X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=9488a1c9a188327ed4ab8687b9eaa819f0606c17;hb=814c97be10a4c55b0bb642668f9ef8e1f80d5a6c;hp=40fc4bcbb7cd2d213551e5bb7bc77e5b0650b3b7;hpb=12fb7d9470cefe81e135eb79a17288ca055ec0ed;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 40fc4bc..9488a1c 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -42,7 +42,6 @@ import java.net.URL; import java.util.ArrayList; import java.util.HashSet; import java.util.List; -import java.util.Map; import java.util.Set; import javax.swing.ButtonGroup; @@ -78,7 +77,6 @@ import org.forester.io.parsers.nhx.NHXParser; import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; import org.forester.io.parsers.phyloxml.PhyloXmlParser; -import org.forester.io.parsers.phyloxml.PhyloXmlUtil; import org.forester.io.parsers.tol.TolParser; import org.forester.io.parsers.util.ParserUtils; import org.forester.io.writers.SequenceWriter; @@ -104,8 +102,8 @@ import org.forester.util.ForesterUtil; public final class MainFrameApplication extends MainFrame { - private final static int FRAME_X_SIZE = 800; - private final static int FRAME_Y_SIZE = 800; + private final static int FRAME_X_SIZE = 900; + private final static int FRAME_Y_SIZE = 900; // Filters for the file-open dialog (classes defined in this file) private static final long serialVersionUID = -799735726778865234L; private static final boolean PREPROCESS_TREES = false; @@ -118,7 +116,6 @@ public final class MainFrameApplication extends MainFrame { // Application-only print menu items private JMenuItem _collapse_below_threshold; private JMenuItem _collapse_below_branch_length; - private JMenuItem _collapse_by_taxonomic_rank; private ButtonGroup _radio_group_1; private ButtonGroup _radio_group_2; // Others: @@ -435,12 +432,7 @@ public final class MainFrameApplication extends MainFrame { } collapseBelowThreshold(); } - else if ( o == _collapse_by_taxonomic_rank ) { - if ( isSubtreeDisplayed() ) { - return; - } - collapseByTaxonomicRank(); - } + else if ( o == _collapse_below_branch_length ) { if ( isSubtreeDisplayed() ) { return; @@ -768,10 +760,7 @@ public final class MainFrameApplication extends MainFrame { l.add( d ); } if ( !l.isEmpty() ) { - if ( node.getNodeData().getProperties() != null ) { - node.getNodeData().getProperties() - .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); - } + node.getNodeData().setVector( l ); } } @@ -983,7 +972,7 @@ public final class MainFrameApplication extends MainFrame { } } - private void collapse( final Phylogeny phy ) { + private void collapseBelowThreshold( final Phylogeny phy ) { final PhylogenyNodeIterator it = phy.iteratorPostorder(); final List to_be_removed = new ArrayList(); double min_support = Double.MAX_VALUE; @@ -1051,27 +1040,6 @@ public final class MainFrameApplication extends MainFrame { } } - private void collapseByTaxonomicRank() { - if ( _mainpanel.getCurrentTreePanel() != null ) { - final Map present_ranks = AptxUtil.getRankCounts( _mainpanel.getCurrentTreePanel().getPhylogeny()); - final String[] ranks = AptxUtil.getAllPossibleRanks(present_ranks); - String rank = ( String ) JOptionPane - .showInputDialog( this, - "What rank should the collapsing be based on", - "Rank Selection", - JOptionPane.QUESTION_MESSAGE, - null, - ranks, - null ); - if ( !ForesterUtil.isEmpty( rank ) ) { - if ( rank.indexOf( '(' ) > 0 ) { - rank = rank.substring( 0, rank.indexOf( '(' ) ).trim(); - } - _mainpanel.getCurrentTreePanel().collapseByTaxonomicRank( rank ); - } - } - } - private void collapseBelowBranchLengthThreshold() { if ( getCurrentTreePanel() != null ) { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); @@ -1135,7 +1103,7 @@ public final class MainFrameApplication extends MainFrame { } if ( success && ( m >= 0.0 ) ) { setMinNotCollapseConfidenceValue( m ); - collapse( phy ); + collapseBelowThreshold( phy ); } } } @@ -1381,14 +1349,9 @@ public final class MainFrameApplication extends MainFrame { _mainpanel.getControlPanel().showWhole(); _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } - else { - getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - } + + getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + activateSaveAllIfNeeded(); System.gc(); } @@ -1844,12 +1807,10 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) ); _options_jmenu .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); - _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); _radio_group_1 = new ButtonGroup(); _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); - _radio_group_1.add( _uniform_cladograms_rbmi ); - _radio_group_1.add( _non_lined_up_cladograms_rbmi ); + _radio_group_1.add( _non_lined_up_cladograms_rbmi ); _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) ); _options_jmenu @@ -1858,8 +1819,21 @@ public final class MainFrameApplication extends MainFrame { .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); _options_jmenu .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + + _options_jmenu + .add( _collapsed_with_average_height_cbmi = new JCheckBoxMenuItem( "Proportional Height of Collapsed Subtrees" ) ); + + + _options_jmenu + .add( _show_abbreviated_labels_for_collapsed_nodes_cbmi = new JCheckBoxMenuItem( "Add Abbreviated Labels to Collapsed Subtrees" ) ); + + + _options_jmenu .add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); + + + if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { _options_jmenu .add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); @@ -1962,12 +1936,13 @@ public final class MainFrameApplication extends MainFrame { customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() ); customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() ); + customizeCheckBoxMenuItem( _collapsed_with_average_height_cbmi, getOptions().isCollapsedWithAverageHeigh() ); + customizeCheckBoxMenuItem( _show_abbreviated_labels_for_collapsed_nodes_cbmi, getOptions().isShowAbbreviatedLabelsForCollapsedNodes() ); + customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi, getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ); - customizeRadioButtonMenuItem( _uniform_cladograms_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, - getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); + getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP ); customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); customizeCheckBoxMenuItem( _label_direction_cbmi, getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL ); @@ -2058,12 +2033,9 @@ public final class MainFrameApplication extends MainFrame { _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" ); customizeJMenuItem( _delete_not_selected_nodes_item ); _tools_menu.addSeparator(); - _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); + _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Single Taxonomy-Subtrees" ) ); customizeJMenuItem( _collapse_species_specific_subtrees ); - _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" ); - _tools_menu.add( _collapse_by_taxonomic_rank = new JMenuItem( "Collapse By Taxonomic Rank" ) ); - customizeJMenuItem( _collapse_by_taxonomic_rank ); - _collapse_by_taxonomic_rank.setToolTipText( "To (reversibly) collapse subtrees by taxonomic rank" ); + _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse subtrees associated with only one taxonomy (such as species specific subtrees)" ); _tools_menu .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) ); customizeJMenuItem( _collapse_below_threshold );