X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=e45dfc8195f21969b8ddd76e98cd29b79dc643f5;hb=9d627b6d40d2f38258ffe2cdebd82a2e8c1b9ea6;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..e45dfc8 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -90,12 +90,16 @@ 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 +137,14 @@ 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; // --------------------------- // Display options for trees // --------------------------- @@ -151,7 +156,7 @@ 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 +170,10 @@ 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" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -363,6 +369,9 @@ 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( "display_sequences" ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); @@ -374,6 +383,9 @@ 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 +435,20 @@ 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; } @@ -781,6 +807,10 @@ 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 +819,28 @@ 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 +853,62 @@ 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; } @@ -951,6 +1051,31 @@ 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() ) ); } @@ -1418,10 +1543,18 @@ 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; }