From 06b38f91bc061d8ab1dfea3b6238c94c95a30d26 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 10 Oct 2014 21:27:52 +0000 Subject: [PATCH] in progress (special coloring is still true) --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 9 +++++++-- .../org/forester/archaeopteryx/Configuration.java | 20 ++++++++++++-------- .../src/org/forester/archaeopteryx/Constants.java | 4 ++-- .../src/org/forester/archaeopteryx/MainFrame.java | 11 +++++++++-- .../forester/archaeopteryx/MainFrameApplet.java | 6 ++++-- .../archaeopteryx/MainFrameApplication.java | 8 ++++---- .../src/org/forester/archaeopteryx/Options.java | 11 +++++++++++ .../src/org/forester/archaeopteryx/TreePanel.java | 7 +++++-- 8 files changed, 54 insertions(+), 22 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 7ea1610..2796e00 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -122,6 +122,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private ButtonGroup _radio_group_1; private JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; private JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; + private JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; private JMenuItem _cycle_node_shape_mi; private JMenuItem _cycle_node_fill_mi; private JMenuItem _choose_node_size_mi; @@ -751,13 +752,14 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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 ); - ///// _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + _options_jmenu + .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); _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 ) ); @@ -782,7 +784,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); - ///// _options_jmenu.addSeparator(); _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); @@ -807,6 +808,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() .isShowDefaultNodeShapesInternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -1309,6 +1312,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) && _show_default_node_shapes_external_cbmi.isSelected() ); + options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index c4978d9..da1bdc4 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -238,6 +238,7 @@ public final class Configuration { private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; private boolean _show_annotation_ref_source = true; private boolean _show_default_node_shapes_external = false; + private boolean _show_default_node_shapes_for_marked_nodes = false; private boolean _show_default_node_shapes_internal = false; private boolean _show_domain_labels = true; private boolean _show_overview = true; @@ -746,6 +747,10 @@ public final class Configuration { return _show_default_node_shapes_external; } + public boolean isShowDefaultNodeShapesForMarkedNodes() { + return _show_default_node_shapes_for_marked_nodes; + } + public boolean isShowDefaultNodeShapesInternal() { return _show_default_node_shapes_internal; } @@ -1380,20 +1385,15 @@ public final class Configuration { else if ( key.equals( "gui_button_border_color" ) ) { _gui_button_border_color = Color.decode( ( String ) st.nextElement() ); } - else if ( key.equals( "show_default_node_shapes" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" ); - final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() ); - setShowDefaultNodeShapesInternal( b ); - setShowDefaultNodeShapesExternal( b ); - } else if ( key.equals( "show_default_node_shapes_internal" ) ) { setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); } else if ( key.equals( "show_default_node_shapes_external" ) ) { setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); } + else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) { + setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); + } else if ( key.equals( "default_node_size" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); setDefaultNodeShapeSize( i ); @@ -1761,6 +1761,10 @@ public final class Configuration { _show_default_node_shapes_external = show_default_node_shapes_external; } + public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) { + _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes; + } + public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { _show_default_node_shapes_internal = show_default_node_shapes_internal; } diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index b9c91cd..86ac819 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -42,8 +42,8 @@ public final class Constants { public final static boolean __SYNTH_LF = false; // TODO remove me public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; - final static String VERSION = "0.9899 beta"; - final static String PRG_DATE = "140925"; + final static String VERSION = "0.9900 beta"; + final static String PRG_DATE = "141010"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica", "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 2411d9d..dedc7ac 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -107,8 +107,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { 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_EXT = "External Node Shapes"; - static final String DISPLAY_NODE_BOXES_LABEL_INT = "Internal Node Shapes"; + static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes"; + static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes"; + 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"; @@ -193,6 +194,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _choose_minimal_confidence_mi; JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; JMenuItem _cycle_node_shape_mi; JMenuItem _cycle_node_fill_mi; JMenuItem _choose_node_size_mi; @@ -429,6 +431,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } + else if ( o == _show_default_node_shapes_for_marked_cbmi ) { + updateOptions( getOptions() ); + } else if ( o == _non_lined_up_cladograms_rbmi ) { updateOptions( getOptions() ); showWhole(); @@ -1308,6 +1313,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) && _show_default_node_shapes_external_cbmi.isSelected() ); + options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index 8314448..43fdc2e 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -208,13 +208,14 @@ public final class MainFrameApplet extends MainFrame { _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 ); - //////////// _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.