X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FControlPanel.java;h=509e24d99b78f9969d8833a83f8c8dbcc4da6cb8;hb=e6ea1a1dcb0a9b96cad1bc08c3b80a6f876344d2;hp=9549aef7ed5bfc6bc8d5455ab98d66c90c84bcd8;hpb=d33a5a1d64863f9b0207e1da71151396cea74a38;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 9549aef..509e24d 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -91,10 +91,12 @@ final class ControlPanel extends JPanel implements ActionListener { private List _click_to_names; private int _collapse_cb_item; private JCheckBox _color_acc_species; + private JCheckBox _color_acc_sequence; private JCheckBox _color_according_to_annotation; private boolean _color_branches; - private JCheckBox _color_branches_cb; + private JCheckBox _use_visual_styles_cb; private int _color_subtree_cb_item; + private int _change_node_font_item; // The settings from the conf file private final Configuration _configuration; private int _copy_subtree_item; @@ -116,12 +118,19 @@ final class ControlPanel extends JPanel implements ActionListener { private int _open_pdb_item; private int _open_seq_web_item; private int _open_tax_web_item; + private int _color_node_font_item; private JButton _order; private boolean _order_of_appearance; private int _paste_subtree_item; private int _reroot_cb_item; private JButton _return_to_super_tree; - + // Search + private JLabel _search_found_label_0; + private JLabel _search_found_label_1; + private JButton _search_reset_button_0; + private JButton _search_reset_button_1; + private JTextField _search_tf_0; + private JTextField _search_tf_1; private int _select_nodes_item; private Sequence _selected_query_seq; private JCheckBox _seq_relation_confidence_switch; @@ -129,14 +138,6 @@ final class ControlPanel extends JPanel implements ActionListener { private JCheckBox _show_annotation; private JCheckBox _show_binary_character_counts; private JCheckBox _show_binary_characters; - // Search - private JLabel _search_found_label_0; - private JButton _search_reset_button_0; - private JTextField _search_tf_0; - private JLabel _search_found_label_1; - private JButton _search_reset_button_1; - private JTextField _search_tf_1; - // Indices for the click-to options in the combo box private int _show_data_item; private JCheckBox _show_domain_architectures; @@ -156,6 +157,7 @@ final class ControlPanel extends JPanel implements ActionListener { private JButton _show_whole; private int _sort_descendents_item; private Map _species_colors; + private Map _sequence_colors; private int _subtree_cb_item; private int _swap_cb_item; private JButton _uncollapse_all; @@ -189,6 +191,19 @@ final class ControlPanel extends JPanel implements ActionListener { @Override public void actionPerformed( final ActionEvent e ) { try { + if ( e.getSource() == _color_acc_sequence ) { + if ( _color_acc_species != null ) { + _color_acc_species.setSelected( false ); + } + } + else if ( e.getSource() == _color_acc_species ) { + if ( _color_acc_sequence != null ) { + _color_acc_sequence.setSelected( false ); + } + + } + + final TreePanel tp = getMainPanel().getCurrentTreePanel(); if ( tp == null ) { return; @@ -291,6 +306,10 @@ final class ControlPanel extends JPanel implements ActionListener { search1(); displayedPhylogenyMightHaveChanged( true ); } + + + + else { displayedPhylogenyMightHaveChanged( true ); } @@ -310,9 +329,13 @@ final class ControlPanel extends JPanel implements ActionListener { public JCheckBox getColorAccSpeciesCb() { return _color_acc_species; } + + public JCheckBox getColorAccSequenceCb() { + return _color_acc_sequence; + } - public JCheckBox getColorBranchesCb() { - return _color_branches_cb; + public JCheckBox getUseVisualStylesCb() { + return _use_visual_styles_cb; } public JCheckBox getDisplayAsPhylogramCb() { @@ -532,10 +555,17 @@ final class ControlPanel extends JPanel implements ActionListener { case Configuration.color_according_to_species: _color_acc_species = new JCheckBox( title ); _color_acc_species - .setToolTipText( "To colorize taxonomy and sequence labels as a function of taxonomy" ); + .setToolTipText( "To colorize node labels as a function of taxonomy" ); addJCheckBox( _color_acc_species, ch_panel ); add( ch_panel ); break; + case Configuration.color_according_to_sequence: + _color_acc_sequence = new JCheckBox( title ); + _color_acc_sequence + .setToolTipText( "To colorize node labels as a function of sequence name" ); + addJCheckBox( _color_acc_sequence, ch_panel ); + add( ch_panel ); + break; case Configuration.color_according_to_annotation: _color_according_to_annotation = new JCheckBox( title ); _color_according_to_annotation @@ -593,10 +623,11 @@ final class ControlPanel extends JPanel implements ActionListener { addJCheckBox( getShowEventsCb(), ch_panel ); add( ch_panel ); break; - case Configuration.color_branches: - _color_branches_cb = new JCheckBox( title ); - getColorBranchesCb().setToolTipText( "To use branch color values, if present" ); - addJCheckBox( getColorBranchesCb(), ch_panel ); + case Configuration.use_style: + _use_visual_styles_cb = new JCheckBox( title ); + getUseVisualStylesCb() + .