// 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;
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;
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;
import java.util.Hashtable;
import java.util.List;
import java.util.Set;
+import java.util.SortedSet;
import javax.swing.BorderFactory;
import javax.swing.JApplet;
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.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.NodeVisualization;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
-import org.forester.phylogeny.data.PhylogenyData;
+import org.forester.phylogeny.data.NodeData.NODE_DATA;
+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.PropertiesMap;
import org.forester.phylogeny.data.Property;
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 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<Integer> _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 PhylogenyNode _root;
- final private Arc2D _arc = new Arc2D.Double();
- final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
- final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
- final private Set<Integer> _collapsed_external_nodeid_set = new HashSet<Integer>();
- HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
- 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;
+ 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_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 double TWO_PI = 2 * Math.PI;
+ private final static int WIGGLE = 2;
+ HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
+ final private Arc2D _arc = new Arc2D.Double();
+ private AffineTransform _at;
+ private int _circ_max_depth;
+ final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
+ private JColorChooser _color_chooser = null;
+ private Configuration _configuration = null;
+ private ControlPanel _control_panel = null;
+ private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
+ private Set<Long> _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 = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
+ private double _domain_structure_width = Constants.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<Long> _found_nodes_0 = null;
+ private Set<Long> _found_nodes_1 = null;
+ private final FontRenderContext _frc = new FontRenderContext( null,
+ false,
+ false );
+ 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 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 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<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
+ final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
+ 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 Image offscreenImage;
// private Graphics offscreenGraphics;
// private Dimension offscreenDimension;
.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 );
+ @Override
+ final public void actionPerformed( final ActionEvent e ) {
+ boolean done = false;
+ final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
+ 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 ] ) {
+ // Set this as the new default click-to action
+ _main_panel.getControlPanel().setClickToAction( index );
+ final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
+ .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
+ handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
+ done = true;
+ }
+ }
+ repaint();
+ requestFocusInWindow();
+ }
+
+ public synchronized Hashtable<String, BufferedImage> 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;
+ }
+
+ @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() ) {
+ if ( notches < 0 ) {
+ getTreeFontSet().increaseFontSize();
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ else {
+ getTreeFontSet().decreaseFontSize( 1, false );
+ 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() );
}
- 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;
+ 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();
+ }
+
+ @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
+ 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<String, BufferedImage> 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 );
+ }
+
+ 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, final boolean recalc_longest_ext_node_info ) {
+ // updateStyle(); not needed?
+ if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
+ initNodeData();
+ if ( recalc_longest_ext_node_info ) {
+ calculateLongestExtNodeInfo();
+ if ( getOptions().isAllowFontSizeChange() ) {
+ 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();
}
- if ( i < 0 ) {
- JOptionPane.showMessageDialog( this,
- "Attempt to use negative index for vector data",
- "Problem with Vector Data",
- JOptionPane.ERROR_MESSAGE );
- return;
+ }
+ else {
+ while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() <= ( getTreeFontSet()
+ .getLargeFontMemory().getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ calculateLongestExtNodeInfo();
}
- vector[ i ] = d;
- ++counter;
- stats.addValue( d );
}
}
- final List<Double> vector_l = new ArrayList<Double>( counter );
- for( int i = 0; i < counter; ++i ) {
- vector_l.add( vector[ i ] );
+ _length_of_longest_text = calcLengthOfLongestText();
+ }
+ 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();
+ //
+ if ( getOptions().isAllowFontSizeChange() ) {
+ 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_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
+ * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
+ if ( max_length < 40 ) {
+ max_length = 40;
+ }
+ 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 ( 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 ( sum >= max_length ) {
+ _longest_ext_node_info = max_length;
+ return;
+ }
+ if ( sum > longest ) {
+ longest = sum;
+ }
+ }
+ _ext_node_with_longest_txt_info = longest_txt_node;
+ if ( longest >= max_length ) {
+ _longest_ext_node_info = max_length;
+ }
+ else {
+ _longest_ext_node_info = longest;
+ }
+ }
+
+ 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 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;
+ }
+ }
+
+ 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;
+ }
+
+ 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<Double> vector_l = new ArrayList<Double>( 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;
+ }
+ }
+
+ 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 collapseSpeciesSpecificSubtrees() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ setWaitCursor();
+ TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+ updateSetOfCollapsedExternalNodes();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ calculateLongestExtNodeInfo();
+ setNodeInPreorderToNull();
+ resetPreferredSize();
+ _main_panel.adjustJScrollPane();
+ setArrowCursor();
+ repaint();
+ }
+
+ 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 Colorization Completed (" + rank + ")",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ String msg = "Could not taxonomy 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. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
+ msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
+ JOptionPane.showMessageDialog( this, msg, "Taxonomy 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 decreaseDomainStructureEvalueThreshold() {
+ 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
+ */
+ 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 getDomainStructureEvalueThreshold() {
+ return _domain_structure_e_value_thr_exp;
+ }
+
+ final Set<Long> getFoundNodes0() {
+ return _found_nodes_0;
+ }
+
+ final Set<Long> getFoundNodes1() {
+ return _found_nodes_1;
+ }
+
+ 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 double getStartingAngle() {
+ return _urt_starting_angle;
+ }
+
+ DescriptiveStatistics getStatisticsForExpressionValues() {
+ return _statistics_for_vector_data;
+ }
+
+ final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
+ }
+ // return non-colorized color
+ return getTreeColorSet().getTaxonomyColor();
+ }
+
+ final Color getSequenceBasedColor( final PhylogenyNode node ) {
+ if ( node.getNodeData().isHasSequence() ) {
+ return calculateSequenceBasedColor( node.getNodeData().getSequence() );
+ }
+ // return non-colorized color
+ return getTreeColorSet().getSequenceColor();
+ }
+
+ public final TreeColorSet getTreeColorSet() {
+ return getMainPanel().getTreeColorSet();
+ }
+
+ 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 increaseDomainStructureEvalueThreshold() {
+ 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 ) ) {
+ 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 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 boolean isApplet() {
+ return getMainPanel() instanceof MainPanelApplets;
+ }
+
+ 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() );
+ }
+
+ 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<Long>() );
+ }
+ 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
+ _highlight_node = null;
+ }
+ }
+ 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 JApplet obtainApplet() {
