// 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.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.HashSet;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map.Entry;
import java.util.Set;
+import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
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.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Event;
+import org.forester.phylogeny.data.NodeData.NODE_DATA;
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.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.SequenceIdParser;
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 );
+ private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
+ private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
+ private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
+ private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
+ private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
+ private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
+ private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
+ 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 = 2000;
+ private final static int CONFIDENCE_LEFT_MARGIN = 4;
+ 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<Long> _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 Path2D.Float _polygon = new Path2D.Float();
+ 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<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
+ final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
+ final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
+ HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, 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 StringBuffer _popup_buffer = new StringBuffer();
+ final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
+ Font.PLAIN,
+ 12 );
+ private Sequence _query_sequence = null;
+ private final FontRenderContext _frc = new FontRenderContext( null,
+ false,
+ false );
// expression values menu:
- private DescriptiveStatistics _statistics_for_vector_data;
- private PhylogenyNode[] _nodes_in_preorder = null;
+ private DescriptiveStatistics _statistics_for_vector_data;
+ private PhylogenyNode[] _nodes_in_preorder = null;
+ private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
+ private int _current_external_nodes_data_buffer_change_counter = 0;
+ private Set<Long> _current_external_nodes = null;
// 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 );
- }
- 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;
- }
- }
-
+ @Override
final public void actionPerformed( final ActionEvent e ) {
boolean done = false;
final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
requestFocusInWindow();
}
- final private void addEmptyNode( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- final String label = getASimpleTextRepresentationOfANode( node );
- String msg = "";
- if ( ForesterUtil.isEmpty( label ) ) {
- msg = "How to add the new, empty node?";
- }
- else {
- msg = "How to add the new, empty node to node" + label + "?";
- }
- final Object[] options = { "As sibling", "As descendant", "Cancel" };
- final int r = JOptionPane.showOptionDialog( this,
- msg,
- "Addition of Empty New Node",
- JOptionPane.CLOSED_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[ 2 ] );
- boolean add_as_sibling = true;
- if ( r == 1 ) {
- add_as_sibling = false;
- }
- else if ( r != 0 ) {
- return;
- }
- final Phylogeny phy = new Phylogeny();
- phy.setRoot( new PhylogenyNode() );
- phy.setRooted( true );
- if ( add_as_sibling ) {
- if ( node.isRoot() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot add sibling to root",
- "Attempt to add sibling to root",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- phy.addAsSibling( node );
- }
- else {
- phy.addAsChild( node );
- }
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- repaint();
+ public synchronized Hashtable<String, BufferedImage> getImageMap() {
+ return getMainPanel().getImageMap();
}
- final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
- final boolean is_vertical,
- final Graphics g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
- || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
- && ( getCutOrCopiedTree() != null )
- && ( getCopiedAndPastedNodes() != null )
- && !to_pdf
- && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
- }
- else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
- }
- else if ( to_pdf ) {
- g.setColor( getTreeColorSet().getBranchColorForPdf() );
- }
- else {
- g.setColor( getTreeColorSet().getBranchColor() );
- }
+ final public MainPanel getMainPanel() {
+ return _main_panel;
}
- final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
- if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- return ( PhylogenyMethods.getBranchColorValue( node ) );
- }
- else {
- return ( getTreeColorSet().getBranchColor() );
- }
+ /**
+ * Get a pointer to the phylogeny
+ *
+ * @return a pointer to the phylogeny
+ */
+ public final Phylogeny getPhylogeny() {
+ return _phylogeny;
}
- final private void blast( final PhylogenyNode node ) {
- if ( !isCanBlast( node ) ) {
- JOptionPane.showMessageDialog( this,
- "No sequence information present",
- "Cannot Blast",
- JOptionPane.WARNING_MESSAGE );
- return;
+ @Override
+ final public void mouseWheelMoved( final MouseWheelEvent e ) {
+ final int notches = e.getWheelRotation();
+ if ( inOvVirtualRectangle( e ) ) {
+ if ( !isInOvRect() ) {
+ setInOvRect( true );
+ repaint();
+ }
}
- if ( node.getNodeData().isHasSequence() ) {
- final String query = Blast.obtainQueryForBlast( node );
- boolean nucleotide = false;
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
- if ( !node.getNodeData().getSequence().getType().toLowerCase().equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
- nucleotide = true;
- }
+ else {
+ if ( isInOvRect() ) {
+ setInOvRect( false );
+ repaint();
+ }
+ }
+ if ( e.isControlDown() ) {
+ if ( notches < 0 ) {
+ getTreeFontSet().increaseFontSize();
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- nucleotide = !ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() );
+ else {
+ getTreeFontSet().decreaseFontSize( 1, false );
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- if ( !ForesterUtil.isEmpty( query ) ) {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- try {
- Blast.openNcbiBlastWeb( query, nucleotide, applet, this );
+ }
+ 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 );
+ }
}
- catch ( final Exception e ) {
- e.printStackTrace();
+ 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 );
+ }
}
- if ( Constants.ALLOW_DDBJ_BLAST ) {
- try {
- System.out.println( "trying: " + query );
- final Blast s = new Blast();
- s.ddbjBlast( query );
+ }
+ else {
+ if ( notches < 0 ) {
+ for( int i = 0; i < ( -notches ); ++i ) {
+ getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
- catch ( final Exception e ) {
- e.printStackTrace();
+ }
+ else {
+ for( int i = 0; i < notches; ++i ) {
+ getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
}
}
- }
-
- final void calcMaxDepth() {
- if ( _phylogeny != null ) {
- _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ 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();
}
- /**
- * Calculate the length of the distance between the given node and its
- * parent.
