X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=978b1322b9a99aa598ad7da03ba3d1da28d25f74;hb=886c0c0a7a7cef72503df9f21762db1dab594362;hp=fc2c074aeecd4dff78bba6e58bfafe1c1ce6afb6;hpb=ebc019e52cc784faa96c1360f23e0d4b8c12ecf5;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index fc2c074..3b3977d 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -30,13 +30,14 @@ import java.awt.Color; import java.awt.Cursor; import java.awt.Dimension; import java.awt.Font; +import java.awt.FontMetrics; import java.awt.GradientPaint; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Point; -import java.awt.Polygon; import java.awt.Rectangle; import java.awt.RenderingHints; +import java.awt.Stroke; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; @@ -48,12 +49,14 @@ import java.awt.event.MouseEvent; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.awt.font.FontRenderContext; +import java.awt.font.TextAttribute; import java.awt.font.TextLayout; import java.awt.geom.AffineTransform; import java.awt.geom.Arc2D; import java.awt.geom.CubicCurve2D; import java.awt.geom.Ellipse2D; import java.awt.geom.Line2D; +import java.awt.geom.Path2D; import java.awt.geom.QuadCurve2D; import java.awt.geom.Rectangle2D; import java.awt.image.BufferedImage; @@ -66,6 +69,7 @@ import java.io.UnsupportedEncodingException; import java.net.URI; import java.net.URISyntaxException; import java.net.URLEncoder; +import java.text.AttributedString; import java.text.DecimalFormat; import java.text.DecimalFormatSymbols; import java.text.NumberFormat; @@ -74,11 +78,13 @@ import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; +import java.util.Map; import java.util.Set; +import java.util.SortedSet; import javax.swing.BorderFactory; -import javax.swing.JApplet; import javax.swing.JColorChooser; import javax.swing.JDialog; import javax.swing.JMenuItem; @@ -89,153 +95,263 @@ import javax.swing.JTextArea; import javax.swing.Popup; import javax.swing.PopupFactory; +import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON; import org.forester.archaeopteryx.ControlPanel.NodeClickAction; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; -import org.forester.archaeopteryx.Options.NodeFill; -import org.forester.archaeopteryx.Options.NodeShape; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture; +import org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence; import org.forester.archaeopteryx.phylogeny.data.RenderableVector; import org.forester.archaeopteryx.tools.Blast; import org.forester.archaeopteryx.tools.ImageLoader; import org.forester.io.parsers.phyloxml.PhyloXmlUtil; +import org.forester.io.writers.SequenceWriter; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.data.Accession; import org.forester.phylogeny.data.Annotation; import org.forester.phylogeny.data.BranchColor; import org.forester.phylogeny.data.Confidence; +import org.forester.phylogeny.data.DomainArchitecture; import org.forester.phylogeny.data.Event; -import org.forester.phylogeny.data.PhylogenyData; -import org.forester.phylogeny.data.PropertiesMap; -import org.forester.phylogeny.data.Property; +import org.forester.phylogeny.data.NodeDataField; +import org.forester.phylogeny.data.NodeVisualData; +import org.forester.phylogeny.data.NodeVisualData.NodeFill; +import org.forester.phylogeny.data.NodeVisualData.NodeShape; +import org.forester.phylogeny.data.PhylogenyDataUtil; +import org.forester.phylogeny.data.ProteinDomain; import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.data.SequenceRelation; import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.data.Uri; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.phylogeny.iterators.PreorderTreeIterator; -import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; +import org.forester.util.SequenceAccessionTools; +import org.forester.util.TaxonomyUtil; public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable { - private static final float PI = ( float ) ( Math.PI ); - private static final double TWO_PI = 2 * Math.PI; - private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI ); - private static final float HALF_PI = ( float ) ( Math.PI / 2.0 ); - private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 ); - private static final short OV_BORDER = 10; - final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR ); - final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR ); - final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR ); - final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR ); - final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR ); - private final static long serialVersionUID = -978349745916505029L; - private final static int EURO_D = 10; - private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node"; - private final static int MIN_ROOT_LENGTH = 3; - private final static int MAX_SUBTREES = 100; - private final static int MAX_NODE_FRAMES = 10; - private final static int MOVE = 20; - private final static NumberFormat FORMATTER_CONFIDENCE; - private final static NumberFormat FORMATTER_BRANCH_LENGTH; - private final static int WIGGLE = 2; - private final int _half_box_size_plus_wiggle; - private final static int LIMIT_FOR_HQ_RENDERING = 1000; - private final static int CONFIDENCE_LEFT_MARGIN = 4; - // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not - // being static anymore (02/20/2009). - private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, - RenderingHints.VALUE_RENDER_DEFAULT ); - private File _treefile = null; - private Configuration _configuration = null; - private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ]; - private int _node_frame_index = 0; - private Phylogeny _phylogeny = null; - private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ]; - private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ]; - private int _subtree_index = 0; - private MainPanel _main_panel = null; - private Set _found_nodes = null; - private PhylogenyNode _highlight_node = null; - private JPopupMenu _node_popup_menu = null; - private JMenuItem _node_popup_menu_items[] = null; - private int _longest_ext_node_info = 0; - private float _x_correction_factor = 0.0f; - private float _ov_x_correction_factor = 0.0f; - private float _x_distance = 0.0f; - private float _y_distance = 0.0f; - private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; - private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH; - private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP; - private float _last_drag_point_x = 0; - private float _last_drag_point_y = 0; - private ControlPanel _control_panel = null; - private int _external_node_index = 0; - private final Polygon _polygon = new Polygon(); - private final StringBuilder _sb = new StringBuilder(); - private JColorChooser _color_chooser = null; - private double _scale_distance = 0.0; - private String _scale_label = null; - private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float(); - private final QuadCurve2D _quad_curve = new QuadCurve2D.Float(); - private final Line2D _line = new Line2D.Float(); - private final Ellipse2D _ellipse = new Ellipse2D.Float(); - private final Rectangle2D _rectangle = new Rectangle2D.Float(); - private Options _options = null; - private float _ov_max_width = 0; - private float _ov_max_height = 0; - private int _ov_x_position = 0; - private int _ov_y_position = 0; - private int _ov_y_start = 0; - private float _ov_y_distance = 0; - private float _ov_x_distance = 0; - private boolean _ov_on = false; - private double _urt_starting_angle = ( float ) ( Math.PI / 2 ); - private float _urt_factor = 1; - private float _urt_factor_ov = 1; - private final boolean _phy_has_branch_lengths; - private final Rectangle2D _ov_rectangle = new Rectangle2D.Float(); - private boolean _in_ov_rect = false; - private boolean _in_ov = false; - private final Rectangle _ov_virtual_rectangle = new Rectangle(); - final private static double _180_OVER_PI = 180.0 / Math.PI; - private static final float ROUNDED_D = 8; - private int _circ_max_depth; - private int _circ_num_ext_nodes; - private PhylogenyNode _root; - final private Arc2D _arc = new Arc2D.Double(); - final private HashMap _urt_nodeid_angle_map = new HashMap(); - final private HashMap _urt_nodeid_index_map = new HashMap(); - HashMap _nodeid_dist_to_leaf = new HashMap(); - private AffineTransform _at; - private double _max_distance_to_root = -1; - private int _dynamic_hiding_factor = 0; - private boolean _edited = false; - private Popup _node_desc_popup; - private JTextArea _rollover_popup; - private final int _box_size; - private final int _half_box_size; - //private final short _skip_counter = 0; - private final StringBuffer _popup_buffer = new StringBuffer(); - final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(), - Font.PLAIN, - 12 ); - private static final boolean DRAW_MEAN_COUNTS = true; //TODO remove me later - private Sequence _query_sequence = null; - private final FontRenderContext _frc = new FontRenderContext( null, - false, - false ); - // expression values menu: - private DescriptiveStatistics _statistics_for_vector_data; - private PhylogenyNode[] _nodes_in_preorder = null; - // private Image offscreenImage; - // private Graphics offscreenGraphics; - // private Dimension offscreenDimension; + final private class NodeColorizationActionListener implements ActionListener { + + List _additional_nodes = null; + JColorChooser _chooser = null; + PhylogenyNode _node = null; + + NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) { + _chooser = chooser; + _node = node; + } + + NodeColorizationActionListener( final JColorChooser chooser, + final PhylogenyNode node, + final List additional_nodes ) { + _chooser = chooser; + _node = node; + _additional_nodes = additional_nodes; + } + + @Override + public void actionPerformed( final ActionEvent e ) { + final Color c = _chooser.getColor(); + if ( c != null ) { + colorizeNodes( c, _node, _additional_nodes ); + } + } + } + + final private class SubtreeColorizationActionListener implements ActionListener { + + List _additional_nodes = null; + JColorChooser _chooser = null; + PhylogenyNode _node = null; + + SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) { + _chooser = chooser; + _node = node; + } + + SubtreeColorizationActionListener( final JColorChooser chooser, + final PhylogenyNode node, + final List additional_nodes ) { + _chooser = chooser; + _node = node; + _additional_nodes = additional_nodes; + } + + @Override + public void actionPerformed( final ActionEvent e ) { + final Color c = _chooser.getColor(); + if ( c != null ) { + colorizeSubtree( c, _node, _additional_nodes ); + } + } + } + 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 ); + final static Cursor MOVE_CURSOR = Cursor + .getPredefinedCursor( Cursor.MOVE_CURSOR ); + final static Cursor WAIT_CURSOR = Cursor + .getPredefinedCursor( Cursor.WAIT_CURSOR ); + final private static double _180_OVER_PI = 180.0 / Math.PI; + private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI + / 32 ); + private final static int CONFIDENCE_LEFT_MARGIN = 4; + private final static int EURO_D = 10; + private final static NumberFormat FORMATTER_BRANCH_LENGTH; + private final static NumberFormat FORMATTER_CONFIDENCE; + private static final float HALF_PI = ( float ) ( Math.PI + / 2.0 ); + private final static int LIMIT_FOR_HQ_RENDERING = 2000; + private final static int MAX_NODE_FRAMES = 10; + private final static int MAX_SUBTREES = 100; + private final static int MIN_ROOT_LENGTH = 3; + private final static int MOVE = 20; + private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node"; + private static final float ONEHALF_PI = ( float ) ( 1.5 + * Math.PI ); + private static final short OV_BORDER = 10; + private final static double OVERVIEW_FOUND_NODE_BOX_SIZE = 2; + private final static double OVERVIEW_FOUND_NODE_BOX_SIZE_HALF = 1; + private static final float PI = ( float ) ( Math.PI ); + final private static Font POPUP_FONT = new Font( Configuration + .getDefaultFontFamilyName(), Font.PLAIN, 12 ); + private static final float ROUNDED_D = 8; + private final static long serialVersionUID = -978349745916505029L; + private static final BasicStroke STROKE_0025 = new BasicStroke( 0.025f ); + private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f ); + private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f ); + private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f ); + private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f ); + private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f ); + private static final BasicStroke STROKE_1 = new BasicStroke( 1f ); + private static final BasicStroke STROKE_2 = new BasicStroke( 2f ); + private static final BasicStroke STROKE_01_DASHED = new BasicStroke( 0.1f, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, + 0, + new float[] { + 2.0f }, + 0f ); + private static final BasicStroke STROKE_005_DASHED = new BasicStroke( 0.05f, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, + 0, + new float[] { + 2.0f }, + 0f ); + private static final BasicStroke STROKE_001_DASHED = new BasicStroke( 0.01f, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, + 0, + new float[] { + 2.0f }, + 0f ); + private static final double TWO_PI = 2 * Math.PI; + private final static int WIGGLE = 3; + private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me + HashMap _nodeid_dist_to_leaf = new HashMap(); + final private Arc2D _arc = new Arc2D.Double(); + private AffineTransform _at; + private int _clicked_x; + private int _circ_max_depth; + final private Set _collapsed_external_nodeid_set = new HashSet(); + private JColorChooser _color_chooser = null; + private Configuration _configuration = null; + private ControlPanel _control_panel = null; + private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float(); + private Set _current_external_nodes = null; + private StringBuilder _current_external_nodes_data_buffer = new StringBuilder(); + private int _current_external_nodes_data_buffer_change_counter = 0; + private int _domain_structure_e_value_thr_exp = AptxConstants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP; + private double _domain_structure_width = AptxConstants.DOMAIN_STRUCTURE_DEFAULT_WIDTH; + private int _dynamic_hiding_factor = 0; + private boolean _edited = false; + private final Ellipse2D _ellipse = new Ellipse2D.Float(); + private int _external_node_index = 0; + private Set _found_nodes_0 = null; + private Set _found_nodes_1 = null; + private final FontRenderContext _frc = new FontRenderContext( null, + false, + false ); + private float _furthest_node_x; + private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; + private PhylogenyNode _highlight_node = null; + private boolean _in_ov = false; + private boolean _in_ov_rect = false; + private float _last_drag_point_x = 0; + private float _last_drag_point_y = 0; + private final Line2D _line = new Line2D.Float(); + private int _longest_ext_node_info = 0; + private PhylogenyNode _ext_node_with_longest_txt_info = null; + private MainPanel _main_panel = null; + private double _max_distance_to_root = -1; + private Popup _node_desc_popup; + private int _node_frame_index = 0; + private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ]; + private JPopupMenu _node_popup_menu = null; + private JMenuItem _node_popup_menu_items[] = null; + private PhylogenyNode[] _nodes_in_preorder = null; + private Options _options = null; + private float _ov_max_height = 0; + private float _ov_max_width = 0; + private boolean _ov_on = false; + private final Rectangle2D _ov_rectangle = new Rectangle2D.Float(); + private final Rectangle _ov_virtual_rectangle = new Rectangle(); + private float _ov_x_correction_factor = 0.0f; + private float _ov_x_distance = 0; + private int _ov_x_position = 0; + private float _ov_y_distance = 0; + private int _ov_y_position = 0; + private int _ov_y_start = 0; + private boolean _partition_tree = false; + private final boolean _phy_has_branch_lengths; + private Phylogeny _phylogeny = null; + private final Path2D.Float _polygon = new Path2D.Float(); + private final StringBuffer _popup_buffer = new StringBuffer(); + private final QuadCurve2D _quad_curve = new QuadCurve2D.Float(); + private Sequence _query_sequence = null; + private final Rectangle2D _rectangle = new Rectangle2D.Float(); + private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, + RenderingHints.VALUE_RENDER_DEFAULT ); + private JTextArea _rollover_popup; + private PhylogenyNode _root; + private float _root_x; + private final StringBuilder _sb = new StringBuilder(); + private double _scale_distance = 0.0; + private String _scale_label = null; + private DescriptiveStatistics _statistics_for_vector_data; + private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ]; + private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ]; + private int _subtree_index = 0; + private File _treefile = null; + private float _urt_factor = 1; + private float _urt_factor_ov = 1; + final private HashMap _urt_nodeid_angle_map = new HashMap(); + final private HashMap _urt_nodeid_index_map = new HashMap(); + private double _urt_starting_angle = ( float ) ( Math.PI + / 2 ); + private float _x_correction_factor = 0.0f; + private float _x_distance = 0.0f; + private float _y_distance = 0.0f; + private int _length_of_longest_text; + private int _longest_domain; + private Map _attributed_string_map = null; + private int _depth_collapse_level = -1; + private int _rank_collapse_level = -1; + + + static { final DecimalFormatSymbols dfs = new DecimalFormatSymbols(); dfs.setDecimalSeparator( '.' ); @@ -267,14 +383,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _main_panel = tjp; _configuration = configuration; _phylogeny = t; - _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny ); - _box_size = tjp.getOptions().getDefaultNodeShapeSize(); - _half_box_size = tjp.getOptions().getDefaultNodeShapeSize() / 2; - _half_box_size_plus_wiggle = _half_box_size + WIGGLE; + _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny ); init(); // if ( !_phylogeny.isEmpty() ) { _phylogeny.recalculateNumberOfExternalDescendants( true ); - checkForVectorProperties( _phylogeny ); // } setBackground( getTreeColorSet().getBackgroundColor() ); final MouseListener mouse_listener = new MouseListener( this ); @@ -283,74 +395,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee addMouseWheelListener( this ); calculateScaleDistance(); FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() ); - FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration - .getNumberOfDigitsAfterCommaForBranchLengthValues() ); - } - - public void checkForVectorProperties( final Phylogeny phy ) { - final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); - for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - if ( node.getNodeData().getProperties() != null ) { - final PropertiesMap pm = node.getNodeData().getProperties(); - final double[] vector = new double[ pm.getProperties().size() ]; - int counter = 0; - for( final String ref : pm.getProperties().keySet() ) { - if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) { - final Property p = pm.getProperty( ref ); - final String value_str = p.getValue(); - final String index_str = ref - .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() ); - double d = -100; - try { - d = Double.parseDouble( value_str ); - } - catch ( final NumberFormatException e ) { - JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str - + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE ); - return; - } - int i = -1; - try { - i = Integer.parseInt( index_str ); - } - catch ( final NumberFormatException e ) { - JOptionPane.showMessageDialog( this, - "Could not parse \"" + index_str - + "\" into index for vector data", - "Problem with Vector Data", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( i < 0 ) { - JOptionPane.showMessageDialog( this, - "Attempt to use negative index for vector data", - "Problem with Vector Data", - JOptionPane.ERROR_MESSAGE ); - return; - } - vector[ i ] = d; - ++counter; - stats.addValue( d ); - } - } - final List vector_l = new ArrayList( counter ); - for( int i = 0; i < counter; ++i ) { - vector_l.add( vector[ i ] ); - } - node.getNodeData().setVector( vector_l ); - } - } - if ( stats.getN() > 0 ) { - _statistics_for_vector_data = stats; - } + FORMATTER_BRANCH_LENGTH + .setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() ); } + @Override final public void actionPerformed( final ActionEvent e ) { - int index; boolean done = false; final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource(); - for( index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) { + for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) { // NOTE: index corresponds to the indices of click-to options // in the control panel. if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) { @@ -366,12 +419,196 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee requestFocusInWindow(); } + public synchronized Hashtable getImageMap() { + return getMainPanel().getImageMap(); + } + + final public MainPanel getMainPanel() { + return _main_panel; + } + + /** + * Get a pointer to the phylogeny + * + * @return a pointer to the phylogeny + */ + public final Phylogeny getPhylogeny() { + return _phylogeny; + } + + public final TreeColorSet getTreeColorSet() { + return getMainPanel().getTreeColorSet(); + } + + @Override + final public void mouseWheelMoved( final MouseWheelEvent e ) { + final int notches = e.getWheelRotation(); + if ( inOvVirtualRectangle( e ) ) { + if ( !isInOvRect() ) { + setInOvRect( true ); + repaint(); + } + } + else { + if ( isInOvRect() ) { + setInOvRect( false ); + repaint(); + } + } + if ( e.isControlDown() && e.isShiftDown() ) { + if ( notches < 0 ) { + getTreeFontSet().increaseFontSize(); + } + else { + getTreeFontSet().decreaseFontSize( 1, false ); + } + getControlPanel().displayedPhylogenyMightHaveChanged( true ); + resetPreferredSize(); + updateOvSizes(); + repaint(); + } + else if ( e.isShiftDown() && e.isAltDown() ) { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + else { + for( int i = 0; i < notches; ++i ) { + getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + } + else if ( e.isShiftDown() ) { + if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + else { + for( int i = 0; i < notches; ++i ) { + setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT ); + if ( getStartingAngle() < 0 ) { + setStartingAngle( TWO_PI + getStartingAngle() ); + } + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + } + else { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + else { + for( int i = 0; i < notches; ++i ) { + getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + } + } + else { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, + AptxConstants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR ); + getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + else { + for( int i = 0; i < notches; ++i ) { + getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); + getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + } + requestFocus(); + requestFocusInWindow(); + requestFocus(); + } + + @Override + final public void paintComponent( final Graphics g ) { + final Graphics2D g2d = ( Graphics2D ) g; + g2d.setRenderingHints( _rendering_hints ); + paintPhylogeny( g2d, false, false, 0, 0, 0, 0 ); + } + + @Override + final public int print( final Graphics g, final PageFormat page_format, final int page_index ) + throws PrinterException { + if ( page_index > 0 ) { + return ( NO_SUCH_PAGE ); + } + else { + final Graphics2D g2d = ( Graphics2D ) g; + g2d.translate( page_format.getImageableX(), page_format.getImageableY() ); + // Turn off double buffering !? + paintPhylogeny( g2d, true, false, 0, 0, 0, 0 ); + // Turn double buffering back on !? + return ( PAGE_EXISTS ); + } + } + + public final void setEdited( final boolean edited ) { + _edited = edited; + } + + public synchronized void setImageMap( final Hashtable image_map ) { + getMainPanel().setImageMap( image_map ); + } + + /** + * Set a phylogeny tree. + * + * @param t + * an instance of a Phylogeny + */ + public final void setTree( final Phylogeny t ) { + setNodeInPreorderToNull(); + _phylogeny = t; + } + + public final void setWaitCursor() { + setCursor( WAIT_CURSOR ); + repaint(); + } + + @Override + public void update( final Graphics g ) { + paint( g ); + } + + private void abbreviateScientificName( final String sn, final StringBuilder sb ) { + final String[] a = sn.split( "\\s+" ); + sb.append( a[ 0 ].substring( 0, 1 ) ); + sb.append( a[ 1 ].substring( 0, 2 ) ); + if ( a.length > 2 ) { + for( int i = 2; i < a.length; i++ ) { + sb.append( " " ); + sb.append( a[ i ] ); + } + } + } + final private void addEmptyNode( final PhylogenyNode node ) { if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { errorMessageNoCutCopyPasteInUnrootedDisplay(); return; } - final String label = getASimpleTextRepresentationOfANode( node ); + final String label = createASimpleTextRepresentationOfANode( node ); String msg = ""; if ( ForesterUtil.isEmpty( label ) ) { msg = "How to add the new, empty node?"; @@ -411,15 +648,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { phy.addAsChild( node ); } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); repaint(); } + final private void addToCurrentExternalNodes( final long i ) { + if ( _current_external_nodes == null ) { + _current_external_nodes = new HashSet(); + } + _current_external_nodes.add( i ); + } + final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node, final boolean is_vertical, final Graphics g, @@ -430,14 +674,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.setColor( Color.BLACK ); } else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE ) - || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) ) - && ( getCutOrCopiedTree() != null ) - && ( getCopiedAndPastedNodes() != null ) - && !to_pdf - && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) { - g.setColor( getTreeColorSet().getFoundColor() ); - } - else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { + || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) + || ( action == NodeClickAction.ADD_NEW_NODE ) ) && ( getCutOrCopiedTree() != null ) + && ( getCopiedAndPastedNodes() != null ) && !to_pdf && !to_graphics_file + && getCopiedAndPastedNodes().contains( node.getId() ) ) { + g.setColor( getTreeColorSet().getFoundColor0() ); + } + else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); } else if ( to_pdf ) { @@ -448,39 +691,49 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) { - if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - return ( PhylogenyMethods.getBranchColorValue( node ) ); - } - else { - return ( getTreeColorSet().getBranchColor() ); - } - } - final private void blast( final PhylogenyNode node ) { if ( !isCanBlast( node ) ) { JOptionPane.showMessageDialog( this, - "No sequence information present", + "Insufficient information present", "Cannot Blast", - JOptionPane.WARNING_MESSAGE ); + JOptionPane.INFORMATION_MESSAGE ); return; } - if ( node.getNodeData().isHasSequence() ) { - String name = ""; - if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) { - name = node.getNodeData().getSequence().getName(); - } - else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { - name = node.getNodeData().getSequence().getSymbol(); - } - else if ( node.getNodeData().getSequence().getAccession() != null ) { - name = node.getNodeData().getSequence().getAccession().getValue(); - } - if ( !ForesterUtil.isEmpty( name ) ) { + else { + final String query = Blast.obtainQueryForBlast( node ); + System.out.println( "query for BLAST is: " + query ); + char type = '?'; + if ( !ForesterUtil.isEmpty( query ) ) { + if ( node.getNodeData().isHasSequence() ) { + if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) { + if ( node.getNodeData().getSequence().getType().toLowerCase() + .