+ return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ }
+
+ 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 ( ( _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 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( final PhylogenyNode element : _nodes_in_preorder ) {
+ paintNodeRectangular( g, element, 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 ) ( ( 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() );
+ }
+
+ /**
+ * 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<Long, Short>();
+ }
+
+ 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().getHeight() ) + getXdistance() );
+ }
+ 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 ) );
+ }
+ }
+ 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<Long>() );
+ }
+ 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;
+ }
+
+ final void setFoundNodes0( final Set<Long> found_nodes ) {
+ _found_nodes_0 = found_nodes;
+ }
+
+ final void setFoundNodes1( final Set<Long> 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 {
+ _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
+ _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
+ }
+ }
+
+ final void setTinyFonts() {
+ getTreeFontSet().tinyFonts();
+ }
+
+ 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.TAXONOMY;
+ if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
+ .isShowTaxonomyCommonNames() ) ) {
+ if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
+ .isShowSeqSymbols() ) ) {
+ pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
+ }
+ else if ( getControlPanel().isShowNodeNames() ) {
+ pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
}
- node.getNodeData().setVector( vector_l );
}
+ PhylogenyMethods.sortNodeDescendents( node, pri );
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
}
- if ( stats.getN() > 0 ) {
- _statistics_for_vector_data = stats;
+ repaint();
+ }
+
+ final void subTree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot get a sub/super tree in unrooted display",
+ "Attempt to get sub/super tree in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ if ( node.isExternal() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot get a subtree of a external node",
+ "Attempt to get subtree of external node",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot get a subtree of the root node",
+ "Attempt to get subtree of root node",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ 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 = TreePanelUtil.subTree( node, _phylogeny );
+ updateSubSuperTreeButton();
+ }
+ else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
+ superTree();
}
+ _main_panel.getControlPanel().showWhole();
+ repaint();
}
- final public void actionPerformed( final ActionEvent e ) {
- boolean done = false;
- final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
- 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 ] ) {
- // Set this as the new default click-to action
- _main_panel.getControlPanel().setClickToAction( index );
- final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
- .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
- handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
- done = true;
- }
+ final void superTree() {
+ setNodeInPreorderToNull();
+ final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
+ for( final PhylogenyNode n : temp_root.getDescendants() ) {
+ n.setParent( temp_root );
+ }
+ _sub_phylogenies[ _subtree_index ] = null;
+ _sub_phylogenies_temp_roots[ _subtree_index ] = null;
+ _phylogeny = _sub_phylogenies[ --_subtree_index ];
+ updateSubSuperTreeButton();
+ }
+
+ final void swap( final PhylogenyNode node ) {
+ if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
+ return;
+ }
+ if ( node.getNumberOfDescendants() > 2 ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot swap descendants of nodes with more than 2 descendants",
+ "Cannot swap descendants",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( !node.isExternal() ) {
+ node.swapChildren();
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
}
repaint();
- requestFocusInWindow();
+ }
+
+ final void taxColor() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ setWaitCursor();
+ TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
+ }
+ setEdited( true );
+ setArrowCursor();
+ repaint();
+ }
+
+ final void updateOvSettings() {
+ switch ( getOptions().getOvPlacement() ) {
+ case LOWER_LEFT:
+ setOvXPosition( OV_BORDER );
+ setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
+ setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
+ break;
+ case LOWER_RIGHT:
+ setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
+ setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
+ setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
+ break;
+ case UPPER_RIGHT:
+ setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
+ setOvYPosition( OV_BORDER );
+ setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
+ break;
+ default:
+ setOvXPosition( OV_BORDER );
+ setOvYPosition( OV_BORDER );
+ setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
+ break;
+ }
+ }
+
+ final void updateOvSizes() {
+ if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
+ setOvOn( true );
+ float l = getLongestExtNodeInfo();
+ final float w_ratio = getOvMaxWidth() / getWidth();
+ l *= w_ratio;
+ final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
+ setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
+ float ov_xdist = 0;
+ if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
+ ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
+ }
+ else {
+ ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
+ }
+ float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
+ if ( ov_xdist < 0.0 ) {
+ ov_xdist = 0.0f;
+ }
+ if ( ydist < 0.0 ) {
+ ydist = 0.0f;
+ }
+ setOvXDistance( ov_xdist );
+ final double height = _phylogeny.getHeight();
+ if ( height > 0 ) {
+ final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
+ setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
+ }
+ else {
+ setOvXcorrectionFactor( 0 );
+ }
+ }
+ else {
+ setOvOn( false );
+ }
+ }
+
+ 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();
+ }
+ else {
+ getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
+ }
+ }
+
+ final void zoomInDomainStructure() {
+ if ( _domain_structure_width < 2000 ) {
+ _domain_structure_width *= 1.2;
+ }
+ }
+
+ final void zoomOutDomainStructure() {
+ if ( _domain_structure_width > 20 ) {
+ _domain_structure_width *= 0.8;
+ }
+ }
+
+ 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 ) {
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?";
}
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<Long>();
+ }
+ _current_external_nodes.add( i );
+ }
+
final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
final boolean is_vertical,
final Graphics g,
&& ( getCopiedAndPastedNodes() != null )
&& !to_pdf
&& !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
}
- else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
else if ( to_pdf ) {
}
}
- 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() ) {
+ 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';
+ }
+ }
JApplet applet = null;
if ( isApplet() ) {
applet = obtainApplet();
}
- Blast.NcbiBlastWeb( query, applet, this );
+ try {
+ Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
if ( Constants.ALLOW_DDBJ_BLAST ) {
try {
System.out.println( "trying: " + query );
}
}
- 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 Color calculateColorForAnnotation( final PhylogenyData ann ) {
+ final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
Color c = getTreeColorSet().getAnnotationColor();
if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
- c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() );
- 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()
- + " " );
- }
+ final StringBuilder sb = new StringBuilder();
+ for( final Annotation a : ann ) {
+ sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
}
- 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() + " " );
+ 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 ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
+ if ( c == null ) {
+ c = getTreeColorSet().getAnnotationColor();
}
}
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
- sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
- }
- 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 );
}
+ return c;
}
final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
}
}
- 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 calculateTaxonomyBasedColor( final Taxonomy tax ) {
- String species = tax.getTaxonomyCode();
- if ( ForesterUtil.isEmpty( species ) ) {
- species = tax.getScientificName();
- if ( ForesterUtil.isEmpty( species ) ) {
- species = tax.getCommonName();
- }
- }
- if ( ForesterUtil.isEmpty( species ) ) {
- return getTreeColorSet().getTaxonomyColor();
- }
- // Look in species hash