- *
- * @param node
- * @param ext_node_x
- * @factor
- * @return the distance value
- */
- final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
- if ( getControlPanel().isDrawPhylogram() ) {
- if ( node.getDistanceToParent() < 0.0 ) {
- return 0.0f;
- }
- return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
+ @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 {
- if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
- return getXdistance();
- }
- return getXdistance() * factor;
+ 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 private Color calculateColorForAnnotation( final PhylogenyData ann ) {
- Color c = getTreeColorSet().getAnnotationColor();
- if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
- c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() );
- if ( c == null ) {
- c = getTreeColorSet().getAnnotationColor();
+ 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();
+ }
+ }
+ else {
+ while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
+ .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ 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();
+ //
+ 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();
+ // }
+ // }
+ }
+ }
+ //
}
- return c;
}
final void calculateLongestExtNodeInfo() {
if ( getControlPanel().isShowAnnotation()
&& ( node.getNodeData().getSequence().getAnnotations() != null )
&& !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
- sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
- .asSimpleText()
+ sum += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
+ .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
+ " " );
}
if ( getControlPanel().isShowDomainArchitectures()
}
}
- final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
- if ( getControlPanel().isDrawPhylogram() ) {
- if ( node.getDistanceToParent() < 0.0 ) {
- return 0.0f;
- }
- return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
- }
- else {
- if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
- return getOvXDistance();
- }
- return getOvXDistance() * factor;
- }
- }
-
final void calculateScaleDistance() {
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
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 ) ) {
+ if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
return getTreeColorSet().getTaxonomyColor();
}
- // Look in species hash
- Color c = getControlPanel().getSpeciesColors().get( species );
+ 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 ) {
- c = AptxUtil.calculateColorFromString( species );
- getControlPanel().getSpeciesColors().put( species, c );
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = TreePanelUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
+ getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
+ }
+ else {
+ c = TreePanelUtil.calculateColorFromString( tax.getScientificName(), true );
+ getControlPanel().getSpeciesColors().put( tax.getScientificName(), 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",
- "Cannot launch web browser",
- JOptionPane.WARNING_MESSAGE );
+ 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() );
}
/**
}
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
- AptxUtil.collapseSubtree( node, collapse );
+ TreePanelUtil.collapseSubtree( node, collapse );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
return;
}
setWaitCursor();
- AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+ TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
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;
- }
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
- }
- for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
- }
- repaint();
- }
-
- final private void colorSubtree( final PhylogenyNode node ) {
- Color intitial_color = null;
- if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
- && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
- intitial_color = PhylogenyMethods.getBranchColorValue( node );
- }
- else {
- intitial_color = getTreeColorSet().getBranchColor();
- }
- _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 );
- }
-
- final void confColor() {
+ final void colorRank( final String rank ) {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
}
setWaitCursor();
AptxUtil.removeBranchColors( _phylogeny );
- AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
- }
- setArrowCursor();
- repaint();
- }
-
- final void colorRank( final String rank ) {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- setWaitCursor();
- AptxUtil.removeBranchColors( _phylogeny );
- final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
if ( colorizations > 0 ) {
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
else {
msg += "colorized one subtree";
}
+ setEdited( true );
JOptionPane.showMessageDialog( this,
msg,
"Taxonomy Colorization Completed (" + rank + ")",
}
}
- final private void copySubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- setNodeInPreorderToNull();
- setCutOrCopiedTree( _phylogeny.copy( node ) );
- final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
- final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
- for( final PhylogenyNode n : nodes ) {
- node_ids.add( n.getId() );
- }
- node_ids.add( node.getId() );
- setCopiedAndPastedNodes( node_ids );
- repaint();
- }
-
- final private void cutSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- if ( node.isRoot() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot cut entire tree as subtree",
- "Attempt to cut entire tree",
- JOptionPane.ERROR_MESSAGE );
+ final void confColor() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
}
- final String label = getASimpleTextRepresentationOfANode( node );
- final int r = JOptionPane.showConfirmDialog( null,
- "Cut subtree" + label + "?",
- "Confirm Cutting of Subtree",
- JOptionPane.YES_NO_OPTION );
- if ( r != JOptionPane.OK_OPTION ) {
- return;
+ setWaitCursor();
+ AptxUtil.removeBranchColors( _phylogeny );
+ TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getColorBranchesCb() != null ) {
+ _control_panel.getColorBranchesCb().setSelected( true );
}
- setNodeInPreorderToNull();
- setCopiedAndPastedNodes( null );
- setCutOrCopiedTree( _phylogeny.copy( node ) );
- _phylogeny.deleteSubtree( node, true );
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
+ setArrowCursor();
repaint();
}
- final private void cycleColors() {
- getMainPanel().getTreeColorSet().cycleColorScheme();
- for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
- tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
- }
- }
-
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 );
- setOvMaxHeight( getOvMaxHeight() - 5 );
- updateOvSettings();
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- }
-
- final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- if ( node.isRoot() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot delete entire tree",
- "Attempt to delete entire tree",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final String label = getASimpleTextRepresentationOfANode( node );
- final Object[] options = { "Node only", "Entire subtree", "Cancel" };
- final int r = JOptionPane.showOptionDialog( this,
- "Delete" + label + "?",
- "Delete Node/Subtree",
- JOptionPane.CLOSED_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[ 2 ] );
- setNodeInPreorderToNull();
- boolean node_only = true;
- if ( r == 1 ) {
- node_only = false;
- }
- else if ( r != 0 ) {
- return;
- }
- if ( node_only ) {
- PhylogenyMethods.removeNode( node, _phylogeny );
- }
- else {
- _phylogeny.deleteSubtree( node, true );
- }
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- repaint();
- }
-
- final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
- makePopupMenus( node );
- _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
- _node_popup_menu.show( this, x, y );
- }
-
- final private void drawArc( final double x,
- final double y,
- final double width,
- final double heigth,
- final double start_angle,
- final double arc_angle,
- final Graphics2D g ) {
- _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
- g.draw( _arc );
- }
-
- final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
- if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
- return;
- }
- _line.setLine( x1, y1, x2, y2 );
- g.draw( _line );
- }
-
- final private void drawOval( final double x,
- final double y,
- final double width,
- final double heigth,
- final Graphics2D g ) {
- _ellipse.setFrame( x, y, width, heigth );
- g.draw( _ellipse );
- }
-
- final private void drawOvalFilled( final double x,
- final double y,
- final double width,
- final double heigth,
- final Graphics2D g ) {
- _ellipse.setFrame( x, y, width, heigth );
- g.fill( _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 );
- }
-
- final private void drawRectFilled( final double x,
- final double y,
- final double width,
- final double heigth,
- final Graphics2D g ) {
- _rectangle.setFrame( x, y, width, heigth );
- 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 Graphics2D g,