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) { + type = 'p'; + } + else { + type = 'n'; + } + } + else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { + if ( ForesterUtil + .seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) { + type = 'p'; + } + else { + type = 'n'; + } + } + } + if ( type == '?' ) { + if ( SequenceAccessionTools.isProteinDbQuery( query ) ) { + type = 'p'; + } + else { + type = 'n'; + } + } try { - System.out.println( "trying: " + name ); - final Blast s = new Blast(); - s.go( name ); + Blast.openNcbiBlastWeb( query, type == 'n', this ); } catch ( final Exception e ) { e.printStackTrace(); @@ -489,16 +742,25 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final void calcMaxDepth() { - if ( _phylogeny != null ) { - _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + private final int calcDynamicHidingFactor() { + return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().getHeight() / ( 1.5 * getYdistance() ) ) ); + } + + final private int calcLengthOfLongestText() { + final StringBuilder sb = new StringBuilder(); + if ( _ext_node_with_longest_txt_info != null ) { + nodeDataAsSB( _ext_node_with_longest_txt_info, sb ); + if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) { + nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb ); + } } + return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() ); } /** * Calculate the length of the distance between the given node and its * parent. - * + * * @param node * @param ext_node_x * @factor @@ -519,90 +781,28 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final private Color calculateColorForAnnotation( final PhylogenyData ann ) { + final private Color calculateColorForAnnotation( final SortedSet ann ) { Color c = getTreeColorSet().getAnnotationColor(); if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) { - c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() ); - if ( c == null ) { - c = getTreeColorSet().getAnnotationColor(); + final StringBuilder sb = new StringBuilder(); + for( final Annotation a : ann ) { + sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() ); + } + final String ann_str = sb.toString(); + if ( !ForesterUtil.isEmpty( ann_str ) ) { + c = getControlPanel().getAnnotationColors().get( ann_str ); + if ( c == null ) { + c = AptxUtil.calculateColorFromString( ann_str, false ); + getControlPanel().getAnnotationColors().put( ann_str, c ); + } + if ( c == null ) { + c = getTreeColorSet().getAnnotationColor(); + } } } return c; } - final void calculateLongestExtNodeInfo() { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { - return; - } - int longest = 20; - for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { - int sum = 0; - if ( node.isCollapse() ) { - continue; - } - if ( getControlPanel().isShowNodeNames() ) { - sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " ); - } - if ( node.getNodeData().isHasSequence() ) { - if ( getControlPanel().isShowSequenceAcc() - && ( node.getNodeData().getSequence().getAccession() != null ) ) { - sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession() - .getValue() - + " " ); - } - if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { - sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " ); - } - if ( getControlPanel().isShowGeneSymbols() - && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) { - sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " ); - } - if ( getControlPanel().isShowAnnotation() - && ( node.getNodeData().getSequence().getAnnotations() != null ) - && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) { - sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 ) - .asSimpleText() - + " " ); - } - } - if ( node.getNodeData().isHasTaxonomy() ) { - final Taxonomy tax = node.getNodeData().getTaxonomy(); - if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { - sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " ); - } - if ( getControlPanel().isShowTaxonomyScientificNames() - && !ForesterUtil.isEmpty( tax.getScientificName() ) ) { - sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " ); - } - if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) { - sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" ); - } - } - if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { - sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters() - .getGainedCharactersAsStringBuffer().toString() ); - } - if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() ) - .getRenderingSize().getWidth(); - } - if ( sum >= Constants.EXT_NODE_INFO_LENGTH_MAX ) { - setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX ); - return; - } - if ( sum > longest ) { - longest = sum; - } - } - if ( longest >= Constants.EXT_NODE_INFO_LENGTH_MAX ) { - setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX ); - } - else { - setLongestExtNodeInfo( longest ); - } - } - final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) { if ( getControlPanel().isDrawPhylogram() ) { if ( node.getDistanceToParent() < 0.0 ) { @@ -618,160 +818,160 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final void calculateScaleDistance() { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { - return; + final private void cannotOpenBrowserWarningMessage( final String type_type ) { + JOptionPane.showMessageDialog( this, + "Cannot launch web browser for " + type_type + " data of this node", + "Cannot launch web browser", + JOptionPane.WARNING_MESSAGE ); + } + + private void changeNodeFont( final PhylogenyNode node ) { + final FontChooser fc = new FontChooser(); + Font f = null; + if ( ( node.getNodeData().getNodeVisualData() != null ) && !node.getNodeData().getNodeVisualData().isEmpty() ) { + f = node.getNodeData().getNodeVisualData().getFont(); } - final double height = getMaxDistanceToRoot(); - if ( height > 0 ) { - if ( ( height <= 0.5 ) ) { - setScaleDistance( 0.01 ); - } - else if ( height <= 5.0 ) { - setScaleDistance( 0.1 ); - } - else if ( height <= 50.0 ) { - setScaleDistance( 1 ); - } - else if ( height <= 500.0 ) { - setScaleDistance( 10 ); - } - else { - setScaleDistance( 100 ); - } + if ( f != null ) { + fc.setFont( f ); } else { - setScaleDistance( 0.0 ); + fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); } - String scale_label = String.valueOf( getScaleDistance() ); - if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) { - scale_label += " [" + _phylogeny.getDistanceUnit() + "]"; + List nodes = new ArrayList(); + if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { + nodes = getFoundNodesAsListOfPhylogenyNodes(); } - setScaleLabel( scale_label ); - } - - final Color calculateTaxonomyBasedColor( final Taxonomy tax ) { - String species = tax.getTaxonomyCode(); - if ( ForesterUtil.isEmpty( species ) ) { - species = tax.getScientificName(); - if ( ForesterUtil.isEmpty( species ) ) { - species = tax.getCommonName(); - } + if ( !nodes.contains( node ) ) { + nodes.add( node ); } - if ( ForesterUtil.isEmpty( species ) ) { - return getTreeColorSet().getTaxonomyColor(); + final int count = nodes.size(); + String title = "Change the font for "; + if ( count == 1 ) { + title += "one node"; } - // Look in species hash - Color c = getControlPanel().getSpeciesColors().get( species ); - if ( c == null ) { - c = Util.calculateColorFromString( species ); - getControlPanel().getSpeciesColors().put( species, c ); + else { + title += ( count + " nodes" ); } - return c; - } - - final private void cannotOpenBrowserWarningMessage( final String type_type ) { - JOptionPane.showMessageDialog( this, - "Cannot launch web browser for " + type_type + " data of this node", - "Cannot launch web browser", - JOptionPane.WARNING_MESSAGE ); + fc.showDialog( this, title ); + if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) { + for( final PhylogenyNode n : nodes ) { + if ( n.getNodeData().getNodeVisualData() == null ) { + n.getNodeData().setNodeVisualData( new NodeVisualData() ); + } + final NodeVisualData vd = n.getNodeData().getNodeVisualData(); + final Font ff = fc.getFont(); + vd.setFontName( ff.getFamily().trim() ); + int s = ff.getSize(); + if ( s < 0 ) { + s = 0; + } + if ( s > Byte.MAX_VALUE ) { + s = Byte.MAX_VALUE; + } + vd.setFontSize( s ); + vd.setFontStyle( ff.getStyle() ); + } + if ( _control_panel.getUseVisualStylesCb() != null ) { + getControlPanel().getUseVisualStylesCb().setSelected( true ); + } + } + setEdited( true ); + repaint(); } - /** - * Collapse the tree from the given node - * - * @param node - * a PhylogenyNode - */ - final void collapse( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - JOptionPane.showMessageDialog( this, - "Cannot collapse in unrooted display type", - "Attempt to collapse in unrooted display", - JOptionPane.WARNING_MESSAGE ); - return; + final private void colorizeNodes( final Color c, + final PhylogenyNode node, + final List additional_nodes ) { + _control_panel.setColorBranches( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); } - if ( !node.isExternal() && !node.isRoot() ) { - final boolean collapse = !node.isCollapse(); - Util.collapseSubtree( node, collapse ); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - calculateLongestExtNodeInfo(); - _nodes_in_preorder = null; - resetPreferredSize(); - updateOvSizes(); - _main_panel.adjustJScrollPane(); - repaint(); + if ( node != null ) { + colorizeNodesHelper( c, node ); } - } - - final void collapseSpeciesSpecificSubtrees() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; + if ( additional_nodes != null ) { + for( final PhylogenyNode n : additional_nodes ) { + colorizeNodesHelper( c, n ); + } } - setWaitCursor(); - Util.collapseSpeciesSpecificSubtrees( _phylogeny ); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - calculateLongestExtNodeInfo(); - _nodes_in_preorder = null; - resetPreferredSize(); - _main_panel.adjustJScrollPane(); - setArrowCursor(); repaint(); } - final private void colorizeSubtree( final Color c, final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - JOptionPane.showMessageDialog( this, - "Cannot colorize subtree in unrooted display type", - "Attempt to colorize subtree in unrooted display", - JOptionPane.WARNING_MESSAGE ); - return; - } + final private void colorizeSubtree( final Color c, + final PhylogenyNode node, + final List additional_nodes ) { _control_panel.setColorBranches( true ); - if ( _control_panel.getColorBranchesCb() != null ) { - _control_panel.getColorBranchesCb().setSelected( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); + } + if ( node != null ) { + for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) { + it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + } } - for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) { - it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + if ( additional_nodes != null ) { + for( final PhylogenyNode an : additional_nodes ) { + for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) { + it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + } + } } repaint(); } - final private void colorSubtree( final PhylogenyNode node ) { - Color intitial_color = null; - if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) - && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) { - intitial_color = PhylogenyMethods.getBranchColorValue( node ); + private void colorNodeFont( final PhylogenyNode node ) { + _color_chooser.setPreviewPanel( new JPanel() ); + NodeColorizationActionListener al; + int count = 1; + if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { + final List additional_nodes = getFoundNodesAsListOfPhylogenyNodes(); + al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes ); + count = additional_nodes.size(); + if ( !additional_nodes.contains( node ) ) { + count++; + } } else { - intitial_color = getTreeColorSet().getBranchColor(); + al = new NodeColorizationActionListener( _color_chooser, node ); } - _color_chooser.setColor( intitial_color ); - _color_chooser.setPreviewPanel( new JPanel() ); - final JDialog dialog = JColorChooser - .createDialog( this, - "Subtree colorization", - true, - _color_chooser, - new SubtreeColorizationActionListener( _color_chooser, node ), - null ); + String title = "Change the (node and font) color for "; + if ( count == 1 ) { + title += "one node"; + } + else { + title += ( count + " nodes" ); + } + final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null ); + setEdited( true ); dialog.setVisible( true ); } - final void confColor() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + final private void colorSubtree( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + JOptionPane.showMessageDialog( this, + "Cannot colorize subtree in unrooted display type", + "Attempt to colorize subtree in unrooted display", + JOptionPane.WARNING_MESSAGE ); return; } - setWaitCursor(); - Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); - _control_panel.setColorBranches( true ); - if ( _control_panel.getColorBranchesCb() != null ) { - _control_panel.getColorBranchesCb().setSelected( true ); + _color_chooser.setPreviewPanel( new JPanel() ); + final SubtreeColorizationActionListener al; + final boolean color_found = getOptions().isColorAllFoundNodesWhenColoringSubtree(); + if ( color_found && ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) ) { + final List additional_nodes = getFoundNodesAsListOfPhylogenyNodes(); + al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes ); } - setArrowCursor(); - repaint(); + else { + al = new SubtreeColorizationActionListener( _color_chooser, node ); + } + final JDialog dialog = JColorChooser.createDialog( this, + "Subtree colorization", + true, + _color_chooser, + al, + null ); + setEdited( true ); + dialog.setVisible( true ); } final private void copySubtree( final PhylogenyNode node ) { @@ -779,10 +979,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee errorMessageNoCutCopyPasteInUnrootedDisplay(); return; } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); setCutOrCopiedTree( _phylogeny.copy( node ) ); final List nodes = PhylogenyMethods.getAllDescendants( node ); - final Set node_ids = new HashSet( nodes.size() ); + final Set node_ids = new HashSet( nodes.size() ); for( final PhylogenyNode n : nodes ) { node_ids.add( n.getId() ); } @@ -791,6 +991,24 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } + final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) { + final String tax = PhylogenyMethods.getSpecies( node ); + String label = node.getName(); + if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) { + label = label + " " + tax; + } + else if ( !ForesterUtil.isEmpty( tax ) ) { + label = tax; + } + else { + label = ""; + } + if ( !ForesterUtil.isEmpty( label ) ) { + label = " [" + label + "]"; + } + return label; + } + final private void cutSubtree( final PhylogenyNode node ) { if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { errorMessageNoCutCopyPasteInUnrootedDisplay(); @@ -803,7 +1021,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.ERROR_MESSAGE ); return; } - final String label = getASimpleTextRepresentationOfANode( node ); + final String label = createASimpleTextRepresentationOfANode( node ); final int r = JOptionPane.showConfirmDialog( null, "Cut subtree" + label + "?", "Confirm Cutting of Subtree", @@ -811,11 +1029,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( r != JOptionPane.OK_OPTION ) { return; } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); setCopiedAndPastedNodes( null ); setCutOrCopiedTree( _phylogeny.copy( node ) ); _phylogeny.deleteSubtree( node, true ); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -829,12 +1047,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final void decreaseDomainStructureEvalueThreshold() { - if ( _domain_structure_e_value_thr_exp > -20 ) { - _domain_structure_e_value_thr_exp -= 1; - } - } - final private void decreaseOvSize() { if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) { setOvMaxWidth( getOvMaxWidth() - 5 ); @@ -849,14 +1061,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee errorMessageNoCutCopyPasteInUnrootedDisplay(); return; } - if ( node.isRoot() ) { + if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) { JOptionPane.showMessageDialog( this, "Cannot delete entire tree", "Attempt to delete entire tree", JOptionPane.ERROR_MESSAGE ); return; } - final String label = getASimpleTextRepresentationOfANode( node ); + final String label = createASimpleTextRepresentationOfANode( node ); final Object[] options = { "Node only", "Entire subtree", "Cancel" }; final int r = JOptionPane.showOptionDialog( this, "Delete" + label + "?", @@ -866,7 +1078,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee null, options, options[ 2 ] ); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); boolean node_only = true; if ( r == 1 ) { node_only = false; @@ -881,7 +1093,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _phylogeny.deleteSubtree( node, true ); } _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -905,7 +1117,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.draw( _arc ); } - final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) { + final private void drawLine( final double x1, + final double y1, + final double x2, + final double y2, + final Graphics2D g ) { if ( ( x1 == x2 ) && ( y1 == y2 ) ) { return; } @@ -931,7 +1147,28 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.fill( _ellipse ); } - final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) { + final private void drawOvalGradient( final float x, + final float y, + final float width, + final float heigth, + final Graphics2D g, + final Color color_1, + final Color color_2, + final Color color_border ) { + _ellipse.setFrame( x, y, width, heigth ); + g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) ); + g.fill( _ellipse ); + if ( color_border != null ) { + g.setPaint( color_border ); + g.draw( _ellipse ); + } + } + + final private void drawRect( final float x, + final float y, + final float width, + final float heigth, + final Graphics2D g ) { _rectangle.setFrame( x, y, width, heigth ); g.draw( _rectangle ); } @@ -945,23 +1182,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.fill( _rectangle ); } - //TODO FIXME - final private void drawRectGradient( final double x, - final double y, - final double width, - final double heigth, + final private void drawRectGradient( final float x, + final float y, + final float width, + final float heigth, final Graphics2D g, final Color color_1, final Color color_2, final Color color_border ) { _rectangle.setFrame( x, y, width, heigth ); - g.setPaint( new GradientPaint( ( float ) x, - ( float ) y, - color_1, - ( float ) ( x + width ), - ( float ) ( y + heigth ), - color_2, - false ) ); + g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) ); g.fill( _rectangle ); if ( color_border != null ) { g.setPaint( color_border ); @@ -969,101 +1199,91 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - //TODO FIXME - final private void drawOvalGradient( final double x, - final double y, - final double width, - final double heigth, - final Graphics2D g, - final Color color_1, - final Color color_2, - final Color color_border ) { - _ellipse.setFrame( x, y, width, heigth ); - g.setPaint( new GradientPaint( ( float ) x, - ( float ) y, - color_1, - ( float ) ( x + width ), - ( float ) ( y + heigth ), - color_2, - false ) ); - g.fill( _ellipse ); - if ( color_border != null ) { - g.setPaint( color_border ); - g.draw( _ellipse ); - } - } - - final private void errorMessageNoCutCopyPasteInUnrootedDisplay() { - JOptionPane.showMessageDialog( this, - "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display", - "Attempt to cut/copy/paste/add/delete in unrooted display", - JOptionPane.ERROR_MESSAGE ); - } - - /** - * Find the node, if any, at the given location - * - * @param x - * @param y - * @return pointer to the node at x,y, null if not found - */ - final PhylogenyNode findNode( final int x, final int y ) { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { - return null; - } - for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) ) - && ( ( node.getXcoord() - _half_box_size_plus_wiggle ) <= x ) - && ( ( node.getXcoord() + _half_box_size_plus_wiggle ) >= x ) - && ( ( node.getYcoord() - _half_box_size_plus_wiggle ) <= y ) - && ( ( node.getYcoord() + _half_box_size_plus_wiggle ) >= y ) ) { - return node; + private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) { + final List us = new ArrayList(); + for( final Taxonomy t : node.getNodeData().getTaxonomies() ) { + for( final Uri uri : t.getUris() ) { + us.add( uri ); } } - return null; - } - - final private String getASimpleTextRepresentationOfANode( final PhylogenyNode node ) { - final String tax = PhylogenyMethods.getSpecies( node ); - String label = node.getName(); - if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) { - label = label + " " + tax; - } - else if ( !ForesterUtil.isEmpty( tax ) ) { - label = tax; - } - else { - label = ""; - } - if ( !ForesterUtil.isEmpty( label ) ) { - label = " [" + label + "]"; + double offset = 0; + for( final Uri uri : us ) { + if ( uri != null ) { + final String uri_str = uri.getValue().toString().toLowerCase(); + if ( getImageMap().containsKey( uri_str ) ) { + final BufferedImage bi = getImageMap().get( uri_str ); + if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) { + double scaling_factor = 1; + if ( getOptions().isAllowMagnificationOfTaxonomyImages() + || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) { + scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight(); + } + // y = y - ( 0.9 * getYdistance() ); + final double hs = bi.getHeight() * scaling_factor; + double ws = ( bi.getWidth() * scaling_factor ) + offset; + final double my_y = y - ( 0.5 * hs ); + final int x_w = ( int ) ( x + ws + 0.5 ); + final int y_h = ( int ) ( my_y + hs + 0.5 ); + if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) { + g.drawImage( bi, + ( int ) ( x + 0.5 + offset ), + ( int ) ( my_y + 0.5 ), + x_w, + y_h, + 0, + 0, + bi.getWidth(), + bi.getHeight(), + null ); + ws += 8; + } + else { + ws = 0.0; + } + offset = ws; + } + } + } } - return label; + return offset; } - final Configuration getConfiguration() { - return _configuration; + final private void errorMessageNoCutCopyPasteInUnrootedDisplay() { + JOptionPane.showMessageDialog( this, + "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display", + "Attempt to cut/copy/paste/add/delete in unrooted display", + JOptionPane.ERROR_MESSAGE ); } - final ControlPanel getControlPanel() { - return _control_panel; + private final Color getColorForFoundNode( final PhylogenyNode n ) { + if ( isInCurrentExternalNodes( n ) ) { + return getTreeColorSet().getFoundColor0(); + } + else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) { + return getTreeColorSet().getFoundColor0(); + } + else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) { + return getTreeColorSet().getFoundColor1(); + } + else { + return getTreeColorSet().getFoundColor0and1(); + } } - final private Set getCopiedAndPastedNodes() { + final private Set getCopiedAndPastedNodes() { return getMainPanel().getCopiedAndPastedNodes(); } - final private Phylogeny getCutOrCopiedTree() { - return getMainPanel().getCutOrCopiedTree(); + final private Set getCurrentExternalNodes() { + return _current_external_nodes; } - final int getDomainStructureEvalueThreshold() { - return _domain_structure_e_value_thr_exp; + final private Phylogeny getCutOrCopiedTree() { + return getMainPanel().getCutOrCopiedTree(); } - final Set getFoundNodes() { - return _found_nodes; + private FontMetrics getFontMetricsForLargeDefaultFont() { + return getTreeFontSet().getFontMetricsLarge(); } final private float getLastDragPointX() { @@ -1074,25 +1294,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _last_drag_point_y; } - final int getLongestExtNodeInfo() { - return _longest_ext_node_info; - } - - final public MainPanel getMainPanel() { - return _main_panel; - } - - final private short getMaxBranchesToLeaf( final PhylogenyNode node ) { - if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) { - final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node ); - _nodeid_dist_to_leaf.put( node.getId(), m ); - return m; - } - else { - return _nodeid_dist_to_leaf.get( node.getId() ); - } - } - final private double getMaxDistanceToRoot() { if ( _max_distance_to_root < 0 ) { recalculateMaxDistanceToRoot(); @@ -1100,13 +1301,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _max_distance_to_root; } - final Options getOptions() { - if ( _options == null ) { - _options = getControlPanel().getOptions(); - } - return _options; - } - final private float getOvMaxHeight() { return _ov_max_height; } @@ -1115,14 +1309,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _ov_max_width; } - final Rectangle2D getOvRectangle() { - return _ov_rectangle; - } - - final Rectangle getOvVirtualRectangle() { - return _ov_virtual_rectangle; - } - final private float getOvXcorrectionFactor() { return _ov_x_correction_factor; } @@ -1147,17 +1333,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _ov_y_start; } - /** - * Get a pointer to the phylogeny - * - * @return a pointer to the phylogeny - */ - public final Phylogeny getPhylogeny() { - return _phylogeny; - } - - final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { - return _graphics_type; + final private List getPdbAccs( final PhylogenyNode node ) { + final List pdb_ids = new ArrayList(); + if ( node.getNodeData().isHasSequence() ) { + final Sequence seq = node.getNodeData().getSequence(); + if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) { + final SortedSet cross_refs = seq.getCrossReferences(); + for( final Accession acc : cross_refs ) { + if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) { + pdb_ids.add( acc ); + } + } + } + } + return pdb_ids; } final private double getScaleDistance() { @@ -1168,35 +1357,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _scale_label; } - final double getStartingAngle() { - return _urt_starting_angle; - } - - /** - * Find a color for this species name. - * - * @param species - * @return the species color - */ - final Color getTaxonomyBasedColor( final PhylogenyNode node ) { - if ( node.getNodeData().isHasTaxonomy() ) { - return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() ); - } - // return non-colorized color - return getTreeColorSet().getTaxonomyColor(); - } - - /** - * @return pointer to colorset for tree drawing - */ - final TreeColorSet getTreeColorSet() { - return getMainPanel().getTreeColorSet(); - } - - final File getTreeFile() { - return _treefile; - } - final private TreeFontSet getTreeFontSet() { return getMainPanel().getTreeFontSet(); } @@ -1209,18 +1369,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _urt_factor_ov; } - final float getXcorrectionFactor() { - return _x_correction_factor; - } - - final float getXdistance() { - return _x_distance; - } - - final float getYdistance() { - return _y_distance; - } - final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) { switch ( action ) { case SHOW_DATA: @@ -1241,6 +1389,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee case COLOR_SUBTREE: colorSubtree( node ); break; + case COLOR_NODE_FONT: + colorNodeFont( node ); + break; + case CHANGE_NODE_FONT: + changeNodeFont( node ); + break; case OPEN_SEQ_WEB: openSeqWeb( node ); break; @@ -1250,6 +1404,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee case OPEN_TAX_WEB: openTaxWeb( node ); break; + case OPEN_PDB_WEB: + openPdbWeb( node ); + break; case CUT_SUBTREE: cutSubtree( node ); break; @@ -1268,21 +1425,35 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee case EDIT_NODE_DATA: showNodeEditFrame( node ); break; + case SELECT_NODES: + selectNode( node ); + break; + case SORT_DESCENDENTS: + sortDescendants( node ); + break; + case GET_EXT_DESC_DATA: + showExtDescNodeData( node, '_' ); + break; + case UNCOLLAPSE_ALL: + uncollapseAll( node ); + break; + case ORDER_SUBTREE: + orderSubtree( node ); + break; default: throw new IllegalArgumentException( "unknown action: " + action ); } } - final void increaseDomainStructureEvalueThreshold() { - if ( _domain_structure_e_value_thr_exp < 3 ) { - _domain_structure_e_value_thr_exp += 1; - } + final private void increaseCurrentExternalNodesDataBufferChangeCounter() { + _current_external_nodes_data_buffer_change_counter++; } final private void increaseOvSize() { - if ( ( getOvMaxWidth() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) - && ( getOvMaxHeight() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect() - .getHeight() / 2 ) ) { + if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() + / 2 ) ) + && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect() + .getHeight() / 2 ) ) ) { setOvMaxWidth( getOvMaxWidth() + 5 ); setOvMaxHeight( getOvMaxHeight() + 5 ); updateOvSettings(); @@ -1290,16 +1461,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final void inferCommonPartOfScientificNames() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - setWaitCursor(); - Util.inferCommonPartOfScientificNames( _phylogeny ); - setArrowCursor(); - repaint(); - } - final private void init() { _color_chooser = new JColorChooser(); _rollover_popup = new JTextArea(); @@ -1309,7 +1470,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setTreeFile( null ); setEdited( false ); initializeOvSettings(); - setStartingAngle( TWO_PI * 3 / 4 ); + resetDepthCollapseDepthValue(); + resetRankCollapseRankValue(); + setStartingAngle( ( TWO_PI * 3 ) / 4 ); final ImageLoader il = new ImageLoader( this ); new Thread( il ).start(); } @@ -1319,126 +1482,39 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setOvMaxWidth( getConfiguration().getOvMaxWidth() ); } - final void initNodeData() { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { - return; - } - double max_original_domain_structure_width = 0.0; - for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { - if ( node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - RenderableDomainArchitecture rds = null; - if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { - rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(), - getConfiguration() ); - node.getNodeData().getSequence().setDomainArchitecture( rds ); - } - else { - rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); - } - if ( getControlPanel().isShowDomainArchitectures() ) { - final double dsw = rds.getOriginalSize().getWidth(); - if ( dsw > max_original_domain_structure_width ) { - max_original_domain_structure_width = dsw; - } - } - } - } - if ( getControlPanel().isShowDomainArchitectures() ) { - final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width; - for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { - if ( node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData() - .getSequence().getDomainArchitecture(); - rds.setRenderingFactorWidth( ds_factor_width ); - rds.setParameter( _domain_structure_e_value_thr_exp ); - } - } - } - } - - final boolean inOv( final MouseEvent e ) { - return ( ( e.getX() > getVisibleRect().x + getOvXPosition() + 1 ) - && ( e.getX() < getVisibleRect().x + getOvXPosition() + getOvMaxWidth() - 1 ) - && ( e.getY() > getVisibleRect().y + getOvYPosition() + 1 ) && ( e.getY() < getVisibleRect().y - + getOvYPosition() + getOvMaxHeight() - 1 ) ); - } - - final boolean inOvRectangle( final MouseEvent e ) { - return ( ( e.getX() >= getOvRectangle().getX() - 1 ) - && ( e.getX() <= getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) - && ( e.getY() >= getOvRectangle().getY() - 1 ) && ( e.getY() <= getOvRectangle().getY() - + getOvRectangle().getHeight() + 1 ) ); - } - final private boolean inOvVirtualRectangle( final int x, final int y ) { - return ( ( x >= getOvVirtualRectangle().x - 1 ) - && ( x <= getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) - && ( y >= getOvVirtualRectangle().y - 1 ) && ( y <= getOvVirtualRectangle().y - + getOvVirtualRectangle().height + 1 ) ); + return ( ( x >= ( getOvVirtualRectangle().x - 1 ) ) + && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) ) + && ( y >= ( getOvVirtualRectangle().y - 1 ) ) + && ( y <= ( getOvVirtualRectangle().y + getOvVirtualRectangle().height + 1 ) ) ); } final private boolean inOvVirtualRectangle( final MouseEvent e ) { return ( inOvVirtualRectangle( e.getX(), e.getY() ) ); } - final boolean isApplet() { - return getMainPanel() instanceof MainPanelApplets; - } - final private boolean isCanBlast( final PhylogenyNode node ) { - return ( node.getNodeData().isHasSequence() && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil - .isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) - || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil.isEmpty( node - .getNodeData().getSequence().getSymbol() ) ) ); - } - - final boolean isCanCollapse() { - return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); - } - - final boolean isCanColorSubtree() { - return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); - } - - final boolean isCanCopy() { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); - } - - final boolean isCanCut( final PhylogenyNode node ) { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node - .isRoot() ); - } - - final boolean isCanDelete() { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); + if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) { + return false; + } + return Blast.isContainsQueryForBlast( node ); } - final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) { - if ( node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getAccession() != null ) - && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) - && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) - && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource() - .toLowerCase() ) ) { - return true; + final private String isCanOpenSeqWeb( final PhylogenyNode node ) { + final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node ); + if ( a != null ) { + return a.getValue(); } - return false; + return null; } final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) { - if ( node.getNodeData().isHasTaxonomy() - && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null ) - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() ) - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration() - .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) ) - || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) - || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) - || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node - .getNodeData().getTaxonomy().getIdentifier() != null ) - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node - .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) { + if ( node.getNodeData().isHasTaxonomy() && ( ( !ForesterUtil + .isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) + || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) + || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) + || ( ( node.getNodeData().getTaxonomy().getIdentifier() != null ) + && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) { return true; } else { @@ -1446,69 +1522,47 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final boolean isCanPaste() { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() - && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() ); - } - - final boolean isCanReroot() { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) ); + final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) { + return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) ); } - final boolean isCanSubtree( final PhylogenyNode node ) { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node - .isRoot() || ( _subtree_index > 0 ) ) ); + private boolean isInFoundNodes( final PhylogenyNode n ) { + return isInFoundNodes0( n ) || isInFoundNodes1( n ); } - final boolean isEdited() { - return _edited; + final private boolean isInFoundNodes0( final PhylogenyNode node ) { + return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ); } - final private boolean isInFoundNodes( final PhylogenyNode node ) { - return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ); + final private boolean isInFoundNodes1( final PhylogenyNode node ) { + return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) ); } final private boolean isInOv() { return _in_ov; } - final boolean isInOvRect() { - return _in_ov_rect; - } - final private boolean isNodeDataInvisible( final PhylogenyNode node ) { int y_dist = 40; if ( getControlPanel().isShowTaxonomyImages() ) { y_dist = 40 + ( int ) getYdistance(); } - return ( ( node.getYcoord() < getVisibleRect().getMinY() - y_dist ) - || ( node.getYcoord() > getVisibleRect().getMaxY() + y_dist ) || ( ( node.getParent() != null ) && ( node - .