X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=d81100a1c415dc05a351ad59c22871f5161a4b51;hb=b1a74bd076c917d428002284a53a2c6f390226fb;hp=bb896aec78254e3e03cafff44688a98cf03947f9;hpb=885253f33f05af39d0d529659d534f5a3365159e;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index bb896ae..d81100a 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -62,10 +62,6 @@ public final class Configuration { private boolean _use_tabbed_display = false; private boolean _hide_controls_and_menus = false; private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; - private File _mafft = null; - private File _clustalo = null; - private File _fastme = null; - private SortedMap _weblinks = null; private SortedMap _display_colors = null; private boolean _antialias_screen = true; @@ -94,12 +90,17 @@ 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_kalign = 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; @@ -435,6 +436,22 @@ public final class Configuration { return _default_bootstrap_samples; } + public File getpathToLocalMafft() { + return _path_to_local_mafft; + } + + public File getPathToLocalKalign() { + return _path_to_local_kalign; + } + + public File getPathToLocalFastme() { + return _path_to_local_fastme; + } + + public File getPathToLocalRaxml() { + return _path_to_local_raxml; + } + int getDefaultDisplayClicktoOption() { return default_clickto; } @@ -805,6 +822,30 @@ 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 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; + } + + 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; } @@ -931,18 +972,6 @@ public final class Configuration { _ui = UI.UNKNOWN; } } - else if ( key.equals( "path_to_mafft" ) ) { - setPathToMafft( new File( (String) st.nextElement() ) ); - } - else if ( key.equals( "path_to_clustalo" ) ) { - setPathToClustalOmega( new File( (String) st.nextElement() ) ); - } - else if ( key.equals( "path_to_fastme" ) ) { - setPathToFastME( new File( (String) st.nextElement() ) ); - } - else if ( key.equals( "path_to_mafft" ) ) { - setPathToMafft( new File( (String) st.nextElement() ) ); - } else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) { setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) ); } @@ -1027,6 +1056,36 @@ 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( "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 ) ) { + 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() ) ); } @@ -1518,38 +1577,6 @@ public final class Configuration { return DEFAULT_FONT_FAMILY; } - - public File getPathToMafft() { - return _mafft; - } - - - - public File getPathToClustalOmega() { - return _clustalo; - } - - - public File getPathToFastME() { - return _fastme; - } - - - public void setPathToMafft( final File mafft ) { - _mafft = mafft; - } - - - - public void setPathToClustalOmega( final File clustalo ) { - _clustalo = clustalo ; - } - - - public void setPathToFastME( final File fastme ) { - _fastme = fastme; - } - static enum TRIPLET { TRUE, FALSE, UNKNOWN }