X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=0e8f3281f33fc5ec832f545f71e1b1b3152560d3;hb=c4f9dc6343e1fee8846c893b968065d9d9178655;hp=0b5433b713c38d4fa8b899f01457eae8b8907abf;hpb=605b9b5326538a70a7afe353368b206516292575;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 0b5433b..0e8f328 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -24,6 +24,7 @@ package org.forester.archaeopteryx; +import java.awt.Component; import java.awt.Container; import java.awt.Font; import java.awt.event.ActionEvent; @@ -33,7 +34,6 @@ import java.util.List; import java.util.Locale; import java.util.Map; -import javax.swing.Icon; import javax.swing.JApplet; import javax.swing.JCheckBoxMenuItem; import javax.swing.JFrame; @@ -47,53 +47,55 @@ 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.phylogeny.Phylogeny; +import org.forester.phylogeny.data.NodeVisualization.NodeFill; +import org.forester.phylogeny.data.NodeVisualization.NodeShape; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; public abstract class MainFrame extends JFrame implements ActionListener { - static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; - static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME - static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE; - private static final long serialVersionUID = 3655000897845508358L; - final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), - Font.PLAIN, - 10 ); - static final String TYPE_MENU_HEADER = "Type"; - static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; - static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; - static final String CURVED_TYPE_CBMI_LABEL = "Curved"; - static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; - static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; - static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; - static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO - static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO - static final String OPTIONS_HEADER = "Options"; - static final String SEARCH_SUBHEADER = "Search:"; - static final String DISPLAY_SUBHEADER = "Display:"; - static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; - static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; - static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; - static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values"; - static final String DISPLAY_SCALE_LABEL = "Display 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 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 SCREEN_ANTIALIAS_LABEL = "Antialias"; - static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; - static final String BG_GRAD_LABEL = "Background Color Gradient"; - static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Shapes"; - static final String SHOW_OVERVIEW_LABEL = "Show Overview"; - static final String FONT_SIZE_MENU_LABEL = "Font Size"; - static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; - static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels"; - 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"; - static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; - static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy"; - static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes"; - static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type"; - static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size"; + static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; + static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME + static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE; + private static final long serialVersionUID = 3655000897845508358L; + final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), + Font.PLAIN, + 10 ); + static final String TYPE_MENU_HEADER = "Type"; + static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; + static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; + static final String CURVED_TYPE_CBMI_LABEL = "Curved"; + static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; + static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; + static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; + static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO + static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO + static final String OPTIONS_HEADER = "Options"; + static final String SEARCH_SUBHEADER = "Search:"; + static final String DISPLAY_SUBHEADER = "Display:"; + static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; + static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; + static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; + static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values"; + static final String DISPLAY_SCALE_LABEL = "Display 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 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 SCREEN_ANTIALIAS_LABEL = "Antialias"; + static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; + static final String BG_GRAD_LABEL = "Background Color Gradient"; + static final String DISPLAY_NODE_BOXES_LABEL = "Display Node Shapes"; + static final String SHOW_OVERVIEW_LABEL = "Show Overview"; + static final String FONT_SIZE_MENU_LABEL = "Font Size"; + static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; + static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels"; + 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"; + static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; + static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy"; + static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes"; + static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type"; + static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; @@ -114,10 +116,12 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _midpoint_root_item; JMenuItem _taxcolor_item; JMenuItem _confcolor_item; + JMenuItem _color_rank_jmi; JMenuItem _infer_common_sn_names_item; JMenuItem _collapse_species_specific_subtrees; - JMenuItem _collapse_below_threshold; //TODO implememt me + JMenuItem _collapse_below_threshold; //TODO implememt me JMenuItem _obtain_detailed_taxonomic_information_jmi; + JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi; JMenuItem _obtain_uniprot_seq_information_jmi; JMenuItem _move_node_names_to_tax_sn_jmi; JMenuItem _move_node_names_to_seq_names_jmi; @@ -136,24 +140,22 @@ public abstract class MainFrame extends JFrame implements ActionListener { // _ screen display 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 _show_branch_length_values_cbmi; - JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me + JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me JCheckBoxMenuItem _show_overview_cbmi; JCheckBoxMenuItem _show_domain_labels; JCheckBoxMenuItem _abbreviate_scientific_names; JCheckBoxMenuItem _color_labels_same_as_parent_branch; JMenuItem _overview_placment_mi; JMenuItem _choose_minimal_confidence_mi; - JCheckBoxMenuItem _show_default_node_shapes_cbmi; JMenuItem _cycle_node_shape_mi; JMenuItem _cycle_node_fill_mi; JMenuItem _choose_node_size_mi; - JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; + JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; // _ print JCheckBoxMenuItem _graphics_export_visible_only_cbmi; JCheckBoxMenuItem _antialias_print_cbmi; @@ -230,6 +232,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _confcolor_item ) { confColor(); } + else if ( o == _color_rank_jmi ) { + colorRank(); + } else if ( o == _infer_common_sn_names_item ) { if ( isSubtreeDisplayed() ) { return; @@ -312,9 +317,18 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _choose_minimal_confidence_mi ) { chooseMinimalConfidence(); } + else if ( o == _choose_node_size_mi ) { + chooseNodeSize( getOptions(), this ); + } else if ( o == _overview_placment_mi ) { MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() ); } + else if ( o == _cycle_node_fill_mi ) { + MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() ); + } + else if ( o == _cycle_node_shape_mi ) { + MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() ); + } else if ( o == _screen_antialias_cbmi ) { updateOptions( getOptions() ); updateScreenTextAntialias( getMainPanel().getTreePanels() ); @@ -337,7 +351,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _non_lined_up_cladograms_rbmi ) { updateOptions( getOptions() ); showWhole(); @@ -578,6 +591,40 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + static void chooseNodeSize( final Options options, final Component parent ) { + final String s = ( String ) JOptionPane.showInputDialog( parent, + "Please enter the default size for node shapes.\n" + + "[current value: " + + options.getDefaultNodeShapeSize() + "]\n", + "Node Shape Size", + JOptionPane.QUESTION_MESSAGE, + null, + null, + options.getDefaultNodeShapeSize() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + if ( success && ( m >= 0.0 ) ) { + final short size = ForesterUtil.roundToShort( m ); + if ( size >= 0.0 ) { + options.setDefaultNodeShapeSize( size ); + } + } + } + } + void close() { removeTextFrame(); if ( _mainpanel != null ) { @@ -596,6 +643,30 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + void colorRank() { + if ( _mainpanel.getCurrentTreePanel() != null ) { + final String[] ranks = Util.getAllRanks( _mainpanel.getCurrentTreePanel().getPhylogeny() ); + if ( ranks.length < 1 ) { + JOptionPane.showMessageDialog( this, + "No rank information was found", + "No Rank Inoformation", + JOptionPane.WARNING_MESSAGE ); + return; + } + final String rank = ( String ) JOptionPane + .showInputDialog( this, + "What rank should the colorization be based on", + "Rank Selection", + JOptionPane.PLAIN_MESSAGE, + null, + ranks, + null ); + if ( !ForesterUtil.isEmpty( rank ) ) { + _mainpanel.getCurrentTreePanel().colorRank( rank ); + } + } + } + void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) { if ( item != null ) { item.setFont( MainFrame.menu_font ); @@ -865,11 +936,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) && _color_labels_same_as_parent_branch.isSelected() ); - //TODO FIXME ~~ - options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null ) && _show_default_node_shapes_cbmi.isSelected() ); - options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); - - //TODO FIXME ~~ + options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null ) + && _show_default_node_shapes_cbmi.isSelected() ); + options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) + && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -1071,7 +1141,38 @@ public abstract class MainFrame extends JFrame implements ActionListener { default: throw new RuntimeException( "unknown placement: " + op.getOvPlacement() ); } - tree_panel.updateOvSettings(); + if ( tree_panel != null ) { + tree_panel.updateOvSettings(); + } + } + + static void cycleNodeFill( final Options op, final TreePanel tree_panel ) { + switch ( op.getDefaultNodeFill() ) { + case GRADIENT: + op.setDefaultNodeFill( NodeFill.SOLID ); + break; + case NONE: + op.setDefaultNodeFill( NodeFill.GRADIENT ); + break; + case SOLID: + op.setDefaultNodeFill( NodeFill.NONE ); + break; + default: + throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() ); + } + } + + static void cycleNodeShape( final Options op, final TreePanel tree_panel ) { + switch ( op.getDefaultNodeShape() ) { + case CIRCLE: + op.setDefaultNodeShape( NodeShape.RECTANGLE ); + break; + case RECTANGLE: + op.setDefaultNodeShape( NodeShape.CIRCLE ); + break; + default: + throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() ); + } } static void help( final Map weblinks ) { @@ -1172,12 +1273,32 @@ public abstract class MainFrame extends JFrame implements ActionListener { TextFrame.instantiate( sb.toString() ); } - static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) { - if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) { - mi.setText( "Overview Placement... (current: " + tree_panel.getOptions().getOvPlacement() + ")" ); + static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { + mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); + } + else { + mi.setText( "Cycle Overview Placement..." ); + } + } + + static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) { + mi.setText( "Cycle Node Shape Fill Type... (current: " + + options.getDefaultNodeFill().toString().toLowerCase() + ")" ); } else { - mi.setText( "Overview Placement..." ); + mi.setText( "Cycle Node Shape Fill Type..." ); + } + } + + static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) { + mi.setText( "Cycle Node Shape Fill Type... (current: " + + options.getDefaultNodeShape().toString().toLowerCase() + ")" ); + } + else { + mi.setText( "Cycle Node Shape Fill Type..." ); } } @@ -1207,6 +1328,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" ); } + static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) { + mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" ); + } + static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel, final JCheckBoxMenuItem scale, final JCheckBoxMenuItem branch_lengths,