import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.font.FontRenderContext;
+import java.awt.font.TextAttribute;
import java.awt.font.TextLayout;
import java.awt.geom.AffineTransform;
import java.awt.geom.Arc2D;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URLEncoder;
+import java.text.AttributedString;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
import javax.swing.BorderFactory;
-import javax.swing.JApplet;
import javax.swing.JColorChooser;
import javax.swing.JDialog;
import javax.swing.JMenuItem;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
+import org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence;
import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
import org.forester.archaeopteryx.tools.Blast;
import org.forester.archaeopteryx.tools.ImageLoader;
import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.DomainArchitecture;
import org.forester.phylogeny.data.Event;
-import org.forester.phylogeny.data.NodeData.NODE_DATA;
+import org.forester.phylogeny.data.NodeDataField;
import org.forester.phylogeny.data.NodeVisualData;
import org.forester.phylogeny.data.NodeVisualData.NodeFill;
import org.forester.phylogeny.data.NodeVisualData.NodeShape;
import org.forester.phylogeny.data.PhylogenyDataUtil;
-import org.forester.phylogeny.data.PropertiesMap;
-import org.forester.phylogeny.data.Property;
+import org.forester.phylogeny.data.ProteinDomain;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.SequenceRelation;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.data.Uri;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PreorderTreeIterator;
-import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
- final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
- final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
- final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
- final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
- final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
- final private static double _180_OVER_PI = 180.0 / Math.PI;
- private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
- private final static int CONFIDENCE_LEFT_MARGIN = 4;
- private final static int EURO_D = 10;
- private final static NumberFormat FORMATTER_BRANCH_LENGTH;
- private final static NumberFormat FORMATTER_CONFIDENCE;
- private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
- private final static int LIMIT_FOR_HQ_RENDERING = 2000;
- private final static int MAX_NODE_FRAMES = 10;
- private final static int MAX_SUBTREES = 100;
- private final static int MIN_ROOT_LENGTH = 3;
- private final static int MOVE = 20;
- private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
- private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
- private static final short OV_BORDER = 10;
- private final static double OVERVIEW_FOUND_NODE_BOX_SIZE = 2;
- private final static double OVERVIEW_FOUND_NODE_BOX_SIZE_HALF = 1;
- private static final float PI = ( float ) ( Math.PI );
- final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
- Font.PLAIN,
- 12 );
- private static final float ROUNDED_D = 8;
- private final static long serialVersionUID = -978349745916505029L;
- private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
- private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
- private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
- private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
- private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
- private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
- private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
- private static final double TWO_PI = 2 * Math.PI;
- private final static int WIGGLE = 2;
- HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
- final private Arc2D _arc = new Arc2D.Double();
- private AffineTransform _at;
- private int _circ_max_depth;
- final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
- private JColorChooser _color_chooser = null;
- private Configuration _configuration = null;
- private ControlPanel _control_panel = null;
- private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
- private Set<Long> _current_external_nodes = null;
- private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
- private int _current_external_nodes_data_buffer_change_counter = 0;
- private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
- private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
- private int _dynamic_hiding_factor = 0;
- private boolean _edited = false;
- private final Ellipse2D _ellipse = new Ellipse2D.Float();
- private int _external_node_index = 0;