- Color c = getControlPanel().getSpeciesColors().get( species );
- if ( c == null ) {
- c = AptxUtil.calculateColorFromString( species );
- getControlPanel().getSpeciesColors().put( species, c );
- }
- return c;
- }
-
final private void cannotOpenBrowserWarningMessage( final String type_type ) {
JOptionPane.showMessageDialog( this,
"Cannot launch web browser for " + type_type + " data of this node",
JOptionPane.WARNING_MESSAGE );
}
- /**
- * 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;
+ 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();
}
- if ( !node.isExternal() && !node.isRoot() ) {
- final boolean collapse = !node.isCollapse();
- AptxUtil.collapseSubtree( node, collapse );
- updateSetOfCollapsedExternalNodes( _phylogeny );
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- calculateLongestExtNodeInfo();
- setNodeInPreorderToNull();
- _control_panel.displayedPhylogenyMightHaveChanged( true );
- resetPreferredSize();
- updateOvSizes();
- _main_panel.adjustJScrollPane();
- repaint();
+ if ( f != null ) {
+ fc.setFont( f );
}
- }
-
- final void collapseSpeciesSpecificSubtrees() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
+ else {
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ }
+ fc.showDialog( this, "Select Font" );
+ if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
+ List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ nodes = getFoundNodesAsListOfPhylogenyNodes();
+ }
+ nodes.add( node );
+ 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 );
+ }
}
- setWaitCursor();
- AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
- updateSetOfCollapsedExternalNodes( _phylogeny );
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- calculateLongestExtNodeInfo();
- setNodeInPreorderToNull();
- 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 colorizeNodes( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> 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 ) {
+ colorizeNodesHelper( c, node );
}
- for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode n : additional_nodes ) {
+ colorizeNodesHelper( c, n );
+ }
}
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 );
+ final private void colorizeSubtree( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
- else {
- intitial_color = getTreeColorSet().getBranchColor();
+ if ( node != null ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
}
- _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 );
- dialog.setVisible( true );
+ 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 void confColor() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
+ private void colorNodeFont( final PhylogenyNode node ) {
+ _color_chooser.setPreviewPanel( new JPanel() );
+ NodeColorizationActionListener al;
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
}
- setWaitCursor();
- AptxUtil.removeBranchColors( _phylogeny );
- AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ else {
+ al = new NodeColorizationActionListener( _color_chooser, node );
}
- setArrowCursor();
- repaint();
+ final JDialog dialog = JColorChooser.createDialog( this, "Node colorization", true, _color_chooser, al, null );
+ dialog.setVisible( true );
}
- final void colorRank( final String rank ) {
- 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();
- AptxUtil.removeBranchColors( _phylogeny );
- final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
- if ( colorizations > 0 ) {
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
- }
- if ( _control_panel.getColorAccSpeciesCb() != null ) {
- _control_panel.getColorAccSpeciesCb().setSelected( false );
- }
- _options.setColorLabelsSameAsParentBranch( 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";
- }
- JOptionPane.showMessageDialog( this,
- msg,
- "Taxonomy Colorization Completed (" + rank + ")",
- JOptionPane.INFORMATION_MESSAGE );
+ _color_chooser.setPreviewPanel( new JPanel() );
+ SubtreeColorizationActionListener al;
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
- String msg = "Could not taxonomy 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. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
- msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
- JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
+ al = new SubtreeColorizationActionListener( _color_chooser, node );
}
+ final JDialog dialog = JColorChooser
+ .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+ dialog.setVisible( true );
}
final private void copySubtree( final PhylogenyNode node ) {
setNodeInPreorderToNull();
setCutOrCopiedTree( _phylogeny.copy( node ) );
final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
- final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
+ final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
for( final PhylogenyNode n : nodes ) {
node_ids.add( n.getId() );
}
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();
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",
setCopiedAndPastedNodes( null );
setCutOrCopiedTree( _phylogeny.copy( node ) );
_phylogeny.deleteSubtree( node, true );
- _phylogeny.hashIDs();
+ _phylogeny.clearHashIdToNodeMap();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
}
}
- 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 );
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 + "?",
_phylogeny.deleteSubtree( node, true );
}
_phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
+ _phylogeny.clearHashIdToNodeMap();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
setEdited( true );
g.fill( _ellipse );
}
+ 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 );
g.fill( _rectangle );
}
- final private void drawRectGradient( 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 ) {
- _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.fill( _rectangle );
- if ( color_border != null ) {
- g.setPaint( color_border );
- g.draw( _rectangle );
- }
- }
-
- final private void drawOvalGradient( 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 ) {
- _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 );
+ final Color color_border ) {
+ _rectangle.setFrame( x, y, width, heigth );
+ 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 );
- g.draw( _ellipse );
+ g.draw( _rectangle );
+ }
+ }
+
+ private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
+ final List<Uri> us = new ArrayList<Uri>();
+ for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
+ for( final Uri uri : t.getUris() ) {
+ us.add( uri );
+ }
+ }
+ 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 offset;
}
final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
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;
- }
- 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;
- }
+ private final Color getColorForFoundNode( final PhylogenyNode n ) {
+ if ( isInCurrentExternalNodes( n ) ) {
+ return getTreeColorSet().getFoundColor0();
}
- 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 ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor0();
}
- else if ( !ForesterUtil.isEmpty( tax ) ) {
- label = tax;
+ else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor1();
}
else {
- label = "";
- }
- if ( !ForesterUtil.isEmpty( label ) ) {
- label = " [" + label + "]";
+ return getTreeColorSet().getFoundColor0and1();
}
- return label;
- }
-
- final Configuration getConfiguration() {
- return _configuration;
}
- final ControlPanel getControlPanel() {
- return _control_panel;
+ final private Set<Long> getCopiedAndPastedNodes() {
+ return getMainPanel().getCopiedAndPastedNodes();
}
- final private Set<Integer> getCopiedAndPastedNodes() {
- return getMainPanel().getCopiedAndPastedNodes();
+ final private Set<Long> getCurrentExternalNodes() {
+ return _current_external_nodes;
}
final private Phylogeny getCutOrCopiedTree() {
return getMainPanel().getCutOrCopiedTree();
}
- final int getDomainStructureEvalueThreshold() {
- return _domain_structure_e_value_thr_exp;
+ private FontMetrics getFontMetricsForLargeDefaultFont() {
+ return getTreeFontSet().getFontMetricsLarge();
}
- final Set<Integer> getFoundNodes() {
- return _found_nodes;
+ List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ if ( getFoundNodes0() != null ) {
+ for( final Long id : getFoundNodes0() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ }
+ if ( getFoundNodes1() != null ) {
+ for( final Long id : getFoundNodes1() ) {
+ if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ }
+ }
+ return additional_nodes;
}
final private float getLastDragPointX() {
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 );
return _max_distance_to_root;
}
- final Options getOptions() {
- if ( _options == null ) {
- _options = getControlPanel().getOptions();
- }
- return _options;
- }
-
final private float getOvMaxHeight() {
return _ov_max_height;
}
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;
}
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<Accession> getPdbAccs( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = new ArrayList<Accession>();