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) ); + return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) ) + || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) + || ( ( node.getParent() != null ) && ( node.getParent().getXcoord() > getVisibleRect().getMaxX() ) ) ); } final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) { - return ( ( node.getYcoord() < getVisibleRect().getMinY() - 20 ) - || ( node.getYcoord() > getVisibleRect().getMaxY() + 20 ) - || ( node.getXcoord() < getVisibleRect().getMinX() - 20 ) || ( node.getXcoord() > getVisibleRect() - .getMaxX() + 20 ) ); + return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) ) + || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) ) + || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) + || ( node.getXcoord() > ( getVisibleRect().getMaxX() + 20 ) ) ); } final private boolean isNonLinedUpCladogram() { return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP; } - final boolean isOvOn() { - return _ov_on; - } - - final boolean isPhyHasBranchLengths() { - return _phy_has_branch_lengths; - } - - final private boolean isUniformBranchLengthsForCladogram() { - return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP; - } - final private void keyPressedCalls( final KeyEvent e ) { if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) { if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) { @@ -1520,102 +1574,104 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setInOvRect( false ); } } - if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) { + if ( e.isAltDown() ) { if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) - || ( e.getKeyCode() == KeyEvent.VK_F ) ) { - getMainPanel().getTreeFontSet().mediumFonts(); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + || ( e.getKeyCode() == KeyEvent.VK_C ) || ( e.getKeyCode() == KeyEvent.VK_BACK_SPACE ) ) { + getControlPanel().showWhole(); } - else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { - getMainPanel().getTreeFontSet().decreaseFontSize(); + else if ( e.isShiftDown() + && ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) ) { + getMainPanel().getTreeFontSet().decreaseFontSize( 1, false ); getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); } - else if ( plusPressed( e.getKeyCode() ) ) { + else if ( e.isShiftDown() && plusPressed( e.getKeyCode() ) ) { getMainPanel().getTreeFontSet().increaseFontSize(); getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); } - } - else { - if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) - || ( e.getKeyCode() == KeyEvent.VK_F ) ) { - getControlPanel().showWhole(); + else if ( e.getKeyCode() == KeyEvent.VK_O ) { + getControlPanel().orderPressed( this ); } - else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN ) - || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) { - if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) { - if ( e.getKeyCode() == KeyEvent.VK_UP ) { - getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { - getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { - getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR, - Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { - getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR, - Constants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - else { - final int d = 80; - int dx = 0; - int dy = -d; - if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { - dy = d; - } - else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { - dx = -d; - dy = 0; - } - else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { - dx = d; - dy = 0; - } - final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); - scroll_position.x = scroll_position.x + dx; - scroll_position.y = scroll_position.y + dy; - if ( scroll_position.x <= 0 ) { - scroll_position.x = 0; - } - else { - final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); - if ( scroll_position.x >= max_x ) { - scroll_position.x = max_x; - } - } - if ( scroll_position.y <= 0 ) { - scroll_position.y = 0; - } - else { - final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); - if ( scroll_position.y >= max_y ) { - scroll_position.y = max_y; - } - } - repaint(); - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); - } + else if ( e.getKeyCode() == KeyEvent.VK_R ) { + getControlPanel().returnedToSuperTreePressed(); + } + else if ( e.getKeyCode() == KeyEvent.VK_U ) { + getControlPanel().uncollapseAll( this ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_UP ) { + getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { + getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { + getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { + getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, + AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); } else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { - getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR, - Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); + getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); } else if ( plusPressed( e.getKeyCode() ) ) { - getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR, - Constants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, + AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); } + } + else { + if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN ) + || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) { + final int d = 80; + int dx = 0; + int dy = -d; + if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { + dy = d; + } + else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { + dx = -d; + dy = 0; + } + else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { + dx = d; + dy = 0; + } + final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); + scroll_position.x = scroll_position.x + dx; + scroll_position.y = scroll_position.y + dy; + if ( scroll_position.x <= 0 ) { + scroll_position.x = 0; + } + else { + final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); + if ( scroll_position.x >= max_x ) { + scroll_position.x = max_x; + } + } + if ( scroll_position.y <= 0 ) { + scroll_position.y = 0; + } + else { + final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); + if ( scroll_position.y >= max_y ) { + scroll_position.y = max_y; + } + } + repaint(); + getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); + } else if ( e.getKeyCode() == KeyEvent.VK_S ) { if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { @@ -1642,16 +1698,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - if ( ae.getlabelDirectionCbmi() != null ) { - ae.getlabelDirectionCbmi().setSelected( selected ); - } - } - else { - getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected ); - } + getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected ); repaint(); } else if ( e.getKeyCode() == KeyEvent.VK_X ) { @@ -1672,8 +1719,19 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) { decreaseOvSize(); } - e.consume(); } + if ( e.getKeyCode() == KeyEvent.VK_HOME || e.getKeyCode() == KeyEvent.VK_ESCAPE ) { + getControlPanel().showWhole(); + } + else if ( e.getKeyCode() == KeyEvent.VK_PAGE_UP ) { + getMainPanel().getTreeFontSet().increaseFontSize(); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + else if ( e.getKeyCode() == KeyEvent.VK_PAGE_DOWN ) { + getMainPanel().getTreeFontSet().decreaseFontSize( 1, false ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + e.consume(); } final private void makePopupMenus( final PhylogenyNode node ) { @@ -1684,15 +1742,58 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final String title = clickto_names.get( i ); _node_popup_menu_items[ i ] = new JMenuItem( title ); if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) ); + final String id = isCanOpenSeqWeb( node ); + if ( !ForesterUtil.isEmpty( id ) ) { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" ); + _node_popup_menu_items[ i ].setEnabled( true ); + } + else { + _node_popup_menu_items[ i ].setEnabled( false ); + } + } + else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) { + final List accs = getPdbAccs( node ); + _node_popup_menu_items[ i ] = new JMenuItem( title ); + if ( !ForesterUtil.isEmpty( accs ) ) { + if ( accs.size() == 1 ) { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" ); + _node_popup_menu_items[ i ].setEnabled( true ); + } + else if ( accs.size() == 2 ) { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" ); + _node_popup_menu_items[ i ].setEnabled( true ); + } + else if ( accs.size() == 3 ) { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 1 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" ); + _node_popup_menu_items[ i ].setEnabled( true ); + } + else { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 1 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" ); + _node_popup_menu_items[ i ].setEnabled( true ); + } + } + else { + _node_popup_menu_items[ i ].setEnabled( false ); + } + } + else if ( title.startsWith( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] ) ) { + _node_popup_menu_items[ i ] + .setText( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] + ": " + + getOptions().getExtDescNodeDataToReturn().toString() ); } else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) { _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) ); } else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) { - if ( Constants.__RELEASE || Constants.__SNAPSHOT_RELEASE ) { - continue; - } _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) ); } else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) { @@ -1733,7 +1834,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _node_popup_menu_items[ i ].setEnabled( isCanReroot() ); } else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( isCanCollapse() ); + _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) ); } else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) { _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() ); @@ -1741,352 +1842,177 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) { _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) ); } + else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 ); + } + else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 ); + } + else if ( title.equals( Configuration.clickto_options[ Configuration.uncollapse_all ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( isCanUncollapseAll( node ) ); + } _node_popup_menu_items[ i ].addActionListener( this ); _node_popup_menu.add( _node_popup_menu_items[ i ] ); } } - final void midpointRoot() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - if ( !_phylogeny.isRerootable() ) { - JOptionPane.showMessageDialog( this, - "This is not rerootable", - "Not rerootable", - JOptionPane.WARNING_MESSAGE ); - return; - } - _nodes_in_preorder = null; - setWaitCursor(); - PhylogenyMethods.midpointRoot( _phylogeny ); - resetNodeIdToDistToLeafMap(); - setArrowCursor(); - repaint(); - } - - final void mouseClicked( final MouseEvent e ) { - if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) { - final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth(); - final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight(); - double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - getOvRectangle().getWidth() / 2.0 ) - * w_ratio; - double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - getOvRectangle().getHeight() / 2.0 ) - * h_ratio; - if ( x < 0 ) { - x = 0; - } - if ( y < 0 ) { - y = 0; - } - final double max_x = getWidth() - getVisibleRect().width; - final double max_y = getHeight() - getVisibleRect().height; - if ( x > max_x ) { - x = max_x; - } - if ( y > max_y ) { - y = max_y; + private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) { + if ( node != null ) { + if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getName() ); } - getMainPanel().getCurrentScrollPane().getViewport() - .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); - setInOvRect( true ); - repaint(); - } - else { - final PhylogenyNode node = findNode( e.getX(), e.getY() ); - if ( node != null ) { - if ( !node.isRoot() && node.getParent().isCollapse() ) { - return; + if ( node.getNodeData().isHasSequence() ) { + if ( getControlPanel().isShowSeqSymbols() + && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getNodeData().getSequence().getSymbol() ); } - _highlight_node = node; - // Check if shift key is down - if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) { - // Yes, so add to _found_nodes - if ( getFoundNodes() == null ) { - setFoundNodes( new HashSet() ); + if ( getControlPanel().isShowGeneNames() + && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); } - getFoundNodes().add( node.getId() ); - // Check if control key is down + sb.append( node.getNodeData().getSequence().getGeneName() ); } - else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) { - // Yes, so pop-up menu - displayNodePopupMenu( node, e.getX(), e.getY() ); - // Handle unadorned click + if ( getControlPanel().isShowSeqNames() + && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getNodeData().getSequence().getName() ); } - else { - // Check for right mouse button - if ( e.getModifiers() == 4 ) { - displayNodePopupMenu( node, e.getX(), e.getY() ); + if ( getControlPanel().isShowSequenceAcc() + && ( node.getNodeData().getSequence().getAccession() != null ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); } - else { - // if not in _found_nodes, clear _found_nodes - handleClickToAction( _control_panel.getActionWhenNodeClicked(), node ); + if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) { + sb.append( node.getNodeData().getSequence().getAccession().getSource() ); + sb.append( ":" ); } + sb.append( node.getNodeData().getSequence().getAccession().getValue() ); } } - else { - // no node was clicked - _highlight_node = null; + if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( propertiesToString( node ) ); } } - repaint(); } - final void mouseDragInBrowserPanel( final MouseEvent e ) { - setCursor( MOVE_CURSOR ); - final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); - scroll_position.x -= ( e.getX() - getLastDragPointX() ); - scroll_position.y -= ( e.getY() - getLastDragPointY() ); - if ( scroll_position.x < 0 ) { - scroll_position.x = 0; + private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) { + if ( _control_panel.isShowTaxonomyRank() && !ForesterUtil.isEmpty( taxonomy.getRank() ) ) { + sb.append( "[" ); + sb.append( taxonomy.getRank() ); + sb.append( "] " ); } - else { - final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); - if ( scroll_position.x > max_x ) { - scroll_position.x = max_x; - } + if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) { + sb.append( taxonomy.getTaxonomyCode() ); + sb.append( " " ); } - if ( scroll_position.y < 0 ) { - scroll_position.y = 0; + if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) { + if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) + && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { + if ( getOptions().isAbbreviateScientificTaxonNames() + && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) { + abbreviateScientificName( taxonomy.getScientificName(), sb ); + } + else { + sb.append( taxonomy.getScientificName() ); + } + sb.append( " (" ); + sb.append( taxonomy.getCommonName() ); + sb.append( ") " ); + } + else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) { + if ( getOptions().isAbbreviateScientificTaxonNames() + && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) { + abbreviateScientificName( taxonomy.getScientificName(), sb ); + } + else { + sb.append( taxonomy.getScientificName() ); + } + sb.append( " " ); + } + else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { + sb.append( taxonomy.getCommonName() ); + sb.append( " " ); + } } - else { - final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); - if ( scroll_position.y > max_y ) { - scroll_position.y = max_y; + else if ( _control_panel.isShowTaxonomyScientificNames() ) { + if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) { + if ( getOptions().isAbbreviateScientificTaxonNames() + && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) { + abbreviateScientificName( taxonomy.getScientificName(), sb ); + } + else { + sb.append( taxonomy.getScientificName() ); + } + sb.append( " " ); } } - if ( isOvOn() || getOptions().isShowScale() ) { - repaint(); + else if ( _control_panel.isShowTaxonomyCommonNames() ) { + if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { + sb.append( taxonomy.getCommonName() ); + sb.append( " " ); + } } - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); } - final void mouseDragInOvRectangle( final MouseEvent e ) { - setCursor( HAND_CURSOR ); - final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth(); - final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight(); - final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); - double dx = ( w_ratio * e.getX() - w_ratio * getLastDragPointX() ); - double dy = ( h_ratio * e.getY() - h_ratio * getLastDragPointY() ); - scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx ); - scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy ); - if ( scroll_position.x <= 0 ) { - scroll_position.x = 0; - dx = 0; + private final String obtainTitleForExtDescNodeData() { + return getOptions().getExtDescNodeDataToReturn().toString(); + } + + final private void openPdbWeb( final PhylogenyNode node ) { + final List pdb_ids = getPdbAccs( node ); + if ( ForesterUtil.isEmpty( pdb_ids ) ) { + cannotOpenBrowserWarningMessage( "PDB" ); + return; } - else { - final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); - if ( scroll_position.x >= max_x ) { - dx = 0; - scroll_position.x = max_x; + final List uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this ); + if ( !ForesterUtil.isEmpty( uri_strs ) ) { + for( final String uri_str : uri_strs ) { + try { + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" ); + } + catch ( final IOException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } + catch ( final URISyntaxException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } } } - if ( scroll_position.y <= 0 ) { - dy = 0; - scroll_position.y = 0; - } else { - final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); - if ( scroll_position.y >= max_y ) { - dy = 0; - scroll_position.y = max_y; - } + cannotOpenBrowserWarningMessage( "PDB" ); } - repaint(); - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); - setLastMouseDragPointX( ( float ) ( e.getX() + dx ) ); - setLastMouseDragPointY( ( float ) ( e.getY() + dy ) ); } - final void mouseMoved( final MouseEvent e ) { - requestFocusInWindow(); - if ( getControlPanel().isNodeDescPopup() ) { - if ( _node_desc_popup != null ) { - _node_desc_popup.hide(); - _node_desc_popup = null; - } + final private void openSeqWeb( final PhylogenyNode node ) { + if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) { + cannotOpenBrowserWarningMessage( "sequence" ); + return; } - if ( getOptions().isShowOverview() && isOvOn() ) { - if ( inOvVirtualRectangle( e ) ) { - if ( !isInOvRect() ) { - setInOvRect( true ); - repaint(); - } + final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this ); + if ( !ForesterUtil.isEmpty( uri_str ) ) { + try { + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" ); } - else { - if ( isInOvRect() ) { - setInOvRect( false ); - repaint(); - } - } - } - if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) { - if ( !isInOv() ) { - setInOv( true ); - } - } - else { - if ( isInOv() ) { - setInOv( false ); - } - final PhylogenyNode node = findNode( e.getX(), e.getY() ); - if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) { - // cursor is over a tree node - if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) { - setCursor( CUT_CURSOR ); - } - else { - setCursor( HAND_CURSOR ); - if ( getControlPanel().isNodeDescPopup() ) { - showNodeDataPopup( e, node ); - } - } - } - else { - setCursor( ARROW_CURSOR ); - } - } - } - - final void mouseReleasedInBrowserPanel( final MouseEvent e ) { - setCursor( ARROW_CURSOR ); - } - - final public void mouseWheelMoved( final MouseWheelEvent e ) { - final int notches = e.getWheelRotation(); - if ( inOvVirtualRectangle( e ) ) { - if ( !isInOvRect() ) { - setInOvRect( true ); - repaint(); - } - } - else { - if ( isInOvRect() ) { - setInOvRect( false ); - repaint(); - } - } - if ( e.isControlDown() ) { - if ( notches < 0 ) { - getTreeFontSet().increaseFontSize(); - getControlPanel().displayedPhylogenyMightHaveChanged( true ); - } - else { - getTreeFontSet().decreaseFontSize(); - getControlPanel().displayedPhylogenyMightHaveChanged( true ); - } - } - else if ( e.isShiftDown() ) { - if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - if ( notches < 0 ) { - for( int i = 0; i < ( -notches ); ++i ) { - setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - else { - for( int i = 0; i < notches; ++i ) { - setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT ); - if ( getStartingAngle() < 0 ) { - setStartingAngle( TWO_PI + getStartingAngle() ); - } - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - } - else { - if ( notches < 0 ) { - for( int i = 0; i < ( -notches ); ++i ) { - getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - else { - for( int i = 0; i < notches; ++i ) { - getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - } - } - else { - if ( notches < 0 ) { - for( int i = 0; i < ( -notches ); ++i ) { - getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR, - Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR ); - getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - else { - for( int i = 0; i < notches; ++i ) { - getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR, - Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - } - requestFocus(); - requestFocusInWindow(); - requestFocus(); - } - - final void multiplyUrtFactor( final float f ) { - _urt_factor *= f; - } - - final JApplet obtainApplet() { - return ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - } - - final private void openSeqWeb( final PhylogenyNode node ) { - if ( !isCanOpenSeqWeb( node ) ) { - cannotOpenBrowserWarningMessage( "sequence" ); - return; - } - String uri_str = null; - final Sequence seq = node.getNodeData().getSequence(); - final String source = seq.getAccession().getSource().toLowerCase(); - String url; - if ( source.toLowerCase().equals( "ncbi" ) ) { - url = Constants.NCBI_ALL_DATABASE_SEARCH; - } - else { - final WebLink weblink = getConfiguration().getWebLink( source ); - url = weblink.getUrl().toString(); - } - try { - uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 ); - } - catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); - e.printStackTrace(); - } - if ( !ForesterUtil.isEmpty( uri_str ) ) { - try { - JApplet applet = null; - if ( isApplet() ) { - applet = obtainApplet(); - } - Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" ); - } - catch ( final IOException e ) { - Util.showErrorMessage( this, e.toString() ); - e.printStackTrace(); + catch ( final IOException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); } catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2102,73 +2028,70 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } String uri_str = null; final Taxonomy tax = node.getNodeData().getTaxonomy(); - if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) - && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) { - final String type = tax.getIdentifier().getProvider().toLowerCase(); - final WebLink weblink = getConfiguration().getWebLink( type ); + if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) + && tax.getIdentifier().getValue().startsWith( "http://" ) ) { try { - uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 ); + uri_str = new URI( tax.getIdentifier().getValue() ).toString(); } - catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + catch ( final URISyntaxException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + uri_str = null; e.printStackTrace(); } } else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) - && tax.getIdentifier().getValue().startsWith( "http://" ) ) { + && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) + && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) + || tax.getIdentifier().getProvider().equalsIgnoreCase( "uniprot" ) ) ) { try { - uri_str = new URI( tax.getIdentifier().getValue() ).toString(); + uri_str = "http://www.uniprot.org/taxonomy/" + + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF_8 ); } - catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); - uri_str = null; + catch ( final UnsupportedEncodingException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) { try { - uri_str = "http://www.eol.org/search?q=" - + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 ); + uri_str = "http://www.uniprot.org/taxonomy/?query=" + + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { try { uri_str = "http://www.uniprot.org/taxonomy/?query=" - + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 ); + + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) { try { - uri_str = "http://www.eol.org/search?q=" - + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 ); + uri_str = "http://www.uniprot.org/taxonomy/?query=" + + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF_8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } if ( !ForesterUtil.isEmpty( uri_str ) ) { try { - JApplet applet = null; - if ( isApplet() ) { - applet = obtainApplet(); - } - Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" ); + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_tax" ); } catch ( final IOException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2177,71 +2100,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final void paintBranchCircular( final PhylogenyNode p, - final PhylogenyNode c, - final Graphics2D g, - final boolean radial_labels, - final boolean to_pdf, - final boolean to_graphics_file ) { - final double angle = _urt_nodeid_angle_map.get( c.getId() ); - final double root_x = _root.getXcoord(); - final double root_y = _root.getYcoord(); - final double dx = root_x - p.getXcoord(); - final double dy = root_y - p.getYcoord(); - final double parent_radius = Math.sqrt( dx * dx + dy * dy ); - final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; - assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file ); - if ( ( c.isFirstChildNode() || c.isLastChildNode() ) - && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) { - final double r2 = 2.0 * parent_radius; - drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); - } - drawLine( c.getXcoord(), - c.getYcoord(), - root_x + ( Math.cos( angle ) * parent_radius ), - root_y + ( Math.sin( angle ) * parent_radius ), - g ); - paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c ) ); - if ( c.isExternal() ) { - final boolean is_in_found_nodes = isInFoundNodes( c ); - if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes - && ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor != 1 ) ) { - return; - } - paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes ); - } - } - - final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) { - final double angle = _urt_nodeid_angle_map.get( c.getId() ); - final double root_x = _root.getXSecondary(); - final double root_y = _root.getYSecondary(); - final double dx = root_x - p.getXSecondary(); - final double dy = root_y - p.getYSecondary(); - final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; - final double parent_radius = Math.sqrt( dx * dx + dy * dy ); - g.setColor( getTreeColorSet().getOvColor() ); - if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) { - final double r2 = 2.0 * parent_radius; - drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); - } - drawLine( c.getXSecondary(), - c.getYSecondary(), - root_x + ( Math.cos( angle ) * parent_radius ), - root_y + ( Math.sin( angle ) * parent_radius ), - g ); - if ( isInFoundNodes( c ) ) { - g.setColor( getTreeColorSet().getFoundColor() ); - drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g ); - } - } - final private void paintBranchLength( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf, final boolean to_graphics_file ) { g.setFont( getTreeFontSet().getSmallFont() ); - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) { g.setColor( Color.BLACK ); } else { @@ -2249,21 +2113,29 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( !node.isRoot() ) { if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g ); + TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), + node.getParent().getXcoord() + EURO_D, + node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), + g ); } else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g ); + TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), + node.getParent().getXcoord() + ROUNDED_D, + node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), + g ); } else { - TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g ); + TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), + node.getParent().getXcoord() + 3, + node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), + g ); } } else { - TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord() - - getTreeFontSet()._small_max_descent, g ); + TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), + 3, + node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), + g ); } } @@ -2284,8 +2156,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) { final float dx = x2 - x1; final float dy = y2 - y1; - _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1 - + ( dy * 0.8f ), x2, y2 ); + _cubic_curve.setCurve( x1, + y1, + x1 + ( dx * 0.4f ), + y1 + ( dy * 0.2f ), + x1 + ( dx * 0.6f ), + y1 + ( dy * 0.8f ), + x2, + y2 ); ( g ).draw( _cubic_curve ); } else { @@ -2302,7 +2180,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Paint a branch which consists of a vertical and a horizontal bar - * @param is_ind_found_nodes + * @param is_ind_found_nodes */ final private void paintBranchRectangular( final Graphics2D g, final float x1, @@ -2323,63 +2201,28 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) { final float dx = x2 - x1; final float dy = y2 - y1; - _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1 - + ( dy * 0.8f ), x2, y2 ); + _cubic_curve.setCurve( x1, + y1, + x1 + ( dx * 0.4f ), + y1 + ( dy * 0.2f ), + x1 + ( dx * 0.6f ), + y1 + ( dy * 0.8f ), + x2, + y2 ); g.draw( _cubic_curve ); } else { final float x2a = x2; final float x1a = x1; - // draw the vertical line - // boolean draw_horizontal = true; float y2_r = 0; if ( node.isFirstChildNode() || node.isLastChildNode() || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { - //boolean draw_vertical = true; - // final PhylogenyNode parent = node.getParent(); - //TODO fix below -- actually this might not be necessay anymore? test pdf, though! - // if ( ( ( ( getOptions().isShowDefaultNodeShapes() ) && !to_pdf && !to_graphics_file ) || ( ( getControlPanel() - // .