X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FControlPanel.java;h=98d5b5417c28916d3acdd3b4051117006c6a9277;hb=74409250720d04a225c98497ff395e04757d8c81;hp=174ba3520a74359fa52525786964cbf875a85033;hpb=4ca4ac162d7a3caa78a08c28213a0451968cd1ad;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 174ba35..98d5b54 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -81,6 +81,7 @@ final class ControlPanel extends JPanel implements ActionListener { Font.PLAIN, 9 ); private static final String RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree"; + private static final String SEARCH_TIP_TEXT = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches)."; private static final long serialVersionUID = -8463483932821545633L; private NodeClickAction _action_when_node_clicked; private int _add_new_node_item; @@ -125,7 +126,7 @@ final class ControlPanel extends JPanel implements ActionListener { private int _paste_subtree_item; private int _reroot_cb_item; private JButton _return_to_super_tree; - // Search + // Search private JLabel _search_found_label_0; private JLabel _search_found_label_1; private JButton _search_reset_button_0; @@ -142,6 +143,8 @@ final class ControlPanel extends JPanel implements ActionListener { // Indices for the click-to options in the combo box private int _show_data_item; private JCheckBox _show_domain_architectures; + private JCheckBox _show_mol_seqs; + private JCheckBox _write_branch_length_values; private JCheckBox _show_events; private JCheckBox _show_gene_names; private JCheckBox _show_node_names; @@ -221,11 +224,12 @@ final class ControlPanel extends JPanel implements ActionListener { } displayedPhylogenyMightHaveChanged( true ); } - else if ( e.getSource() == _show_domain_architectures ) { + else if ( e.getSource() == _show_domain_architectures ) { search0(); search1(); displayedPhylogenyMightHaveChanged( true ); } + else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) { if ( e.getSource() == getDisplayAsPhylogramCb() ) { setDrawPhylogram( getDisplayAsPhylogramCb().isSelected() ); @@ -249,6 +253,7 @@ final class ControlPanel extends JPanel implements ActionListener { displayedPhylogenyMightHaveChanged( false ); } else if ( e.getSource() == _show_whole ) { + displayedPhylogenyMightHaveChanged( true ); showWhole(); } else if ( e.getSource() == _return_to_super_tree ) { @@ -256,14 +261,12 @@ final class ControlPanel extends JPanel implements ActionListener { showWhole(); } else if ( e.getSource() == _order ) { - DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; - if ( ( !isShowTaxonomyScientificNames() && !isShowTaxonomyCode() && !isShowTaxonomyCommonNames() ) ) { - if ( ( isShowSequenceAcc() || isShowSeqNames() || isShowSeqSymbols() ) ) { - pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; - } - else if ( isShowNodeNames() ) { - pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; - } + DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; + if ( isShowTaxonomyScientificNames() || isShowTaxonomyCode() ) { + pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; + } + else if ( isShowSeqNames() || isShowSeqSymbols() || isShowGeneNames() ) { + pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; } PhylogenyMethods.orderAppearance( tp.getPhylogeny().getRoot(), _order_of_appearance, true, pri ); _order_of_appearance = !_order_of_appearance; @@ -273,7 +276,7 @@ final class ControlPanel extends JPanel implements ActionListener { tp.getPhylogeny().recalculateNumberOfExternalDescendants( true ); tp.resetNodeIdToDistToLeafMap(); tp.setEdited( true ); - displayedPhylogenyMightHaveChanged( false ); + displayedPhylogenyMightHaveChanged( true ); } else if ( e.getSource() == _uncollapse_all ) { uncollapseAll( tp ); @@ -288,11 +291,15 @@ final class ControlPanel extends JPanel implements ActionListener { displayedPhylogenyMightHaveChanged( true ); } else if ( e.getSource() == _decr_domain_structure_evalue_thr ) { - _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThreshold(); + _mainpanel.getCurrentTreePanel().decreaseDomainStructureEvalueThresholdExp(); + search0(); + search1(); displayedPhylogenyMightHaveChanged( true ); } else if ( e.getSource() == _incr_domain_structure_evalue_thr ) { - _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThreshold(); + _mainpanel.getCurrentTreePanel().increaseDomainStructureEvalueThresholdExp(); + search0(); + search1(); displayedPhylogenyMightHaveChanged( true ); } else if ( e.getSource() == _search_tf_0 ) { @@ -632,11 +639,21 @@ final class ControlPanel extends JPanel implements ActionListener { addJCheckBox( _width_branches, ch_panel ); add( ch_panel ); break; + case Configuration.write_branch_length_values: + _write_branch_length_values = new JCheckBox( title ); + addJCheckBox( _write_branch_length_values, ch_panel ); + add( ch_panel ); + break; case Configuration.show_domain_architectures: _show_domain_architectures = new JCheckBox( title ); addJCheckBox( _show_domain_architectures, ch_panel ); add( ch_panel ); break; + case Configuration.show_mol_seqs: + _show_mol_seqs = new JCheckBox( title ); + addJCheckBox( _show_mol_seqs, ch_panel ); + add( ch_panel ); + break; case Configuration.show_seq_names: _show_seq_names = new JCheckBox( title ); addJCheckBox( _show_seq_names, ch_panel ); @@ -754,7 +771,7 @@ final class ControlPanel extends JPanel implements ActionListener { /** * Indicates what action should be execute when a node is clicked - * + * * @return the click-on action */ NodeClickAction getActionWhenNodeClicked() { @@ -873,10 +890,18 @@ final class ControlPanel extends JPanel implements ActionListener { return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() ); } + boolean isWriteBranchLengthValues() { + return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() ); + } + boolean isShowDomainArchitectures() { return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() ); } + public boolean isShowMolSequences() { + return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() ); + } + boolean isShowGeneNames() { return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() ); } @@ -1087,6 +1112,16 @@ final class ControlPanel extends JPanel implements ActionListener { _show_domain_architectures.setSelected( state ); } break; + case Configuration.write_branch_length_values: + if ( _write_branch_length_values != null ) { + _write_branch_length_values.setSelected( state ); + } + break; + case Configuration.show_mol_seqs: + if ( _show_mol_seqs != null ) { + _show_mol_seqs.setSelected( state ); + } + break; case Configuration.show_seq_names: if ( _show_seq_names != null ) { _show_seq_names.setSelected( state ); @@ -1272,10 +1307,6 @@ final class ControlPanel extends JPanel implements ActionListener { _sequence_colors = sequence_colors; } - /* GUILHEM_END */ - /* - * Set up the controls from the config settings. 11/26/05 - */ void setupControls() { // The tree display options: setupDisplayCheckboxes(); @@ -1332,14 +1363,13 @@ final class ControlPanel extends JPanel implements ActionListener { } void setupSearchTools0() { - final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND."; final JLabel search_label = new JLabel( "Search (A):" ); search_label.setFont( ControlPanel.jcb_bold_font ); if ( !getConfiguration().isUseNativeUI() ) { search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() ); } add( search_label ); - search_label.setToolTipText( tip ); + search_label.setToolTipText( SEARCH_TIP_TEXT ); _search_found_label_0 = new JLabel(); getSearchFoundCountsLabel0().setVisible( false ); _search_found_label_0.setFont( ControlPanel.jcb_bold_font ); @@ -1347,7 +1377,7 @@ final class ControlPanel extends JPanel implements ActionListener { _search_found_label_0.setForeground( getConfiguration().getGuiCheckboxTextColor() ); } _search_tf_0 = new JTextField( 3 ); - _search_tf_0.setToolTipText( tip ); + _search_tf_0.setToolTipText( SEARCH_TIP_TEXT ); _search_tf_0.setEditable( true ); if ( !getConfiguration().isUseNativeUI() ) { _search_tf_0.setForeground( getConfiguration().getGuiMenuBackgroundColor() ); @@ -1393,14 +1423,13 @@ final class ControlPanel extends JPanel implements ActionListener { } void setupSearchTools1() { - final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND."; final JLabel search_label = new JLabel( "Search (B):" ); search_label.setFont( ControlPanel.jcb_bold_font ); if ( !getConfiguration().isUseNativeUI() ) { search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() ); } add( search_label ); - search_label.setToolTipText( tip ); + search_label.setToolTipText( SEARCH_TIP_TEXT ); _search_found_label_1 = new JLabel(); getSearchFoundCountsLabel1().setVisible( false ); _search_found_label_1.setFont( ControlPanel.jcb_bold_font ); @@ -1408,7 +1437,7 @@ final class ControlPanel extends JPanel implements ActionListener { _search_found_label_1.setForeground( getConfiguration().getGuiCheckboxTextColor() ); } _search_tf_1 = new JTextField( 3 ); - _search_tf_1.setToolTipText( tip ); + _search_tf_1.setToolTipText( SEARCH_TIP_TEXT ); _search_tf_1.setEditable( true ); if ( !getConfiguration().isUseNativeUI() ) { _search_tf_1.setForeground( getConfiguration().getGuiMenuBackgroundColor() ); @@ -1482,16 +1511,14 @@ final class ControlPanel extends JPanel implements ActionListener { _mainpanel.getCurrentTreePanel().validate(); _mainpanel.validate(); _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width, - _mainpanel.getSizeOfViewport().height, - true ); + _mainpanel.getSizeOfViewport().height ); _mainpanel.getCurrentTreePanel().resetPreferredSize(); _mainpanel.adjustJScrollPane(); _mainpanel.getCurrentTreePanel().repaint(); _mainpanel.getCurrentTreePanel().validate(); _mainpanel.validate(); _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width, - _mainpanel.getSizeOfViewport().height, - true ); + _mainpanel.getSizeOfViewport().height ); _mainpanel.getCurrentTreePanel().resetPreferredSize(); _mainpanel.adjustJScrollPane(); _mainpanel.getCurrentTreePanel().repaint(); @@ -1503,8 +1530,7 @@ final class ControlPanel extends JPanel implements ActionListener { if ( tree_panel != null ) { tree_panel.validate(); tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width, - _mainpanel.getSizeOfViewport().height, - true ); + _mainpanel.getSizeOfViewport().height ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } @@ -1591,7 +1617,7 @@ final class ControlPanel extends JPanel implements ActionListener { void updateDomainStructureEvaluethresholdDisplay() { if ( _domain_structure_evalue_thr_tf != null ) { _domain_structure_evalue_thr_tf.setText( "10^" - + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThreshold() ); + + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThresholdExp() ); } } @@ -1779,7 +1805,7 @@ final class ControlPanel extends JPanel implements ActionListener { getSearchResetButton0().setVisible( true ); String[] queries = null; List nodes = null; - if ( query_str.indexOf( ',' ) >= 0 ) { + if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) { queries = query_str.split( ",+" ); } else { @@ -1793,7 +1819,7 @@ final class ControlPanel extends JPanel implements ActionListener { continue; } query = query.trim(); - if ( query.indexOf( '+' ) >= 0 ) { + if ( ( query.indexOf( '+' ) >= 0 ) && !getOptions().isSearchWithRegex() ) { nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ), tree, getOptions().isSearchCaseSensitive(), @@ -1801,11 +1827,16 @@ final class ControlPanel extends JPanel implements ActionListener { isShowDomainArchitectures() ) ); } else { + final TreePanel tp = getMainPanel().getCurrentTreePanel(); + + nodes.addAll( PhylogenyMethods.searchData( query, tree, getOptions().isSearchCaseSensitive(), !getOptions().isMatchWholeTermsOnly(), - isShowDomainArchitectures() ) ); + getOptions().isSearchWithRegex(), + isShowDomainArchitectures(), + tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) : 0 ) ); } } if ( getOptions().isInverseSearchResult() ) { @@ -1833,7 +1864,7 @@ final class ControlPanel extends JPanel implements ActionListener { getSearchResetButton1().setVisible( true ); String[] queries = null; List nodes = null; - if ( query_str.indexOf( ',' ) >= 0 ) { + if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) { queries = query_str.split( ",+" ); } else { @@ -1847,7 +1878,7 @@ final class ControlPanel extends JPanel implements ActionListener { continue; } query = query.trim(); - if ( query.indexOf( '+' ) >= 0 ) { + if ( ( query.indexOf( '+' ) >= 0 ) && !getOptions().isSearchWithRegex() ) { nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ), tree, getOptions().isSearchCaseSensitive(), @@ -1855,11 +1886,14 @@ final class ControlPanel extends JPanel implements