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
+ final SortedSet<Accession> 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() {
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();
}
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:
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;
case OPEN_TAX_WEB:
openTaxWeb( node );
break;
+ case OPEN_PDB_WEB:
+ openPdbWeb( node );
+ break;
case CUT_SUBTREE:
cutSubtree( node );
break;
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;
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();
}
}
- final void inferCommonPartOfScientificNames() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- setWaitCursor();
- AptxUtil.inferCommonPartOfScientificNames( _phylogeny );
- setArrowCursor();
- repaint();
- }
-
final private void init() {
_color_chooser = new JColorChooser();
_rollover_popup = new JTextArea();
setTreeFile( null );
setEdited( false );
initializeOvSettings();
- setStartingAngle( TWO_PI * 3 / 4 );
+ setStartingAngle( ( TWO_PI * 3 ) / 4 );
final ImageLoader il = new ImageLoader( this );
new Thread( il ).start();
}
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 ) );
- }
-
- 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() ) || !ForesterUtil.isEmpty( node
- .getNodeData().getSequence().getMolecularSequence() ) ) );
- }
-
- 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 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 ) ) );
}
- final boolean isCanCut( final PhylogenyNode node ) {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
- .isRoot() );
+ final private boolean inOvVirtualRectangle( final MouseEvent e ) {
+ return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
}
- final boolean isCanDelete() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
+ final private boolean isCanBlast( final PhylogenyNode node ) {
+ 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().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://" ) ) ) ) {
+ .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+ .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
return true;
}
else {
}
}
- 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
+ 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;
}
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
- getMainPanel().getTreeFontSet().decreaseFontSize();
+ getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else if ( plusPressed( e.getKeyCode() ) ) {
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<Accession> 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.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( 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;
- }
- setNodeInPreorderToNull();
- 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;
- }
- 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 ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Integer>() );
- }
- getFoundNodes().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
- _highlight_node = null;
- }
- }
- 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 ( 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() ) ) {
- // 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();
+ private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
+ if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
}
+ sb.append( node.getName() );
}
- else {
- if ( isInOvRect() ) {
- setInOvRect( false );
- repaint();
+ 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() );
}
- }
- if ( e.isControlDown() ) {
- if ( notches < 0 ) {
- getTreeFontSet().increaseFontSize();
- getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getGeneName() );
}
- else {
- getTreeFontSet().decreaseFontSize();
- getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ 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( ":" );
+ }
+ sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
}
- 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 );
- }
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( propertiesToString( node ) );
+ }
+ }
+
+ private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
+ 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(), sb );
}
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 );
- }
+ sb.append( taxonomy.getScientificName() );
}
+ sb.append( " (" );
+ sb.append( taxonomy.getCommonName() );
+ sb.append( ") " );
}
- else {
- if ( notches < 0 ) {
- for( int i = 0; i < ( -notches ); ++i ) {
- getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
}
else {
- for( int i = 0; i < notches; ++i ) {
- getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
+ sb.append( taxonomy.getScientificName() );
}
+ sb.append( " " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
}
}
- 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 if ( _control_panel.isShowTaxonomyScientificNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
}
- }
- 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 );
+ else {
+ sb.append( taxonomy.getScientificName() );
}
+ sb.append( " " );
+ }
+ }
+ else if ( _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
}
}
- requestFocus();
- requestFocusInWindow();
- requestFocus();
- }
-
- final void multiplyUrtFactor( final float f ) {
- _urt_factor *= f;
}
- final JApplet obtainApplet() {
- return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ private final String obtainTitleForExtDescNodeData() {
+ switch ( getOptions().getExtDescNodeDataToReturn() ) {
+ case NODE_NAME:
+ return "Node Names";
+ case GENE_NAME:
+ return "Gene Names";
+ case SEQUENCE_NAME:
+ return "Sequence Names";
+ case SEQUENCE_SYMBOL:
+ return "Sequence Symbols";
+ case SEQUENCE_MOL_SEQ:
+ return "Molecular Sequences";
+ case SEQUENCE_MOL_SEQ_FASTA:
+ return "Molecular Sequences (Fasta)";
+ case SEQUENCE_ACC:
+ return "Sequence Accessors";
+ case TAXONOMY_SCIENTIFIC_NAME:
+ return "Scientific Names";
+ case TAXONOMY_CODE:
+ return "Taxonomy Codes";
+ case TAXONOMY_COMM0N_NAME:
+ return "Taxonomy Common Names";
+ case UNKNOWN:
+ return "User Selected Data";
+ default:
+ throw new IllegalArgumentException( "unknown data element: "
+ + getOptions().getExtDescNodeDataToReturn() );
+ }
}
- final private void openSeqWeb( final PhylogenyNode node ) {
- if ( !isCanOpenSeqWeb( node ) ) {
- cannotOpenBrowserWarningMessage( "sequence" );
+ final private void openPdbWeb( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = getPdbAccs( node );
+ if ( ForesterUtil.isEmpty( pdb_ids ) ) {
+ cannotOpenBrowserWarningMessage( "PDB" );
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;
+ final List<String> 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 ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
+ }
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ }
}
else {
- final WebLink weblink = getConfiguration().getWebLink( source );
- url = weblink.getUrl().toString();
- }
- try {
- uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
+ cannotOpenBrowserWarningMessage( "PDB" );
}
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
+ }
+
+ final private void openSeqWeb( final PhylogenyNode node ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
+ cannotOpenBrowserWarningMessage( "sequence" );
+ return;
}
+ final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
}
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 ) {
+ 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://" ) ) {
+ else if ( ( tax.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && !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.UTF8 );
}
- catch ( final URISyntaxException e ) {
+ catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
- uri_str = null;
e.printStackTrace();
}
}
else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
try {
- uri_str = "http://www.eol.org/search?q="
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
}
else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
try {
- uri_str = "http://www.eol.org/search?q="
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
}
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_tax" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
}
}
- 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,
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 );
+ .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 );
+ .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 );
+ .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
}
else {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
- - getTreeFontSet()._small_max_descent, g );
+ - getTreeFontSet().getSmallMaxDescent(), g );
}
}
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( !to_graphics_file
&& !to_pdf
- && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
- .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
+ && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
+ .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
// Do nothing.