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) ) - // && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) ) - // && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent - // .isDuplication() ) ) { - // if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) - // && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { - // if ( Math.abs( y2 - y1 ) <= _half_box_size ) { - // draw_vertical = false; - // } - // else { - // if ( y1 < y2 ) { - // y1 += _half_box_size; - // } - // else { - // if ( !to_pdf ) { - // y1 -= _half_box_size + 1; - // } - // else { - // y1 -= _half_box_size; - // } - // } - // } - // } - // if ( ( x2 - x1 ) <= _half_box_size ) { - // draw_horizontal = false; - // } - // else if ( !draw_vertical ) { - // x1a += _half_box_size; - // } - // if ( ( ( x2 - x1a ) > _half_box_size ) - // && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node - // .isDuplication() ) ) { - // x2a -= _half_box_size; - // } - // } - //if ( draw_vertical ) { - if ( !to_graphics_file - && !to_pdf - && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect() - .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) { + if ( !to_graphics_file && !to_pdf + && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) + && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) + || ( ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) + && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) { // Do nothing. } else { @@ -2410,15 +2253,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee drawLine( x1, y1, x1, y2, g ); } } - //} } // draw the horizontal line - if ( !to_graphics_file && !to_pdf - && ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) { + if ( !to_graphics_file && !to_pdf && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) + || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) { return; } float x1_r = 0; - // if ( draw_horizontal ) { if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) { if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { x1_r = x1a + ROUNDED_D; @@ -2454,7 +2295,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); } } - //} if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { if ( x1_r > x2a ) { x1_r = x2a; @@ -2469,59 +2309,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.draw( _arc ); } } - //TODO new ***** if ( node.isExternal() ) { - //TODO new ***** - paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) ); - } - } - - final void paintCircular( final Phylogeny phy, - final double starting_angle, - final int center_x, - final int center_y, - final int radius, - final Graphics2D g, - final boolean to_pdf, - final boolean to_graphics_file ) { - _circ_num_ext_nodes = phy.getNumberOfExternalNodes(); - _root = phy.getRoot(); - _root.setXcoord( center_x ); - _root.setYcoord( center_y ); - final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL; - double current_angle = starting_angle; - int i = 0; - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) ); - n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) ); - _urt_nodeid_angle_map.put( n.getId(), current_angle ); - _urt_nodeid_index_map.put( n.getId(), i++ ); - current_angle += ( TWO_PI / _circ_num_ext_nodes ); - } - paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file ); - paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) ); - } - - final void paintCircularLite( final Phylogeny phy, - final double starting_angle, - final int center_x, - final int center_y, - final int radius, - final Graphics2D g ) { - _circ_num_ext_nodes = phy.getNumberOfExternalNodes(); - _root = phy.getRoot(); - _root.setXSecondary( center_x ); - _root.setYSecondary( center_y ); - double current_angle = starting_angle; - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) ); - n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) ); - _urt_nodeid_angle_map.put( n.getId(), current_angle ); - current_angle += ( TWO_PI / _circ_num_ext_nodes ); + paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file ); } - paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g ); } final private double paintCirculars( final PhylogenyNode n, @@ -2533,9 +2323,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final Graphics2D g, final boolean to_pdf, final boolean to_graphics_file ) { - if ( n.isExternal() ) { + if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) { - System.out.println( "no " + n + ", ERROR!" );//TODO + System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO } return _urt_nodeid_angle_map.get( n.getId() ); } @@ -2555,11 +2345,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } double r = 0; if ( !n.isRoot() ) { - r = 1 - ( ( ( double ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth ); + r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth ); } final double theta = sum / descs.size(); - n.setXcoord( ( float ) ( center_x + r * radius * Math.cos( theta ) ) ); - n.setYcoord( ( float ) ( center_y + r * radius * Math.sin( theta ) ) ); + n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) ); + n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) ); _urt_nodeid_angle_map.put( n.getId(), theta ); for( final PhylogenyNode desc : descs ) { paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file ); @@ -2584,11 +2374,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } float r = 0; if ( !n.isRoot() ) { - r = 1 - ( ( ( float ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth ); + r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth ); } final double theta = _urt_nodeid_angle_map.get( n.getId() ); - n.setXSecondary( ( float ) ( center_x + radius * r * Math.cos( theta ) ) ); - n.setYSecondary( ( float ) ( center_y + radius * r * Math.sin( theta ) ) ); + n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) ); + n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) ); for( final PhylogenyNode desc : descs ) { paintBranchCircularLite( n, desc, g ); } @@ -2600,89 +2390,122 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean to_graphics_file, final boolean to_pdf, final boolean is_in_found_nodes ) { - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else if ( is_in_found_nodes ) { - g.setColor( getTreeColorSet().getFoundColor() ); + //// + //// TODO + //// + Color c = null; + int res[] = null; + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + res = calcFoundNodesInSubtree( node ); } - else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - g.setColor( getTaxonomyBasedColor( node ) ); + if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + c = Color.BLACK; } - else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches() + //TODO + //FIXME + // else if ( is_in_found_nodes ) { + // c = getColorForFoundNode( node ); + // } + // else if ( getControlPanel().isColorAccordingToSequence() ) { + // c = getSequenceBasedColor( node ); + // } + // else if ( getControlPanel().isColorAccordingToTaxonomy() ) { + // c = getTaxonomyBasedColor( node ); + // } + else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); - } - else { - g.setColor( getTreeColorSet().getCollapseFillColor() ); + c = PhylogenyMethods.getBranchColorValue( node ); } - double d = node.getAllExternalDescendants().size(); - if ( d > 1000 ) { - d = ( 3 * _y_distance ) / 3; + else if ( to_pdf ) { + g.setColor( getTreeColorSet().getBranchColorForPdf() ); } else { - d = ( Math.log10( d ) * _y_distance ) / 2.5; + c = getTreeColorSet().getCollapseFillColor(); } - if ( d < _box_size ) { - d = _box_size; + double d = node.getAllExternalDescendants().size(); + float xxx; + double s = 0; + if ( getControlPanel().isDrawPhylogram() ) { + if ( d > 1000 ) { + d = 0.75 * _y_distance; + } + else { + d = 0.25 * Math.log10( d ) * _y_distance; + } + final float half_box_size = 0.5f * getOptions().getDefaultNodeShapeSize(); + if ( d < half_box_size ) { + d = half_box_size; + } + _polygon.reset(); + final float xx = node.getXcoord() - ( getOptions().getDefaultNodeShapeSize() ); + xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1; + _polygon.moveTo( xxx, node.getYcoord() + 0.5 ); + _polygon.lineTo( xxx, node.getYcoord() - 0.5 ); + s = _options.isCollapsedWithAverageHeigh() + ? PhylogenyMethods.calculateAverageTreeHeight( node ) * _x_correction_factor : 1; + _polygon.lineTo( node.getXcoord() + s, node.getYcoord() - d ); + _polygon.lineTo( node.getXcoord() + s, node.getYcoord() + d ); + _polygon.closePath(); } - _polygon.reset(); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - _box_size ), - ForesterUtil.roundToInt( node.getYcoord() ) ); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ), - ForesterUtil.roundToInt( node.getYcoord() - d ) ); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ), - ForesterUtil.roundToInt( node.getYcoord() + d ) ); - g.fillPolygon( _polygon ); - paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); - } - - @Override - final public void paintComponent( final Graphics g ) { - // Dimension currentSize = getSize(); - // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) { - // call the 'java.awt.Component.createImage(...)' method to get an - // image - // offscreenImage = createImage( currentSize.width, currentSize.height ); - // offscreenGraphics = offscreenImage.getGraphics(); - // offscreenDimension = currentSize; - // } - // super.paintComponent( g ); //why? - //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics; - final Graphics2D g2d = ( Graphics2D ) g; - g2d.setRenderingHints( _rendering_hints ); - paintPhylogeny( g2d, false, false, 0, 0, 0, 0 ); - //g.drawImage( offscreenImage, 0, 0, this ); - } - - @Override - public void update( final Graphics g ) { - paint( g ); + else { + if ( d > 1000 ) { + d = _y_distance; + } + else { + d = ( Math.log10( d ) * _y_distance ) / 2.5; + } + final int box_size = getOptions().getDefaultNodeShapeSize() + 1; + if ( d < box_size ) { + d = box_size; + } + final float xx = node.getXcoord() - ( 2 * box_size ); + xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1; + _polygon.reset(); + _polygon.moveTo( xxx, node.getYcoord() ); + _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d ); + _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d ); + _polygon.closePath(); + } + if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) { + g.setColor( c ); + g.fill( _polygon ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) { + g.setColor( getBackground() ); + g.fill( _polygon ); + g.setColor( c ); + g.draw( _polygon ); + } + else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { + g.setPaint( new GradientPaint( xxx, + node.getYcoord(), + getBackground(), + node.getXcoord(), + ( float ) ( node.getYcoord() - d ), + c, + false ) ); + g.fill( _polygon ); + g.setPaint( c ); + g.draw( _polygon ); + } + paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes, s ); } final private void paintConfidenceValues( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf, final boolean to_graphics_file ) { - String conf_str = ""; final List confidences = node.getBranchData().getConfidences(); - if ( confidences.size() == 1 ) { - final double value = node.getBranchData().getConfidence( 0 ).getValue(); - if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) { - return; - } - conf_str = FORMATTER_CONFIDENCE.format( value ); - } - else if ( confidences.size() > 1 ) { - boolean one_ok = false; - boolean not_first = false; - Collections.sort( confidences ); - final StringBuilder sb = new StringBuilder(); - for( final Confidence confidence : confidences ) { + boolean not_first = false; + Collections.sort( confidences ); + final StringBuilder sb = new StringBuilder(); + for( final Confidence confidence : confidences ) { + if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE ) || ( !ForesterUtil.isEmpty( confidence.getType() ) + && confidence.getType().equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) { final double value = confidence.getValue(); if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - if ( value >= getOptions().getMinConfidenceValue() ) { - one_ok = true; + if ( value < getOptions().getMinConfidenceValue() ) { + return; } if ( not_first ) { sb.append( "/" ); @@ -2690,17 +2513,24 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { not_first = true; } - sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil + .round( value, getOptions().getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + if ( getOptions().isShowConfidenceStddev() ) { + if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + sb.append( "(" ); + sb.append( FORMATTER_CONFIDENCE + .format( ForesterUtil.round( confidence.getStandardDeviation(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + sb.append( ")" ); + } + } } } - if ( one_ok ) { - conf_str = sb.toString(); - } } - if ( conf_str.length() > 0 ) { - final double parent_x = node.getParent().getXcoord(); - double x = node.getXcoord(); + if ( sb.length() > 0 ) { + final float parent_x = node.getParent().getXcoord(); + float x = node.getXcoord(); g.setFont( getTreeFontSet().getSmallFont() ); if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { x += EURO_D; @@ -2708,85 +2538,140 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { x += ROUNDED_D; } - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) { g.setColor( Color.BLACK ); } else { g.setColor( getTreeColorSet().getConfidenceColor() ); } - TreePanel - .drawString( conf_str, - parent_x - + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ), - ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1, - g ); + final String conf_str = sb.toString(); + TreePanel.drawString( conf_str, + parent_x + ( ( x - parent_x + - getTreeFontSet().getFontMetricsSmall().stringWidth( conf_str ) ) / 2 ), + ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1, + g ); } } - final private void paintFoundNode( final int x, final int y, final Graphics2D g ) { - g.setColor( getTreeColorSet().getFoundColor() ); - g.fillRect( x - _half_box_size, y - _half_box_size, _box_size, _box_size ); - } - final private void paintGainedAndLostCharacters( final Graphics2D g, final PhylogenyNode node, final String gained, final String lost ) { if ( node.getParent() != null ) { - final double parent_x = node.getParent().getXcoord(); - final double x = node.getXcoord(); + final float parent_x = node.getParent().getXcoord(); + final float x = node.getXcoord(); g.setFont( getTreeFontSet().getLargeFont() ); g.setColor( getTreeColorSet().getGainedCharactersColor() ); - if ( Constants.SPECIAL_CUSTOM ) { + if ( AptxConstants.SPECIAL_CUSTOM ) { g.setColor( Color.BLUE ); } + TreePanel.drawString( gained, + parent_x + ( ( x - parent_x + - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ), + ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ), + g ); + g.setColor( getTreeColorSet().getLostCharactersColor() ); TreePanel - .drawString( gained, - parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ), - ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ), + .drawString( lost, + parent_x + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) + / 2 ), + ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), g ); - g.setColor( getTreeColorSet().getLostCharactersColor() ); - TreePanel.drawString( lost, - parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ), - ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ), - g ); + } + } + + private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) { + final RenderableMsaSequence rs = RenderableMsaSequence + .createInstance( node.getNodeData().getSequence().getMolecularSequence(), + node.getNodeData().getSequence().getType(), + getConfiguration() ); + if ( rs != null ) { + final int default_height = 8; + final float y = getYdistance(); + final int h = ( y / 2 ) < default_height ? ForesterUtil.roundToInt( y * 2 ) : default_height; + rs.setRenderingHeight( h > 1 ? h : 1 ); + if ( getControlPanel().isDrawPhylogram() ) { + rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + else { + rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } } } /** * Draw a box at the indicated node. - * + * * @param x * @param y * @param node * @param g */ - final private void paintNodeBox( final double x, - final double y, + final private void paintNodeBox( final float x, + final float y, final PhylogenyNode node, final Graphics2D g, final boolean to_pdf, - final boolean to_graphics_file, - final boolean is_in_found_nodes ) { + final boolean to_graphics_file ) { if ( node.isCollapse() ) { return; } // if this node should be highlighted, do so if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) { - g.setColor( getTreeColorSet().getFoundColor() ); + g.setColor( getTreeColorSet().getFoundColor0() ); drawOval( x - 8, y - 8, 16, 16, g ); drawOval( x - 9, y - 8, 17, 17, g ); drawOval( x - 9, y - 9, 18, 18, g ); } - if ( is_in_found_nodes ) { - paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g ); - } - else { + 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 ) + || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) + || ( node.getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) ) + || ( getControlPanel().isEvents() && node.isHasAssignedEvent() + && ( node.getNodeData().getEvent().isDuplication() + || node.getNodeData().getEvent().isSpeciation() + || node.getNodeData().getEvent().isSpeciationOrDuplication() ) ) ) { + NodeVisualData vis = null; + if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) + && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) { + vis = node.getNodeData().getNodeVisualData(); + } + float box_size = getOptions().getDefaultNodeShapeSize(); + if ( ( vis != null ) && ( vis.getSize() != NodeVisualData.DEFAULT_SIZE ) ) { + box_size = vis.getSize(); + } + final float half_box_size = box_size / 2.0f; Color outline_color = null; if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { outline_color = Color.BLACK; } - else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) { + else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { + outline_color = getColorForFoundNode( node ); + } + else if ( vis != null ) { + if ( vis.getNodeColor() != null ) { + outline_color = vis.getNodeColor(); + } + else if ( vis.getFontColor() != null ) { + outline_color = vis.getFontColor(); + } + } + else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) { final Event event = node.getNodeData().getEvent(); if ( event.isDuplication() ) { outline_color = getTreeColorSet().getDuplicationBoxColor(); @@ -2798,277 +2683,320 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee outline_color = getTreeColorSet().getDuplicationOrSpeciationColor(); } } - else if ( getOptions().isTaxonomyColorizeNodeShapes() ) { - outline_color = getTaxonomyBasedColor( node ); - } - else { + if ( outline_color == null ) { outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node ); + if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) { + outline_color = getTreeColorSet().getBranchColorForPdf(); + } } - if ( ( ( getOptions().isShowDefaultNodeShapes() ) /*&& !to_pdf && !to_graphics_file*/) - || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) { - if ( to_pdf || to_graphics_file ) { - if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) { - //TODO FIXME - //drawOvalFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g ); - drawOvalGradient( x - _half_box_size, - y - _half_box_size, - _box_size, - _box_size, - g, - outline_color, - getBackground(), - outline_color ); - } + NodeShape shape = null; + if ( vis != null ) { + if ( vis.getShape() == NodeShape.CIRCLE ) { + shape = NodeShape.CIRCLE; } - else { - //TODO FIXME - //drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g ); - if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) { - if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { - drawOvalGradient( x - _half_box_size, - y - _half_box_size, - _box_size, - _box_size, - g, - outline_color, - getBackground(), - outline_color ); - } - else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) { - drawOvalGradient( x - _half_box_size, - y - _half_box_size, - _box_size, - _box_size, - g, - getBackground(), - getBackground(), - outline_color ); - } - else if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) { - g.setColor( outline_color ); - drawOvalFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g ); - } + else if ( vis.getShape() == NodeShape.RECTANGLE ) { + shape = NodeShape.RECTANGLE; + } + } + if ( shape == null ) { + if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) { + shape = NodeShape.CIRCLE; + } + else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) { + shape = NodeShape.RECTANGLE; + } + } + NodeFill fill = null; + if ( vis != null ) { + if ( vis.getFillType() == NodeFill.SOLID ) { + fill = NodeFill.SOLID; + } + else if ( vis.getFillType() == NodeFill.NONE ) { + fill = NodeFill.NONE; + } + else if ( vis.getFillType() == NodeFill.GRADIENT ) { + fill = NodeFill.GRADIENT; + } + } + if ( fill == null ) { + if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) { + fill = NodeFill.SOLID; + } + else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) { + fill = NodeFill.NONE; + } + else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { + fill = NodeFill.GRADIENT; + } + } + Color vis_fill_color = null; + if ( ( vis != null ) && ( vis.getNodeColor() != null ) ) { + vis_fill_color = vis.getNodeColor(); + } + if ( shape == NodeShape.CIRCLE ) { + if ( fill == NodeFill.GRADIENT ) { + drawOvalGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + to_pdf ? Color.WHITE : outline_color, + to_pdf ? outline_color : getBackground(), + outline_color ); + } + else if ( fill == NodeFill.NONE ) { + Color background = getBackground(); + if ( to_pdf ) { + background = Color.WHITE; } - else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) { - if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { - drawRectGradient( x - _half_box_size, - y - _half_box_size, - _box_size, - _box_size, - g, - outline_color, - getBackground(), - outline_color ); - } - else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) { - drawRectGradient( x - _half_box_size, - y - _half_box_size, - _box_size, - _box_size, - g, - getBackground(), - getBackground(), - outline_color ); - } - else if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) { - g.setColor( outline_color ); - drawRectFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g ); - } + drawOvalGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + background, + background, + outline_color ); + } + else if ( fill == NodeVisualData.NodeFill.SOLID ) { + if ( vis_fill_color != null ) { + g.setColor( vis_fill_color ); + } + else { + g.setColor( outline_color ); + } + drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); + } + } + else if ( shape == NodeVisualData.NodeShape.RECTANGLE ) { + if ( fill == NodeVisualData.NodeFill.GRADIENT ) { + drawRectGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + to_pdf ? Color.WHITE : outline_color, + to_pdf ? outline_color : getBackground(), + outline_color ); + } + else if ( fill == NodeVisualData.NodeFill.NONE ) { + Color background = getBackground(); + if ( to_pdf ) { + background = Color.WHITE; + } + drawRectGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + background, + background, + outline_color ); + } + else if ( fill == NodeVisualData.NodeFill.SOLID ) { + if ( vis_fill_color != null ) { + g.setColor( vis_fill_color ); + } + else { + g.setColor( outline_color ); } + drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); } } } } - final private void paintNodeData( final Graphics2D g, - final PhylogenyNode node, - final boolean to_graphics_file, - final boolean to_pdf, - final boolean is_in_found_nodes ) { + final private int paintNodeData( final Graphics2D g, + final PhylogenyNode node, + final boolean to_graphics_file, + final boolean to_pdf, + final boolean is_in_found_nodes, + final double add ) { if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) { - return; + return 0; } - if ( getOptions().isShowBranchLengthValues() + if ( getControlPanel().isWriteBranchLengthValues() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) ) { + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) + && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { paintBranchLength( g, node, to_pdf, to_graphics_file ); } if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) { - return; + return 0; + } + if ( !getControlPanel().isShowExternalData() && ( node.isExternal() || node.isCollapse() ) ) { + return 0; } + _sb.setLength( 0 ); int x = 0; - if ( getControlPanel().isShowTaxonomyImages() - && ( getImageMap() != null ) - && !getImageMap().isEmpty() - && node.getNodeData().isHasTaxonomy() - && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy() - .getUris().isEmpty() ) ) { - x += drawTaxonomyImage( node.getXcoord() + 2 + _half_box_size, node.getYcoord(), node, g ); - } - if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel() - .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) { + if ( add > 0 ) { + x += add; + } + final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2; + if ( getControlPanel().isShowTaxonomyImages() && ( getImageMap() != null ) && !getImageMap().isEmpty() + && node.getNodeData().isHasTaxonomy() && ( ( node.getNodeData().getTaxonomy().getUris() != null ) + && !node.getNodeData().getTaxonomy().getUris().isEmpty() ) ) { + x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g ); + } + if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() + || getControlPanel().isShowTaxonomyCommonNames() || getControlPanel().isShowTaxonomyRank() ) + && node.getNodeData().isHasTaxonomy() ) { x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x ); } - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else if ( is_in_found_nodes ) { - g.setColor( getTreeColorSet().getFoundColor() ); - } - else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - g.setColor( getTaxonomyBasedColor( node ) ); - } - else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches() - && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); - } - else if ( to_pdf ) { - g.setColor( Color.BLACK ); - } - else { - g.setColor( getTreeColorSet().getSequenceColor() ); - } + setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() ); + final boolean saw_species = _sb.length() > 0; _sb.setLength( 0 ); + nodeDataAsSB( node, _sb ); if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) { - _sb.append( " [" ); - _sb.append( node.getAllExternalDescendants().size() ); - _sb.append( "]" ); - } - if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { - if ( _sb.length() > 0 ) { - _sb.append( " " ); - } - _sb.append( node.getName() ); - } - if ( node.getNodeData().isHasSequence() ) { - if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) { - if ( _sb.length() > 0 ) { - _sb.append( " " ); - } - _sb.append( node.getNodeData().getSequence().getSymbol() ); - } - if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { - if ( _sb.length() > 0 ) { - _sb.append( " " ); + if ( ( _sb.length() == 0 ) && !saw_species ) { + if ( getOptions().isShowAbbreviatedLabelsForCollapsedNodes() + && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() + || getControlPanel().isShowSeqNames() || getControlPanel().isShowNodeNames() ) ) { + final PhylogenyNode first = PhylogenyMethods.getFirstExternalNode( node ); + final PhylogenyNode last = PhylogenyMethods.getLastExternalNode( node ); + if ( getControlPanel().isShowTaxonomyCode() && first.getNodeData().isHasTaxonomy() + && last.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getTaxonomyCode() ) + && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + addLabelForCollapsed( first.getNodeData().getTaxonomy().getTaxonomyCode(), + last.getNodeData().getTaxonomy().getTaxonomyCode(), + node.getAllExternalDescendants().size(), + node ); + } + else if ( getControlPanel().isShowTaxonomyScientificNames() && first.getNodeData().isHasTaxonomy() + && last.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getScientificName() ) + && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getScientificName() ) ) { + addLabelForCollapsed( first.getNodeData().getTaxonomy().getScientificName(), + last.getNodeData().getTaxonomy().getScientificName(), + node.getAllExternalDescendants().size(), + node ); + } + else if ( getControlPanel().isShowSeqNames() && first.getNodeData().isHasSequence() + && last.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( first.getNodeData().getSequence().getName() ) + && !ForesterUtil.isEmpty( last.getNodeData().getSequence().getName() ) ) { + addLabelForCollapsed( first.getNodeData().getSequence().getName(), + last.getNodeData().getSequence().getName(), + node.getAllExternalDescendants().size(), + node ); + } + else if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( first.getName() ) + && !ForesterUtil.isEmpty( last.getName() ) ) { + addLabelForCollapsed( first.getName(), + last.getName(), + node.getAllExternalDescendants().size(), + node ); + } } - _sb.append( node.getNodeData().getSequence().getName() ); } - if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) { - if ( _sb.length() > 0 ) { - _sb.append( " " ); - } - if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) { - _sb.append( node.getNodeData().getSequence().getAccession().getSource() ); - _sb.append( ":" ); + else if ( ( _sb.length() > 0 ) || saw_species ) { + // _sb.setLength( 0 ); + _sb.append( " [" ); + _sb.append( node.getAllExternalDescendants().size() ); + _sb.append( "]" ); + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + int[] res = calcFoundNodesInSubtree( node ); + if ( res[ 0 ] > 0 ) { + _sb.append( " [" ); + _sb.append( res[ 0 ] ); + _sb.append( "/" ); + _sb.append( res[ 1 ] ); + _sb.append( "]" ); + } } - _sb.append( node.getNodeData().getSequence().getAccession().getValue() ); } } - g.setFont( getTreeFontSet().getLargeFont() ); - if ( is_in_found_nodes ) { - g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) ); + else { + // _sb.setLength( 0 ); } - double down_shift_factor = 3.0; + // nodeDataAsSB( node, _sb ); + final boolean using_visual_font = setFont( g, node, is_in_found_nodes ); + float down_shift_factor = 3.0f; if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) { down_shift_factor = 1; } - final double pos_x = node.getXcoord() + x + 2 + _half_box_size; - final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) ); + float pos_x; + if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM + && ( node.isExternal() || node.isCollapse() ) ) { + pos_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x + ( 2 * TreePanel.MOVE ) + getXdistance() + + 3 ); + } + else { + pos_x = node.getXcoord() + x + 2 + half_box_size; + } + float pos_y; + if ( !using_visual_font ) { + pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) ); + } + else { + pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) ); + } + if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM + && ( node.isExternal() || node.isCollapse() ) ) { + drawConnection( node.getXcoord(), pos_x - x, node.getYcoord(), 5, 20, g, to_pdf ); + if ( node.isCollapse() ) { + pos_x -= add; + } + } final String sb_str = _sb.toString(); // GUILHEM_BEG ______________ if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence() && ( _query_sequence != null ) ) { - int nodeTextBoundsWidth = 0; - if ( sb_str.length() > 0 ) { - final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how... - nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth(); - } - if ( node.getNodeData().getSequence().equals( _query_sequence ) ) { - if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence - g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 ); - g.setColor( getTreeColorSet().getBackgroundColor() ); - } + x = paintSequenceRelation( g, node, x, half_box_size, pos_x, pos_y, sb_str ); + } + // GUILHEM_END _____________ + if ( sb_str.length() > 0 ) { + if ( !isAllowAttributedStrings() ) { + TreePanel.drawString( sb_str, pos_x, pos_y, g ); } else { - final List seqRelations = node.getNodeData().getSequence().getSequenceRelations(); - for( final SequenceRelation seqRelation : seqRelations ) { - final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation - .getRef1().isEqual( _query_sequence ) ) - && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox() - .getSelectedItem() ); - if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query - final double linePosX = node.getXcoord() + 2 + _half_box_size; - final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation - .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue() - + ")"; - if ( sConfidence != null ) { - double confidenceX = pos_x; - if ( sb_str.length() > 0 ) { - confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth() - + CONFIDENCE_LEFT_MARGIN; - } - if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code - final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc ) - .getBounds().getWidth(); - TreePanel.drawString( sConfidence, confidenceX, pos_y, g ); - x += CONFIDENCE_LEFT_MARGIN + confidenceWidth; - } - } - if ( x + nodeTextBoundsWidth > 0 ) /* we only underline if there is something displayed */ - { - if ( nodeTextBoundsWidth == 0 ) { - nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */ - } - else { - nodeTextBoundsWidth += 2; - } - g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x - + nodeTextBoundsWidth, 3 + ( int ) pos_y ); - break; - } - } - } + drawStringX( sb_str, pos_x, pos_y, g ); } } - if ( sb_str.length() > 0 ) { - TreePanel.drawString( sb_str, pos_x, pos_y, g ); + if ( _sb.length() > 0 ) { + if ( !using_visual_font && !is_in_found_nodes ) { + x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5; + } + else { + x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5; + } } - // GUILHEM_END _____________ - // COMMENTED_OUT_BY_GUILHEM_BEG _______________ - // TODO FIXME need to check this one! - //if ( _sb.length() > 0 ) { - // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord() - // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); - //} - // COMMENTED_OUT_BY_GUILHEM_END ________________ if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) { - if ( _sb.length() > 0 ) { - x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5; - } - final Annotation ann = node.getNodeData().getSequence().getAnnotation( 0 ); + final SortedSet ann = node.getNodeData().getSequence().getAnnotations(); if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { g.setColor( Color.BLACK ); } - else { + else if ( getControlPanel().isColorAccordingToAnnotation() ) { g.setColor( calculateColorForAnnotation( ann ) ); } - final String ann_str = ann.asSimpleText().toString(); - TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + _half_box_size, node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); + final String ann_str = TreePanelUtil.createAnnotationString( ann, + getOptions().isShowAnnotationRefSource() ); + TreePanel.drawString( ann_str, + node.getXcoord() + x + 3 + half_box_size, + node.getYcoord() + + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), + g ); _sb.setLength( 0 ); _sb.append( ann_str ); + if ( _sb.length() > 0 ) { + if ( !using_visual_font && !is_in_found_nodes ) { + x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5; + } + else { + x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5; + } + } } if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() ) && node.getNodeData().isHasBinaryCharacters() ) { - if ( _sb.length() > 0 ) { - x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5; - } if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { g.setColor( Color.BLACK ); } @@ -3077,90 +3005,182 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( getControlPanel().isShowBinaryCharacters() ) { TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() - .toString(), node.getXcoord() + x + 1 + _half_box_size, node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); - paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters() - .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() - .getLostCharactersAsStringBuffer().toString() ); + .toString(), + node.getXcoord() + x + 1 + half_box_size, + node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() + / down_shift_factor ), + g ); + paintGainedAndLostCharacters( g, + node, + node.getNodeData().getBinaryCharacters() + .getGainedCharactersAsStringBuffer().toString(), + node.getNodeData().getBinaryCharacters() + .getLostCharactersAsStringBuffer().toString() ); } else { - if ( DRAW_MEAN_COUNTS && node.isInternal() ) { - final List ec = node.getAllExternalDescendants(); - double sum = 0; - int count = 0; - for( final PhylogenyNode phylogenyNode : ec ) { - count++; - if ( phylogenyNode.getNodeData().getBinaryCharacters() != null ) { - sum += phylogenyNode.getNodeData().getBinaryCharacters().getPresentCount(); - } - } - final double mean = ForesterUtil.round( sum / count, 1 ); - TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " [" - + mean + "]", node.getXcoord() + x + 4 + _half_box_size, node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); - } - else { - TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), - node.getXcoord() + x + 4 + _half_box_size, - node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), - g ); - } - paintGainedAndLostCharacters( g, node, "+" - + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" - + node.getNodeData().getBinaryCharacters().getLostCount() ); + TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), + node.getXcoord() + x + 4 + half_box_size, + node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() + / down_shift_factor ), + g ); + paintGainedAndLostCharacters( g, + node, + "+" + node.getNodeData().getBinaryCharacters().getGainedCount(), + "-" + node.getNodeData().getBinaryCharacters().getLostCount() ); } } } + return x; } - private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) { - final List us = new ArrayList(); - for( final Taxonomy t : node.getNodeData().getTaxonomies() ) { - for( final Uri uri : t.getUris() ) { - us.add( uri ); + private final int paintSequenceRelation( final Graphics2D g, + final PhylogenyNode node, + int x, + final int half_box_size, + final float pos_x, + final float pos_y, + final String sb_str ) { + int nodeTextBoundsWidth = 0; + if ( sb_str.length() > 0 ) { + final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how... + nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth(); + } + if ( node.getNodeData().getSequence().equals( _query_sequence ) ) { + if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence + g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 ); + g.setColor( getTreeColorSet().getBackgroundColor() ); } } - double offset = 0; - for( final Uri uri : us ) { - if ( uri != null ) { - final String uri_str = uri.getValue().toString().toLowerCase(); - if ( getImageMap().containsKey( uri_str ) ) { - final BufferedImage bi = getImageMap().get( uri_str ); - if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) { - double scaling_factor = 1; - if ( getOptions().isAllowMagnificationOfTaxonomyImages() - || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) { - scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight(); + else { + final List seqRelations = node.getNodeData().getSequence().getSequenceRelations(); + for( final SequenceRelation seqRelation : seqRelations ) { + final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) + || seqRelation.getRef1().isEqual( _query_sequence ) ) + && seqRelation.getType() + .equals( getControlPanel().getSequenceRelationTypeBox().getSelectedItem() ); + if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query + final double linePosX = node.getXcoord() + 2 + half_box_size; + final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() + || ( seqRelation.getConfidence() == null ) ) ? null + : " (" + seqRelation.getConfidence().getValue() + ")"; + if ( sConfidence != null ) { + float confidenceX = pos_x; + if ( sb_str.length() > 0 ) { + confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth() + + CONFIDENCE_LEFT_MARGIN; } - // y = y - ( 0.9 * getYdistance() ); - final double hs = bi.getHeight() * scaling_factor; - double ws = bi.getWidth() * scaling_factor + offset; - final double my_y = y - ( 0.5 * hs ); - final int x_w = ( int ) ( x + ws + 0.5 ); - final int y_h = ( int ) ( my_y + hs + 0.5 ); - if ( ( x_w - x > 7 ) && ( y_h - my_y > 7 ) ) { - g.drawImage( bi, - ( int ) ( x + 0.5 + offset ), - ( int ) ( my_y + 0.5 ), - x_w, - y_h, - 0, - 0, - bi.getWidth(), - bi.getHeight(), - null ); - ws += 8; + if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code + final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc ) + .getBounds().getWidth(); + TreePanel.drawString( sConfidence, confidenceX, pos_y, g ); + x += CONFIDENCE_LEFT_MARGIN + confidenceWidth; + } + } + if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */ + { + if ( nodeTextBoundsWidth == 0 ) { + nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */ } else { - ws = 0.0; + nodeTextBoundsWidth += 2; } - offset = ws; + g.drawLine( ( int ) linePosX + 1, + 3 + ( int ) pos_y, + ( int ) linePosX + x + nodeTextBoundsWidth, + 3 + ( int ) pos_y ); + break; } } } } - return offset; + return x; + } + + private final void drawConnection( final float x1, + final float x2, + final float y, + final int dist_left, + final int dist_right, + final Graphics2D g, + final boolean pdf ) { + if ( ( ( x1 + dist_left ) < ( x2 - dist_right ) ) ) { + final Stroke strok = g.getStroke(); + Color col = null; + if ( strok == STROKE_005 ) { + g.setStroke( STROKE_001_DASHED ); + } + else if ( strok == STROKE_01 ) { + g.setStroke( STROKE_005_DASHED ); + } + else { + g.setStroke( STROKE_01_DASHED ); + } + if ( pdf ) { + col = g.getColor(); + g.setColor( lighter( col ) ); + } + drawLine( x1 + dist_left, y, x2 - dist_right, y, g ); + g.setStroke( strok ); + if ( pdf ) { + g.setColor( col ); + } + } + } + + public static Color lighter( final Color color ) { + if ( ( color.getRed() == 0 ) && ( color.getGreen() == 0 ) && ( color.getBlue() == 0 ) ) { + return new Color( 200, 200, 200 ); + } + else { + return color; + } + } + + private final void addLabelForCollapsed( final String first, + final String last, + final int size, + final PhylogenyNode node ) { + _sb.append( first.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? first + : first.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) ); + _sb.append( " ... " ); + _sb.append( last.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? last + : last.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) ); + _sb.append( " (" + size + ")" ); + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + ///// + ///// + int[] res = calcFoundNodesInSubtree( node ); + if ( res[ 0 ] > 0 ) { + _sb.append( " [" ); + _sb.append( res[ 0 ] ); + _sb.append( "/" ); + _sb.append( res[ 1 ] ); + _sb.append( "]" ); + } + } + } + + private final int[] calcFoundNodesInSubtree( final PhylogenyNode node ) { + final List all_descs = PhylogenyMethods.getAllDescendants( node ); + int res[] = new int[ 2 ]; + int found = 0; + int total = 0; + for( final PhylogenyNode desc : all_descs ) { + if ( desc.isHasNodeData() ) { + if ( ( _found_nodes_0 != null && _found_nodes_0.contains( desc.getId() ) ) + || ( _found_nodes_1 != null && _found_nodes_1.contains( desc.getId() ) ) ) { + ++found; + } + ++total; + } + } + res[ 0 ] = found; + res[ 1 ] = total; + return res; + } + + private final boolean isAllowAttributedStrings() { + return false; } final private void paintNodeDataUnrootedCirc( final Graphics2D g, @@ -3173,23 +3193,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) { return; } - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else if ( is_in_found_nodes ) { - g.setColor( getTreeColorSet().getFoundColor() ); - } - else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - g.setColor( getTaxonomyBasedColor( node ) ); - } - else { - g.setColor( getTreeColorSet().getSequenceColor() ); - } _sb.setLength( 0 ); _sb.append( " " ); if ( node.getNodeData().isHasTaxonomy() - && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel() - .isShowTaxonomyCommonNames() ) ) { + && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() + || getControlPanel().isShowTaxonomyCommonNames() ) ) { final Taxonomy taxonomy = node.getNodeData().getTaxonomy(); if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) { _sb.append( taxonomy.getTaxonomyCode() ); @@ -3237,7 +3245,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _sb.append( node.getName() ); } if ( node.getNodeData().isHasSequence() ) { - if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) { + if ( getControlPanel().isShowSequenceAcc() + && ( node.getNodeData().getSequence().getAccession() != null ) ) { if ( _sb.length() > 0 ) { _sb.append( " " ); } @@ -3247,18 +3256,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } _sb.append( node.getNodeData().getSequence().getAccession().getValue() ); } - if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { + if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { if ( _sb.length() > 0 ) { _sb.append( " " ); } _sb.append( node.getNodeData().getSequence().getName() ); } } - g.setFont( getTreeFontSet().getLargeFont() ); - if ( is_in_found_nodes ) { - g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) ); - } + //g.setFont( getTreeFontSet().getLargeFont() ); + //if ( is_in_found_nodes ) { + // g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) ); + // } if ( _sb.length() > 1 ) { + setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() ); + final boolean using_visual_font = setFont( g, node, is_in_found_nodes ); final String sb_str = _sb.toString(); double m = 0; if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { @@ -3270,7 +3281,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _at = g.getTransform(); boolean need_to_reset = false; final float x_coord = node.getXcoord(); - final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f ); + float y_coord; + if ( !using_visual_font ) { + y_coord = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / 3.0f ); + } + else { + y_coord = node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / 3.0f ); + } if ( radial_labels ) { need_to_reset = true; boolean left = false; @@ -3280,13 +3297,24 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } g.rotate( m, x_coord, node.getYcoord() ); if ( left ) { - g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 ); + if ( !using_visual_font ) { + g.translate( -( getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth() ), + 0 ); + } + else { + g.translate( -( getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth() ), 0 ); + } } } else { if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) { need_to_reset = true; - g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 ); + if ( !using_visual_font ) { + g.translate( -getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth(), 0 ); + } + else { + g.translate( -getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth(), 0 ); + } } } TreePanel.drawString( sb_str, x_coord, y_coord, g ); @@ -3298,34 +3326,28 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) { if ( node.isCollapse() ) { - if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) { - paintCollapsedNode( g, node, false, false, false ); - } return; } - if ( isInFoundNodes( node ) ) { - g.setColor( getTreeColorSet().getFoundColor() ); - drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g ); + if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { + g.setColor( getColorForFoundNode( node ) ); + drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, + node.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, + OVERVIEW_FOUND_NODE_BOX_SIZE, + OVERVIEW_FOUND_NODE_BOX_SIZE, + g ); } float new_x = 0; if ( !node.isExternal() && !node.isCollapse() ) { boolean first_child = true; float y2 = 0.0f; - final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node ); + //final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node ); for( int i = 0; i < node.getNumberOfDescendants(); ++i ) { final PhylogenyNode child_node = node.getChildNode( i ); - int factor_x; - if ( !isUniformBranchLengthsForCladogram() ) { - factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes(); - } - else { - factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node ); - } + final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes(); if ( first_child ) { first_child = false; - y2 = node.getYSecondary() - - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node - .getNumberOfExternalNodes() ) ); + y2 = node.getYSecondary() - ( getOvYDistance() + * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) ); } else { y2 += getOvYDistance() * child_node.getNumberOfExternalNodes(); @@ -3349,10 +3371,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean to_pdf, final boolean dynamically_hide, final int dynamic_hiding_factor, - final boolean to_graphics_file ) { - final boolean is_in_found_nodes = isInFoundNodes( node ); + final boolean to_graphics_file, + final boolean disallow_shortcutting ) { + final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node ); if ( node.isCollapse() ) { - if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) { + if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) { paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); } return; @@ -3361,11 +3384,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee ++_external_node_index; } // Confidence values - if ( getControlPanel().isShowBootstrapValues() - && !node.isExternal() - && !node.isRoot() + if ( getControlPanel().isShowConfidenceValues() && !node.isExternal() && !node.isRoot() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) && node.getBranchData().isHasConfidences() ) { paintConfidenceValues( g, node, to_pdf, to_graphics_file ); } @@ -3375,10 +3397,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } float new_x = 0; float new_x_min = Float.MAX_VALUE; - final boolean disallow_shortcutting = dynamic_hiding_factor < 40; float min_dist = 1.5f; if ( !disallow_shortcutting ) { - // System.out.println( dynamic_hiding_factor ); if ( dynamic_hiding_factor > 4000 ) { min_dist = 4; } @@ -3392,20 +3412,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !node.isExternal() && !node.isCollapse() ) { boolean first_child = true; float y2 = 0.0f; - final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node ); for( int i = 0; i < node.getNumberOfDescendants(); ++i ) { final PhylogenyNode child_node = node.getChildNode( i ); - int factor_x; - if ( !isUniformBranchLengthsForCladogram() ) { - factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes(); - } - else { - factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node ); - } + final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes(); if ( first_child ) { first_child = false; - y2 = node.getYcoord() - - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) ); + y2 = node.getYcoord() - ( _y_distance + * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) ); } else { y2 += _y_distance * child_node.getNumberOfExternalNodes(); @@ -3418,7 +3431,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final float diff_y = node.getYcoord() - y2; final float diff_x = node.getXcoord() - new_x; if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist ) - || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) { + || ( diff_x < -min_dist ) ) { paintBranchRectangular( g, node.getXcoord(), new_x, @@ -3432,97 +3445,138 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee child_node.setYcoord( y2 ); y2 += _y_distance * child_node.getNumberOfExternalNodes(); } - //TODO new ***** - paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) ); - //TODO new ***** + paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file ); } - if ( dynamically_hide - && !is_in_found_nodes - && ( ( node.isExternal() && ( _external_node_index % dynamic_hiding_factor != 1 ) ) || ( !node - .isExternal() && ( ( new_x_min < 20 ) || ( _y_distance * node.getNumberOfExternalNodes() < getTreeFontSet()._fm_large - .getHeight() ) ) ) ) ) { + if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) + && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { + paintMolecularSequences( g, node, to_pdf ); + } + if ( dynamically_hide && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) + || ( !node.isExternal() && ( ( new_x_min < 20 ) + || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont() + .getHeight() ) ) ) ) ) { return; } - paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); - paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf ); + final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes, 0 ); + paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf ); } - final private void paintNodeWithRenderableData( final Graphics2D g, + final private void paintNodeWithRenderableData( final int x, + final Graphics2D g, final PhylogenyNode node, final boolean to_graphics_file, final boolean to_pdf ) { - if ( isNodeDataInvisible( node ) && !to_graphics_file ) { + if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) { return; } if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) { return; } + if ( ( !getControlPanel().isShowExternalData() && node.isExternal() ) ) { + return; + } if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) && ( node.getNodeData() + .getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { RenderableDomainArchitecture rds = null; - if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) { - try { - rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); - } - catch ( final ClassCastException cce ) { - cce.printStackTrace(); - return; - } - rds.setRenderingHeight( 6 ); - int x = 0; - if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) { - x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " ); - } - if ( getControlPanel().isShowGeneNames() ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " ); - } - if ( getControlPanel().isShowGeneSymbols() ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " ); - } - if ( getControlPanel().isShowSequenceAcc() ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession() - .toString() - + " " ); + try { + rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); + } + catch ( final ClassCastException cce ) { + cce.printStackTrace(); + } + if ( rds != null ) { + final int default_height = 7; + float y = getYdistance(); + if ( getControlPanel().isDynamicallyHideData() ) { + y = getTreeFontSet().getFontMetricsLarge().getHeight(); + } + final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height; + rds.setRenderingHeight( h > 1 ? h : 2 ); + if ( getControlPanel().isDrawPhylogram() ) { + if ( getOptions().isLineUpRendarableNodeData() ) { + if ( getOptions().isRightLineUpDomains() ) { + rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + + _length_of_longest_text + 50 //TODO why plus 50? + + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ) ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + else { + rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + + _length_of_longest_text + 50 ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + } + else { + rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); + } } - if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " ); + else { + if ( getOptions().isRightLineUpDomains() ) { + rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) + - 20 ) + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + else { + rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } } - rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf ); } } - ////////////// if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) { final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(), getStatisticsForExpressionValues(), getConfiguration() ); - int x = 0; - PhylogenyNode my_node = node; - if ( !getControlPanel().isDrawPhylogram() ) { - my_node = getPhylogeny().getFirstExternalNode(); - } - if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) { - x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " ); - } - if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) { - x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " ); + if ( rv != null ) { + double domain_add = 0; + if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + domain_add = _domain_structure_width + 10; + } + if ( getControlPanel().isDrawPhylogram() ) { + rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf ); + } + else { + rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + + domain_add ), node.getYcoord() - 3, g, this, to_pdf ); + } } - rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf ); } - ////////////// + //if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) + // && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) + // && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { + // paintMolecularSequences( g, node, to_pdf ); + //} } final private void paintOvRectangle( final Graphics2D g ) { - final float w_ratio = ( float ) getWidth() / getVisibleRect().width; - final float h_ratio = ( float ) getHeight() / getVisibleRect().height; - final float x_ratio = ( float ) getWidth() / getVisibleRect().x; - final float y_ratio = ( float ) getHeight() / getVisibleRect().y; + final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width; + final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height; + final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x; + final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y; final float width = getOvMaxWidth() / w_ratio; final float height = getOvMaxHeight() / h_ratio; - final float x = getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / x_ratio; - final float y = getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / y_ratio; - g.setColor( getTreeColorSet().getFoundColor() ); + final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio ); + final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio ); + g.setColor( getTreeColorSet().getFoundColor0() ); getOvRectangle().setRect( x, y, width, height ); + final Stroke s = g.getStroke(); + g.setStroke( STROKE_1 ); if ( ( width < 6 ) && ( height < 6 ) ) { drawRectFilled( x, y, 6, 6, g ); getOvVirtualRectangle().setRect( x, y, 6, 6 ); @@ -3542,229 +3596,27 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } getOvVirtualRectangle().setRect( x, y, width, height ); } - } - - final void paintPhylogeny( final Graphics2D g, - final boolean to_pdf, - final boolean to_graphics_file, - final int graphics_file_width, - final int graphics_file_height, - final int graphics_file_x, - final int graphics_file_y ) { - if ( _control_panel.isShowSequenceRelations() ) { - _query_sequence = _control_panel.getSelectedQuerySequence(); - } - // Color the background - if ( !to_pdf ) { - final Rectangle r = getVisibleRect(); - if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) { - g.setColor( getTreeColorSet().getBackgroundColor() ); - if ( !to_graphics_file ) { - g.fill( r ); - } - else { - if ( getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.WHITE ); - } - g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); - } - } - else { - if ( !to_graphics_file ) { - g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y - + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) ); - g.fill( r ); - } - else { - g.setPaint( new GradientPaint( graphics_file_x, - graphics_file_y, - getTreeColorSet().getBackgroundColor(), - graphics_file_x, - graphics_file_y + graphics_file_height, - getTreeColorSet().getBackgroundColorGradientBottom() ) ); - g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); - } - } - g.setStroke( new BasicStroke( 1 ) ); - } - else { - g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) ); - } - if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) - && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - _external_node_index = 0; - // Position starting X of tree - if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) { - _phylogeny.getRoot().setXcoord( TreePanel.MOVE ); - } - else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) { - _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot() - .getDistanceToParent() * getXcorrectionFactor() ) ) ); - } - else { - _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() ); - } - // Position starting Y of tree - _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() ) - + ( TreePanel.MOVE / 2.0f ) ); - final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ); - if ( getControlPanel().isDynamicallyHideData() ) { - if ( dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); - } - else { - getControlPanel().setDynamicHidingIsOn( false ); - } - } - if ( _nodes_in_preorder == null ) { - _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ]; - int i = 0; - for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { - _nodes_in_preorder[ i++ ] = it.next(); - } - } - //final PhylogenyNodeIterator it; - //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { - // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData() - // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file ); - //} - for( int i = 0; i < _nodes_in_preorder.length; ++i ) { - paintNodeRectangular( g, _nodes_in_preorder[ i ], to_pdf, getControlPanel().isDynamicallyHideData() - && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file ); - } - if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) { - if ( !( to_graphics_file || to_pdf ) ) { - paintScale( g, - getVisibleRect().x, - getVisibleRect().y + getVisibleRect().height, - to_pdf, - to_graphics_file ); - } - else { - paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); - } - } - if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { - paintPhylogenyLite( g ); - } - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - if ( getControlPanel().getDynamicallyHideData() != null ) { - getControlPanel().setDynamicHidingIsOn( false ); - } - final double angle = getStartingAngle(); - final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL; - _dynamic_hiding_factor = 0; - if ( getControlPanel().isDynamicallyHideData() ) { - _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny() - .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) ); - } - if ( getControlPanel().getDynamicallyHideData() != null ) { - if ( _dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); - } - else { - getControlPanel().setDynamicHidingIsOn( false ); - } - } - paintUnrooted( _phylogeny.getRoot(), - angle, - ( float ) ( angle + 2 * Math.PI ), - radial_labels, - g, - to_pdf, - to_graphics_file ); - if ( getOptions().isShowScale() ) { - if ( !( to_graphics_file || to_pdf ) ) { - paintScale( g, - getVisibleRect().x, - getVisibleRect().y + getVisibleRect().height, - to_pdf, - to_graphics_file ); - } - else { - paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); - } - } - if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { - g.setColor( getTreeColorSet().getOvColor() ); - paintUnrootedLite( _phylogeny.getRoot(), - angle, - angle + 2 * Math.PI, - g, - ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) ); - paintOvRectangle( g ); - } - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { - final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) ); - final int d = radius + MOVE + getLongestExtNodeInfo(); - _dynamic_hiding_factor = 0; - if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) { - _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny() - .