X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=758f053a74bf372521022062217da227634a8edc;hb=4a71774e563925de62c37378a6c32c3275f2e287;hp=0336c92d7223c2112aa8b59e547d333458baf281;hpb=2153d77fe476de9ceeb3b1e7fb3438c2ce373963;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 0336c92..758f053 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -36,6 +36,7 @@ import java.util.ArrayList; import java.util.LinkedList; import java.util.List; import java.util.Locale; +import java.util.Map; import java.util.NoSuchElementException; import javax.swing.Box; @@ -93,7 +94,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { final static MsaFileFilter msafilter = new MsaFileFilter(); final static SequencesFileFilter seqsfilter = new SequencesFileFilter(); final static DefaultFilter defaultfilter = new DefaultFilter(); - static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; + static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "rotate with mousewheel + Shift (or A and S), D toggles between horizontal and radial labels"; static final String PHYLOXML_REF_TOOL_TIP = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME static final String APTX_REF_TOOL_TIP = AptxConstants.APTX_REFERENCE; private static final long serialVersionUID = 3655000897845508358L; @@ -118,8 +119,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group"; static final String DISPLAY_SCALE_LABEL = "Scale"; - static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms"; - static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms"; + static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladogram"; static final String LABEL_DIRECTION_LABEL = "Radial Labels"; static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types"; static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits."; @@ -131,7 +131,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data"; static final String SHOW_OVERVIEW_LABEL = "Overview"; static final String FONT_SIZE_MENU_LABEL = "Font Size"; - static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; + static final String NONUNIFORM_CLADOGRAMS_LABEL = "Lined Up Cladogram"; static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels"; static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources"; static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent"; @@ -183,6 +183,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _confcolor_item; JMenuItem _color_rank_jmi; JMenuItem _collapse_species_specific_subtrees; + JMenuItem _obtain_detailed_taxonomic_information_jmi; JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi; JMenuItem _obtain_seq_information_jmi; @@ -209,7 +210,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { JCheckBoxMenuItem _screen_antialias_cbmi; JCheckBoxMenuItem _background_gradient_cbmi; JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; - JRadioButtonMenuItem _uniform_cladograms_rbmi; JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me @@ -230,6 +230,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JCheckBoxMenuItem _show_confidence_stddev_cbmi; JCheckBoxMenuItem _right_line_up_domains_cbmi; JCheckBoxMenuItem _line_up_renderable_data_cbmi; + JCheckBoxMenuItem _collapsed_with_average_height_cbmi; // _ print JCheckBoxMenuItem _graphics_export_visible_only_cbmi; JCheckBoxMenuItem _antialias_print_cbmi; @@ -498,10 +499,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { updateOptions( getOptions() ); showWhole(); } - else if ( o == _uniform_cladograms_rbmi ) { - updateOptions( getOptions() ); - showWhole(); - } else if ( o == _ext_node_dependent_cladogram_rbmi ) { updateOptions( getOptions() ); showWhole(); @@ -577,6 +574,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { } updateOptions( getOptions() ); } + + else if ( o == _collapsed_with_average_height_cbmi ) { + if ( _collapsed_with_average_height_cbmi.isSelected() ) { + _collapsed_with_average_height_cbmi.setSelected( true ); + } + updateOptions( getOptions() ); + } else if ( o == _right_line_up_domains_cbmi ) { if ( _right_line_up_domains_cbmi.isSelected() ) { _line_up_renderable_data_cbmi.setSelected( true ); @@ -1210,6 +1214,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { customizeCheckBoxMenuItem( _convex_type_cbmi, false ); customizeCheckBoxMenuItem( _unrooted_type_cbmi, false ); customizeCheckBoxMenuItem( _circular_type_cbmi, false ); + _triangular_type_cbmi.setToolTipText( "not suitable for phylograms" ); + _curved_type_cbmi.setToolTipText( "not suitable for phylograms" ); _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE ); initializeTypeMenu( getOptions() ); @@ -1291,8 +1297,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { void colorRank() { if ( _mainpanel.getCurrentTreePanel() != null ) { - final String[] ranks = AptxUtil.getAllPossibleRanks(); - final String rank = ( String ) JOptionPane + 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 colorization be based on", "Rank Selection", @@ -1301,6 +1308,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { ranks, null ); if ( !ForesterUtil.isEmpty( rank ) ) { + if ( rank.indexOf( '(' ) > 0 ) { + rank = rank.substring( 0, rank.indexOf( '(' ) ).trim(); + } _mainpanel.getCurrentTreePanel().colorRank( rank ); } } @@ -1832,11 +1842,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } - else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) { - options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); - } else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) { - options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); + options.setCladogramType( CLADOGRAM_TYPE.LINED_UP ); } options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null ) && _search_case_senstive_cbmi.isSelected() ); @@ -1933,6 +1940,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _parse_beast_style_extended_nexus_tags_cbmi != null ) && _parse_beast_style_extended_nexus_tags_cbmi.isEnabled() ) { options.setParseBeastStyleExtendedNexusTags(_parse_beast_style_extended_nexus_tags_cbmi.isSelected() ); } + if ( ( _collapsed_with_average_height_cbmi != null ) && _collapsed_with_average_height_cbmi.isEnabled() ) { + options.setCollapsedWithAverageHeigh(_collapsed_with_average_height_cbmi.isSelected() ); + } + } void updateTypeCheckboxes( final Options options, final Object o ) {