}
else {
}
// draw the horizontal line
if ( !to_graphics_file && !to_pdf
- && ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) {
+ && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
return;
}
float x1_r = 0;
}
}
if ( node.isExternal() ) {
- 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 ) {
- 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, isInFoundNodes( _root ) );
- }
-
- void updateSetOfCollapsedExternalNodes( final Phylogeny phy ) {
- _collapsed_external_nodeid_set.clear();
- 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() );
- continue E;
- }
- n = n.getParent();
- }
- }
- }
-
- 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 );
+ 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,
}
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 );
}
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 );
}
c = Color.BLACK;
}
else if ( is_in_found_nodes ) {
- c = getTreeColorSet().getFoundColor();
+ c = getColorForFoundNode( node );
+ }
+ else if ( getControlPanel().isColorAccordingToSequence() ) {
+ c = getSequenceBasedColor( node );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
c = getTaxonomyBasedColor( node );
}
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
c = PhylogenyMethods.getBranchColorValue( node );
}
else {
d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- final int box_size = getOptions().getDefaultNodeShapeSize();
+ final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
if ( d < box_size ) {
d = box_size;
}
+ final float xx = node.getXcoord() - ( 2 * box_size );
+ final float xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
_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 ) );
- if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ _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.fillPolygon( _polygon );
+ g.fill( _polygon );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
g.setColor( getBackground() );
- g.fillPolygon( _polygon );
+ g.fill( _polygon );
g.setColor( c );
- g.drawPolygon( _polygon );
+ g.draw( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
- .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
+ 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 );
}
- @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 );
- }
-
final private void paintConfidenceValues( final Graphics2D g,
final PhylogenyNode node,
final boolean to_pdf,
final boolean to_graphics_file ) {
final List<Confidence> 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();
- String conf_str = "";
for( final Confidence confidence : confidences ) {
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( "/" );
}
}
}
- //}
- 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;
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 ) {
- final int box_size = getOptions().getDefaultNodeShapeSize();
- final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
- 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 ) {
}
TreePanel
.drawString( gained,
- parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
- ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
+ parent_x
+ + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
+ ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
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 );
+ TreePanel
+ .drawString( lost,
+ parent_x
+ + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ),
+ ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
+ g );
}
}
* @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() )
+ || ( 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() && AptxUtil.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();
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();
}
}
- final int box_size = getOptions().getDefaultNodeShapeSize();
- final int half_box_size = box_size / 2;
- if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
+ NodeShape shape = null;
+ if ( vis != null ) {
+ if ( vis.getShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( vis.getShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ if ( shape == null ) {
if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
- if ( getOptions().getDefaultNodeFill() == 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 );
+ 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().getDefaultNodeFill() == NodeFill.NONE ) {
- Color background = getBackground();
- if ( to_pdf ) {
- background = Color.WHITE;
- }
- drawOvalGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- background,
- background,
- outline_color );
+ 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 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ else {
g.setColor( outline_color );
- drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
+ 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 ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeVisualization.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;
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualization.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 );
+ 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 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ else {
g.setColor( outline_color );
- drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
+ 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 ) {
if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
- return;
+ return 0;
}
if ( getOptions().isShowBranchLengthValues()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
paintBranchLength( g, node, to_pdf, to_graphics_file );
}
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
- return;
+ return 0;
}
+ _sb.setLength( 0 );
int x = 0;
final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
if ( getControlPanel().isShowTaxonomyImages()
.isShowTaxonomyCommonNames() ) && 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() );
- }
- _sb.setLength( 0 );
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
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( " " );
- }
- _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( ":" );
- }
- _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
- }
- }
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
if ( _sb.length() > 0 ) {
- _sb.append( " " );
+ _sb.setLength( 0 );
+ _sb.append( " (" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( ")" );
}
- _sb.append( propertiesToString( node ) );
}
- 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 ) );
+ final float 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 ) );
+ }
final String sb_str = _sb.toString();
// GUILHEM_BEG ______________
if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
.getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
+ ")";
if ( sConfidence != null ) {
- double confidenceX = pos_x;
+ float confidenceX = pos_x;
if ( sb_str.length() > 0 ) {
confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
+ CONFIDENCE_LEFT_MARGIN;
x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
}
}
- if ( x + nodeTextBoundsWidth > 0 ) /* we only underline if there is something displayed */
+ 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 */
}
}
}
- }
- if ( sb_str.length() > 0 ) {
- TreePanel.drawString( sb_str, pos_x, pos_y, g );
- }
- // 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 );
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else {
- 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 );
- _sb.setLength( 0 );
- _sb.append( ann_str );
- }
- 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 );
- }
- else {
- g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
- }
- 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() );
- }
- else {
- if ( DRAW_MEAN_COUNTS && node.isInternal() ) {
- final List<PhylogenyNode> 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() );
- }
- }
- }
- }
-
- private StringBuffer propertiesToString( final PhylogenyNode node ) {
- final PropertiesMap properties = node.getNodeData().getProperties();