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( _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 ) ); @@ -239,7 +240,6 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); - ////// _options_jmenu.addSeparator(); _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); @@ -255,6 +255,8 @@ public final class MainFrameApplet extends MainFrame { .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() .isShowDefaultNodeShapesExternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 125471d..e0d7990 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -901,13 +901,14 @@ public final class MainFrameApplication extends MainFrame { _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 ); - /////// _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) ); _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .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( _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 ) ); @@ -930,7 +931,6 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); - /////// _options_jmenu.addSeparator(); _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) ); _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) ); @@ -956,7 +956,6 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) ); _options_jmenu .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) ); - // _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) ); _options_jmenu .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) ); @@ -975,7 +974,6 @@ public final class MainFrameApplication extends MainFrame { _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi ); _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi ); _radio_group_2.add( _extract_taxonomy_agressive_rbmi ); - // _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) ); _options_jmenu .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) ); @@ -993,6 +991,8 @@ public final class MainFrameApplication extends MainFrame { .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() .isShowDefaultNodeShapesInternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 387bba6..36d0224 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -78,6 +78,7 @@ final public class Options { private boolean _search_case_sensitive; private boolean _show_annotation_ref_source; private boolean _show_confidence_stddev; + private boolean _show_default_node_shapes_for_marked_nodes; private boolean _show_default_node_shapes_external; private boolean _show_default_node_shapes_internal; private boolean _show_domain_labels; @@ -279,6 +280,10 @@ final public class Options { return _show_default_node_shapes_external; } + boolean isShowDefaultNodeShapesForMarkedNodes() { + return _show_default_node_shapes_for_marked_nodes; + } + boolean isShowDefaultNodeShapesInternal() { return _show_default_node_shapes_internal; } @@ -421,6 +426,10 @@ final public class Options { _show_default_node_shapes_internal = show_default_node_shapes_internal; } + void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) { + _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes; + } + final void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } @@ -446,6 +455,7 @@ final public class Options { _background_color_gradient = false; _show_default_node_shapes_internal = false; _show_default_node_shapes_external = false; + _show_default_node_shapes_for_marked_nodes = false; if ( AptxUtil.isUsOrCanada() ) { _print_size_x = Constants.US_LETTER_SIZE_X; _print_size_y = Constants.US_LETTER_SIZE_Y; @@ -551,6 +561,7 @@ final public class Options { } instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() ); instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() ); + instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() ); if ( configuration.getExtDescNodeDataToReturn() != null ) { instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() ); } diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index df7306b..bb31d7e 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -136,6 +136,7 @@ import org.forester.util.TaxonomyUtil; public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable { + public final static boolean SPECIAL_DOMAIN_COLORING = true; final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR ); final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR ); final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR ); @@ -173,7 +174,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private static final BasicStroke STROKE_2 = new BasicStroke( 2f ); private static final double TWO_PI = 2 * Math.PI; private final static int WIGGLE = 2; - private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me + private static final String SHOW_ONLY_THIS_CONF_TYPE = "posterior probability"; //TODO remove me HashMap _nodeid_dist_to_leaf = new HashMap(); final private Arc2D _arc = new Arc2D.Double(); private AffineTransform _at; @@ -255,7 +256,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private float _y_distance = 0.0f; private int _length_of_longest_text; private int _longest_domain; - public final static boolean SPECIAL_DOMAIN_COLORING = true; // private Image offscreenImage; // private Graphics offscreenGraphics; // private Dimension offscreenDimension; @@ -4166,6 +4166,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() ) || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() ) + || ( getOptions().isShowDefaultNodeShapesForMarkedNodes() + && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData() + .getNodeVisualData().isEmpty() ) ) || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node .getNodeData().getNodeVisualData().getNodeColor() != null ) || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE ) -- 1.7.10.2