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) ); - } - if ( getControlPanel().getDynamicallyHideData() != null ) { - if ( _dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); - } - else { - getControlPanel().setDynamicHidingIsOn( false ); - } - } - paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file ); - if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { - final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2 - : getOvMaxWidth() / 2 ); - double x_scale = 1.0; - double y_scale = 1.0; - int x_pos = getVisibleRect().x + getOvXPosition(); - int y_pos = getVisibleRect().y + getOvYPosition(); - if ( getWidth() > getHeight() ) { - x_scale = ( double ) getHeight() / getWidth(); - x_pos = ForesterUtil.roundToInt( x_pos / x_scale ); - } - else { - y_scale = ( double ) getWidth() / getHeight(); - y_pos = ForesterUtil.roundToInt( y_pos / y_scale ); - } - _at = g.getTransform(); - g.scale( x_scale, y_scale ); - paintCircularLite( _phylogeny, - getStartingAngle(), - x_pos + radius_ov, - y_pos + radius_ov, - ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle() - .getWidth() ) ) ), - g ); - g.setTransform( _at ); - paintOvRectangle( g ); - } - } + g.setStroke( s ); } final private void paintPhylogenyLite( final Graphics2D g ) { - //System.out.println( getVisibleRect().x + " " + getVisibleRect().y ); - _phylogeny - .getRoot() - .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle() - .getWidth() ) ) ) ); + _phylogeny.getRoot().setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + + ( MOVE / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ) ); _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) ); - //final PhylogenyNodeIterator it; - //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { - // paintNodeLite( g, it.next() ); - //} - for( int i = 0; i < _nodes_in_preorder.length; ++i ) { - paintNodeLite( g, _nodes_in_preorder[ i ] ); + final Stroke s = g.getStroke(); + g.setStroke( STROKE_05 ); + for( final PhylogenyNode element : _nodes_in_preorder ) { + paintNodeLite( g, element ); } + g.setStroke( s ); paintOvRectangle( g ); } /** * Paint the root branch. (Differs from others because it will always be a * single horizontal line). - * @param to_graphics_file - * + * @param to_graphics_file + * * @return new x1 value */ final private void paintRootBranch( final Graphics2D g, @@ -3788,7 +3640,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final double w = PhylogenyMethods.getBranchWidthValue( root ); drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g ); } - paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) ); + paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file ); } final private void paintScale( final Graphics2D g, @@ -3808,12 +3660,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { g.setColor( getTreeColorSet().getBranchLengthColor() ); } + final Stroke s = g.getStroke(); + g.setStroke( STROKE_1 ); drawLine( x1, y1, x1, y2, g ); drawLine( x2, y1, x2, y2, g ); drawLine( x1, y3, x2, y3, g ); if ( getScaleLabel() != null ) { g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 ); } + g.setStroke( s ); } final private int paintTaxonomy( final Graphics2D g, @@ -3821,116 +3676,47 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean is_in_found_nodes, final boolean to_pdf, final boolean to_graphics_file, - final double x_shift ) { + final float x_shift ) { final Taxonomy taxonomy = node.getNodeData().getTaxonomy(); - g.setFont( getTreeFontSet().getLargeItalicFont() ); - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else if ( is_in_found_nodes ) { - g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) ); - g.setColor( getTreeColorSet().getFoundColor() ); - } - else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - g.setColor( getTaxonomyBasedColor( node ) ); - } - else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches() - && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); - } - else if ( to_pdf ) { - g.setColor( Color.BLACK ); + final boolean using_visual_font = setFont( g, node, is_in_found_nodes ); + setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() ); + float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift; + if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM + && node.isExternal() ) { + start_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift + ( 2 * TreePanel.MOVE ) + getXdistance() + + 3 ); + } + float start_y; + if ( !using_visual_font ) { + start_y = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() + / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) ); } else { - g.setColor( getTreeColorSet().getTaxonomyColor() ); + start_y = node.getYcoord() + + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) ); } - final double start_x = node.getXcoord() + 3 + _half_box_size + x_shift; - final double start_y = node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) ); _sb.setLength( 0 ); - if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) { - _sb.append( taxonomy.getTaxonomyCode() ); - _sb.append( " " ); - } - if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) { - if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) - && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { - if ( getOptions().isAbbreviateScientificTaxonNames() - && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) { - abbreviateScientificName( taxonomy.getScientificName() ); - } - else { - _sb.append( taxonomy.getScientificName() ); - } - _sb.append( " (" ); - _sb.append( taxonomy.getCommonName() ); - _sb.append( ") " ); - } - else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) { - if ( getOptions().isAbbreviateScientificTaxonNames() - && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) { - abbreviateScientificName( taxonomy.getScientificName() ); - } - else { - _sb.append( taxonomy.getScientificName() ); - } - _sb.append( " " ); - } - else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { - _sb.append( taxonomy.getCommonName() ); - _sb.append( " " ); - } - } - else if ( _control_panel.isShowTaxonomyScientificNames() ) { - if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) { - if ( getOptions().isAbbreviateScientificTaxonNames() - && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) { - abbreviateScientificName( taxonomy.getScientificName() ); - } - else { - _sb.append( taxonomy.getScientificName() ); - } - _sb.append( " " ); - } - } - else if ( _control_panel.isShowTaxonomyCommonNames() ) { - if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { - _sb.append( taxonomy.getCommonName() ); - _sb.append( " " ); - } - } - final String label = _sb.toString(); - /* GUILHEM_BEG */ - if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 ) - && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) { - // invert font color and background color to show that this is the query sequence - final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null, - false, - false ) ) - .getBounds(); - g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 ); - g.setColor( getTreeColorSet().getBackgroundColor() ); + nodeTaxonomyDataAsSB( taxonomy, _sb ); + final String label = _sb.toString(); + /* GUILHEM_BEG */ + if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 ) + && ( node.getNodeData().isHasSequence() ) + && node.getNodeData().getSequence().equals( _query_sequence ) ) { + // invert font color and background color to show that this is the query sequence + final Rectangle2D nodeTextBounds = new TextLayout( label, + g.getFont(), + new FontRenderContext( null, false, false ) ) + .getBounds(); + g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 ); + g.setColor( getTreeColorSet().getBackgroundColor() ); } /* GUILHEM_END */ TreePanel.drawString( label, start_x, start_y, g ); - if ( is_in_found_nodes ) { - return getTreeFontSet()._fm_large_italic_bold.stringWidth( label ); - } - else { - return getTreeFontSet()._fm_large_italic.stringWidth( label ); - } - } - - private void abbreviateScientificName( final String sn ) { - final String[] a = sn.split( "\\s+" ); - _sb.append( a[ 0 ].substring( 0, 1 ) ); - _sb.append( a[ 1 ].substring( 0, 2 ) ); - if ( a.length > 2 ) { - for( int i = 2; i < a.length; i++ ) { - _sb.append( " " ); - _sb.append( a[ i ] ); - } + if ( !using_visual_font && !is_in_found_nodes ) { + return getFontMetricsForLargeDefaultFont().stringWidth( label ); } + return getFontMetrics( g.getFont() ).stringWidth( label ); } final private void paintUnrooted( final PhylogenyNode n, @@ -3951,7 +3737,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee to_graphics_file, radial_labels, ( high_angle + low_angle ) / 2, - isInFoundNodes( n ) ); + isInFoundNodes( n ) || isInCurrentExternalNodes( n ) ); return; } final float num_enclosed = n.getNumberOfExternalNodes(); @@ -3990,19 +3776,19 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { length = getUrtFactor(); } - final double mid_angle = current_angle + arc_size / 2; - final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length ); - final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length ); + final double mid_angle = current_angle + ( arc_size / 2 ); + final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) ); + final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) ); desc.setXcoord( new_x ); desc.setYcoord( new_y ); paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file ); current_angle += arc_size; assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file ); drawLine( x, y, new_x, new_y, g ); - paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) ); + paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file ); } if ( n.isRoot() ) { - paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) ); + paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file ); } } @@ -4012,8 +3798,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final Graphics2D g, final float urt_ov_factor ) { if ( n.isRoot() ) { - final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / 2 ); - final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / 2 ); + final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) ); + final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) ); n.setXSecondary( x_pos ); n.setYSecondary( y_pos ); } @@ -4040,14 +3826,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { length = urt_ov_factor; } - final double mid_angle = current_angle + arc_size / 2; - final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length ); - final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length ); + final double mid_angle = current_angle + ( arc_size / 2 ); + final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) ); + final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) ); desc.setXSecondary( new_x ); desc.setYSecondary( new_y ); - if ( isInFoundNodes( desc ) ) { - g.setColor( getTreeColorSet().getFoundColor() ); - drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g ); + if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) { + g.setColor( getColorForFoundNode( desc ) ); + drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, + desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, + OVERVIEW_FOUND_NODE_BOX_SIZE, + OVERVIEW_FOUND_NODE_BOX_SIZE, + g ); g.setColor( getTreeColorSet().getOvColor() ); } paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor ); @@ -4068,7 +3858,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.ERROR_MESSAGE ); return; } - final String label = getASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() ); + final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() ); final Object[] options = { "As sibling", "As descendant", "Cancel" }; final int r = JOptionPane.showOptionDialog( this, "How to paste subtree" + label + "?", @@ -4087,7 +3877,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final Phylogeny buffer_phy = getCutOrCopiedTree().copy(); buffer_phy.setAllNodesToNotCollapse(); - buffer_phy.preOrderReId(); + PhylogenyMethods.preOrderReId( buffer_phy ); buffer_phy.setRooted( true ); boolean need_to_show_whole = false; if ( paste_as_sibling ) { @@ -4110,18 +3900,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } if ( getCopiedAndPastedNodes() == null ) { - setCopiedAndPastedNodes( new HashSet() ); + setCopiedAndPastedNodes( new HashSet() ); } final List nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy ); - final Set node_ids = new HashSet( nodes.size() ); + final Set node_ids = new HashSet( nodes.size() ); for( final PhylogenyNode n : nodes ) { node_ids.add( n.getId() ); } node_ids.add( node.getId() ); getCopiedAndPastedNodes().addAll( node_ids ); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -4131,124 +3921,50 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } - final public int print( final Graphics g, final PageFormat page_format, final int page_index ) - throws PrinterException { - if ( page_index > 0 ) { - return ( NO_SUCH_PAGE ); - } - else { - final Graphics2D g2d = ( Graphics2D ) g; - g2d.translate( page_format.getImageableX(), page_format.getImageableY() ); - // Turn off double buffering !? - paintPhylogeny( g2d, true, false, 0, 0, 0, 0 ); - // Turn double buffering back on !? - return ( PAGE_EXISTS ); - } - } - - final void recalculateMaxDistanceToRoot() { - _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() ); + private final StringBuffer propertiesToString( final PhylogenyNode node ) { + return node.getNodeData().getProperties().asText(); } - /** - * Remove all edit-node frames - */ - final void removeAllEditNodeJFrames() { - for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) { - if ( _node_frames[ i ] != null ) { - _node_frames[ i ].dispose(); - _node_frames[ i ] = null; - } + private void setColor( final Graphics2D g, + final PhylogenyNode node, + final boolean to_graphics_file, + final boolean to_pdf, + final boolean is_in_found_nodes, + final Color default_color ) { + if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.BLACK ); } - _node_frame_index = 0; - } - - /** - * Remove a node-edit frame. - */ - final void removeEditNodeFrame( final int i ) { - _node_frame_index--; - _node_frames[ i ] = null; - if ( i < _node_frame_index ) { - for( int j = 0; j < _node_frame_index - 1; j++ ) { - _node_frames[ j ] = _node_frames[ j + 1 ]; - } - _node_frames[ _node_frame_index ] = null; + else if ( is_in_found_nodes ) { + g.setColor( getColorForFoundNode( node ) ); } - } - - final void reRoot( final PhylogenyNode node ) { - if ( !getPhylogeny().isRerootable() ) { - JOptionPane.showMessageDialog( this, - "This is not rerootable", - "Not rerootable", - JOptionPane.WARNING_MESSAGE ); - return; + else if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) + && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) { + g.setColor( node.getNodeData().getNodeVisualData().getFontColor() ); } - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - JOptionPane.showMessageDialog( this, - "Cannot reroot in unrooted display type", - "Attempt to reroot tree in unrooted display", - JOptionPane.WARNING_MESSAGE ); - return; + else if ( getControlPanel().isColorAccordingToSequence() ) { + g.setColor( getSequenceBasedColor( node ) ); } - getPhylogeny().reRoot( node ); - getPhylogeny().recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - _nodes_in_preorder = null; - resetPreferredSize(); - getMainPanel().adjustJScrollPane(); - repaint(); - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { - getControlPanel().showWhole(); + else if ( getControlPanel().isColorAccordingToTaxonomy() ) { + g.setColor( getTaxonomyBasedColor( node ) ); } - } - - final void resetNodeIdToDistToLeafMap() { - _nodeid_dist_to_leaf = new HashMap(); - } - - final void resetPreferredSize() { - if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) { - return; + else if ( getControlPanel().isColorAccordingToAnnotation() + && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) + && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) { + g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) ); } - int x = 0; - int y = 0; - y = TreePanel.MOVE - + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 ); - if ( getControlPanel().isDrawPhylogram() ) { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil - .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() ); + else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles() + && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { + g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); + } + else if ( to_pdf ) { + g.setColor( Color.BLACK ); } else { - if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil.roundToInt( getXdistance() - * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); - } - else { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil.roundToInt( getXdistance() - * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); - } + g.setColor( default_color ); } - setPreferredSize( new Dimension( x, y ) ); - } - - public final void setArrowCursor() { - setCursor( ARROW_CURSOR ); - repaint(); - } - - final void setControlPanel( final ControlPanel atv_control ) { - _control_panel = atv_control; } - final private void setCopiedAndPastedNodes( final Set nodeIds ) { + final private void setCopiedAndPastedNodes( final Set nodeIds ) { getMainPanel().setCopiedAndPastedNodes( nodeIds ); } @@ -4256,42 +3972,25 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getMainPanel().setCutOrCopiedTree( cut_or_copied_tree ); } - public final void setEdited( final boolean edited ) { - _edited = edited; - } - - final void setFoundNodes( final Set found_nodes ) { - _found_nodes = found_nodes; + private boolean setFont( final Graphics2D g, final PhylogenyNode node, final boolean is_in_found_nodes ) { + Font visual_font = null; + if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) { + visual_font = node.getNodeData().getNodeVisualData().getFont(); + g.setFont( visual_font != null ? visual_font : getTreeFontSet().getLargeFont() ); + } + else { + g.setFont( getTreeFontSet().getLargeFont() ); + } + if ( is_in_found_nodes ) { + g.setFont( g.getFont().deriveFont( Font.BOLD ) ); + } + return visual_font != null; } final private void setInOv( final boolean in_ov ) { _in_ov = in_ov; } - final void setInOvRect( final boolean in_ov_rect ) { - _in_ov_rect = in_ov_rect; - } - - final void setLargeFonts() { - getTreeFontSet().largeFonts(); - } - - final void setLastMouseDragPointX( final float x ) { - _last_drag_point_x = x; - } - - final void setLastMouseDragPointY( final float y ) { - _last_drag_point_y = y; - } - - final void setLongestExtNodeInfo( final int i ) { - _longest_ext_node_info = i; - } - - final void setMediumFonts() { - getTreeFontSet().mediumFonts(); - } - final private void setOvMaxHeight( final float ov_max_height ) { _ov_max_height = ov_max_height; } @@ -4300,10 +3999,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _ov_max_width = ov_max_width; } - final void setOvOn( final boolean ov_on ) { - _ov_on = ov_on; - } - final private void setOvXcorrectionFactor( final float f ) { _ov_x_correction_factor = f; } @@ -4328,72 +4023,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _ov_y_start = ov_y_start; } - /** - * Set parameters for printing the displayed tree - * - * @param x - * @param y - */ - final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) { - // updateStyle(); not needed? - if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { - initNodeData(); - if ( recalc_longest_ext_node_info ) { - calculateLongestExtNodeInfo(); - } - int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes(); - final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); - if ( ext_nodes == 1 ) { - ext_nodes = max_depth; - if ( ext_nodes < 1 ) { - ext_nodes = 1; - } - } - updateOvSizes(); - float xdist = 0; - float ov_xdist = 0; - if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { - xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) ); - ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) ); - } - else { - xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) ); - ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) ); - } - float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) ); - if ( xdist < 0.0 ) { - xdist = 0.0f; - } - if ( ov_xdist < 0.0 ) { - ov_xdist = 0.0f; - } - if ( ydist < 0.0 ) { - ydist = 0.0f; - } - setXdistance( xdist ); - setYdistance( ydist ); - setOvXDistance( ov_xdist ); - final double height = _phylogeny.getHeight(); - if ( height > 0 ) { - final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height ); - setXcorrectionFactor( corr > 0 ? corr : 0 ); - final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height ); - setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); - } - else { - setXcorrectionFactor( 0 ); - setOvXcorrectionFactor( 0 ); - } - _circ_max_depth = max_depth; - setUpUrtFactor(); - } - } - - final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) { - _graphics_type = graphics_type; - setTextAntialias(); - } - final private void setScaleDistance( final double scale_distance ) { _scale_distance = scale_distance; } @@ -4402,67 +4031,33 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _scale_label = scale_label; } - final void setSmallFonts() { - getTreeFontSet().smallFonts(); - } - - final void setStartingAngle( final double starting_angle ) { - _urt_starting_angle = starting_angle; - } - - final void setSuperTinyFonts() { - getTreeFontSet().superTinyFonts(); - } - - final void setTextAntialias() { - if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { - if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) { - _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY ); - } - else { - _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED ); - } + private final void setupStroke( final Graphics2D g ) { + if ( getYdistance() < 0.0001 ) { + g.setStroke( STROKE_0025 ); } - if ( getMainPanel().getOptions().isAntialiasScreen() ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) { - _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); - } - else { - _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON ); - } - try { - _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, - RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB ); - } - catch ( final Throwable e ) { - _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON ); - } + if ( getYdistance() < 0.001 ) { + g.setStroke( STROKE_005 ); + } + else if ( getYdistance() < 0.01 ) { + g.setStroke( STROKE_01 ); + } + else if ( getYdistance() < 0.5 ) { + g.setStroke( STROKE_025 ); + } + else if ( getYdistance() < 1 ) { + g.setStroke( STROKE_05 ); + } + else if ( getYdistance() < 2 ) { + g.setStroke( STROKE_075 ); + } + else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) { + g.setStroke( STROKE_1 ); } else { - _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF ); - _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); + g.setStroke( STROKE_2 ); } } - final void setTinyFonts() { - getTreeFontSet().tinyFonts(); - } - - /** - * Set a phylogeny tree. - * - * @param t - * an instance of a Phylogeny - */ - public final void setTree( final Phylogeny t ) { - _nodes_in_preorder = null; - _phylogeny = t; - } - - final void setTreeFile( final File treefile ) { - _treefile = treefile; - } - final private void setUpUrtFactor() { final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width : getVisibleRect().height; @@ -4489,28 +4084,222 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _urt_factor_ov = urt_factor_ov; } - public final void setWaitCursor() { - setCursor( WAIT_CURSOR ); - repaint(); - } - - final void setXcorrectionFactor( final float f ) { - _x_correction_factor = f; - } - - final void setXdistance( final float x ) { - _x_distance = x; - } - - final void setYdistance( final float y ) { - _y_distance = y; + private void showExtDescNodeData( final PhylogenyNode node, final char separator ) { + final List data = new ArrayList(); + final List nodes = node.getAllExternalDescendants(); + if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { + for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) { + if ( !nodes.contains( n ) ) { + nodes.add( n ); + } + } + } + for( final PhylogenyNode n : nodes ) { + switch ( getOptions().getExtDescNodeDataToReturn() ) { + case NODE_NAME: + if ( !ForesterUtil.isEmpty( n.getName() ) ) { + data.add( n.getName() ); + } + break; + case SEQUENCE_NAME: + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { + data.add( n.getNodeData().getSequence().getName() ); + } + break; + case GENE_NAME: + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { + data.add( n.getNodeData().getSequence().getGeneName() ); + } + break; + case SEQUENCE_SYMBOL: + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { + data.add( n.getNodeData().getSequence().getSymbol() ); + } + break; + case SEQUENCE_MOL_SEQ_FASTA: + final StringBuilder sb = new StringBuilder(); + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { + final StringBuilder ann = new StringBuilder(); + if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( n.getName() ) ) { + ann.append( n.getName() ); + ann.append( separator ); + } + if ( n.getNodeData().isHasTaxonomy() ) { + if ( getControlPanel().isShowTaxonomyCode() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() ); + ann.append( separator ); + } + if ( getControlPanel().isShowTaxonomyScientificNames() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { + ann.append( n.getNodeData().getTaxonomy().getScientificName() ); + ann.append( separator ); + } + if ( getControlPanel().isShowTaxonomyCommonNames() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) { + ann.append( n.getNodeData().getTaxonomy().getCommonName() ); + ann.append( separator ); + } + } + if ( getControlPanel().isShowSeqSymbols() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { + ann.append( n.getNodeData().getSequence().getSymbol() ); + ann.append( separator ); + } + if ( getControlPanel().isShowSeqNames() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { + ann.append( n.getNodeData().getSequence().getName() ); + ann.append( separator ); + } + if ( getControlPanel().isShowGeneNames() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { + ann.append( n.getNodeData().getSequence().getGeneName() ); + ann.append( separator ); + } + if ( getControlPanel().isShowSequenceAcc() + && n.getNodeData().getSequence().getAccession() != null ) { + ann.append( n.getNodeData().getSequence().getAccession().asText() ); + ann.append( separator ); + } + + final String ann_str; + if ( ann.length() > 0 && ann.charAt( ann.length() - 1 ) == separator ) { + ann_str = ann.substring( 0, ann.length() - 1 ); + } + else { + ann_str = ann.toString(); + } + sb.append( SequenceWriter.toFasta( ann_str, + n.getNodeData().getSequence().getMolecularSequence(), + 60 ) ); + data.add( sb.toString() ); + } + break; + case SEQUENCE_ACC: + if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null ) + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) { + data.add( n.getNodeData().getSequence().getAccession().toString() ); + } + break; + case TAXONOMY_SCIENTIFIC_NAME: + if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { + data.add( n.getNodeData().getTaxonomy().getScientificName() ); + } + break; + case TAXONOMY_CODE: + if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() ); + } + break; + case DOMAINS_ALL: + case DOMAINS_COLLAPSED_PER_PROTEIN: + if ( n.getNodeData().isHasSequence() + && ( n.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + final DomainArchitecture da = n.getNodeData().getSequence().getDomainArchitecture(); + final Set s = new HashSet(); + for( int i = 0; i < da.getDomains().size(); ++i ) { + final ProteinDomain d = da.getDomain( i ); + if ( d.getConfidence() <= Math.pow( 10, getDomainStructureEvalueThresholdExp() ) ) { + final String name = d.getName(); + if ( !( s.contains( name ) ) ) { + data.add( name ); + if ( getOptions() + .getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) { + s.add( name ); + } + } + } + } + } + break; + case SEQ_ANNOTATIONS: + if ( n.getNodeData().isHasSequence() ) { + if ( n.getNodeData().isHasSequence() + && ( n.getNodeData().getSequence().getAnnotations() != null ) ) { + final SortedSet a = n.getNodeData().getSequence().getAnnotations(); + for( int i = 0; i < a.size(); ++i ) { + data.add( n.getNodeData().getSequence().getAnnotation( i ).toString() ); + } + } + } + break; + case GO_TERM_IDS: + if ( n.getNodeData().isHasSequence() ) { + if ( n.getNodeData().isHasSequence() + && ( n.getNodeData().getSequence().getAnnotations() != null ) ) { + final SortedSet a = n.getNodeData().getSequence().getAnnotations(); + for( int i = 0; i < a.size(); ++i ) { + final Annotation ann = n.getNodeData().getSequence().getAnnotation( i ); + final String ref = ann.getRef(); + if ( ref.toUpperCase().startsWith( "GO:" ) ) { + data.add( ref ); + } + } + } + } + break; + case UNKNOWN: + TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data ); + break; + default: + throw new IllegalArgumentException( "unknown data element: " + + getOptions().getExtDescNodeDataToReturn() ); + } + } // for loop + final StringBuilder sb = new StringBuilder(); + final int size = TreePanelUtil.nodeDataIntoStringBuffer( data, getOptions(), sb ); + if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) + || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) { + if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { + System.out.println( sb ); + } + if ( sb.length() < 1 ) { + clearCurrentExternalNodesDataBuffer(); + } + else { + setCurrentExternalNodesDataBuffer( sb ); + } + } + else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { + if ( sb.length() < 1 ) { + TreePanelUtil.showInformationMessage( this, + "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")", + "Descendants of selected node do not contain selected data" ); + clearCurrentExternalNodesDataBuffer(); + } + else { + setCurrentExternalNodesDataBuffer( sb ); + String title; + if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) { + title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data" + : obtainTitleForExtDescNodeData() ) + " for " + data.size() + " nodes, unique entries: " + + size; + } + else { + title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data" + : obtainTitleForExtDescNodeData() ) + " for " + data.size() + "/" + + node.getNumberOfExternalNodes() + " external descendats of node " + node + + ", unique entries: " + size; + } + final String s = sb.toString().trim(); + getMainPanel().getMainFrame().showTextFrame( s, title ); + } + } } final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) { try { if ( ( node.getName().length() > 0 ) - || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) - || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) + || ( node.getNodeData().isHasTaxonomy() + && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) + || ( node.getNodeData().isHasSequence() + && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) { _popup_buffer.setLength( 0 ); @@ -4519,7 +4308,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee lines++; _popup_buffer.append( node.getName() ); } - if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) { + if ( node.getNodeData().isHasTaxonomy() + && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) { lines++; boolean enc_data = false; final Taxonomy tax = node.getNodeData().getTaxonomy(); @@ -4591,7 +4381,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _popup_buffer.append( "]" ); } if ( !enc_data ) { - if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) { + if ( ( tax.getIdentifier() != null ) + && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) { if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) { _popup_buffer.append( "[" ); _popup_buffer.append( tax.getIdentifier().getProvider() ); @@ -4601,7 +4392,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } } - if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) { + if ( node.getNodeData().isHasSequence() + && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) { lines++; boolean enc_data = false; if ( _popup_buffer.length() > 0 ) { @@ -4629,6 +4421,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _popup_buffer.append( "]" ); enc_data = true; } + if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) { + if ( enc_data ) { + _popup_buffer.append( " [" ); + } + else { + _popup_buffer.append( "[" ); + } + _popup_buffer.append( seq.getGeneName() ); + _popup_buffer.append( "]" ); + enc_data = true; + } if ( !ForesterUtil.isEmpty( seq.getName() ) ) { if ( enc_data ) { _popup_buffer.append( " " ); @@ -4662,22 +4465,38 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _popup_buffer.append( confidence.getType() ); _popup_buffer.append( "] " ); } - _popup_buffer - .