- final Color color_1,
- final Color color_2,
- final Color color_border ) {
- _ellipse.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint( ( float ) x,
- ( float ) y,
- color_1,
- ( float ) ( x + width ),
- ( float ) ( y + heigth ),
- color_2,
- false ) );
- g.fill( _ellipse );
- if ( color_border != null ) {
- g.setPaint( color_border );
- g.draw( _ellipse );
- }
- }
-
- final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
- JOptionPane.showMessageDialog( this,
- "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
- "Attempt to cut/copy/paste/add/delete in unrooted display",
- JOptionPane.ERROR_MESSAGE );
- }
-
/**
* Find the node, if any, at the given location
*
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return null;
}
- final int half_box_size_plus_wiggle = getOptions().getDefaultNodeShapeSize() / 2 + WIGGLE;
+ 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 ) )
return null;
}
- final private String getASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
- final String tax = PhylogenyMethods.getSpecies( node );
- String label = node.getName();
- if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
- label = label + " " + tax;
- }
- else if ( !ForesterUtil.isEmpty( tax ) ) {
- label = tax;
- }
- else {
- label = "";
- }
- if ( !ForesterUtil.isEmpty( label ) ) {
- label = " [" + label + "]";
- }
- return label;
- }
-
final Configuration getConfiguration() {
return _configuration;
}
return _control_panel;
}
- final private Set<Integer> getCopiedAndPastedNodes() {
- return getMainPanel().getCopiedAndPastedNodes();
+ String getCurrentExternalNodesDataBufferAsString() {
+ return _current_external_nodes_data_buffer.toString();
}
- final private Phylogeny getCutOrCopiedTree() {
- return getMainPanel().getCutOrCopiedTree();
+ int getCurrentExternalNodesDataBufferChangeCounter() {
+ return _current_external_nodes_data_buffer_change_counter;
}
final int getDomainStructureEvalueThreshold() {
return _domain_structure_e_value_thr_exp;
}
- final Set<Integer> getFoundNodes() {
+ final Set<Long> getFoundNodes() {
return _found_nodes;
}
- final private float getLastDragPointX() {
- return _last_drag_point_x;
- }
-
- final private float getLastDragPointY() {
- return _last_drag_point_y;
- }
-
- final int getLongestExtNodeInfo() {
- return _longest_ext_node_info;
- }
-
- final public MainPanel getMainPanel() {
- return _main_panel;
- }
-
- final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
- if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
- final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
- _nodeid_dist_to_leaf.put( node.getId(), m );
- return m;
+ final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
+ if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ return ( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
- return _nodeid_dist_to_leaf.get( node.getId() );
+ return ( getTreeColorSet().getBranchColor() );
}
}
- final private double getMaxDistanceToRoot() {
- if ( _max_distance_to_root < 0 ) {
- recalculateMaxDistanceToRoot();
- }
- return _max_distance_to_root;
+ final int getLongestExtNodeInfo() {
+ return _longest_ext_node_info;
}
final Options getOptions() {
return _options;
}
- final private float getOvMaxHeight() {
- return _ov_max_height;
- }
-
- final private float getOvMaxWidth() {
- return _ov_max_width;
- }
-
final Rectangle2D getOvRectangle() {
return _ov_rectangle;
}
return _ov_virtual_rectangle;
}
- final private float getOvXcorrectionFactor() {
- return _ov_x_correction_factor;
- }
-
- final private float getOvXDistance() {
- return _ov_x_distance;
- }
-
- final private int getOvXPosition() {
- return _ov_x_position;
- }
-
- final private float getOvYDistance() {
- return _ov_y_distance;
- }
-
- final private int getOvYPosition() {
- return _ov_y_position;
- }
-
- final private int getOvYStart() {
- 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 double getScaleDistance() {
- return _scale_distance;
- }
-
- final private String getScaleLabel() {
- return _scale_label;
- }
-
final double getStartingAngle() {
return _urt_starting_angle;
}
+ DescriptiveStatistics getStatisticsForExpressionValues() {
+ return _statistics_for_vector_data;
+ }
+
/**
* Find a color for this species name.
*
return _treefile;
}
- final private TreeFontSet getTreeFontSet() {
- return getMainPanel().getTreeFontSet();
- }
-
- final private float getUrtFactor() {
- return _urt_factor;
- }
-
- final private float getUrtFactorOv() {
- return _urt_factor_ov;
- }
-
final float getXcorrectionFactor() {
return _x_correction_factor;
}
return _y_distance;
}
- final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
- switch ( action ) {
- case SHOW_DATA:
- showNodeFrame( node );
- break;
- case COLLAPSE:
- collapse( node );
- break;
- case REROOT:
- reRoot( node );
- break;
- case SUBTREE:
- subTree( node );
- break;
- case SWAP:
- swap( node );
- break;
- case COLOR_SUBTREE:
- colorSubtree( node );
- break;
- case OPEN_SEQ_WEB:
- openSeqWeb( node );
- break;
- case BLAST:
- blast( node );
- break;
- case OPEN_TAX_WEB:
- openTaxWeb( node );
- break;
- case CUT_SUBTREE:
- cutSubtree( node );
- break;
- case COPY_SUBTREE:
- copySubtree( node );
- break;
- case PASTE_SUBTREE:
- pasteSubtree( node );
- break;
- case DELETE_NODE_OR_SUBTREE:
- deleteNodeOrSubtree( node );
- break;
- case ADD_NEW_NODE:
- addEmptyNode( node );
- break;
- case EDIT_NODE_DATA:
- showNodeEditFrame( node );
- break;
- case SORT_DESCENDENTS:
- sortDescendants( node );
- break;
- case GET_EXT_DESC_DATA:
- getExtDescNodeData( node );
- break;
- default:
- throw new IllegalArgumentException( "unknown action: " + action );
- }
- }
-
- private void getExtDescNodeData( final PhylogenyNode node ) {
- for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
- switch ( getOptions().getExtDescNodeDataToReturn() ) {
- case NODE_NAME:
- System.out.println( n.getName() );
- break;
- case SEQUENCE_NAME:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- System.out.println( n.getNodeData().getSequence().getName() );
- }
- break;
- case SEQUENCE_SYMBOL:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
- System.out.println( n.getNodeData().getSequence().getSymbol() );
- }
- break;
- case SEQUENCE_MOL_SEQ:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
- System.out.println( n.getNodeData().getSequence().getMolecularSequence() );
- }
- break;
- case SEQUENCE_ACC:
- if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null ) ) {
- System.out.println( n.getNodeData().getSequence().getAccession().toString() );
- }
- break;
- default:
- throw new IllegalArgumentException( "unknown data element: "
- + getOptions().getExtDescNodeDataToReturn() );
- }
- }
- }
-
final void increaseDomainStructureEvalueThreshold() {
if ( _domain_structure_e_value_thr_exp < 3 ) {
_domain_structure_e_value_thr_exp += 1;
}
}
- final private void increaseOvSize() {
- if ( ( getOvMaxWidth() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 )
- && ( getOvMaxHeight() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
- .getHeight() / 2 ) ) {
- setOvMaxWidth( getOvMaxWidth() + 5 );
- setOvMaxHeight( getOvMaxHeight() + 5 );
- updateOvSettings();
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- }
-
- 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();
- _rollover_popup.setFont( POPUP_FONT );
- resetNodeIdToDistToLeafMap();
- setTextAntialias();
- setTreeFile( null );
- setEdited( false );
- initializeOvSettings();
- setStartingAngle( TWO_PI * 3 / 4 );
- final ImageLoader il = new ImageLoader( this );
- new Thread( il ).start();
- }
-
- final private void initializeOvSettings() {
- setOvMaxHeight( getConfiguration().getOvMaxHeight() );
- setOvMaxWidth( getConfiguration().getOvMaxWidth() );
- }
-
final void initNodeData() {
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
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 ) );
+ 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() ) );
+ 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 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().getMolecularSequence() ) ) && Blast
- .isContainsQueryForBlast( node ) );
- }
-
final boolean isCanCollapse() {
return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
}
- 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;
- }
- return false;
- }
-
- final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
- if ( node.getNodeData().isHasTaxonomy()
- && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
- .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
- || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
- || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
- || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
- .getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
- .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
- return true;
- }
- else {
- return false;
- }
- }
-
final boolean isCanPaste() {
return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
&& ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
.isRoot() || ( _subtree_index > 0 ) ) );
}
- final boolean isEdited() {
- return _edited;
- }
-
- final private boolean isInFoundNodes( final PhylogenyNode node ) {
- return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
+ final boolean isCurrentTreeIsSubtree() {
+ return ( _subtree_index > 0 );
}
- final private boolean isInOv() {
- return _in_ov;
+ final boolean isEdited() {
+ return _edited;
}
final boolean isInOvRect() {
return _in_ov_rect;
}
- final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
- int y_dist = 40;
- if ( getControlPanel().isShowTaxonomyImages() ) {
- y_dist = 40 + ( int ) getYdistance();
- }
- return ( ( node.getYcoord() < getVisibleRect().getMinY() - y_dist )
- || ( node.getYcoord() > getVisibleRect().getMaxY() + y_dist ) || ( ( node.getParent() != null ) && ( node
- .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
- }
-
- 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 ) );
- }
-
- final private boolean isNonLinedUpCladogram() {
- return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
- }
-
- final boolean isOvOn() {
- return _ov_on;
+ final boolean isOvOn() {
+ return _ov_on;
}
final boolean isPhyHasBranchLengths() {
return _phy_has_branch_lengths;
}
- final private boolean isUniformBranchLengthsForCladogram() {
- return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
- }
-
- final private void keyPressedCalls( final KeyEvent e ) {
- if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
- if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
- if ( !isInOvRect() ) {
- setInOvRect( true );
- }
- }
- else if ( isInOvRect() ) {
- setInOvRect( false );
- }
- }
- if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
- if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
- || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
- getMainPanel().getTreeFontSet().mediumFonts();
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
- }
- else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
- getMainPanel().getTreeFontSet().decreaseFontSize();
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
- }
- else if ( plusPressed( e.getKeyCode() ) ) {
- getMainPanel().getTreeFontSet().increaseFontSize();
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
- }
- }
- else {
- if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
- || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
- getControlPanel().showWhole();
- }
- else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
- || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
- if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
- if ( e.getKeyCode() == KeyEvent.VK_UP ) {
- getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
- getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
- getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
- Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
- getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- }
- else {
- final int d = 80;
- int dx = 0;
- int dy = -d;
- if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
- dy = d;
- }
- else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
- dx = -d;
- dy = 0;
- }
- else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
- dx = d;
- dy = 0;
- }
- final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
- scroll_position.x = scroll_position.x + dx;
- scroll_position.y = scroll_position.y + dy;
- if ( scroll_position.x <= 0 ) {
- scroll_position.x = 0;
- }
- else {
- final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
- if ( scroll_position.x >= max_x ) {
- scroll_position.x = max_x;
- }
- }
- if ( scroll_position.y <= 0 ) {
- scroll_position.y = 0;
- }
- else {
- final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
- if ( scroll_position.y >= max_y ) {
- scroll_position.y = max_y;
- }
- }
- repaint();
- getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
- }
- }
- else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
- getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
- Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( plusPressed( e.getKeyCode() ) ) {
- getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_S ) {
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- }
- else if ( e.getKeyCode() == KeyEvent.VK_A ) {
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
- if ( getStartingAngle() < 0 ) {
- setStartingAngle( TWO_PI + getStartingAngle() );
- }
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- }
- else if ( e.getKeyCode() == KeyEvent.VK_D ) {
- boolean selected = false;
- if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
- getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
- selected = true;
- }
- else {
- getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
- }
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- if ( ae.getlabelDirectionCbmi() != null ) {
- ae.getlabelDirectionCbmi().setSelected( selected );
- }
- }
- else {
- getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
- }
- repaint();
- }
- else if ( e.getKeyCode() == KeyEvent.VK_X ) {
- switchDisplaygetPhylogenyGraphicsType();
- repaint();
- }
- else if ( e.getKeyCode() == KeyEvent.VK_C ) {
- cycleColors();
- repaint();
- }
- else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
- MainFrame.cycleOverview( getOptions(), this );
- repaint();
- }
- else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
- increaseOvSize();
- }
- else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
- decreaseOvSize();
- }
- e.consume();
- }
- }
-
- final private void makePopupMenus( final PhylogenyNode node ) {
- _node_popup_menu = new JPopupMenu();
- final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
- _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
- for( int i = 0; i < clickto_names.size(); i++ ) {
- 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 ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
- }
- _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
- }
- _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
- }
- _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
- }
- _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
- }
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
- }
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
- }
- _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;
PhylogenyMethods.midpointRoot( _phylogeny );
resetNodeIdToDistToLeafMap();
setArrowCursor();
+ setEdited( true );
repaint();
}
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 )
+ double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
* w_ratio;
- double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - getOvRectangle().getHeight() / 2.0 )
+ double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
* h_ratio;
if ( x < 0 ) {
x = 0;
if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
// Yes, so add to _found_nodes
if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Integer>() );
+ setFoundNodes( new HashSet<Long>() );
}
getFoundNodes().add( node.getId() );
// Check if control key is down
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() );
+ 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 ) {
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();
if ( !isInOv() ) {
setInOv( true );
}
- }
- else {
- if ( isInOv() ) {
- setInOv( false );
+ }
+ 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, isInFoundNodes( c )
+ || isInCurrentExternalNodes( c ) );
+ if ( c.isExternal() ) {
+ final boolean is_in_found_nodes = isInFoundNodes( 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( getTreeColorSet().getFoundColor() );
+ drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, 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, isInFoundNodes( _root ) );
+ }
+
+ final void paintCircularLite( final Phylogeny phy,
+ final double starting_angle,
+ final int center_x,
+ final int center_y,
+ final int radius,
+ final Graphics2D g ) {
+ 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 ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
+ .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
+ }
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ if ( _dynamic_hiding_factor > 1 ) {
+ getControlPanel().setDynamicHidingIsOn( true );
+ }
+ else {
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ }
+ paintUnrooted( _phylogeny.getRoot(),
+ angle,
+ ( float ) ( angle + ( 2 * Math.PI ) ),
+ radial_labels,
+ g,
+ to_pdf,
+ to_graphics_file );
+ if ( getOptions().isShowScale() ) {
+ if ( !( to_graphics_file || to_pdf ) ) {
+ paintScale( g,
+ getVisibleRect().x,
+ getVisibleRect().y + getVisibleRect().height,
+ to_pdf,
+ to_graphics_file );
+ }
+ else {
+ paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ }
+ }
+ if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
+ g.setColor( getTreeColorSet().getOvColor() );
+ paintUnrootedLite( _phylogeny.getRoot(),
+ angle,
+ angle + ( 2 * Math.PI ),