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" ); + addJCheckBox( getUseVisualStylesCb(), ch_panel ); add( ch_panel ); break; case Configuration.width_branches: @@ -761,7 +792,7 @@ final class ControlPanel extends JPanel implements ActionListener { JLabel getSearchFoundCountsLabel0() { return _search_found_label_0; } - + JLabel getSearchFoundCountsLabel1() { return _search_found_label_1; } @@ -769,7 +800,7 @@ final class ControlPanel extends JPanel implements ActionListener { JButton getSearchResetButton0() { return _search_reset_button_0; } - + JButton getSearchResetButton1() { return _search_reset_button_1; } @@ -777,7 +808,7 @@ final class ControlPanel extends JPanel implements ActionListener { JTextField getSearchTextField0() { return _search_tf_0; } - + JTextField getSearchTextField1() { return _search_tf_1; } @@ -789,6 +820,10 @@ final class ControlPanel extends JPanel implements ActionListener { Map getSpeciesColors() { return _species_colors; } + + Map getSequenceColors() { + return _sequence_colors; + } boolean isAntialiasScreenText() { return true; @@ -801,9 +836,13 @@ final class ControlPanel extends JPanel implements ActionListener { boolean isColorAccordingToTaxonomy() { return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() ); } + + boolean isColorAccordingToSequence() { + return ( ( _color_acc_sequence != null ) && _color_acc_sequence.isSelected() ); + } - boolean isColorBranches() { - return ( ( ( getColorBranchesCb() != null ) && getColorBranchesCb().isSelected() ) || ( ( getColorBranchesCb() == null ) && _color_branches ) ); + boolean isUseVisualStyles() { + return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) ); } boolean isDrawPhylogram() { @@ -908,8 +947,6 @@ final class ControlPanel extends JPanel implements ActionListener { if ( query != null ) { query = query.trim(); } - - if ( !ForesterUtil.isEmpty( query ) ) { search0( main_panel, tree, query ); } @@ -920,7 +957,7 @@ final class ControlPanel extends JPanel implements ActionListener { searchReset0(); } } - + void search1() { final MainPanel main_panel = getMainPanel(); final Phylogeny tree = main_panel.getCurrentPhylogeny(); @@ -931,7 +968,6 @@ final class ControlPanel extends JPanel implements ActionListener { if ( query != null ) { query = query.trim(); } - if ( !ForesterUtil.isEmpty( query ) ) { search1( main_panel, tree, query ); } @@ -942,15 +978,13 @@ final class ControlPanel extends JPanel implements ActionListener { searchReset1(); } } - - void searchReset0() { if ( getMainPanel().getCurrentTreePanel() != null ) { getMainPanel().getCurrentTreePanel().setFoundNodes0( null ); } } - + void searchReset1() { if ( getMainPanel().getCurrentTreePanel() != null ) { getMainPanel().getCurrentTreePanel().setFoundNodes1( null ); @@ -982,6 +1016,11 @@ final class ControlPanel extends JPanel implements ActionListener { _color_acc_species.setSelected( state ); } break; + case Configuration.color_according_to_sequence: + if ( _color_acc_sequence != null ) { + _color_acc_sequence.setSelected( state ); + } + break; case Configuration.color_according_to_annotation: if ( _color_according_to_annotation != null ) { _color_according_to_annotation.setSelected( state ); @@ -1037,9 +1076,9 @@ final class ControlPanel extends JPanel implements ActionListener { getShowEventsCb().setSelected( state ); } break; - case Configuration.color_branches: - if ( getColorBranchesCb() != null ) { - getColorBranchesCb().setSelected( state ); + case Configuration.use_style: + if ( getUseVisualStylesCb() != null ) { + getUseVisualStylesCb().setSelected( state ); } break; case Configuration.width_branches: @@ -1173,6 +1212,12 @@ final class ControlPanel extends JPanel implements ActionListener { else if ( action == _open_pdb_item ) { setActionWhenNodeClicked( NodeClickAction.OPEN_PDB_WEB ); } + else if ( action == _color_node_font_item ) { + setActionWhenNodeClicked( NodeClickAction.COLOR_NODE_FONT ); + } + else if ( action == _change_node_font_item ) { + setActionWhenNodeClicked( NodeClickAction.CHANGE_NODE_FONT ); + } else { throw new RuntimeException( "unknown action: " + action ); } @@ -1213,7 +1258,7 @@ final class ControlPanel extends JPanel implements ActionListener { void setSearchFoundCountsOnLabel0( final int counts ) { getSearchFoundCountsLabel0().setText( "Found: " + counts ); } - + void setSearchFoundCountsOnLabel1( final int counts ) { getSearchFoundCountsLabel1().setText( "Found: " + counts ); } @@ -1228,6 +1273,10 @@ final class ControlPanel extends JPanel implements ActionListener { void setSpeciesColors( final Map species_colors ) { _species_colors = species_colors; } + + void setSequenceColors( final Map sequence_colors ) { + _sequence_colors = sequence_colors; + } /* GUILHEM_END */ /* @@ -1409,8 +1458,7 @@ final class ControlPanel extends JPanel implements ActionListener { s_panel_2.add( _search_found_label_1 ); addJButton( _search_reset_button_1, s_panel_2 ); } - - + void showAnnotations() { if ( _show_annotation != null ) { _show_annotation.setSelected( true ); @@ -1421,6 +1469,9 @@ final class ControlPanel extends JPanel implements ActionListener { if ( _color_acc_species != null ) { _color_acc_species.setSelected( false ); } + if ( _color_acc_sequence != null ) { + _color_acc_sequence.setSelected( false ); + } _mainpanel.getCurrentTreePanel().repaint(); } @@ -1720,6 +1771,7 @@ final class ControlPanel extends JPanel implements ActionListener { private void init() { _draw_phylogram = new ArrayList(); setSpeciesColors( new HashMap() ); + setSequenceColors( new HashMap() ); setAnnotationColors( new HashMap() ); } @@ -1780,7 +1832,7 @@ final class ControlPanel extends JPanel implements ActionListener { searchReset0(); } } - + private void search1( final MainPanel main_panel, final Phylogeny tree, final String query_str ) { getSearchFoundCountsLabel1().setVisible( true ); getSearchResetButton1().setEnabled( true ); @@ -1894,6 +1946,24 @@ final class ControlPanel extends JPanel implements ActionListener { } cb_index++; } + if ( _configuration.doDisplayClickToOption( Configuration.color_node_font ) ) { + _color_node_font_item = cb_index; + addClickToOption( Configuration.color_node_font, + _configuration.getClickToTitle( Configuration.color_node_font ) ); + if ( default_option == Configuration.color_node_font ) { + selected_index = cb_index; + } + cb_index++; + } + if ( _configuration.doDisplayClickToOption( Configuration.change_node_font ) ) { + _change_node_font_item = cb_index; + addClickToOption( Configuration.change_node_font, + _configuration.getClickToTitle( Configuration.change_node_font ) ); + if ( default_option == Configuration.change_node_font ) { + selected_index = cb_index; + } + cb_index++; + } if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) { _color_subtree_cb_item = cb_index; addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) ); @@ -2076,6 +2146,18 @@ final class ControlPanel extends JPanel implements ActionListener { setCheckbox( Configuration.display_internal_data, _configuration.doCheckOption( Configuration.display_internal_data ) ); } + + + if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) { + addCheckbox( Configuration.color_according_to_sequence, + _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) ); + setCheckbox( Configuration.color_according_to_sequence, + _configuration.doCheckOption( Configuration.color_according_to_sequence ) ); + } + + + + if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) { addCheckbox( Configuration.color_according_to_species, _configuration.getDisplayTitle( Configuration.color_according_to_species ) ); @@ -2088,9 +2170,9 @@ final class ControlPanel extends JPanel implements ActionListener { setCheckbox( Configuration.color_according_to_annotation, _configuration.doCheckOption( Configuration.color_according_to_annotation ) ); } - if ( _configuration.doDisplayOption( Configuration.color_branches ) ) { - addCheckbox( Configuration.color_branches, _configuration.getDisplayTitle( Configuration.color_branches ) ); - setCheckbox( Configuration.color_branches, _configuration.doCheckOption( Configuration.color_branches ) ); + if ( _configuration.doDisplayOption( Configuration.use_style ) ) { + addCheckbox( Configuration.use_style, _configuration.getDisplayTitle( Configuration.use_style ) ); + setCheckbox( Configuration.use_style, _configuration.doCheckOption( Configuration.use_style ) ); } if ( _configuration.doDisplayOption( Configuration.width_branches ) ) { addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) ); @@ -2239,6 +2321,8 @@ final class ControlPanel extends JPanel implements ActionListener { SHOW_DATA, SORT_DESCENDENTS, SUBTREE, - SWAP; + SWAP, + CHANGE_NODE_FONT, + COLOR_NODE_FONT; } }