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), - getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + _popup_buffer.append( " (sd=" ); + _popup_buffer.append( FORMATTER_CONFIDENCE + .format( ForesterUtil.round( confidence.getStandardDeviation(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + _popup_buffer.append( ")" ); + } + } + } + if ( node.getNodeData().isHasProperties() ) { + if ( _popup_buffer.length() > 0 ) { + _popup_buffer.append( "\n" ); } + _popup_buffer.append( node.getNodeData().getProperties().asText() ); } if ( _popup_buffer.length() > 0 ) { if ( !getConfiguration().isUseNativeUI() ) { _rollover_popup .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) ); _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() ); - if ( isInFoundNodes( node ) ) { - _rollover_popup.setForeground( getTreeColorSet().getFoundColor() ); + if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) { + _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() ); } - else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - _rollover_popup.setForeground( getTaxonomyBasedColor( node ) ); + else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) { + _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() ); + } + else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) { + _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() ); } else { _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() ); @@ -4687,11 +4506,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) ); } _rollover_popup.setText( _popup_buffer.toString() ); - _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null, - _rollover_popup, - e.getLocationOnScreen().x + 10, - e.getLocationOnScreen().y - - ( lines * 20 ) ); + _node_desc_popup = PopupFactory.getSharedInstance() + .getPopup( null, + _rollover_popup, + e.getLocationOnScreen().x + 10, + e.getLocationOnScreen().y - ( lines * 20 ) ); _node_desc_popup.show(); } } @@ -4701,26 +4520,1627 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final private void showNodeEditFrame( final PhylogenyNode n ) { - if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) { - // pop up edit box for single node - _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" ); - _node_frame_index++; + final private void showNodeEditFrame( final PhylogenyNode n ) { + if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) { + // pop up edit box for single node + _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" ); + _node_frame_index++; + } + else { + JOptionPane.showMessageDialog( this, "too many node windows are open" ); + } + } + + final private void showNodeFrame( final PhylogenyNode n ) { + if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) { + // pop up edit box for single node + _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index ); + _node_frame_index++; + } + else { + JOptionPane.showMessageDialog( this, "too many node windows are open" ); + } + } + + final private void switchDisplaygetPhylogenyGraphicsType() { + switch ( getPhylogenyGraphicsType() ) { + case RECTANGULAR: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); + break; + case EURO_STYLE: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); + break; + case ROUNDED: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); + break; + case CURVED: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); + break; + case TRIANGULAR: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); + break; + case CONVEX: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + break; + case UNROOTED: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); + break; + case CIRCULAR: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + break; + default: + throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() ); + } + if ( getControlPanel().getDynamicallyHideData() != null ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + getControlPanel().getDynamicallyHideData().setEnabled( false ); + } + else { + getControlPanel().getDynamicallyHideData().setEnabled( true ); + } + } + if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + getControlPanel().setDrawPhylogramEnabled( true ); + } + else { + getControlPanel().setDrawPhylogramEnabled( false ); + } + getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); + } + + final void calcMaxDepth() { + if ( _phylogeny != null ) { + _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + } + } + + /** + * Set parameters for printing the displayed tree + * + */ + final void calcParametersForPainting( final int x, final int y ) { + // updateStyle(); not needed? + if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { + initNodeData(); + calculateLongestExtNodeInfo(); + if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) ) + && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { + while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) + && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) { + getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), true ); + calculateLongestExtNodeInfo(); + } + } + else { + while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) ) && ( getTreeFontSet().getLargeFont() + .getSize() <= ( getTreeFontSet().getLargeFontMemory().getSize() + - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { + getMainPanel().getTreeFontSet().increaseFontSize(); + calculateLongestExtNodeInfo(); + } + } + //_length_of_longest_text = calcLengthOfLongestText(); + int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes(); + final int max_depth = PhylogenyMethods.calculateMaxDepthConsiderCollapsed( _phylogeny ) + 1; + if ( ext_nodes == 1 ) { + ext_nodes = max_depth; + if ( ext_nodes < 1 ) { + ext_nodes = 1; + } + } + updateOvSizes(); + float xdist = 0; + float ov_xdist = 0; + if ( !isNonLinedUpCladogram() ) { + xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) ); + ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) ); + } + else { + xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) ); + ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) ); + } + float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) ); + if ( xdist < 0.0 ) { + xdist = 0.0f; + } + if ( ov_xdist < 0.0 ) { + ov_xdist = 0.0f; + } + if ( ydist < 0.0 ) { + ydist = 0.0f; + } + setXdistance( xdist ); + setYdistance( ydist ); + setOvXDistance( ov_xdist ); + final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() ); + //final double height = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + if ( height > 0 ) { + final float corr = ( float ) ( ( x - ( 2.0 * TreePanel.MOVE ) - getLongestExtNodeInfo() + - getXdistance() ) / height ); + setXcorrectionFactor( corr > 0 ? corr : 0 ); + final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height ); + setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); + } + else { + setXcorrectionFactor( 0 ); + setOvXcorrectionFactor( 0 ); + } + _circ_max_depth = max_depth; + setUpUrtFactor(); + // + if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + // int dynamic_hiding_factor = calcDynamicHidingFactor(); + // if ( dynamic_hiding_factor > 1 ) { + // while ( dynamic_hiding_factor > 1 + // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) { + // getTreeFontSet().decreaseFontSize( 1, true ); + // dynamic_hiding_factor = calcDynamicHidingFactor(); + // } + // } + // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) { + // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) { + // getTreeFontSet().increaseFontSize(); + // dynamic_hiding_factor = calcDynamicHidingFactor(); + // } + // } + } + // + } + } + + final void calculateLongestExtNodeInfo() { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return; + } + int max_possible_length = ForesterUtil + .roundToInt( ( getSize().getWidth() - ( 2 * MOVE ) ) * AptxConstants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); + if ( max_possible_length < 20 ) { + max_possible_length = 20; + } + int longest = 30; + int longest_txt = 0; + _longest_domain = 0; + PhylogenyNode longest_txt_node = _phylogeny.getFirstExternalNode(); + for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { + int sum = 0; + if ( node.isCollapse() ) { + continue; + } + final StringBuilder sb = new StringBuilder(); + nodeDataAsSB( node, sb ); + if ( node.getNodeData().isHasTaxonomy() ) { + nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb ); + } + final int txt = sb.length(); + if ( txt > longest_txt ) { + longest_txt = txt; + longest_txt_node = node; + } + boolean use_vis = false; + final Graphics2D g = ( Graphics2D ) getGraphics(); + if ( g != null && getControlPanel().isUseVisualStyles() ) { + use_vis = setFont( g, node, false ); + } + if ( !use_vis ) { + sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() ); + } + else { + sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() ); + } + if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { + sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters() + .getGainedCharactersAsStringBuffer().toString() ); + } + if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) + && ( node.getNodeData().getVector().size() > 0 ) ) { + if ( getConfiguration() != null ) { + sum += getConfiguration().getVectorDataWidth() + 10; + } + else { + sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10; + } + } + if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + // FIXME + // TODO this might need some clean up + final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture(); + sum += ( ( _domain_structure_width + / ( ( RenderableDomainArchitecture ) d ).getOriginalSize().getWidth() ) * d.getTotalLength() ) + + 10; + if ( d.getTotalLength() > _longest_domain ) { + _longest_domain = d.getTotalLength(); + } + } + if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) + && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { + // FIXME + sum += RenderableMsaSequence.DEFAULT_WIDTH + 30; + } + if ( sum >= max_possible_length ) { + _longest_ext_node_info = max_possible_length; + // return; //FIXME why? + } + if ( sum > longest ) { + longest = sum; + } + } + _ext_node_with_longest_txt_info = longest_txt_node; + if ( longest >= max_possible_length ) { + _longest_ext_node_info = max_possible_length; + } + else { + _longest_ext_node_info = longest; + } + _length_of_longest_text = calcLengthOfLongestText(); + } + + final void calculateScaleDistance() { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return; + } + final double height = getMaxDistanceToRoot(); + if ( height > 0 ) { + if ( ( height <= 0.5 ) ) { + setScaleDistance( 0.01 ); + } + else if ( height <= 5.0 ) { + setScaleDistance( 0.1 ); + } + else if ( height <= 50.0 ) { + setScaleDistance( 1 ); + } + else if ( height <= 500.0 ) { + setScaleDistance( 10 ); + } + else { + setScaleDistance( 100 ); + } + } + else { + setScaleDistance( 0.0 ); + } + String scale_label = String.valueOf( getScaleDistance() ); + if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) { + scale_label += " [" + _phylogeny.getDistanceUnit() + "]"; + } + setScaleLabel( scale_label ); + } + + final Color calculateSequenceBasedColor( final Sequence seq ) { + if ( ForesterUtil.isEmpty( seq.getName() ) ) { + return getTreeColorSet().getSequenceColor(); + } + Color c = null; + final String seq_name = seq.getName(); + c = getControlPanel().getSequenceColors().get( seq_name ); + if ( c == null ) { + c = AptxUtil.calculateColorFromString( seq_name, false ); + getControlPanel().getSequenceColors().put( seq_name, c ); + } + return c; + } + + final Color calculateTaxonomyBasedColor( final Taxonomy tax ) { + if ( getOptions().isColorByTaxonomicGroup() ) { + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + boolean ex = false; + String group = null; + try { + group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() ); + } + catch ( final Exception e ) { + ex = true; + } + if ( !ex && !ForesterUtil.isEmpty( group ) ) { + final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group ); + if ( c != null ) { + return c; + } + } + } + return getTreeColorSet().getTaxonomyColor(); + } + else { + if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) { + return getTreeColorSet().getTaxonomyColor(); + } + Color c = null; + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() ); + } + if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) { + c = getControlPanel().getSpeciesColors().get( tax.getScientificName() ); + } + if ( c == null ) { + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true ); + getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c ); + } + else { + c = AptxUtil.calculateColorFromString( tax.getScientificName(), true ); + getControlPanel().getSpeciesColors().put( tax.getScientificName(), c ); + } + } + return c; + } + } + + void clearCurrentExternalNodesDataBuffer() { + setCurrentExternalNodesDataBuffer( new StringBuilder() ); + } + + /** + * Collapse the tree from the given node + * + * @param node + * a PhylogenyNode + */ + final void collapse( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + JOptionPane.showMessageDialog( this, + "Cannot collapse in unrooted display type", + "Attempt to collapse in unrooted display", + JOptionPane.WARNING_MESSAGE ); + return; + } + if ( !node.isExternal() && !node.isRoot() ) { + final boolean collapse = !node.isCollapse(); + TreePanelUtil.collapseSubtree( node, collapse ); + updateSetOfCollapsedExternalNodes(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + calculateLongestExtNodeInfo(); + setNodeInPreorderToNull(); + _control_panel.displayedPhylogenyMightHaveChanged( true ); + resetPreferredSize(); + updateOvSizes(); + _main_panel.adjustJScrollPane(); + repaint(); + } + } + + final void uncollapseAll( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + JOptionPane.showMessageDialog( this, + "Cannot uncollapse in unrooted display type", + "Attempt to uncollapse in unrooted display", + JOptionPane.WARNING_MESSAGE ); + return; + } + if ( !node.isExternal() ) { + TreePanelUtil.uncollapseSubtree( node ); + updateSetOfCollapsedExternalNodes(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + calculateLongestExtNodeInfo(); + setNodeInPreorderToNull(); + _control_panel.displayedPhylogenyMightHaveChanged( true ); + resetPreferredSize(); + updateOvSizes(); + _main_panel.adjustJScrollPane(); + repaint(); + } + } + + final void collapseSpeciesSpecificSubtrees() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; + } + setWaitCursor(); + TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny ); + updateSetOfCollapsedExternalNodes(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + calculateLongestExtNodeInfo(); + setNodeInPreorderToNull(); + resetPreferredSize(); + resetDepthCollapseDepthValue(); + resetRankCollapseRankValue(); + _main_panel.adjustJScrollPane(); + getControlPanel().showWhole(); + setArrowCursor(); + } + + final void colorRank( final String rank ) { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; + } + setWaitCursor(); + AptxUtil.removeBranchColors( _phylogeny ); + final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this ); + if ( colorizations > 0 ) { + _control_panel.setColorBranches( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); + } + if ( _control_panel.getColorAccSpeciesCb() != null ) { + _control_panel.getColorAccSpeciesCb().setSelected( false ); + } + _options.setColorLabelsSameAsParentBranch( true ); + if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) { + getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true ); + } + _control_panel.repaint(); + } + setArrowCursor(); + repaint(); + if ( colorizations > 0 ) { + String msg = "Taxonomy colorization via " + rank + " completed:\n"; + if ( colorizations > 1 ) { + msg += "colorized " + colorizations + " subtrees"; + } + else { + msg += "colorized one subtree"; + } + setEdited( true ); + JOptionPane.showMessageDialog( this, + msg, + "Taxonomy Rank-Colorization Completed (" + rank + ")", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + String msg = "Could not taxonomy rank-colorize any subtree via " + rank + ".\n"; + msg += "Possible solutions (given that suitable taxonomic information is present):\n"; + msg += "select a different rank (e.g. phylum, genus, ...)\n"; + msg += " and/or\n"; + msg += "execute:\n"; + msg += "1. \"" + MainFrame.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n"; + msg += "2. \"" + MainFrame.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)"; + JOptionPane.showMessageDialog( this, + msg, + "Taxonomy Rank-Colorization Failed", + JOptionPane.WARNING_MESSAGE ); + } + } + + final void confColor() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; + } + setWaitCursor(); + AptxUtil.removeBranchColors( _phylogeny ); + TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); + _control_panel.setColorBranches( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); + } + setArrowCursor(); + repaint(); + } + + final void decreaseDomainStructureEvalueThresholdExp() { + if ( _domain_structure_e_value_thr_exp > -20 ) { + _domain_structure_e_value_thr_exp -= 1; + } + } + + /** + * Find the node, if any, at the given location + * + * @param x + * @param y + * @return pointer to the node at x,y, null if not found + */ + public final PhylogenyNode findNode( final int x, final int y ) { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return null; + } + final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE; + for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) ) + && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x ) + && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x ) + && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y ) + && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) { + return node; + } + } + return null; + } + + final Configuration getConfiguration() { + return _configuration; + } + + final ControlPanel getControlPanel() { + return _control_panel; + } + + String getCurrentExternalNodesDataBufferAsString() { + return _current_external_nodes_data_buffer.toString(); + } + + int getCurrentExternalNodesDataBufferChangeCounter() { + return _current_external_nodes_data_buffer_change_counter; + } + + final int getDomainStructureEvalueThresholdExp() { + return _domain_structure_e_value_thr_exp; + } + + public final Set getFoundNodes0() { + return _found_nodes_0; + } + + public final Set getFoundNodes1() { + return _found_nodes_1; + } + + public List getFoundNodesAsListOfPhylogenyNodes() { + final List additional_nodes = new ArrayList(); + if ( getFoundNodes0() != null ) { + for( final Long id : getFoundNodes0() ) { + final PhylogenyNode n = _phylogeny.getNode( id ); + if ( n != null ) { + additional_nodes.add( n ); + } + } + } + if ( getFoundNodes1() != null ) { + for( final Long id : getFoundNodes1() ) { + if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) { + final PhylogenyNode n = _phylogeny.getNode( id ); + if ( n != null ) { + additional_nodes.add( n ); + } + } + } + } + return additional_nodes; + } + + final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) { + if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { + return ( PhylogenyMethods.getBranchColorValue( node ) ); + } + else { + return ( getTreeColorSet().getBranchColor() ); + } + } + + final int getLongestExtNodeInfo() { + return _longest_ext_node_info; + } + + final Options getOptions() { + if ( _options == null ) { + _options = getControlPanel().getOptions(); + } + return _options; + } + + final Rectangle2D getOvRectangle() { + return _ov_rectangle; + } + + final Rectangle getOvVirtualRectangle() { + return _ov_virtual_rectangle; + } + + final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { + return _graphics_type; + } + + final Color getSequenceBasedColor( final PhylogenyNode node ) { + if ( node.getNodeData().isHasSequence() ) { + return calculateSequenceBasedColor( node.getNodeData().getSequence() ); + } + // return non-colorized color + return getTreeColorSet().getSequenceColor(); + } + + final double getStartingAngle() { + return _urt_starting_angle; + } + + DescriptiveStatistics getStatisticsForExpressionValues() { + return _statistics_for_vector_data; + } + + final Color getTaxonomyBasedColor( final PhylogenyNode node ) { + if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) { + return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() ); + } + // return non-colorized color + return getTreeColorSet().getTaxonomyColor(); + } + + public final File getTreeFile() { + return _treefile; + } + + final float getXcorrectionFactor() { + return _x_correction_factor; + } + + final float getXdistance() { + return _x_distance; + } + + final float getYdistance() { + return _y_distance; + } + + final void increaseDomainStructureEvalueThresholdExp() { + if ( _domain_structure_e_value_thr_exp < 3 ) { + _domain_structure_e_value_thr_exp += 1; + } + } + + final void initNodeData() { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return; + } + double _max_original_domain_structure_width = 0.0; + for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { + if ( node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + RenderableDomainArchitecture rds = null; + if ( !( node.getNodeData().getSequence() + .getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { + if ( SPECIAL_DOMAIN_COLORING ) { + rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() + .getDomainArchitecture(), node.getName() ); + } + else { + rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() + .getDomainArchitecture() ); + } + node.getNodeData().getSequence().setDomainArchitecture( rds ); + } + else { + rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); + } + if ( getControlPanel().isShowDomainArchitectures() ) { + final double dsw = rds.getOriginalSize().getWidth(); + if ( dsw > _max_original_domain_structure_width ) { + _max_original_domain_structure_width = dsw; + } + } + } + } + if ( getControlPanel().isShowDomainArchitectures() ) { + final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width ); + for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { + if ( node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData() + .getSequence().getDomainArchitecture(); + rds.setRenderingFactorWidth( ds_factor_width ); + rds.setParameter( _domain_structure_e_value_thr_exp ); + } + } + } + } + + final boolean inOv( final MouseEvent e ) { + return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) ) + && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) ) + && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) + && ( e.getY() < ( ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) ); + } + + final boolean inOvRectangle( final MouseEvent e ) { + return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) ) + && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) ) + && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) + && ( e.getY() <= ( getOvRectangle().getY() + getOvRectangle().getHeight() + 1 ) ) ); + } + + final boolean isCanCollapse() { + return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + } + + final boolean isCanUncollapseAll( final PhylogenyNode node ) { + if ( node.isExternal() || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) { + return false; + } + if ( node.isCollapse() ) { + return true; + } + final PhylogenyNodeIterator it = new PreorderTreeIterator( node ); + while ( it.hasNext() ) { + if ( it.next().isCollapse() ) { + return true; + } + } + return false; + } + + final boolean isCanColorSubtree() { + return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + } + + final boolean isCanCopy() { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); + } + + final boolean isCanCut( final PhylogenyNode node ) { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() + && !node.isRoot() ); + } + + final boolean isCanDelete() { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); + } + + final boolean isCanPaste() { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() + && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() ); + } + + final boolean isCanReroot() { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) ); + } + + final boolean isCanSubtree( final PhylogenyNode node ) { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() + && ( !node.isRoot() || ( _subtree_index > 0 ) ) ); + } + + final boolean isCurrentTreeIsSubtree() { + return ( _subtree_index > 0 ); + } + + final boolean isEdited() { + return _edited; + } + + final boolean isInOvRect() { + return _in_ov_rect; + } + + final boolean isOvOn() { + return _ov_on; + } + + final boolean isPhyHasBranchLengths() { + return _phy_has_branch_lengths; + } + + final void midpointRoot() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; + } + if ( !_phylogeny.isRerootable() ) { + JOptionPane.showMessageDialog( this, + "This is not rerootable", + "Not rerootable", + JOptionPane.WARNING_MESSAGE ); + return; + } + setNodeInPreorderToNull(); + setWaitCursor(); + PhylogenyMethods.midpointRoot( _phylogeny ); + resetNodeIdToDistToLeafMap(); + setArrowCursor(); + setEdited( true ); + repaint(); + } + + final void mouseClicked( final MouseEvent e ) { + if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) { + final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth(); + final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight(); + double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) ) + * w_ratio; + double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) ) + * h_ratio; + if ( x < 0 ) { + x = 0; + } + if ( y < 0 ) { + y = 0; + } + final double max_x = getWidth() - getVisibleRect().width; + final double max_y = getHeight() - getVisibleRect().height; + if ( x > max_x ) { + x = max_x; + } + if ( y > max_y ) { + y = max_y; + } + getMainPanel().getCurrentScrollPane().getViewport() + .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); + setInOvRect( true ); + repaint(); + } + else { + final PhylogenyNode node = findNode( e.getX(), e.getY() ); + if ( node != null ) { + if ( !node.isRoot() && node.getParent().isCollapse() ) { + return; + } + _highlight_node = node; + // Check if shift key is down + if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) { + // Yes, so add to _found_nodes + if ( getFoundNodes0() == null ) { + setFoundNodes0( new HashSet() ); + } + getFoundNodes0().add( node.getId() ); + // Check if control key is down + } + else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) { + // Yes, so pop-up menu + displayNodePopupMenu( node, e.getX(), e.getY() ); + // Handle unadorned click + } + else { + // Check for right mouse button + if ( e.getModifiers() == 4 ) { + displayNodePopupMenu( node, e.getX(), e.getY() ); + } + else { + // if not in _found_nodes, clear _found_nodes + handleClickToAction( _control_panel.getActionWhenNodeClicked(), node ); + } + } + } + else { + // no node was clicked so partition tree instead + _highlight_node = null; + + _clicked_x = e.getX(); + if (!getPhylogeny().isEmpty()) { + // should be calculated on each partition as the tree can theoretically + // change in the meantime + PhylogenyNode furthestNode = PhylogenyMethods.calculateNodeWithMaxDistanceToRoot( _phylogeny ); + _furthest_node_x = furthestNode.getXcoord(); + _root_x = _phylogeny.getRoot().getXcoord(); + + // don't bother if 0 distance tree or clicked x lies outside of tree + if (_furthest_node_x != _root_x && !(_clicked_x < _root_x || _clicked_x > _furthest_node_x)) + { + _partition_tree = true; + + } + + + } + } + } + repaint(); + } + + final void mouseDragInBrowserPanel( final MouseEvent e ) { + setCursor( MOVE_CURSOR ); + final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); + scroll_position.x -= ( e.getX() - getLastDragPointX() ); + scroll_position.y -= ( e.getY() - getLastDragPointY() ); + if ( scroll_position.x < 0 ) { + scroll_position.x = 0; + } + else { + final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); + if ( scroll_position.x > max_x ) { + scroll_position.x = max_x; + } + } + if ( scroll_position.y < 0 ) { + scroll_position.y = 0; + } + else { + final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); + if ( scroll_position.y > max_y ) { + scroll_position.y = max_y; + } + } + if ( isOvOn() || getOptions().isShowScale() ) { + repaint(); + } + getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); + } + + final void mouseDragInOvRectangle( final MouseEvent e ) { + setCursor( HAND_CURSOR ); + final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth(); + final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight(); + final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); + double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) ); + double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) ); + scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx ); + scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy ); + if ( scroll_position.x <= 0 ) { + scroll_position.x = 0; + dx = 0; + } + else { + final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); + if ( scroll_position.x >= max_x ) { + dx = 0; + scroll_position.x = max_x; + } + } + if ( scroll_position.y <= 0 ) { + dy = 0; + scroll_position.y = 0; + } + else { + final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); + if ( scroll_position.y >= max_y ) { + dy = 0; + scroll_position.y = max_y; + } + } + repaint(); + getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); + setLastMouseDragPointX( ( float ) ( e.getX() + dx ) ); + setLastMouseDragPointY( ( float ) ( e.getY() + dy ) ); + } + + final void mouseMoved( final MouseEvent e ) { + requestFocusInWindow(); + if ( _current_external_nodes != null ) { + _current_external_nodes = null; + repaint(); + } + if ( getControlPanel().isNodeDescPopup() ) { + if ( _node_desc_popup != null ) { + _node_desc_popup.hide(); + _node_desc_popup = null; + } + } + if ( getOptions().isShowOverview() && isOvOn() ) { + if ( inOvVirtualRectangle( e ) ) { + if ( !isInOvRect() ) { + setInOvRect( true ); + repaint(); + } + } + else { + if ( isInOvRect() ) { + setInOvRect( false ); + repaint(); + } + } + } + if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) { + if ( !isInOv() ) { + setInOv( true ); + } + } + else { + if ( isInOv() ) { + setInOv( false ); + } + final PhylogenyNode node = findNode( e.getX(), e.getY() ); + if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) { + if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) { + for( final PhylogenyNode n : node.getAllExternalDescendants() ) { + addToCurrentExternalNodes( n.getId() ); + } + setCursor( HAND_CURSOR ); + repaint(); + } + else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) { + setCursor( CUT_CURSOR ); + } + else { + setCursor( HAND_CURSOR ); + if ( getControlPanel().isNodeDescPopup() ) { + showNodeDataPopup( e, node ); + } + } + } + else { + setCursor( ARROW_CURSOR ); + } + } + } + + final void mouseReleasedInBrowserPanel( final MouseEvent e ) { + setCursor( ARROW_CURSOR ); + } + + final void multiplyUrtFactor( final float f ) { + _urt_factor *= f; + } + + final void paintBranchCircular( final PhylogenyNode p, + final PhylogenyNode c, + final Graphics2D g, + final boolean radial_labels, + final boolean to_pdf, + final boolean to_graphics_file ) { + final double angle = _urt_nodeid_angle_map.get( c.getId() ); + final double root_x = _root.getXcoord(); + final double root_y = _root.getYcoord(); + final double dx = root_x - p.getXcoord(); + final double dy = root_y - p.getYcoord(); + final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) ); + final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; + assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file ); + if ( ( c.isFirstChildNode() || c.isLastChildNode() ) + && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) { + final double r2 = 2.0 * parent_radius; + drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); + } + drawLine( c.getXcoord(), + c.getYcoord(), + root_x + ( Math.cos( angle ) * parent_radius ), + root_y + ( Math.sin( angle ) * parent_radius ), + g ); + paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file ); + if ( c.isExternal() ) { + final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c ) + || isInCurrentExternalNodes( c ); + if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes + && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) { + return; + } + paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes ); + } + } + + final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) { + final double angle = _urt_nodeid_angle_map.get( c.getId() ); + final double root_x = _root.getXSecondary(); + final double root_y = _root.getYSecondary(); + final double dx = root_x - p.getXSecondary(); + final double dy = root_y - p.getYSecondary(); + final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; + final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) ); + g.setColor( getTreeColorSet().getOvColor() ); + if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) { + final double r2 = 2.0 * parent_radius; + drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); + } + drawLine( c.getXSecondary(), + c.getYSecondary(), + root_x + ( Math.cos( angle ) * parent_radius ), + root_y + ( Math.sin( angle ) * parent_radius ), + g ); + if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) { + g.setColor( getColorForFoundNode( c ) ); + drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, + c.