- final StringBuffer sb = new StringBuffer();
- boolean first = true;
- for( final String ref : properties.getPropertyRefs() ) {
- if ( first ) {
- first = false;
- }
- else {
- sb.append( " " );
- }
- final Property p = properties.getProperty( ref );
- sb.append( getPartAfterColon( p.getRef() ) );
- sb.append( "=" );
- sb.append( p.getValue() );
- if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- sb.append( getPartAfterColon( p.getUnit() ) );
- }
- }
- return sb;
- }
-
- final private static String getPartAfterColon( final String s ) {
- final int i = s.indexOf( ':' );
- if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
- return s;
- }
- return s.substring( i + 1, s.length() );
- }
-
- private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
- final List<Uri> us = new ArrayList<Uri>();
- for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
- for( final Uri uri : t.getUris() ) {
- us.add( uri );
- }
- }
- 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;
- }
+ }
+ if ( sb_str.length() > 0 ) {
+ TreePanel.drawString( sb_str, pos_x, pos_y, g );
+ }
+ // GUILHEM_END _____________
+ 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 ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAnnotations() != null )
+ && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
+ final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else if ( getControlPanel().isColorAccordingToAnnotation() ) {
+ g.setColor( calculateColorForAnnotation( ann ) );
+ }
+ 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;
}
}
}
- return offset;
+ 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 ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else {
+ g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
+ }
+ if ( getControlPanel().isShowBinaryCharacters() ) {
+ TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
+ .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 {
+ 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;
}
final private void paintNodeDataUnrootedCirc( final Graphics2D g,
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()
}
_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 ) {
_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;
}
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 );
final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+ if ( !node.isRoot() && !node.getParent().isCollapse() ) {
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() ) {
final boolean dynamically_hide,
final int dynamic_hiding_factor,
final boolean to_graphics_file ) {
- final boolean is_in_found_nodes = isInFoundNodes( node );
+ 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;
}
float new_x = 0;
float new_x_min = Float.MAX_VALUE;
- final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
+ 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;
}
child_node.setYcoord( y2 );
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
+ 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
+ && ( ( 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 );
+ 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() ) ) {
if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
RenderableDomainArchitecture rds = null;
- if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
- try {
- rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
- }
- catch ( final ClassCastException cce ) {
- cce.printStackTrace();
- }
- if ( rds != null ) {
- rds.setRenderingHeight( 6 );
- int x = 0;
- if ( getControlPanel().isShowTaxonomyCode()
- && ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( node ) ) ) ) {
- x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
- }
- if ( getControlPanel().isShowGeneNames()
- && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
- }
- if ( getControlPanel().isShowGeneSymbols()
- && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
- x += getTreeFontSet()._fm_large
- .stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
- }
- if ( getControlPanel().isShowSequenceAcc()
- && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
- .toString()
- + " " );
- }
- if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
- }
- 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() );
- if ( rv != null ) {
- 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() + " " );
- }
- rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, 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 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() );
- getOvRectangle().setRect( x, y, width, height );
- if ( ( width < 6 ) && ( height < 6 ) ) {
- drawRectFilled( x, y, 6, 6, g );
- getOvVirtualRectangle().setRect( x, y, 6, 6 );
- }
- else if ( width < 6 ) {
- drawRectFilled( x, y, 6, height, g );
- getOvVirtualRectangle().setRect( x, y, 6, height );
- }
- else if ( height < 6 ) {
- drawRectFilled( x, y, width, 6, g );
- getOvVirtualRectangle().setRect( x, y, width, 6 );
- }
- else {
- drawRect( x, y, width, height, g );
- if ( isInOvRect() ) {
- drawRect( x + 1, y + 1, width - 2, height - 2, g );
- }
- 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 );
+ 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( getMaxDistanceToRoot() * getXcorrectionFactor() + _length_of_longest_text
+ + ( _longest_domain - rds.getTotalLength() )
+ * rds.getRenderingFactorWidth(),
+ node.getYcoord() - ( h / 2 ),
+ g,
+ this,
+ to_pdf );
+ }
+ else {
+ rds.render( getMaxDistanceToRoot() * getXcorrectionFactor() + _length_of_longest_text,
+ node.getYcoord() - ( h / 2 ),
+ g,
+ this,
+ to_pdf );
+ }
+ }
+ else {
+ rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2 ), g, this, to_pdf );
+ }
}
else {
- paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ if ( getOptions().isRightLineUpDomains() ) {
+ rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text
+ - 20 + ( _longest_domain - rds.getTotalLength() )
+ * rds.getRenderingFactorWidth(),
+ node.getYcoord() - ( h / 2 ),
+ g,
+ this,
+ to_pdf );
+ }
+ else {
+ rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
+ node.getYcoord() - ( h / 2 ),
+ g,
+ this,
+ to_pdf );
+ }
}
}
- 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 );
+ if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
+ && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
+ final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
+ getStatisticsForExpressionValues(),
+ getConfiguration() );
+ if ( rv != null ) {
+ double domain_add = 0;
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ domain_add = _domain_structure_width + 10;
}
- }
- 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 );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ rv.render( node.getXcoord() + x + domain_add, node.getYcoord() - 3, g, this, to_pdf );
}
else {
- y_scale = ( double ) getWidth() / getHeight();
- y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
+ rv.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + domain_add,
+ node.getYcoord() - 3,
+ g,
+ this,
+ to_pdf );
}
- _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 private int calcLengthOfLongestText() {
+ final StringBuilder sb = new StringBuilder();
+ 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() );
+ }
+
+ 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 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().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 );
+ }
+ else if ( width < 6 ) {
+ drawRectFilled( x, y, 6, height, g );
+ getOvVirtualRectangle().setRect( x, y, 6, height );
+ }
+ else if ( height < 6 ) {
+ drawRectFilled( x, y, width, 6, g );
+ getOvVirtualRectangle().setRect( x, y, width, 6 );
+ }
+ else {
+ drawRect( x, y, width, height, g );
+ if ( isInOvRect() ) {
+ drawRect( x + 1, y + 1, width - 2, height - 2, g );
+ }
+ getOvVirtualRectangle().setRect( x, y, width, height );
+ }
+ 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().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 );