- private Set<Long> _found_nodes_0 = null;
- private Set<Long> _found_nodes_1 = null;
- private final FontRenderContext _frc = new FontRenderContext( null,
- false,
- false );
- private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
- private PhylogenyNode _highlight_node = null;
- private boolean _in_ov = false;
- private boolean _in_ov_rect = false;
- private float _last_drag_point_x = 0;
- private float _last_drag_point_y = 0;
- private final Line2D _line = new Line2D.Float();
- private int _longest_ext_node_info = 0;
- private MainPanel _main_panel = null;
- private double _max_distance_to_root = -1;
- private Popup _node_desc_popup;
- private int _node_frame_index = 0;
- private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
- private JPopupMenu _node_popup_menu = null;
- private JMenuItem _node_popup_menu_items[] = null;
- private PhylogenyNode[] _nodes_in_preorder = null;
- private Options _options = null;
- private float _ov_max_height = 0;
- private float _ov_max_width = 0;
- private boolean _ov_on = false;
- private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
- private final Rectangle _ov_virtual_rectangle = new Rectangle();
- private float _ov_x_correction_factor = 0.0f;
- private float _ov_x_distance = 0;
- private int _ov_x_position = 0;
- private float _ov_y_distance = 0;
- private int _ov_y_position = 0;
- private int _ov_y_start = 0;
- private final boolean _phy_has_branch_lengths;
- private Phylogeny _phylogeny = null;
- private final Path2D.Float _polygon = new Path2D.Float();
- private final StringBuffer _popup_buffer = new StringBuffer();
- private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
- private Sequence _query_sequence = null;
- private final Rectangle2D _rectangle = new Rectangle2D.Float();
- private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
- RenderingHints.VALUE_RENDER_DEFAULT );
- private JTextArea _rollover_popup;
- private PhylogenyNode _root;
- private final StringBuilder _sb = new StringBuilder();
- private double _scale_distance = 0.0;
- private String _scale_label = null;
- // expression values menu:
- private DescriptiveStatistics _statistics_for_vector_data;
- private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
- private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
- private int _subtree_index = 0;
- private File _treefile = null;
- private float _urt_factor = 1;
- private float _urt_factor_ov = 1;
- final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
- final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
- private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
- private float _x_correction_factor = 0.0f;
- private float _x_distance = 0.0f;
- private float _y_distance = 0.0f;
- // private Image offscreenImage;
- // private Graphics offscreenGraphics;
- // private Dimension offscreenDimension;
+ final private class NodeColorizationActionListener implements ActionListener {
+
+ List<PhylogenyNode> _additional_nodes = null;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
+
+ NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
+ _chooser = chooser;
+ _node = node;
+ }
+
+ NodeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<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 ) {
+ colorizeNodes( c, _node, _additional_nodes );
+ }
+ }
+ }
+
+ final private class SubtreeColorizationActionListener implements ActionListener {
+
+ List<PhylogenyNode> _additional_nodes = null;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
+
+ SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
+ _chooser = chooser;
+ _node = node;
+ }
+
+ SubtreeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _chooser = chooser;
+ _node = node;
+ _additional_nodes = additional_nodes;
+ }
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ final Color c = _chooser.getColor();
+ if ( c != null ) {
+ colorizeSubtree( c, _node, _additional_nodes );
+ }
+ }
+ }
+ public final static boolean SPECIAL_DOMAIN_COLORING = true;
+ final static Cursor ARROW_CURSOR = Cursor
+ .getPredefinedCursor( Cursor.DEFAULT_CURSOR );
+ final static Cursor CUT_CURSOR = Cursor
+ .getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
+ final static Cursor HAND_CURSOR = Cursor
+ .getPredefinedCursor( Cursor.HAND_CURSOR );
+ final static Cursor MOVE_CURSOR = Cursor
+ .getPredefinedCursor( Cursor.MOVE_CURSOR );
+ final static Cursor WAIT_CURSOR = Cursor
+ .getPredefinedCursor( Cursor.WAIT_CURSOR );
+ final private static double _180_OVER_PI = 180.0 / Math.PI;
+ private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI
+ / 32 );