+ g,
+ ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
+ paintOvRectangle( g );
+ }
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
+ final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
+ final int d = radius + MOVE + getLongestExtNodeInfo();
+ _dynamic_hiding_factor = 0;
+ if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
+ _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
+ .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
+ }
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ if ( _dynamic_hiding_factor > 1 ) {
+ getControlPanel().setDynamicHidingIsOn( true );
+ }
+ else {
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ }
+ paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
+ if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
+ final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
+ : getOvMaxWidth() / 2 );
+ double x_scale = 1.0;
+ double y_scale = 1.0;
+ int x_pos = getVisibleRect().x + getOvXPosition();
+ int y_pos = getVisibleRect().y + getOvYPosition();
+ if ( getWidth() > getHeight() ) {
+ x_scale = ( double ) getHeight() / getWidth();
+ x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
+ }
+ else {
+ y_scale = ( double ) getWidth() / getHeight();
+ y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
+ }
+ _at = g.getTransform();
+ g.scale( x_scale, y_scale );
+ paintCircularLite( _phylogeny,
+ getStartingAngle(),
+ x_pos + radius_ov,
+ y_pos + radius_ov,
+ ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
+ .getWidth() ) ) ),
+ g );
+ g.setTransform( _at );
+ paintOvRectangle( g );
+ }
+ }
+ }
+
+ 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 ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
+ getFoundNodes().remove( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
+ if ( getFoundNodes().size() < 1 ) {
+ getControlPanel().searchReset();
+ }
+ }
+ else {
+ getControlPanel().getSearchFoundCountsLabel().setVisible( true );
+ getControlPanel().getSearchResetButton().setEnabled( true );
+ getControlPanel().getSearchResetButton().setVisible( true );
+ if ( getFoundNodes() == null ) {
+ setFoundNodes( new HashSet<Long>() );
+ }
+ getFoundNodes().add( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().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 setFoundNodes( final Set<Long> found_nodes ) {
+ _found_nodes = 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 setLongestExtNodeInfo( final int i ) {
+ _longest_ext_node_info = i;
+ }
+
+ 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().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.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ }
+ 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 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();
+ }
+
+ final void taxColor() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ setWaitCursor();
+ TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getColorBranchesCb() != null ) {
+ _control_panel.getColorBranchesCb().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 String[] a = sn.split( "\\s+" );
+ _sb.append( a[ 0 ].substring( 0, 1 ) );
+ _sb.append( a[ 1 ].substring( 0, 2 ) );
+ if ( a.length > 2 ) {
+ for( int i = 2; i < a.length; i++ ) {
+ _sb.append( " " );
+ _sb.append( a[ i ] );
+ }
+ }
+ }
+
+ final private void addEmptyNode( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
+ }
+ final String label = createASimpleTextRepresentationOfANode( node );
+ String msg = "";
+ if ( ForesterUtil.isEmpty( label ) ) {
+ msg = "How to add the new, empty node?";
+ }
+ else {
+ msg = "How to add the new, empty node to node" + label + "?";
+ }
+ final Object[] options = { "As sibling", "As descendant", "Cancel" };
+ final int r = JOptionPane.showOptionDialog( this,
+ msg,
+ "Addition of Empty New Node",
+ JOptionPane.CLOSED_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options,
+ options[ 2 ] );
+ boolean add_as_sibling = true;
+ if ( r == 1 ) {
+ add_as_sibling = false;
+ }
+ else if ( r != 0 ) {
+ return;
+ }
+ final Phylogeny phy = new Phylogeny();
+ phy.setRoot( new PhylogenyNode() );
+ phy.setRooted( true );
+ if ( add_as_sibling ) {
+ if ( node.isRoot() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot add sibling to root",
+ "Attempt to add sibling to root",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ phy.addAsSibling( node );
+ }
+ else {
+ phy.addAsChild( node );
+ }
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _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,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
+ || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
+ && ( getCutOrCopiedTree() != null )
+ && ( getCopiedAndPastedNodes() != null )
+ && !to_pdf
+ && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
+ g.setColor( getTreeColorSet().getFoundColor() );
+ }
+ else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ }
+ else if ( to_pdf ) {
+ g.setColor( getTreeColorSet().getBranchColorForPdf() );
+ }
+ else {
+ g.setColor( getTreeColorSet().getBranchColor() );
+ }
+ }
+
+ final private void blast( final PhylogenyNode node ) {
+ if ( !isCanBlast( node ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Insufficient information present",
+ "Cannot Blast",
+ JOptionPane.INFORMATION_MESSAGE );
+ return;
+ }
+ 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 ( SequenceIdParser.isProtein( query ) ) {
+ type = 'p';
+ }
+ else {
+ type = 'n';
+ }
+ }
+ JApplet applet = null;
+ if ( isApplet() ) {
+ applet = obtainApplet();
+ }
+ 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 Blast s = new Blast();
+ s.ddbjBlast( query );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+ }
+
+ private final int calcDynamicHidingFactor() {
+ return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) );
+ }
+
+ /**
+ * Calculate the length of the distance between the given node and its
+ * parent.
+ *
+ * @param node
+ * @param ext_node_x
+ * @factor
+ * @return the distance value
+ */
+ final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( node.getDistanceToParent() < 0.0 ) {
+ return 0.0f;
+ }
+ return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
+ }
+ else {
+ if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
+ return getXdistance();
+ }
+ return getXdistance() * factor;
+ }
+ }
+
+ final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
+ Color c = getTreeColorSet().getAnnotationColor();
+ if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
+ final StringBuilder sb = new StringBuilder();
+ for( final Annotation a : ann ) {
+ sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
+ }
+ final String ann_str = sb.toString();
+ if ( !ForesterUtil.isEmpty( ann_str ) ) {
+ c = getControlPanel().getAnnotationColors().get( ann_str );
+ if ( c == null ) {
+ c = TreePanelUtil.calculateColorFromString( ann_str, false );
+ getControlPanel().getAnnotationColors().put( ann_str, c );
+ }
+ if ( c == null ) {
+ c = getTreeColorSet().getAnnotationColor();
+ }
+ }
+ }
+ return c;
+ }
+
+ final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( node.getDistanceToParent() < 0.0 ) {
+ return 0.0f;
+ }
+ return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
+ }
+ else {
+ if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
+ return getOvXDistance();
+ }
+ return getOvXDistance() * factor;
+ }
+ }
+
+ final private void cannotOpenBrowserWarningMessage( final String type_type ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot launch web browser for " + type_type + " data of this node",
+ "Cannot launch web browser",
+ JOptionPane.WARNING_MESSAGE );
+ }
+
+ final private void colorizeSubtree( 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 ( node != null ) {
+ 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 ) {
+ n.getBranchData().setBranchColor( new BranchColor( c ) );
+ }
+ }
+ repaint();
+ }
+
+ 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;
+ }
+ _color_chooser.setPreviewPanel( new JPanel() );
+ SubtreeColorizationActionListener al;
+ if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
+ }
+ else {
+ 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 ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
+ }
+ setNodeInPreorderToNull();
+ setCutOrCopiedTree( _phylogeny.copy( node ) );
+ final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
+ 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() );
+ setCopiedAndPastedNodes( node_ids );
+ 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();
+ return;
+ }
+ if ( node.isRoot() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot cut entire tree as subtree",
+ "Attempt to cut entire tree",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final String label = createASimpleTextRepresentationOfANode( node );
+ final int r = JOptionPane.showConfirmDialog( null,
+ "Cut subtree" + label + "?",
+ "Confirm Cutting of Subtree",
+ JOptionPane.YES_NO_OPTION );
+ if ( r != JOptionPane.OK_OPTION ) {
+ return;
+ }