}
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,
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,
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() );
+ final float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
+ 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 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + 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( " " );
- }
- }
+ nodeTaxonomyDataAsSB( taxonomy, _sb );
final String label = _sb.toString();
/* GUILHEM_BEG */
if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
}
/* 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,
to_graphics_file,
radial_labels,
( high_angle + low_angle ) / 2,
- isInFoundNodes( n ) );
+ isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
return;
}
final float num_enclosed = n.getNumberOfExternalNodes();
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 );
}
}
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 );
}
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 );
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 + "?",
}
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 ) {
}
}
if ( getCopiedAndPastedNodes() == null ) {
- setCopiedAndPastedNodes( new HashSet<Integer>() );
+ setCopiedAndPastedNodes( new HashSet<Long>() );
}
final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
- final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
+ final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
for( final PhylogenyNode n : nodes ) {
node_ids.add( n.getId() );
}
node_ids.add( node.getId() );
- getCopiedAndPastedNodes().addAll( node_ids );
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- if ( need_to_show_whole ) {
- getControlPanel().showWhole();
- }
- 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() );
- }
-
- /**
- * 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();
- repaint();
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- getControlPanel().showWhole();
- }
- }
-
- final void resetNodeIdToDistToLeafMap() {
- _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
- }
-
- 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().getHeight() ) + getXdistance() );
+ getCopiedAndPastedNodes().addAll( node_ids );
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ if ( need_to_show_whole ) {
+ getControlPanel().showWhole();
}
- else {
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil.roundToInt( getXdistance()
- * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
+ repaint();
+ }
+
+ private final StringBuffer propertiesToString( final PhylogenyNode node ) {
+ final PropertiesMap properties = node.getNodeData().getProperties();
+ final StringBuffer sb = new StringBuffer();
+ boolean first = true;
+ for( final String ref : properties.getPropertyRefs() ) {
+ if ( first ) {
+ first = false;
}
else {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil.roundToInt( getXdistance()
- * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
+ sb.append( " " );
+ }
+ final Property p = properties.getProperty( ref );
+ sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
+ sb.append( "=" );
+ sb.append( p.getValue() );
+ if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
+ sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
- setPreferredSize( new Dimension( x, y ) );
- }
-
- public final void setArrowCursor() {
- setCursor( ARROW_CURSOR );
- repaint();
+ return sb;
}
- final void setControlPanel( final ControlPanel atv_control ) {
- _control_panel = atv_control;
+ 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 );
+ }
+ else if ( is_in_found_nodes ) {
+ g.setColor( getColorForFoundNode( node ) );
+ }
+ else if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
+ && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
+ g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
+ }
+ else if ( getControlPanel().isColorAccordingToSequence() ) {
+ g.setColor( getSequenceBasedColor( node ) );
+ }
+ else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
+ g.setColor( getTaxonomyBasedColor( node ) );
+ }
+ else if ( getControlPanel().isColorAccordingToAnnotation()
+ && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
+ .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
+ g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
+ }
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
+ && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ }
+ else if ( to_pdf ) {
+ g.setColor( Color.BLACK );
+ }
+ else {
+ g.setColor( default_color );
+ }
}
- final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
+ final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
getMainPanel().setCopiedAndPastedNodes( nodeIds );
}
getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
}
- public final void setEdited( final boolean edited ) {
- _edited = edited;
- }
-
- final void setFoundNodes( final Set<Integer> 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;
}
_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;
}
_ov_y_start = ov_y_start;
}
- /**
- * Set parameters for printing the displayed tree
- *
- * @param x
- * @param y
- */
- public 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;
}
_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() < 0.001 ) {
+ g.setStroke( STROKE_005 );
}
- 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 );
- }
+ 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 ) {
+ 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 ) {
- setNodeInPreorderToNull();
- _phylogeny = t;
- }
-
- final void setNodeInPreorderToNull() {
- _nodes_in_preorder = null;
- }
-
- final void setTreeFile( final File treefile ) {
- _treefile = treefile;
- }
-
final private void setUpUrtFactor() {
final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
: getVisibleRect().height;
_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 List<String> data = new ArrayList<String>();
+ final List<PhylogenyNode> 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:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+ data.add( n.getNodeData().getSequence().getMolecularSequence() );
+ }
+ 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 ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ ann.append( n.getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+ ann.append( "SYM=" );
+ ann.append( n.getNodeData().getSequence().getSymbol() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ ann.append( "NAME=" );
+ ann.append( n.getNodeData().getSequence().getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ ann.append( "GN=" );
+ ann.append( n.getNodeData().getSequence().getGeneName() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().getSequence().getAccession() != null ) {
+ ann.append( "ACC=" );
+ ann.append( n.getNodeData().getSequence().getAccession().asText() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ ann.append( "TAXID=" );
+ ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ ann.append( "SN=" );
+ ann.append( n.getNodeData().getTaxonomy().getScientificName() );
+ ann.append( "|" );
+ }
+ }
+ String ann_str;
+ if ( ann.charAt( ann.length() - 1 ) == '|' ) {
+ 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_COMM0N_NAME:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getCommonName() );
+ }
+ break;
+ case TAXONOMY_CODE:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ 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.makeSB( 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() == NODE_DATA.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + " nodes, unique entries: "
+ + size;
+ }
+ else {
+ title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + "/"
+ + node.getNumberOfExternalNodes()
+ + " external descendats of node "
+ + node
+ + ", unique entries: " + size;
+ }
+ final String s = sb.toString().trim();
+ if ( getMainPanel().getMainFrame() == null ) {
+ // Must be "E" applet version.
