X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=d232fdde92ee8b080b32333ec7a52fa4937054a3;hb=a07102813fbac79ba1a534dc9954a8500dc5e5ff;hp=d81100a1c415dc05a351ad59c22871f5161a4b51;hpb=de8fbefc959f11af246340c4f903fb2983a95d4d;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index d81100a..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"; @@ -97,7 +101,6 @@ public final class Configuration { 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_kalign = null; private File _path_to_local_fastme = null; private File _path_to_local_raxml = null; private File _path_to_local_clustalo = null; @@ -146,6 +149,7 @@ public final class Configuration { 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 // --------------------------- @@ -174,7 +178,7 @@ public final class Configuration { { "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" } }; + { "Sort Descendants", "display" }, { "Return", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -209,6 +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 ) { @@ -373,6 +380,9 @@ public final class Configuration { 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" ); @@ -440,10 +450,6 @@ public final class Configuration { return _path_to_local_mafft; } - public File getPathToLocalKalign() { - return _path_to_local_kalign; - } - public File getPathToLocalFastme() { return _path_to_local_fastme; } @@ -703,7 +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 + "]" ); @@ -715,7 +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 + "]" ); @@ -727,7 +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 + "]" ); @@ -739,7 +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 + "]" ); @@ -826,10 +832,6 @@ public final class Configuration { _path_to_local_mafft = path_to_local_mafft; } - private void setPathToLocalKalign( final File path_to_local_kalign ) { - _path_to_local_kalign = path_to_local_kalign; - } - private void setPathToLocalFastme( final File path_to_local_fastme ) { _path_to_local_fastme = path_to_local_fastme; } @@ -938,10 +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(); @@ -1068,12 +1070,6 @@ public final class Configuration { setPathToLocalMafft( new File( str ) ); } } - else if ( key.equals( "kalign_local" ) ) { - final String str = ( ( String ) st.nextElement() ).trim(); - if ( !ForesterUtil.isEmpty( str ) ) { - setPathToLocalKalign( new File( str ) ); - } - } else if ( key.equals( "fastme_local" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); if ( !ForesterUtil.isEmpty( str ) ) { @@ -1135,11 +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" ) ) { @@ -1296,6 +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; @@ -1493,6 +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; } @@ -1501,12 +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 ) { @@ -1584,4 +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; + } }