+ setNodeInPreorderToNull();
+ setCopiedAndPastedNodes( null );
+ setCutOrCopiedTree( _phylogeny.copy( node ) );
+ _phylogeny.deleteSubtree( node, true );
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ repaint();
+ }
+
+ final private void cycleColors() {
+ getMainPanel().getTreeColorSet().cycleColorScheme();
+ for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
+ tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
+ }
+ }
+
+ final private void decreaseOvSize() {
+ if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
+ setOvMaxWidth( getOvMaxWidth() - 5 );
+ setOvMaxHeight( getOvMaxHeight() - 5 );
+ updateOvSettings();
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ }
+
+ final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
+ }
+ 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 = createASimpleTextRepresentationOfANode( node );
+ final Object[] options = { "Node only", "Entire subtree", "Cancel" };
+ final int r = JOptionPane.showOptionDialog( this,
+ "Delete" + label + "?",
+ "Delete Node/Subtree",
+ JOptionPane.CLOSED_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options,
+ options[ 2 ] );
+ setNodeInPreorderToNull();
+ boolean node_only = true;
+ if ( r == 1 ) {
+ node_only = false;
+ }
+ else if ( r != 0 ) {
+ return;
+ }
+ if ( node_only ) {
+ PhylogenyMethods.removeNode( node, _phylogeny );
+ }
+ else {
+ _phylogeny.deleteSubtree( node, true );
+ }
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ repaint();
+ }
+
+ final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
+ makePopupMenus( node );
+ _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
+ _node_popup_menu.show( this, x, y );
+ }
+
+ final private void drawArc( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final double start_angle,
+ final double arc_angle,
+ final Graphics2D g ) {
+ _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
+ g.draw( _arc );
+ }
+
+ final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
+ if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
+ return;
+ }
+ _line.setLine( x1, y1, x2, y2 );
+ g.draw( _line );
+ }
+
+ final private void drawOval( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g ) {
+ _ellipse.setFrame( x, y, width, heigth );
+ g.draw( _ellipse );
+ }
+
+ final private void drawOvalFilled( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g ) {
+ _ellipse.setFrame( x, y, width, heigth );
+ g.fill( _ellipse );
+ }
+
+ final private void drawOvalGradient( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g,
+ final Color color_1,
+ final Color color_2,
+ final Color color_border ) {
+ _ellipse.setFrame( x, y, width, heigth );
+ g.setPaint( new GradientPaint( ( float ) x,
+ ( float ) y,
+ color_1,
+ ( float ) ( x + width ),
+ ( float ) ( y + heigth ),
+ color_2,
+ false ) );
+ g.fill( _ellipse );
+ if ( color_border != null ) {
+ g.setPaint( color_border );
+ g.draw( _ellipse );
+ }
+ }
+
+ final private void 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 );
+ }
+
+ final private void drawRectFilled( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g ) {
+ _rectangle.setFrame( x, y, width, heigth );
+ 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 );
+ }
+ }
+
+ 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.showMessageDialog( this,
+ "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
+ "Attempt to cut/copy/paste/add/delete in unrooted display",
+ JOptionPane.ERROR_MESSAGE );
+ }
+
+ final private Set<Long> getCopiedAndPastedNodes() {
+ return getMainPanel().getCopiedAndPastedNodes();
+ }
+
+ final private Set<Long> getCurrentExternalNodes() {
+ return _current_external_nodes;
+ }
+
+ final private Phylogeny getCutOrCopiedTree() {
+ return getMainPanel().getCutOrCopiedTree();
+ }
+
+ final private float getLastDragPointX() {
+ return _last_drag_point_x;
+ }
+
+ final private float getLastDragPointY() {
+ return _last_drag_point_y;
+ }
+
+ final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
+ if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
+ final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
+ _nodeid_dist_to_leaf.put( node.getId(), m );
+ return m;
+ }
+ else {
+ return _nodeid_dist_to_leaf.get( node.getId() );
+ }
+ }
+
+ final private double getMaxDistanceToRoot() {
+ if ( _max_distance_to_root < 0 ) {
+ recalculateMaxDistanceToRoot();
+ }
+ return _max_distance_to_root;
+ }
+
+ final private float getOvMaxHeight() {
+ return _ov_max_height;
+ }
+
+ final private float getOvMaxWidth() {
+ return _ov_max_width;
+ }
+
+ final private float getOvXcorrectionFactor() {
+ return _ov_x_correction_factor;
+ }
+
+ final private float getOvXDistance() {
+ return _ov_x_distance;
+ }
+
+ final private int getOvXPosition() {
+ return _ov_x_position;
+ }
+
+ final private float getOvYDistance() {
+ return _ov_y_distance;
+ }
+
+ final private int getOvYPosition() {
+ return _ov_y_position;
+ }
+
+ final private int getOvYStart() {
+ return _ov_y_start;
+ }
+
+ final private double getScaleDistance() {
+ return _scale_distance;
+ }
+
+ final private String getScaleLabel() {
+ return _scale_label;
+ }
+
+ final private TreeFontSet getTreeFontSet() {
+ return getMainPanel().getTreeFontSet();
+ }
+
+ final private float getUrtFactor() {
+ return _urt_factor;
+ }
+
+ final private float getUrtFactorOv() {
+ return _urt_factor_ov;
+ }
+
+ final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
+ switch ( action ) {
+ case SHOW_DATA:
+ showNodeFrame( node );
+ break;
+ case COLLAPSE:
+ collapse( node );
+ break;
+ case REROOT:
+ reRoot( node );
+ break;
+ case SUBTREE:
+ subTree( node );
+ break;
+ case SWAP:
+ swap( node );
+ break;
+ case COLOR_SUBTREE:
+ colorSubtree( node );
+ break;
+ case OPEN_SEQ_WEB:
+ openSeqWeb( node );
+ break;
+ case BLAST:
+ blast( node );
+ break;
+ case OPEN_TAX_WEB:
+ openTaxWeb( node );
+ break;
+ case CUT_SUBTREE:
+ cutSubtree( node );
+ break;
+ case COPY_SUBTREE:
+ copySubtree( node );
+ break;
+ case PASTE_SUBTREE:
+ pasteSubtree( node );
+ break;
+ case DELETE_NODE_OR_SUBTREE:
+ deleteNodeOrSubtree( node );
+ break;
+ case ADD_NEW_NODE:
+ addEmptyNode( 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 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 ) ) ) {
+ setOvMaxWidth( getOvMaxWidth() + 5 );
+ setOvMaxHeight( getOvMaxHeight() + 5 );
+ updateOvSettings();
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ }
+
+ final private void init() {
+ _color_chooser = new JColorChooser();
+ _rollover_popup = new JTextArea();
+ _rollover_popup.setFont( POPUP_FONT );
+ resetNodeIdToDistToLeafMap();
+ setTextAntialias();
+ setTreeFile( null );
+ setEdited( false );
+ initializeOvSettings();
+ setStartingAngle( ( TWO_PI * 3 ) / 4 );
+ final ImageLoader il = new ImageLoader( this );
+ new Thread( il ).start();
+ }
+
+ final private void initializeOvSettings() {
+ setOvMaxHeight( getConfiguration().getOvMaxHeight() );
+ setOvMaxWidth( getConfiguration().getOvMaxWidth() );
+ }
+
+ 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 private boolean isCanBlast( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
+ return false;
+ }
+ return Blast.isContainsQueryForBlast( node );
+ }
+
+ final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
+ String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractGenbankAccessor( node );
+ }
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractRefSeqAccessorAccessor( node );
+ }
+ if ( ForesterUtil.isEmpty( v ) ) {
+ v = ForesterUtil.extractGInumber( node );
+ }
+ return v;
+ }
+
+ final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
+ if ( node.getNodeData().isHasTaxonomy()
+ && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
+ || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+ || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
+ .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+ .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
+ return true;
+ }
+ else {
+ return false;
+ }
+ }
+
+ final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
+ return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
+ }
+
+ final private boolean isInFoundNodes( final PhylogenyNode node ) {
+ return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
+ }
+
+ final private boolean isInOv() {
+ return _in_ov;
+ }
+
+ final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
+ int y_dist = 40;
+ if ( getControlPanel().isShowTaxonomyImages() ) {
+ y_dist = 40 + ( int ) getYdistance();
+ }
+ return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
+ || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
+ .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
+ }
+
+ 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 ) ) );
+ }
+
+ final private boolean isNonLinedUpCladogram() {
+ return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
+ }
+
+ final private boolean isUniformBranchLengthsForCladogram() {
+ return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
+ }
+