+ final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ ae.showTextFrame( s, title );
+ }
+ else {
+ 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().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
- || node.getBranchData().isHasConfidences() ) {
+ || ( 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 );
short lines = 0;
if ( node.getName().length() > 0 ) {
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();
}
}
}
- 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 ) {
_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( " " );
for( final String ref : properties.getPropertyRefs() ) {
_popup_buffer.append( "\n" );
final Property p = properties.getProperty( ref );
- _popup_buffer.append( getPartAfterColon( p.getRef() ) );
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
_popup_buffer.append( "=" );
_popup_buffer.append( p.getValue() );
if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
}
_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 ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
}
- else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
+ else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
}
else {
_rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
}
}
- final void subTree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot get a sub/super tree in unrooted display",
- "Attempt to get sub/super tree in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- if ( node.isExternal() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot get a subtree of a external node",
- "Attempt to get subtree of external node",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot get a subtree of the root node",
- "Attempt to get subtree of root node",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- 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 );
- updateSubSuperTreeButton();
- }
- else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
- superTree();
- }
- _main_panel.getControlPanel().showWhole();
- 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() {
- setNodeInPreorderToNull();
- final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
- for( final PhylogenyNode n : temp_root.getDescendants() ) {
- n.setParent( temp_root );
- }
- _sub_phylogenies[ _subtree_index ] = null;
- _sub_phylogenies_temp_roots[ _subtree_index ] = null;
- _phylogeny = _sub_phylogenies[ --_subtree_index ];
- updateSubSuperTreeButton();
- }
-
- final void swap( final PhylogenyNode node ) {
- if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
- return;
- }
- if ( node.getNumberOfDescendants() > 2 ) {
- JOptionPane.showMessageDialog( this,
- "Cannot swap descendants of nodes with more than 2 descendants",
- "Cannot swap descendants",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( !node.isExternal() ) {
- node.swapChildren();
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- }
- repaint();
- }
-
- final void sortDescendants( final PhylogenyNode node ) {
- if ( !node.isExternal() ) {
- DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
- if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
- .isShowTaxonomyCommonNames() ) ) {
- if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
- .isShowGeneSymbols() ) ) {
- pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
- }
- else if ( getControlPanel().isShowNodeNames() ) {
- pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
- }
- }
- PhylogenyMethods.sortNodeDescendents( node, pri );
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.hashIDs();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- }
- repaint();
- }
-
final private void switchDisplaygetPhylogenyGraphicsType() {
switch ( getPhylogenyGraphicsType() ) {
case RECTANGULAR:
}
}
- final void taxColor() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
+ private final static void colorizeNodesHelper( final Color c, final PhylogenyNode node ) {
+ if ( node.getNodeData().getNodeVisualData() == null ) {
+ node.getNodeData().setNodeVisualData( new NodeVisualData() );
}
- setWaitCursor();
- AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
- }
- setArrowCursor();
- repaint();
+ node.getNodeData().getNodeVisualData().setFontColor( new Color( c.getRed(), c.getGreen(), c.getBlue() ) );
}
- final void updateOvSettings() {
- switch ( getOptions().getOvPlacement() ) {
- case LOWER_LEFT:
- setOvXPosition( OV_BORDER );
- setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
- setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
- break;
- case LOWER_RIGHT:
- setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
- setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
- setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
- break;
- case UPPER_RIGHT:
- setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
- setOvYPosition( OV_BORDER );
- setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
- break;
- default:
- setOvXPosition( OV_BORDER );
- setOvYPosition( OV_BORDER );
- setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
- break;
- }
+ final private static void drawString( final String str, final float x, final float y, final Graphics2D g ) {
+ g.drawString( str, x, y );
}
- final void updateOvSizes() {
- if ( ( getWidth() > 1.05 * getVisibleRect().width ) || ( getHeight() > 1.05 * getVisibleRect().height ) ) {
- setOvOn( true );
- float l = getLongestExtNodeInfo();
- final float w_ratio = getOvMaxWidth() / getWidth();
- l *= w_ratio;
- final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
- setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
- float ov_xdist = 0;
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
- ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
- }
- else {
- ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
- }
- float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
- if ( ov_xdist < 0.0 ) {
- ov_xdist = 0.0f;
- }
- if ( ydist < 0.0 ) {
- ydist = 0.0f;
- }
- setOvXDistance( ov_xdist );
- final double height = _phylogeny.getHeight();
- if ( height > 0 ) {
- final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
- setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
- }
- else {
- setOvXcorrectionFactor( 0 );
- }
- }
- else {
- setOvOn( false );
- }
+ 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 ) );
}
- final void updateSubSuperTreeButton() {
- if ( _subtree_index < 1 ) {
- getControlPanel().deactivateButtonToReturnToSuperTree();
- }
- else {
- getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
- }
- }
+ final private class NodeColorizationActionListener implements ActionListener {
- final void zoomInDomainStructure() {
- if ( _domain_structure_width < 2000 ) {
- _domain_structure_width *= 1.2;
- }
- }
+ List<PhylogenyNode> _additional_nodes = null;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
- final void zoomOutDomainStructure() {
- if ( _domain_structure_width > 20 ) {
- _domain_structure_width *= 0.8;
+ NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
+ _chooser = chooser;
+ _node = node;
}
- }
-
- 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 ) );
- }
-
- 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 static boolean isSequenceEmpty( final Sequence seq ) {
- return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
- && ForesterUtil.isEmpty( seq.getSymbol() );
- }
-
- 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() );
- }
- 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 ) );
- }
-
- void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
- _statistics_for_vector_data = statistics_for_expression_values;
- }
+ NodeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _chooser = chooser;
+ _node = node;
+ _additional_nodes = additional_nodes;
+ }
- DescriptiveStatistics getStatisticsForExpressionValues() {
- return _statistics_for_vector_data;
+ @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 {
- JColorChooser _chooser;
- PhylogenyNode _node;
+ List<PhylogenyNode> _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<PhylogenyNode> 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 );
+ colorizeSubtree( c, _node, _additional_nodes );
}
}
}
-
- public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
- getMainPanel().setImageMap( image_map );
- }
-
- public synchronized Hashtable<String, BufferedImage> getImageMap() {
- return getMainPanel().getImageMap();
- }
}
git://source.jalview.org / jalview.git / blobdiff