+ private final static int CONFIDENCE_LEFT_MARGIN = 4;
+ private final static int EURO_D = 10;
+ private final static NumberFormat FORMATTER_BRANCH_LENGTH;
+ private final static NumberFormat FORMATTER_CONFIDENCE;
+ private static final float HALF_PI = ( float ) ( Math.PI
+ / 2.0 );
+ private final static int LIMIT_FOR_HQ_RENDERING = 2000;
+ private final static int MAX_NODE_FRAMES = 10;
+ private final static int MAX_SUBTREES = 100;
+ private final static int MIN_ROOT_LENGTH = 3;
+ private final static int MOVE = 20;
+ private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
+ private static final float ONEHALF_PI = ( float ) ( 1.5
+ * Math.PI );
+ private static final short OV_BORDER = 10;
+ private final static double OVERVIEW_FOUND_NODE_BOX_SIZE = 2;
+ private final static double OVERVIEW_FOUND_NODE_BOX_SIZE_HALF = 1;
+ private static final float PI = ( float ) ( Math.PI );
+ final private static Font POPUP_FONT = new Font( Configuration
+ .getDefaultFontFamilyName(), Font.PLAIN, 12 );
+ private static final float ROUNDED_D = 8;
+ private final static long serialVersionUID = -978349745916505029L;
+ private static final BasicStroke STROKE_0025 = new BasicStroke( 0.025f );
+ private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
+ private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
+ private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
+ private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
+ private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
+ private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
+ private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
+ private static final BasicStroke STROKE_01_DASHED = new BasicStroke( 0.1f,
+ BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_ROUND,
+ 0,
+ new float[] {
+ 2.0f },
+ 0f );
+ private static final BasicStroke STROKE_005_DASHED = new BasicStroke( 0.05f,
+ BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_ROUND,
+ 0,
+ new float[] {
+ 2.0f },
+ 0f );
+ private static final BasicStroke STROKE_001_DASHED = new BasicStroke( 0.01f,
+ BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_ROUND,
+ 0,
+ new float[] {
+ 2.0f },
+ 0f );
+ private static final double TWO_PI = 2 * Math.PI;
+ private final static int WIGGLE = 3;
+ private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me
+ HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
+ final private Arc2D _arc = new Arc2D.Double();
+ private AffineTransform _at;
+ private int _clicked_x;
+ private int _circ_max_depth;
+ final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
+ private JColorChooser _color_chooser = null;
+ private Configuration _configuration = null;
+ private ControlPanel _control_panel = null;
+ private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
+ private Set<Long> _current_external_nodes = null;
+ private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
+ private int _current_external_nodes_data_buffer_change_counter = 0;
+ private int _domain_structure_e_value_thr_exp = AptxConstants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
+ private double _domain_structure_width = AptxConstants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
+ private int _dynamic_hiding_factor = 0;
+ private boolean _edited = false;
+ private final Ellipse2D _ellipse = new Ellipse2D.Float();
+ private int _external_node_index = 0;
+ private Set<Long> _found_nodes_0 = null;
+ private Set<Long> _found_nodes_1 = null;
+ private final FontRenderContext _frc = new FontRenderContext( null,
+ false,
+ false );
+ private float _furthest_node_x;
+ private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
+ private PhylogenyNode _highlight_node = null;
+ private boolean _in_ov = false;
+ private boolean _in_ov_rect = false;
+ private float _last_drag_point_x = 0;
+ private float _last_drag_point_y = 0;
+ private final Line2D _line = new Line2D.Float();
+ private int _longest_ext_node_info = 0;
+ private PhylogenyNode _ext_node_with_longest_txt_info = null;
+ private MainPanel _main_panel = null;
+ private double _max_distance_to_root = -1;
+ private Popup _node_desc_popup;
+ private int _node_frame_index = 0;
+ private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
+ private JPopupMenu _node_popup_menu = null;
+ private JMenuItem _node_popup_menu_items[] = null;
+ private PhylogenyNode[] _nodes_in_preorder = null;
+ private Options _options = null;
+ private float _ov_max_height = 0;
+ private float _ov_max_width = 0;
+ private boolean _ov_on = false;
+ private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
+ private final Rectangle _ov_virtual_rectangle = new Rectangle();