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, + OVERVIEW_FOUND_NODE_BOX_SIZE, + OVERVIEW_FOUND_NODE_BOX_SIZE, + g ); + } + } + + final void paintCircular( final Phylogeny phy, + final double starting_angle, + final int center_x, + final int center_y, + final int radius, + final Graphics2D g, + final boolean to_pdf, + final boolean to_graphics_file ) { + final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size(); + System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() ); + _root = phy.getRoot(); + _root.setXcoord( center_x ); + _root.setYcoord( center_y ); + final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL; + double current_angle = starting_angle; + int i = 0; + for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( !n.isCollapse() ) { + n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) ); + n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) ); + _urt_nodeid_angle_map.put( n.getId(), current_angle ); + _urt_nodeid_index_map.put( n.getId(), i++ ); + current_angle += ( TWO_PI / circ_num_ext_nodes ); + } + else { + //TODO remove me + System.out.println( "is collapse" + n.getName() ); + } + } + paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file ); + paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file ); + } + + final void paintCircularLite( final Phylogeny phy, + final double starting_angle, + final int center_x, + final int center_y, + final int radius, + final Graphics2D g ) { + final int circ_num_ext_nodes = phy.getNumberOfExternalNodes(); + _root = phy.getRoot(); + _root.setXSecondary( center_x ); + _root.setYSecondary( center_y ); + double current_angle = starting_angle; + for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) ); + n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) ); + _urt_nodeid_angle_map.put( n.getId(), current_angle ); + current_angle += ( TWO_PI / circ_num_ext_nodes ); + } + paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g ); + } + + final void paintPhylogeny( final Graphics2D g, + final boolean to_pdf, + final boolean to_graphics_file, + final int graphics_file_width, + final int graphics_file_height, + final int graphics_file_x, + final int graphics_file_y ) { + if (_partition_tree) { +// float threshold = (_clicked_x - _root_x) / (_furthest_node_x - _root_x); +// drawLine( _clicked_x, 0, _clicked_x, getHeight(),g); + + _partition_tree = false; + } + + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return; + } + if ( _control_panel.isShowSequenceRelations() ) { + _query_sequence = _control_panel.getSelectedQuerySequence(); + } + // Color the background + if ( !to_pdf ) { + final Rectangle r = getVisibleRect(); + if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) { + g.setColor( getTreeColorSet().getBackgroundColor() ); + if ( !to_graphics_file ) { + g.fill( r ); + } + else { + if ( getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.WHITE ); + } + g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); + } + } + else { + if ( !to_graphics_file ) { + g.setPaint( new GradientPaint( r.x, + r.y, + getTreeColorSet().getBackgroundColor(), + r.x, + r.y + r.height, + getTreeColorSet().getBackgroundColorGradientBottom() ) ); + g.fill( r ); + } + else { + g.setPaint( new GradientPaint( graphics_file_x, + graphics_file_y, + getTreeColorSet().getBackgroundColor(), + graphics_file_x, + graphics_file_y + graphics_file_height, + getTreeColorSet().getBackgroundColorGradientBottom() ) ); + g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); + } + } + setupStroke( g ); + } + else { + g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) ); + } + if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + _external_node_index = 0; + // Position starting X of tree + if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/ ) { + _phylogeny.getRoot().setXcoord( TreePanel.MOVE ); + } + else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) { + _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + + ( _phylogeny.getRoot().getDistanceToParent() * getXcorrectionFactor() ) ) ); + } + else { + _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() ); + } + // Position starting Y of tree + _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() ) + + ( TreePanel.MOVE / 2.0f ) ); + final int dynamic_hiding_factor = calcDynamicHidingFactor(); + if ( getControlPanel().isDynamicallyHideData() ) { + if ( dynamic_hiding_factor > 1 ) { + getControlPanel().setDynamicHidingIsOn( true ); + } + else { + getControlPanel().setDynamicHidingIsOn( false ); + } + } + if ( _nodes_in_preorder == null ) { + _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ]; + int i = 0; + for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { + _nodes_in_preorder[ i++ ] = it.next(); + } + } + final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) + /* || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()*/ //TODO check if this is really not needed. + || to_graphics_file || to_pdf; + for( final PhylogenyNode element : _nodes_in_preorder ) { + paintNodeRectangular( g, + element, + to_pdf, + getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ), + dynamic_hiding_factor, + to_graphics_file, + disallow_shortcutting ); + } + if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) { + if ( !( to_graphics_file || to_pdf ) ) { + paintScale( g, + getVisibleRect().x, + getVisibleRect().y + getVisibleRect().height, + to_pdf, + to_graphics_file ); + } + else { + paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); + } + } + if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { + paintPhylogenyLite( g ); + } + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + if ( getControlPanel().getDynamicallyHideData() != null ) { + getControlPanel().setDynamicHidingIsOn( false ); + } + final double angle = getStartingAngle(); + final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL; + _dynamic_hiding_factor = 0; + if ( getControlPanel().isDynamicallyHideData() ) { + _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 + * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) ); + } + if ( getControlPanel().getDynamicallyHideData() != null ) { + if ( _dynamic_hiding_factor > 1 ) { + getControlPanel().setDynamicHidingIsOn( true ); + } + else { + getControlPanel().setDynamicHidingIsOn( false ); + } + } + paintUnrooted( _phylogeny.getRoot(), + angle, + ( float ) ( angle + ( 2 * Math.PI ) ), + radial_labels, + g, + to_pdf, + to_graphics_file ); + if ( getOptions().isShowScale() ) { + if ( !( to_graphics_file || to_pdf ) ) { + paintScale( g, + getVisibleRect().x, + getVisibleRect().y + getVisibleRect().height, + to_pdf, + to_graphics_file ); + } + else { + paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); + } + } + if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { + g.setColor( getTreeColorSet().getOvColor() ); + paintUnrootedLite( _phylogeny.getRoot(), + angle, + angle + ( 2 * Math.PI ), + g, + ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) ); + paintOvRectangle( g ); + } + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { + final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) + / 2 ) - ( MOVE + getLongestExtNodeInfo() ) ); + final int d = radius + MOVE + getLongestExtNodeInfo(); + _dynamic_hiding_factor = 0; + if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) { + _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 + * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * radius ) ); + } + if ( getControlPanel().getDynamicallyHideData() != null ) { + if ( _dynamic_hiding_factor > 1 ) { + getControlPanel().setDynamicHidingIsOn( true ); + } + else { + getControlPanel().setDynamicHidingIsOn( false ); + } + } + paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file ); + if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { + final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2 + : getOvMaxWidth() / 2 ); + double x_scale = 1.0; + double y_scale = 1.0; + int x_pos = getVisibleRect().x + getOvXPosition(); + int y_pos = getVisibleRect().y + getOvYPosition(); + if ( getWidth() > getHeight() ) { + x_scale = ( double ) getHeight() / getWidth(); + x_pos = ForesterUtil.roundToInt( x_pos / x_scale ); + } + else { + y_scale = ( double ) getWidth() / getHeight(); + y_pos = ForesterUtil.roundToInt( y_pos / y_scale ); + } + _at = g.getTransform(); + g.scale( x_scale, y_scale ); + paintCircularLite( _phylogeny, + getStartingAngle(), + x_pos + radius_ov, + y_pos + radius_ov, + ( int ) ( radius_ov - ( getLongestExtNodeInfo() + / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ), + g ); + g.setTransform( _at ); + paintOvRectangle( g ); + } + } + } + + final void recalculateMaxDistanceToRoot() { + _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() ); + if ( getPhylogeny().getRoot().getDistanceToParent() > 0 ) { + _max_distance_to_root += getPhylogeny().getRoot().getDistanceToParent(); + } + } + + /** + * Remove all edit-node frames + */ + final void removeAllEditNodeJFrames() { + for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) { + if ( _node_frames[ i ] != null ) { + _node_frames[ i ].dispose(); + _node_frames[ i ] = null; + } + } + _node_frame_index = 0; + } + + /** + * Remove a node-edit frame. + */ + final void removeEditNodeFrame( final int i ) { + _node_frame_index--; + _node_frames[ i ] = null; + if ( i < _node_frame_index ) { + for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) { + _node_frames[ j ] = _node_frames[ j + 1 ]; + } + _node_frames[ _node_frame_index ] = null; + } + } + + final void reRoot( final PhylogenyNode node ) { + if ( !getPhylogeny().isRerootable() ) { + JOptionPane.showMessageDialog( this, + "This is not rerootable", + "Not rerootable", + JOptionPane.WARNING_MESSAGE ); + return; + } + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + JOptionPane.showMessageDialog( this, + "Cannot reroot in unrooted display type", + "Attempt to reroot tree in unrooted display", + JOptionPane.WARNING_MESSAGE ); + return; + } + getPhylogeny().reRoot( node ); + getPhylogeny().recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setNodeInPreorderToNull(); + resetPreferredSize(); + getMainPanel().adjustJScrollPane(); + setEdited( true ); + repaint(); + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { + getControlPanel().showWhole(); + } + } + + final void resetNodeIdToDistToLeafMap() { + _nodeid_dist_to_leaf = new HashMap(); + } + + final void resetPreferredSize() { + if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) { + return; + } + int x = 0; + int y = 0; + y = TreePanel.MOVE + + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 ); + if ( getControlPanel().isDrawPhylogram() ) { + x = TreePanel.MOVE + getLongestExtNodeInfo() + + ForesterUtil.roundToInt( ( getXcorrectionFactor() + * getPhylogeny().calculateHeight( !_options.isCollapsedWithAverageHeigh() ) ) + + getXdistance() ); + } + else { + if ( !isNonLinedUpCladogram() ) { + x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil + .roundToInt( getXdistance() * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); + } + else { + x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil + .roundToInt( getXdistance() * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); + } + } + setPreferredSize( new Dimension( x, y ) ); + } + + final void selectNode( final PhylogenyNode node ) { + if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) { + getFoundNodes0().remove( node.getId() ); + getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() ); + if ( getFoundNodes0().size() < 1 ) { + getControlPanel().searchReset0(); + } + } + else { + getControlPanel().getSearchFoundCountsLabel0().setVisible( true ); + getControlPanel().getSearchResetButton0().setEnabled( true ); + getControlPanel().getSearchResetButton0().setVisible( true ); + if ( getFoundNodes0() == null ) { + setFoundNodes0( new HashSet() ); + } + getFoundNodes0().add( node.getId() ); + getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() ); + } + } + + final void setArrowCursor() { + setCursor( ARROW_CURSOR ); + repaint(); + } + + final void setControlPanel( final ControlPanel atv_control ) { + _control_panel = atv_control; + } + + void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) { + increaseCurrentExternalNodesDataBufferChangeCounter(); + _current_external_nodes_data_buffer = sb; + } + + public final void setFoundNodes0( final Set found_nodes ) { + _found_nodes_0 = found_nodes; + } + + public final void setFoundNodes1( final Set found_nodes ) { + _found_nodes_1 = found_nodes; + } + + final void setInOvRect( final boolean in_ov_rect ) { + _in_ov_rect = in_ov_rect; + } + + final void setLargeFonts() { + getTreeFontSet().largeFonts(); + } + + final void setLastMouseDragPointX( final float x ) { + _last_drag_point_x = x; + } + + final void setLastMouseDragPointY( final float y ) { + _last_drag_point_y = y; + } + + final void setMediumFonts() { + getTreeFontSet().mediumFonts(); + } + + final void setNodeInPreorderToNull() { + _nodes_in_preorder = null; + } + + final void setOvOn( final boolean ov_on ) { + _ov_on = ov_on; + } + + final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) { + _graphics_type = graphics_type; + setTextAntialias(); + } + + final void setSmallFonts() { + getTreeFontSet().smallFonts(); + } + + final void setStartingAngle( final double starting_angle ) { + _urt_starting_angle = starting_angle; + } + + void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) { + _statistics_for_vector_data = statistics_for_expression_values; + } + + final void setSuperTinyFonts() { + getTreeFontSet().superTinyFonts(); + } + + final void setTextAntialias() { + if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { + if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) { + _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY ); + } + else { + _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED ); + } + } + if ( getMainPanel().getOptions().isAntialiasScreen() ) { + _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON ); + // try { + _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB ); + // } + // catch ( final Throwable e ) { + // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON ); + //} } else { - JOptionPane.showMessageDialog( this, "too many node windows are open" ); + _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF ); + _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); } } - final private void showNodeFrame( final PhylogenyNode n ) { - if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) { - // pop up edit box for single node - _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index ); - _node_frame_index++; - } - else { - JOptionPane.showMessageDialog( this, "too many node windows are open" ); + final void setTinyFonts() { + getTreeFontSet().tinyFonts(); + } + + public final void setTreeFile( final File treefile ) { + _treefile = treefile; + } + + final void setXcorrectionFactor( final float f ) { + _x_correction_factor = f; + } + + final void setXdistance( final float x ) { + _x_distance = x; + } + + final void setYdistance( final float y ) { + _y_distance = y; + } + + final void sortDescendants( final PhylogenyNode node ) { + if ( !node.isExternal() ) { + DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; + if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) { + pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; + } + else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols() + || getControlPanel().isShowGeneNames() ) { + pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; + } + PhylogenyMethods.sortNodeDescendents( node, pri ); + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); } + repaint(); } final void subTree( final PhylogenyNode node ) { @@ -4745,13 +6165,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.WARNING_MESSAGE ); return; } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) { _sub_phylogenies[ _subtree_index ] = _phylogeny; _sub_phylogenies_temp_roots[ _subtree_index ] = node; ++_subtree_index; - _phylogeny = subTree( node, _phylogeny ); + _phylogeny = TreePanelUtil.subTree( node, _phylogeny ); + if ( _phylogeny.getRoot().isCollapse() ) { + _phylogeny.getRoot().setCollapse( false ); + } + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); updateSubSuperTreeButton(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + resetRankCollapseRankValue(); + resetDepthCollapseDepthValue(); + getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay(); + getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay(); + getMainPanel().getControlPanel().updateRankCollapseRankDisplay(); } else if ( node.isRoot() && isCurrentTreeIsSubtree() ) { superTree(); @@ -4760,29 +6193,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } - final boolean isCurrentTreeIsSubtree() { - return ( _subtree_index > 0 ); - } - - final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) { - final Phylogeny new_phy = new Phylogeny(); - new_phy.setRooted( true ); - new_phy.setName( source_phy.getName() ); - new_phy.setDescription( source_phy.getDescription() ); - new_phy.setType( source_phy.getType() ); - new_phy.setDistanceUnit( source_phy.getDistanceUnit() ); - new_phy.setConfidence( source_phy.getConfidence() ); - new_phy.setIdentifier( source_phy.getIdentifier() ); - new_phy.setRoot( new_root.copyNodeDataShallow() ); - int i = 0; - for( final PhylogenyNode n : new_root.getDescendants() ) { - new_phy.getRoot().setChildNode( i++, n ); - } - return new_phy; - } - final void superTree() { - _nodes_in_preorder = null; + setNodeInPreorderToNull(); final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ]; for( final PhylogenyNode n : temp_root.getDescendants() ) { n.setParent( temp_root ); @@ -4790,76 +6202,63 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _sub_phylogenies[ _subtree_index ] = null; _sub_phylogenies_temp_roots[ _subtree_index ] = null; _phylogeny = _sub_phylogenies[ --_subtree_index ]; + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + resetRankCollapseRankValue(); + resetDepthCollapseDepthValue(); + getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay(); + getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay(); + getMainPanel().getControlPanel().updateRankCollapseRankDisplay(); updateSubSuperTreeButton(); } - final void swap( final PhylogenyNode node ) { - if ( !node.isExternal() ) { - _phylogeny.swapChildren( node ); - _nodes_in_preorder = null; + final void orderSubtree( final PhylogenyNode node ) { + if ( node.isExternal() ) { + return; + } + DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; + if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) { + pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; + } + else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols() + || getControlPanel().isShowGeneNames() ) { + pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; } + PhylogenyMethods.orderAppearanceX( node, true, pri ); + setNodeInPreorderToNull(); + getPhylogeny().externalNodesHaveChanged(); + getPhylogeny().clearHashIdToNodeMap(); + getPhylogeny().recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); + getControlPanel().displayedPhylogenyMightHaveChanged( true ); repaint(); } - final private void switchDisplaygetPhylogenyGraphicsType() { - switch ( getPhylogenyGraphicsType() ) { - case RECTANGULAR: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); - break; - case EURO_STYLE: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); - break; - case ROUNDED: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); - break; - case CURVED: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); - break; - case TRIANGULAR: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); - break; - case CONVEX: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); - break; - case UNROOTED: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); - break; - case CIRCULAR: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - break; - default: - throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() ); - } - if ( getControlPanel().getDynamicallyHideData() != null ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - getControlPanel().getDynamicallyHideData().setEnabled( false ); - } - else { - getControlPanel().getDynamicallyHideData().setEnabled( true ); - } - } - if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - getControlPanel().setDrawPhylogramEnabled( true ); - } - else { - getControlPanel().setDrawPhylogramEnabled( false ); + final void swap( final PhylogenyNode node ) { + if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) { + return; } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); + if ( node.getNumberOfDescendants() > 2 ) { + JOptionPane.showMessageDialog( this, + "Cannot swap descendants of nodes with more than 2 descendants", + "Cannot swap descendants", + JOptionPane.ERROR_MESSAGE ); + return; } - else { - getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); + if ( !node.isExternal() ) { + node.swapChildren(); + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); } + repaint(); } final void taxColor() { @@ -4867,11 +6266,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this ); + TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this ); _control_panel.setColorBranches( true ); - if ( _control_panel.getColorBranchesCb() != null ) { - _control_panel.getColorBranchesCb().setSelected( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); } + setEdited( true ); setArrowCursor(); repaint(); } @@ -4902,7 +6302,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final void updateOvSizes() { - if ( ( getWidth() > 1.05 * getVisibleRect().width ) || ( getHeight() > 1.05 * getVisibleRect().height ) ) { + if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) + || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) { setOvOn( true ); float l = getLongestExtNodeInfo(); final float w_ratio = getOvMaxWidth() / getWidth(); @@ -4910,7 +6311,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes(); setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) ); float ov_xdist = 0; - if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { + if ( !isNonLinedUpCladogram() ) { ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) ); } else { @@ -4924,7 +6325,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee ydist = 0.0f; } setOvXDistance( ov_xdist ); - final double height = _phylogeny.getHeight(); + final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() ); if ( height > 0 ) { final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height ); setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); @@ -4938,6 +6339,25 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } + void updateSetOfCollapsedExternalNodes() { + final Phylogeny phy = getPhylogeny(); + _collapsed_external_nodeid_set.clear(); + if ( phy != null ) { + E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode ext_node = it.next(); + PhylogenyNode n = ext_node; + while ( !n.isRoot() ) { + if ( n.isCollapse() ) { + _collapsed_external_nodeid_set.add( ext_node.getId() ); + ext_node.setCollapse( true ); + continue E; + } + n = n.getParent(); + } + } + } + } + final void updateSubSuperTreeButton() { if ( _subtree_index < 1 ) { getControlPanel().deactivateButtonToReturnToSuperTree(); @@ -4947,6 +6367,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } + final void updateButtonToUncollapseAll() { + if ( PhylogenyMethods.isHasCollapsedNodes( _phylogeny ) ) { + getControlPanel().activateButtonToUncollapseAll(); + } + else { + getControlPanel().deactivateButtonToUncollapseAll(); + } + } + final void zoomInDomainStructure() { if ( _domain_structure_width < 2000 ) { _domain_structure_width *= 1.2; @@ -4959,62 +6388,152 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) { - g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) ); + private final static void colorizeNodesHelper( final Color c, final PhylogenyNode node ) { + if ( node.getNodeData().getNodeVisualData() == null ) { + node.getNodeData().setNodeVisualData( new NodeVisualData() ); + } + node.getNodeData().getNodeVisualData().setFontColor( new Color( c.getRed(), c.getGreen(), c.getBlue() ) ); + } + + final private static void drawString( final String str, final float x, final float y, final Graphics2D g ) { + g.drawString( str, x, y ); } - final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) { - g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) ); + final private void drawStringX( final String str, final float x, final float y, final Graphics2D g ) { + //TODO + //FIXME + if ( getAttributedStringMap() == null /*&& getAttributedStringMap().containsKey(str) */ ) { + final AttributedString as = new AttributedString( str ); + //Font plainFont = new Font("Times New Roman", Font.PLAIN, 24); + as.addAttribute( TextAttribute.FONT, g.getFont() ); + as.addAttribute( TextAttribute.UNDERLINE, TextAttribute.UNDERLINE_ON, 1, 3 ); + as.addAttribute( TextAttribute.SUPERSCRIPT, TextAttribute.SUPERSCRIPT_SUPER, 3, 4 ); + as.addAttribute( TextAttribute.FOREGROUND, Color.BLUE, 1, 2 ); + as.addAttribute( TextAttribute.FOREGROUND, Color.PINK, 3, 5 ); + as.addAttribute( TextAttribute.STRIKETHROUGH, TextAttribute.STRIKETHROUGH_ON, 2, 4 ); + g.drawString( as.getIterator(), x, y ); + } + else { + g.drawString( str, x, y ); + } } - final private static boolean isSequenceEmpty( final Sequence seq ) { - return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() ) - && ForesterUtil.isEmpty( seq.getSymbol() ); + private final Map getAttributedStringMap() { + return _attributed_string_map; } - final private static boolean isTaxonomyEmpty( final Taxonomy tax ) { - return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() ) - && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax - .getSynonyms().isEmpty() ); + private final void setAttributedStringMap( final Map attributed_string_map ) { + _attributed_string_map = attributed_string_map; } final private static boolean plusPressed( final int key_code ) { return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS ) - || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) ); + || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) + || ( key_code == KeyEvent.VK_1 ) ); } - void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) { - _statistics_for_vector_data = statistics_for_expression_values; + public void decreaseDepthCollapseLevel() { + if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) { + if ( _depth_collapse_level <= 1 ) { + _depth_collapse_level = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + uncollapseAll(); + } + else { + --_depth_collapse_level; + PhylogenyMethods.collapseToDepth( _phylogeny, _depth_collapse_level ); + } + } } - DescriptiveStatistics getStatisticsForExpressionValues() { - return _statistics_for_vector_data; + public void increaseDepthCollapseLevel() { + if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) { + final int max = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + if ( _depth_collapse_level >= max ) { + _depth_collapse_level = 1; + } + else { + ++_depth_collapse_level; + } + PhylogenyMethods.collapseToDepth( _phylogeny, _depth_collapse_level ); + } } - final private class SubtreeColorizationActionListener implements ActionListener { + public void decreaseRankCollapseLevel() { + if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) { + final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( _phylogeny ); + if ( ranks.length > 1 ) { + if ( _rank_collapse_level <= 0 ) { + _rank_collapse_level = ranks.length - 1; + uncollapseAll(); + } + else { + --_rank_collapse_level; + PhylogenyMethods.collapseToRank( _phylogeny, + mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) ); + } + } + } + } - JColorChooser _chooser; - PhylogenyNode _node; + public void increaseRankCollapseLevel() { + if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) { + final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( _phylogeny ); + if ( ranks.length > 1 ) { + if ( _rank_collapse_level >= ( ranks.length - 1 ) ) { + _rank_collapse_level = 0; + PhylogenyMethods.collapseToRank( _phylogeny, + mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) ); + } + else if ( _rank_collapse_level == ( ranks.length - 2 ) ) { + ++_rank_collapse_level; + uncollapseAll(); + } + else { + ++_rank_collapse_level; + PhylogenyMethods.collapseToRank( _phylogeny, + mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) ); + } + } + } + } - SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) { - _chooser = chooser; - _node = node; + private final static int mapToAbsoluteRankLevel( final String present_ranks_sorted[], + final int rank_collapse_level ) { + final String rank_str = present_ranks_sorted[ rank_collapse_level ]; + if ( !TaxonomyUtil.RANK_TO_INT.containsKey( rank_str ) ) { + throw new IllegalStateException( "unexpected exception: cannot find rank " + rank_str ); } + return TaxonomyUtil.RANK_TO_INT.get( rank_str ); + } - @Override - public void actionPerformed( final ActionEvent e ) { - final Color c = _chooser.getColor(); - if ( c != null ) { - colorizeSubtree( c, _node ); - } + private final void uncollapseAll() { + final PhylogenyNodeIterator it = new PreorderTreeIterator( _phylogeny ); + while ( it.hasNext() ) { + it.next().setCollapse( false ); } } - public synchronized void setImageMap( final Hashtable image_map ) { - getMainPanel().setImageMap( image_map ); + final int resetDepthCollapseDepthValue() { + return _depth_collapse_level = -1; } - public synchronized Hashtable getImageMap() { - return getMainPanel().getImageMap(); + final int getDepthCollapseDepthValue() { + return _depth_collapse_level; + } + + final void setDepthCollapseDepthValue( final int depth_collapse_level ) { + _depth_collapse_level = depth_collapse_level; + } + + final int resetRankCollapseRankValue() { + return _rank_collapse_level = -1; + } + + final int getRankCollapseRankValue() { + return _rank_collapse_level; + } + + final void setRankCollapseRankValue( final int rank_collapse_level ) { + _rank_collapse_level = rank_collapse_level; } }