ActionListener { isShowDomainArchitectures() ) ); } else { + final TreePanel tp = getMainPanel().getCurrentTreePanel(); nodes.addAll( PhylogenyMethods.searchData( query, tree, getOptions().isSearchCaseSensitive(), !getOptions().isMatchWholeTermsOnly(), - isShowDomainArchitectures() ) ); + getOptions().isSearchWithRegex(), + isShowDomainArchitectures(), + tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) : 0 ) ); } } if ( getOptions().isInverseSearchResult() ) { @@ -2010,51 +2044,14 @@ final class ControlPanel extends JPanel implements ActionListener { _get_ext_desc_data = cb_index; if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) { addClickToOption( Configuration.get_ext_desc_data, getConfiguration() - .getLabelForGetExtDescendentsData() ); + .getLabelForGetExtDescendentsData() ); } else { - String s = ";"; - switch ( getConfiguration().getExtDescNodeDataToReturn() ) { - case NODE_NAME: - s = "Node Names"; - break; - case SEQUENCE_ACC: - s = "Sequence Accessors"; - break; - case SEQUENCE_MOL_SEQ: - s = "Molecular Sequence"; - break; - case SEQUENCE_MOL_SEQ_FASTA: - s = "Molecular Sequence (Fasta)"; - break; - case SEQUENCE_NAME: - s = "Sequence Names"; - break; - case GENE_NAME: - s = "Gene Names"; - break; - case SEQUENCE_SYMBOL: - s = "Sequence Symbols"; - break; - case TAXONOMY_CODE: - s = "Taxonomy Codes"; - break; - case TAXONOMY_COMM0N_NAME: - s = "Taxonomy Common Names"; - break; - case TAXONOMY_SCIENTIFIC_NAME: - s = "Scientific Names"; - break; - case UNKNOWN: - s = "User Selected Data"; - break; - default: - throw new IllegalStateException( "dont know how to deal with " - + getConfiguration().getExtDescNodeDataToReturn() ); - } - final String label = _configuration.getClickToTitle( Configuration.get_ext_desc_data ) + " " + s; - addClickToOption( Configuration.get_ext_desc_data, label ); + + addClickToOption( Configuration.get_ext_desc_data, + getConfiguration().getClickToTitle( Configuration.get_ext_desc_data ) ); } + if ( default_option == Configuration.get_ext_desc_data ) { selected_index = cb_index; } @@ -2218,6 +2215,18 @@ final class ControlPanel extends JPanel implements ActionListener { addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) ); setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) ); } + if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) { + addCheckbox( Configuration.write_confidence_values, + _configuration.getDisplayTitle( Configuration.write_confidence_values ) ); + setCheckbox( Configuration.write_confidence_values, + _configuration.doCheckOption( Configuration.write_confidence_values ) ); + } + if ( _configuration.doDisplayOption( Configuration.write_branch_length_values ) ) { + addCheckbox( Configuration.write_branch_length_values, + _configuration.getDisplayTitle( Configuration.write_branch_length_values ) ); + setCheckbox( Configuration.write_branch_length_values, + _configuration.doCheckOption( Configuration.write_branch_length_values ) ); + } if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) { addCheckbox( Configuration.show_binary_characters, _configuration.getDisplayTitle( Configuration.show_binary_characters ) ); @@ -2236,11 +2245,9 @@ final class ControlPanel extends JPanel implements ActionListener { setCheckbox( Configuration.show_domain_architectures, _configuration.doCheckOption( Configuration.show_domain_architectures ) ); } - if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) { - addCheckbox( Configuration.write_confidence_values, - _configuration.getDisplayTitle( Configuration.write_confidence_values ) ); - setCheckbox( Configuration.write_confidence_values, - _configuration.doCheckOption( Configuration.write_confidence_values ) ); + if ( _configuration.doDisplayOption( Configuration.show_mol_seqs ) ) { + addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) ); + setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) ); } if ( _configuration.doDisplayOption( Configuration.write_events ) ) { addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) ); @@ -2265,128 +2272,138 @@ final class ControlPanel extends JPanel implements ActionListener { private void setVisibilityOfDomainStrucureControls() { if ( _zoom_in_domain_structure != null ) { - if ( isShowDomainArchitectures() ) { - _domain_display_label.setVisible( true ); - _zoom_in_domain_structure.setVisible( true ); - _zoom_out_domain_structure.setVisible( true ); - _decr_domain_structure_evalue_thr.setVisible( true ); - _incr_domain_structure_evalue_thr.setVisible( true ); - _domain_structure_evalue_thr_tf.setVisible( true ); - if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) { - getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( true ); + final MainFrame mf = getMainFrame(); + if ( mf != null ) { + if ( isShowDomainArchitectures() ) { + _domain_display_label.setVisible( true ); + _zoom_in_domain_structure.setVisible( true ); + _zoom_out_domain_structure.setVisible( true ); + _decr_domain_structure_evalue_thr.setVisible( true ); + _incr_domain_structure_evalue_thr.setVisible( true ); + _domain_structure_evalue_thr_tf.setVisible( true ); + if ( mf._right_line_up_domains_cbmi != null ) { + mf._right_line_up_domains_cbmi.setVisible( true ); + } + if ( mf._show_domain_labels != null ) { + mf._show_domain_labels.setVisible( true ); + } } - if ( getMainPanel().getMainFrame()._show_domain_labels != null ) { - getMainPanel().getMainFrame()._show_domain_labels.setVisible( true ); + else { + _domain_display_label.setVisible( false ); + _zoom_in_domain_structure.setVisible( false ); + _zoom_out_domain_structure.setVisible( false ); + _decr_domain_structure_evalue_thr.setVisible( false ); + _incr_domain_structure_evalue_thr.setVisible( false ); + _domain_structure_evalue_thr_tf.setVisible( false ); + if ( mf._right_line_up_domains_cbmi != null ) { + mf._right_line_up_domains_cbmi.setVisible( false ); + } + if ( mf._show_domain_labels != null ) { + mf._show_domain_labels.setVisible( false ); + } } } - else { - _domain_display_label.setVisible( false ); - _zoom_in_domain_structure.setVisible( false ); - _zoom_out_domain_structure.setVisible( false ); - _decr_domain_structure_evalue_thr.setVisible( false ); - _incr_domain_structure_evalue_thr.setVisible( false ); - _domain_structure_evalue_thr_tf.setVisible( false ); - if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) { - getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false ); - } - if ( getMainPanel().getMainFrame()._show_domain_labels != null ) { - getMainPanel().getMainFrame()._show_domain_labels.setVisible( false ); - } + } + } + + // This takes care of ArchaeopteryxE-issue. + // Can, and will, return null prior to ArchaeopteryxE initialization completion. + final private MainFrame getMainFrame() { + MainFrame mf = getMainPanel().getMainFrame(); + if ( mf == null ) { + // Must be "E" applet version. + final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); + if ( e.getMainPanel() == null ) { + return null; } + mf = e.getMainPanel().getMainFrame(); } + return mf; } void setVisibilityOfX() { - try { + final MainFrame mf = getMainFrame(); + if ( mf != null ) { if ( ( getCurrentTreePanel() != null ) && ( getCurrentTreePanel().getPhylogeny() != null ) ) { if ( AptxUtil.isHasAtLeastOneBranchWithSupportSD( getCurrentTreePanel().getPhylogeny() ) ) { - if ( getMainPanel().getMainFrame()._show_confidence_stddev_cbmi != null ) { - getMainPanel().getMainFrame()._show_confidence_stddev_cbmi.setVisible( true ); + if ( mf._show_confidence_stddev_cbmi != null ) { + mf._show_confidence_stddev_cbmi.setVisible( true ); } } else { - if ( getMainPanel().getMainFrame()._show_confidence_stddev_cbmi != null ) { - getMainPanel().getMainFrame()._show_confidence_stddev_cbmi.setVisible( false ); + if ( mf._show_confidence_stddev_cbmi != null ) { + mf._show_confidence_stddev_cbmi.setVisible( false ); } } if ( AptxUtil.isHasAtLeastOneNodeWithScientificName( getCurrentTreePanel().getPhylogeny() ) ) { - if ( getMainPanel().getMainFrame()._abbreviate_scientific_names != null ) { - getMainPanel().getMainFrame()._abbreviate_scientific_names.setVisible( true ); + if ( mf._abbreviate_scientific_names != null ) { + mf._abbreviate_scientific_names.setVisible( true ); } } else { - if ( getMainPanel().getMainFrame()._abbreviate_scientific_names != null ) { - getMainPanel().getMainFrame()._abbreviate_scientific_names.setVisible( false ); + if ( mf._abbreviate_scientific_names != null ) { + mf._abbreviate_scientific_names.setVisible( false ); } } if ( AptxUtil.isHasAtLeastOneNodeWithSequenceAnnotation( getCurrentTreePanel().getPhylogeny() ) ) { - if ( getMainPanel().getMainFrame()._show_annotation_ref_source != null ) { - getMainPanel().getMainFrame()._show_annotation_ref_source.setVisible( true ); + if ( mf._show_annotation_ref_source != null ) { + mf._show_annotation_ref_source.setVisible( true ); } } else { - if ( getMainPanel().getMainFrame()._show_annotation_ref_source != null ) { - getMainPanel().getMainFrame()._show_annotation_ref_source.setVisible( false ); + if ( mf._show_annotation_ref_source != null ) { + mf._show_annotation_ref_source.setVisible( false ); } } } if ( isDrawPhylogram() || ( ( getCurrentTreePanel() != null ) && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel() .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) ) { - if ( getMainPanel().getMainFrame()._non_lined_up_cladograms_rbmi != null ) { - getMainPanel().getMainFrame()._non_lined_up_cladograms_rbmi.setVisible( false ); + if ( mf._non_lined_up_cladograms_rbmi != null ) { + mf._non_lined_up_cladograms_rbmi.setVisible( false ); } - if ( getMainPanel().getMainFrame()._uniform_cladograms_rbmi != null ) { - getMainPanel().getMainFrame()._uniform_cladograms_rbmi.setVisible( false ); + if ( mf._uniform_cladograms_rbmi != null ) { + mf._uniform_cladograms_rbmi.setVisible( false ); } - if ( getMainPanel().getMainFrame()._ext_node_dependent_cladogram_rbmi != null ) { - getMainPanel().getMainFrame()._ext_node_dependent_cladogram_rbmi.setVisible( false ); + if ( mf._ext_node_dependent_cladogram_rbmi != null ) { + mf._ext_node_dependent_cladogram_rbmi.setVisible( false ); } } else { - if ( getMainPanel().getMainFrame()._non_lined_up_cladograms_rbmi != null ) { - getMainPanel().getMainFrame()._non_lined_up_cladograms_rbmi.setVisible( true ); + if ( mf._non_lined_up_cladograms_rbmi != null ) { + mf._non_lined_up_cladograms_rbmi.setVisible( true ); } - if ( getMainPanel().getMainFrame()._uniform_cladograms_rbmi != null ) { - getMainPanel().getMainFrame()._uniform_cladograms_rbmi.setVisible( true ); + if ( mf._uniform_cladograms_rbmi != null ) { + mf._uniform_cladograms_rbmi.setVisible( true ); } - if ( getMainPanel().getMainFrame()._ext_node_dependent_cladogram_rbmi != null ) { - getMainPanel().getMainFrame()._ext_node_dependent_cladogram_rbmi.setVisible( true ); + if ( mf._ext_node_dependent_cladogram_rbmi != null ) { + mf._ext_node_dependent_cladogram_rbmi.setVisible( true ); } } if ( isDrawPhylogram() ) { - if ( getMainPanel().getMainFrame()._show_scale_cbmi != null ) { - getMainPanel().getMainFrame()._show_scale_cbmi.setVisible( true ); + if ( mf._show_scale_cbmi != null ) { + mf._show_scale_cbmi.setVisible( true ); } } else { - if ( getMainPanel().getMainFrame()._show_scale_cbmi != null ) { - getMainPanel().getMainFrame()._show_scale_cbmi.setVisible( false ); + if ( mf._show_scale_cbmi != null ) { + mf._show_scale_cbmi.setVisible( false ); } } if ( getCurrentTreePanel() != null ) { if ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) { - if ( getMainPanel().getMainFrame()._label_direction_cbmi != null ) { - getMainPanel().getMainFrame()._label_direction_cbmi.setVisible( true ); - } - if ( getMainPanel().getMainFrame()._show_branch_length_values_cbmi != null ) { - getMainPanel().getMainFrame()._show_branch_length_values_cbmi.setVisible( false ); + if ( mf._label_direction_cbmi != null ) { + mf._label_direction_cbmi.setVisible( true ); } } else { - if ( getMainPanel().getMainFrame()._label_direction_cbmi != null ) { - getMainPanel().getMainFrame()._label_direction_cbmi.setVisible( false ); - } - if ( getMainPanel().getMainFrame()._show_branch_length_values_cbmi != null ) { - getMainPanel().getMainFrame()._show_branch_length_values_cbmi.setVisible( true ); + if ( mf._label_direction_cbmi != null ) { + mf._label_direction_cbmi.setVisible( false ); } } } } - catch ( final Exception ignore ) { - //not important... - } } void setVisibilityOfDomainStrucureCB() { @@ -2455,9 +2472,4 @@ final class ControlPanel extends JPanel implements ActionListener { CHANGE_NODE_FONT, COLOR_NODE_FONT; } - - public boolean isShowSequences() { - // TODO Auto-generated method stub - return true; - } }