+ private float _ov_x_correction_factor = 0.0f;
+ private float _ov_x_distance = 0;
+ private int _ov_x_position = 0;
+ private float _ov_y_distance = 0;
+ private int _ov_y_position = 0;
+ private int _ov_y_start = 0;
+ private boolean _partition_tree = false;
+ private float _partition_threshold = 0;
+ private final boolean _phy_has_branch_lengths;
+ private Phylogeny _phylogeny = null;
+ private final Path2D.Float _polygon = new Path2D.Float();
+ private final StringBuffer _popup_buffer = new StringBuffer();
+ private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
+ private Sequence _query_sequence = null;
+ private final Rectangle2D _rectangle = new Rectangle2D.Float();
+ private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_DEFAULT );
+ private JTextArea _rollover_popup;
+ private PhylogenyNode _root;
+ private float _root_x;
+ private final StringBuilder _sb = new StringBuilder();
+ private double _scale_distance = 0.0;
+ private String _scale_label = null;
+ private DescriptiveStatistics _statistics_for_vector_data;
+ private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
+ private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
+ private int _subtree_index = 0;
+ private File _treefile = null;
+ private float _urt_factor = 1;
+ private float _urt_factor_ov = 1;
+ final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
+ final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
+ private double _urt_starting_angle = ( float ) ( Math.PI
+ / 2 );
+ private float _x_correction_factor = 0.0f;
+ private float _x_distance = 0.0f;
+ private float _y_distance = 0.0f;
+ private int _length_of_longest_text;
+ private int _longest_domain;
+ private Map<String, AttributedString> _attributed_string_map = null;
+ private int _depth_collapse_level = -1;
+ private int _rank_collapse_level = -1;
+
+
+
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
init();
// if ( !_phylogeny.isEmpty() ) {
_phylogeny.recalculateNumberOfExternalDescendants( true );
- checkForVectorProperties( _phylogeny );
// }
setBackground( getTreeColorSet().getBackgroundColor() );
final MouseListener mouse_listener = new MouseListener( this );
addMouseWheelListener( this );
calculateScaleDistance();
FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
- FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
- .getNumberOfDigitsAfterCommaForBranchLengthValues() );
+ FORMATTER_BRANCH_LENGTH
+ .setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() );
}
@Override
}
/**
- * Get a pointer to the phylogeny
- *
+ * Get a pointer to the phylogeny
+ *
* @return a pointer to the phylogeny
*/
public final Phylogeny getPhylogeny() {
return _phylogeny;
}
+ public final TreeColorSet getTreeColorSet() {
+ return getMainPanel().getTreeColorSet();
+ }
+
@Override
final public void mouseWheelMoved( final MouseWheelEvent e ) {
final int notches = e.getWheelRotation();
repaint();
}
}
- if ( e.isControlDown() ) {
+ if ( e.isControlDown() && e.isShiftDown() ) {
if ( notches < 0 ) {
getTreeFontSet().increaseFontSize();
- getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else {
getTreeFontSet().decreaseFontSize( 1, false );
- getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ resetPreferredSize();
+ updateOvSizes();
+ repaint();
+ }
+ else if ( e.isShiftDown() && e.isAltDown() ) {
+ if ( notches < 0 ) {
+ for( int i = 0; i < ( -notches ); ++i ) {
+ getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ }
+ else {
+ for( int i = 0; i < notches; ++i ) {
+ getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
+ AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
}
}
else if ( e.isShiftDown() ) {
else {
if ( notches < 0 ) {
for( int i = 0; i < ( -notches ); ++i ) {
- getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
for( int i = 0; i < notches; ++i ) {
- getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
+ getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
if ( notches < 0 ) {
for( int i = 0; i < ( -notches ); ++i ) {
- getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
- getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
+ AptxConstants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
+ getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
for( int i = 0; i < notches; ++i ) {
- getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
- Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
+ getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
+ AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
@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
/**
* Set a phylogeny tree.
