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<String, WebLink> _weblinks = null;
private SortedMap<String, Color> _display_colors = null;
private boolean _antialias_screen = true;
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;
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;
}
_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;
}
_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() ) );
}
"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() ) );
}
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
}
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.archaeopteryx.tools.InferenceManager;
import org.forester.archaeopteryx.tools.ProcessPool;
import org.forester.archaeopteryx.tools.ProcessRunning;
import org.forester.phylogeny.Phylogeny;
Configuration _configuration;
JMenuItem _remove_branch_color_item;
Options _options;
+ InferenceManager _inference_manager;
final ProcessPool _process_pool;
MainFrame() {
_options = options;
}
+ void setInferenceManager( final InferenceManager i ) {
+ _inference_manager = i;
+ }
+
+ InferenceManager getInferenceManager() {
+ return _inference_manager;
+ }
+
+
void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
setTypeMenuToAllUnselected();
switch ( type ) {
// hide until everything is ready
setVisible( false );
setOptions( Options.createInstance( _configuration ) );
+ setInferenceManager( InferenceManager.createInstance( _configuration ) );
setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
_textframe = null;
_species_tree = null;
}
void buildPhylogeneticInferenceMenu() {
- final InferenceManager inference_manager = InferenceManager.getInstance();
+ final InferenceManager im = getInferenceManager();
_inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
_inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
customizeJMenuItem( _inference_from_msa_item );
_inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
- _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
- customizeJMenuItem( _inference_from_seqs_item );
- _inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ if ( im.canDoMsa() ) {
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
+ customizeJMenuItem( _inference_from_seqs_item );
+ _inference_from_seqs_item
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ }
+ else {
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
+ customizeJMenuItem( _inference_from_seqs_item );
+ _inference_from_seqs_item.setEnabled( false );
+ }
_jmenubar.add( _inference_menu );
}
private File getCurrentDir() {
if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
- if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1 ) {
+ if ( ForesterUtil.isWindowns() ) {
try {
_current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
}
package org.forester.archaeopteryx.tools;
-public class InferenceManager {
+import java.io.File;
+import java.io.IOException;
- public static InferenceManager getInstance() {
- // TODO Auto-generated method stub
+import org.forester.archaeopteryx.Configuration;
+import org.forester.util.ForesterUtil;
+
+public final class InferenceManager {
+
+ private final File _path_to_local_mafft;
+ private final File _path_to_local_kalign;
+ private final File _path_to_local_fastme;
+ private final File _path_to_local_raxml;
+ private final File _path_to_local_clustalo;
+
+ public static InferenceManager createInstance( final Configuration c ) {
+ return new InferenceManager( c.getpathToLocalMafft(),
+ c.getPathToLocalKalign(),
+ c.getPathToLocalFastme(),
+ c.getPathToLocalRaxml(),
+ c.getPathToLocalClustalOmega() );
+ }
+
+ public boolean canDoMsa() {
+ return ( getPathToLocalMafft() != null ) || ( getPathToLocalKalign() != null )
+ || ( getPathToLocalClustalo() != null );
+ }
+
+ 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;
+ }
+
+ public File getPathToLocalClustalo() {
+ return _path_to_local_clustalo;
+ }
+
+ private final static File createLocalPath( final File path ) {
+ if ( path == null ) {
+ return null;
+ }
+ try {
+ if ( path.getCanonicalFile().canExecute() && !path.getCanonicalFile().isDirectory() ) {
+ return new File( path.getCanonicalFile().toString() );
+ }
+ }
+ catch ( final IOException e ) {
+ return null;
+ }
return null;
}
+
+ private InferenceManager( final File path_to_local_mafft,
+ final File path_to_local_kalign,
+ final File path_to_local_fastme,
+ final File path_to_local_raxml,
+ final File path_to_local_clustalo ) {
+ _path_to_local_mafft = createLocalPath( path_to_local_mafft ) != null ? createLocalPath( path_to_local_mafft )
+ : createLocalPath( new File( "mafft" ) );
+ _path_to_local_kalign = createLocalPath( path_to_local_kalign ) != null ? createLocalPath( path_to_local_kalign )
+ : createLocalPath( new File( "kalign" ) );
+ _path_to_local_fastme = createLocalPath( path_to_local_fastme ) != null ? createLocalPath( path_to_local_fastme )
+ : createLocalPath( new File( "fastme" ) );
+ _path_to_local_raxml = createLocalPath( path_to_local_raxml ) != null ? createLocalPath( path_to_local_raxml )
+ : createLocalPath( new File( "raxml" ) );
+ _path_to_local_clustalo = createLocalPath( path_to_local_clustalo ) != null ? createLocalPath( path_to_local_clustalo )
+ : createLocalPath( new File( ForesterUtil.isWindowns() ? "clustalo.exe" : "clustalo" ) );
+ }
}
}
}
+ public static boolean isWindowns () {
+ return ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1;
+ }
+
final public static String getForesterLibraryInformation() {
return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")";
}
git://source.jalview.org / jalview.git / commitdiff