parseInt( str ); + i = Integer.parseInt( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); @@ -710,7 +745,7 @@ public final class Configuration { private short parseShort( final String str ) { short i = -1; try { - i = Short.parseShort( str ); + i = Short.parseShort( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); @@ -781,6 +816,10 @@ public final class Configuration { _cladogram_type = cladogram_type; } + public void setColorizeBranches( final boolean b ) { + display_options[ color_branches ][ 2 ] = b ? "yes" : "no"; + } + public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; } @@ -789,6 +828,26 @@ public final class Configuration { _default_bootstrap_samples = default_bootstrap_samples; } + private void setPathToLocalMafft( final File path_to_local_mafft ) { + _path_to_local_mafft = path_to_local_mafft; + } + + private void setPathToLocalFastme( final File path_to_local_fastme ) { + _path_to_local_fastme = path_to_local_fastme; + } + + private void setPathToLocalRaxml( final File path_to_local_raxml ) { + _path_to_local_raxml = path_to_local_raxml; + } + + public File getPathToLocalClustalOmega() { + return _path_to_local_clustalo; + } + + public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) { + _path_to_local_clustalo = path_to_local_clustalo; + } + public void setDefaultNodeFill( final NodeFill default_node_fill ) { _default_node_fill = default_node_fill; } @@ -801,14 +860,62 @@ public final class Configuration { _default_node_shape_size = default_node_shape_size; } + public void setDisplayAsPhylogram( final boolean b ) { + display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; + } + public void setDisplayColors( final SortedMap display_colors ) { _display_colors = display_colors; } + public void setDisplayConfidenceValues( final boolean b ) { + display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayInternalData( final boolean b ) { + display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayNodeNames( final boolean b ) { + display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceAcc( final boolean b ) { + display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplaySequenceNames( final boolean b ) { + display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; + } + public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { _display_sequence_relations = display_sequence_relations; } + public void setDisplaySequenceSymbols( final boolean b ) { + display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyCode( final boolean b ) { + display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyCommonNames( final boolean b ) { + display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyImages( final boolean b ) { + display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; + } + + public void setDisplayTaxonomyScientificNames( final boolean b ) { + display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; + } + + public void setDynamicallyHideData( final boolean b ) { + display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; + } + private void setEditable( final boolean editable ) { _editable = editable; } @@ -833,10 +940,10 @@ public final class Configuration { * 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(); + final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase(); + if ( !st.hasMoreElements() ) { + return; + } // Handle single value settings first: if ( key.equals( "default_click_to" ) ) { final String clickto_name = ( String ) st.nextElement(); @@ -951,6 +1058,30 @@ public final class Configuration { "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 ) ) { + setPathToLocalMafft( new File( str ) ); + } + } + else if ( key.equals( "fastme_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalFastme( new File( str ) ); + } + } + else if ( key.equals( "raxml_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalRaxml( new File( str ) ); + } + } else if ( key.equals( "show_scale" ) ) { setShowScale( parseBoolean( ( String ) st.nextElement() ) ); } @@ -1000,11 +1131,11 @@ public final class Configuration { _use_tabbed_display = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "overview_width" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxWidth( i ); } else if ( key.equals( "overview_height" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxHeight( i ); } else if ( key.equals( "overview_placement_type" ) ) { @@ -1161,6 +1292,60 @@ public final class Configuration { else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) { setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) ); } + else if ( key.equals( "ext_descendents_data_to_return" ) ) { + final String s = ( ( String ) st.nextElement() ).trim(); + if ( s.equalsIgnoreCase( "node_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC ); + } + else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ ); + } + else if ( s.equalsIgnoreCase( "sequence_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL ); + } + else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME ); + } + else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); + } + else if ( s.equalsIgnoreCase( "user_selected" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return]" ); + } + } + else if ( key.equals( "label_for_get_ext_descendents_data" ) ) { + final String s = ( ( String ) st.nextElement() ).trim(); + if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s + + "] for [label_for_get_ext_descendents_data]" ); + } + else { + setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) ); + } + } + else if ( key.equals( "ext_descendents_data_to_return_on" ) ) { + final String s = ( ( String ) st.nextElement() ).trim().toLowerCase(); + if ( s.equals( "console" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE ); + } + else if ( s.equals( "window" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return_on]" ); + } + } else if ( st.countTokens() >= 2 ) { // counts the tokens that are not // yet retrieved! int key_index = -1; @@ -1358,6 +1543,14 @@ public final class Configuration { } } + private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { + _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; + } + + public String getLabelForGetExtDescendentsData() { + return _label_for_get_ext_descendents_data; + } + public void setMinConfidenceValue( final double min_confidence_value ) { _min_confidence_value = min_confidence_value; } @@ -1366,12 +1559,12 @@ public final class Configuration { _node_label_direction = node_label_direction; } - public 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; + public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) { + _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; } - public 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; + public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) { + _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; } private void setOvMaxHeight( final short ov_max_height ) { @@ -1418,10 +1611,18 @@ public final class Configuration { _show_scale = show_scale; } + public void setTaxonomyColorize( final boolean b ) { + display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; + } + public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; } + public void setUseBranchesWidths( final boolean b ) { + display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; + } + private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } @@ -1441,4 +1642,20 @@ public final class Configuration { public enum UI { NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN } + + public NODE_DATA getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; + } + + public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { + _ext_desc_data_to_return = ext_desc_data_to_return; + } + + public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { + return _ext_node_data_return_on; + } + + private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { + _ext_node_data_return_on = ext_node_data_return_on; + } }