+ final private void keyPressedCalls( final KeyEvent e ) {
+ if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
+ if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
+ if ( !isInOvRect() ) {
+ setInOvRect( true );
+ }
+ }
+ else if ( isInOvRect() ) {
+ setInOvRect( false );
+ }
+ }
+ if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
+ if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
+ || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
+ getMainPanel().getTreeFontSet().mediumFonts();
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ else if ( plusPressed( e.getKeyCode() ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ }
+ else {
+ if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
+ || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
+ getControlPanel().showWhole();
+ }
+ else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
+ || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
+ if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
+ if ( e.getKeyCode() == KeyEvent.VK_UP ) {
+ getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
+ getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
+ getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
+ Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
+ getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
+ Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ }
+ else {
+ final int d = 80;
+ int dx = 0;
+ int dy = -d;
+ if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
+ dy = d;
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
+ dx = -d;
+ dy = 0;
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
+ dx = d;
+ dy = 0;
+ }
+ final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
+ scroll_position.x = scroll_position.x + dx;
+ scroll_position.y = scroll_position.y + dy;
+ if ( scroll_position.x <= 0 ) {
+ scroll_position.x = 0;
+ }
+ else {
+ final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
+ if ( scroll_position.x >= max_x ) {
+ scroll_position.x = max_x;
+ }
+ }
+ if ( scroll_position.y <= 0 ) {
+ scroll_position.y = 0;
+ }
+ else {
+ final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
+ if ( scroll_position.y >= max_y ) {
+ scroll_position.y = max_y;
+ }
+ }
+ repaint();
+ getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
+ }
+ }
+ else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
+ getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
+ Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( plusPressed( e.getKeyCode() ) ) {
+ getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
+ Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_S ) {
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_A ) {
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
+ if ( getStartingAngle() < 0 ) {
+ setStartingAngle( TWO_PI + getStartingAngle() );
+ }
+ getControlPanel().displayedPhylogenyMightHaveChanged( 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 if ( e.getKeyCode() == KeyEvent.VK_D ) {
+ boolean selected = false;
+ if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
+ getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
+ selected = true;
}
else {
- setCursor( HAND_CURSOR );
- if ( getControlPanel().isNodeDescPopup() ) {
- showNodeDataPopup( e, node );
+ getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
+ }
+ if ( getMainPanel().getMainFrame() == null ) {
+ // Must be "E" applet version.
+ final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ if ( ae.getlabelDirectionCbmi() != null ) {
+ ae.getlabelDirectionCbmi().setSelected( selected );
}
}
+ else {
+ getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
+ }
+ repaint();
}
- else {
- setCursor( ARROW_CURSOR );
+ else if ( e.getKeyCode() == KeyEvent.VK_X ) {
+ switchDisplaygetPhylogenyGraphicsType();
+ repaint();
}
- }
- }
-
- 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 );
+ else if ( e.getKeyCode() == KeyEvent.VK_C ) {
+ cycleColors();
repaint();
}
- }
- else {
- if ( isInOvRect() ) {
- setInOvRect( false );
+ else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
+ MainFrame.cycleOverview( getOptions(), this );
repaint();
}
- }
- if ( e.isControlDown() ) {
- if ( notches < 0 ) {
- getTreeFontSet().increaseFontSize();
- getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
+ increaseOvSize();
}
- else {
- getTreeFontSet().decreaseFontSize();
- getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
+ decreaseOvSize();
}
+ e.consume();
}
- 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 );
- }
+ }
+
+ final private void makePopupMenus( final PhylogenyNode node ) {
+ _node_popup_menu = new JPopupMenu();
+ final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
+ _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
+ for( int i = 0; i < clickto_names.size(); i++ ) {
+ 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 ] ) ) {
+ 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 {
- for( int i = 0; i < notches; ++i ) {
- setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
- if ( getStartingAngle() < 0 ) {
- setStartingAngle( TWO_PI + getStartingAngle() );
- }
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
+ _node_popup_menu_items[ i ].setEnabled( false );
}
}
- else {
- if ( notches < 0 ) {
- for( int i = 0; i < ( -notches ); ++i ) {
- getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
}
- else {
- for( int i = 0; i < notches; ++i ) {
- getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
+ _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
}
+ _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
}
- }
- 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 ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
}
+ _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
}
- 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 if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
+ }
+ _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
+ }
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
}
}
+ else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
+ }
+ _node_popup_menu_items[ i ].addActionListener( this );
+ _node_popup_menu.add( _node_popup_menu_items[ i ] );
}
- 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 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 ) ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
cannotOpenBrowserWarningMessage( "sequence" );
return;
}
- String uri_str = null;
- final Sequence seq = node.getNodeData().getSequence();
- final String source = seq.getAccession().getSource().toLowerCase();
- String url;
- if ( source.toLowerCase().equals( "ncbi" ) ) {
- url = Constants.NCBI_ALL_DATABASE_SEARCH;
- }
- else {
- final WebLink weblink = getConfiguration().getWebLink( source );
- url = weblink.getUrl().toString();
- }
- try {
- uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ 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() );
e.printStackTrace();
}
catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- }
- else {
- cannotOpenBrowserWarningMessage( "taxonomic" );
- }
- }
-
- 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;
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
}
- 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 );
+ else {
+ cannotOpenBrowserWarningMessage( "taxonomic" );
}
}
|| ( 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 = 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 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, isInFoundNodes( node )
+ || isInCurrentExternalNodes( node ) );
}
- 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 );
}
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 ) );
+ _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() == NodeVisualization.NodeFill.SOLID ) {
g.setColor( c );
- g.fillPolygon( _polygon );
+ g.fill( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeVisualization.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,
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
outline_color = Color.BLACK;
}
- else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
+ else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
outline_color = getTreeColorSet().getDuplicationBoxColor();
}
final int box_size = getOptions().getDefaultNodeShapeSize();
final int half_box_size = box_size / 2;
- if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
+ if ( ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
+ || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+ || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
drawOvalGradient( x - half_box_size,
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
return;
}
+ _sb.setLength( 0 );
int x = 0;
final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
if ( getControlPanel().isShowTaxonomyImages()
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().isColorBranches()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
else {
g.setColor( getTreeColorSet().getSequenceColor() );
}
- _sb.setLength( 0 );
if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- _sb.append( " [" );
- _sb.append( node.getAllExternalDescendants().size() );
- _sb.append( "]" );
+ if ( _sb.length() > 0 ) {
+ _sb.setLength( 0 );
+ _sb.append( "(" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( ")" );
+ }
+ }
+ else {
+ _sb.setLength( 0 );
}
if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
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 */
// 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;
- }
+ // 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 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()
+ + ( 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 {
+ 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() );
}
}
}
- return offset;
}
final private void paintNodeDataUnrootedCirc( final Graphics2D g,
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 {
g.setColor( getTreeColorSet().getSequenceColor() );
}
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 ) ) {
+ if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
g.setColor( getTreeColorSet().getFoundColor() );
drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
}
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;
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, isInFoundNodes( node )
+ || isInCurrentExternalNodes( node ) );
}
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() ) < getTreeFontSet()._fm_large
.getHeight() ) ) ) ) ) {
return;
}
if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
return;
}
- 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 ( ( _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 );
- }
- }
- 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 );
+ 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();
}
- else {
- paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ catch ( final ClassCastException cce ) {
+ cce.printStackTrace();
+ }
+ if ( rds != null ) {
+ rds.setRenderingHeight( 6 );
+ int x = 0;
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ if ( getControlPanel().isShowTaxonomyCode()
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
+ .getTaxonomyCode()
+ + " " );
+ }
+ if ( getControlPanel().isShowTaxonomyScientificNames()
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+ x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
+ .getScientificName()
+ + " " );
+ }
+ if ( getControlPanel().isShowTaxonomyCommonNames()
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+ x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
+ .getCommonName()
+ + " " );
+ }
+ }
+ if ( node.getNodeData().isHasSequence() ) {
+ 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().isShowAnnotation()
+ && ( node.getNodeData().getSequence().getAnnotations() != null )
+ && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
+ x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
+ .getNodeData().getSequence().getAnnotations(), getOptions()
+ .isShowAnnotationRefSource() )
+ + " " );
+ }
+ }
+ if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
+ x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
+ }
+ rds.render( node.getXcoord() + x, node.getYcoord() - 3, 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 ) {
+ int x = 0;
+ PhylogenyNode my_node = node;
+ if ( !getControlPanel().isDrawPhylogram() ) {
+ my_node = getPhylogeny().getFirstExternalNode();
}
- }
- 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().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
+ x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
}
- else {
- y_scale = ( double ) getWidth() / getHeight();
- y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
+ if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
+ x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
}
- _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 );
+ 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 );
+ 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 );
}
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,
}
}
- 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 ] );
- }
- }
- }
-
final private void paintUnrooted( final PhylogenyNode n,
final double low_angle,
final double high_angle,
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, isInFoundNodes( desc )
+ || isInCurrentExternalNodes( desc ) );
}
if ( n.isRoot() ) {
paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
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 ) ) {
+ if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
g.setColor( getTreeColorSet().getFoundColor() );
drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
g.setColor( getTreeColorSet().getOvColor() );
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 ) {
need_to_show_whole = true;
_phylogeny = buffer_phy;
}
- else {
- buffer_phy.addAsChild( node );
- }
- }
- if ( getCopiedAndPastedNodes() == null ) {
- setCopiedAndPastedNodes( new HashSet<Integer>() );
- }
- final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
- final Set<Integer> node_ids = new HashSet<Integer>( 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.clearHashIdToNodeMap();
- _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() );
- }
- 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 ) );
- }
+ else {
+ buffer_phy.addAsChild( node );
+ }
+ }
+ if ( getCopiedAndPastedNodes() == null ) {
+ setCopiedAndPastedNodes( new HashSet<Long>() );
+ }
+ final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
+ 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.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ if ( need_to_show_whole ) {
+ getControlPanel().showWhole();
}
- setPreferredSize( new Dimension( x, y ) );
- }
-
- public final void setArrowCursor() {
- setCursor( ARROW_CURSOR );
repaint();
}
- final void setControlPanel( final ControlPanel atv_control ) {
- _control_panel = atv_control;
+ 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 {
+ 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() ) );
+ }
+ }
+ return sb;
}
- 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;
- }
-
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 )
- && !getMainPanel().getOptions().isShowDefaultNodeShapes()
- && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
- _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;
+ private void showExtDescNodeData( final PhylogenyNode node ) {
+ final List<String> data = new ArrayList<String>();
+ for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
+ 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 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 ( 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 = ann.toString().trim();
+ if ( ann_str.endsWith( "|" ) ) {
+ ann_str = ann_str.substring( 0, ann_str.length() - 1 );
+ }
+ 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 = 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 );
+ final String 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 void setYdistance( final float y ) {
- _y_distance = y;
+ private int makeSB( final List<String> data, final Options optz, final StringBuilder sb ) {
+ final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
+ if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+ && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ if ( map.containsKey( d ) ) {
+ map.put( d, map.get( d ) + 1 );
+ }
+ else {
+ map.put( d, 1 );
+ }
+ }
+ }
+ }
+ int size = 0;
+ if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+ && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ for( final Entry<String, Integer> e : map.entrySet() ) {
+ final String v = e.getKey();
+ final Object c = e.getValue();
+ sb.append( v );
+ sb.append( "\t" );
+ sb.append( c );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ size = map.size();
+ }
+ else {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ sb.append( d );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ size = data.size();
+ }
+ return size;
}
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 ) {
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() ) );
}
}
}
}
}
- 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.clearHashIdToNodeMap();
- _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.clearHashIdToNodeMap();
- _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;
- }
- setWaitCursor();
- AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( 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 );
- }
- }
-
- 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;
- }
- }
-
- 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;
- }
-
- DescriptiveStatistics getStatisticsForExpressionValues() {
- return _statistics_for_vector_data;
- }
-
final private class SubtreeColorizationActionListener implements ActionListener {
- JColorChooser _chooser;
- PhylogenyNode _node;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
+ List<PhylogenyNode> _additional_nodes = 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