- *
+ *
* @param t
* an instance of a Phylogeny
*/
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();
- // }
- // }
- }
+ private void abbreviateScientificName( final String sn, final StringBuilder sb ) {
+ final String[] a = sn.split( "\\s+" );
+ sb.append( a[ 0 ].substring( 0, 1 ) );
+ sb.append( a[ 1 ].substring( 0, 2 ) );
+ if ( a.length > 2 ) {
+ for( int i = 2; i < a.length; i++ ) {
+ sb.append( " " );
+ sb.append( a[ i ] );
}
- //
}
}
- final void calculateLongestExtNodeInfo() {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ final private void addEmptyNode( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
- int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
- * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
- if ( max_length < 40 ) {
- max_length = 40;
- }
- int longest = 30;
- for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
- int sum = 0;
- if ( node.isCollapse() ) {
- continue;
- }
- final StringBuilder sb = new StringBuilder();
- nodeDataAsSB( node, sb );
- if ( node.getNodeData().isHasTaxonomy() ) {
- nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb );
- }
- boolean use_vis = false;
- final Graphics2D g = ( Graphics2D ) getGraphics();
- if ( getControlPanel().isUseVisualStyles() ) {
- use_vis = setFont( g, node, false );
- }
- if ( !use_vis ) {
- sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
- }
- else {
- sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() );
- }
- if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
- .getGainedCharactersAsStringBuffer().toString() );
- }
- if ( sum >= max_length ) {
- setLongestExtNodeInfo( max_length );
- return;
- }
- if ( sum > longest ) {
- longest = sum;
- }
- }
- if ( longest >= max_length ) {
- setLongestExtNodeInfo( max_length );
+ final String label = createASimpleTextRepresentationOfANode( node );
+ String msg = "";
+ if ( ForesterUtil.isEmpty( label ) ) {
+ msg = "How to add the new, empty node?";
}
else {
- setLongestExtNodeInfo( longest );
+ msg = "How to add the new, empty node to node" + label + "?";
}
- }
-
- final void calculateScaleDistance() {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ 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 double height = getMaxDistanceToRoot();
- if ( height > 0 ) {
- if ( ( height <= 0.5 ) ) {
- setScaleDistance( 0.01 );
- }
- else if ( height <= 5.0 ) {
- setScaleDistance( 0.1 );
- }
- else if ( height <= 50.0 ) {
- setScaleDistance( 1 );
- }
- else if ( height <= 500.0 ) {
- setScaleDistance( 10 );
- }
- else {
- setScaleDistance( 100 );
+ 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 {
- setScaleDistance( 0.0 );
+ phy.addAsChild( node );
}
- String scale_label = String.valueOf( getScaleDistance() );
- if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
- scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
+ 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>();
}
- setScaleLabel( scale_label );
+ _current_external_nodes.add( i );
}
- final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
- if ( getOptions().isColorByTaxonomicGroup() ) {
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- boolean ex = false;
- String group = null;
- try {
- group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
- }
- catch ( final Exception e ) {
- ex = true;
- }
- if ( !ex && !ForesterUtil.isEmpty( group ) ) {
- final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
- if ( c != null ) {
- return c;
- }
- }
- }
- return getTreeColorSet().getTaxonomyColor();
+ 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().getFoundColor0() );
+ }
+ else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ }
+ else if ( to_pdf ) {
+ g.setColor( getTreeColorSet().getBranchColorForPdf() );
}
else {
- if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- return getTreeColorSet().getTaxonomyColor();
- }
- Color c = null;
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
- }
- if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
- }
- if ( c == null ) {
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- c = 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;
+ g.setColor( getTreeColorSet().getBranchColor() );
}
}
-
- final Color calculateSequenceBasedColor( final Sequence seq ) {
- if ( ForesterUtil.isEmpty( seq.getName() ) ) {
- return getTreeColorSet().getSequenceColor();
- }
- Color c = null;
- final String seq_name = seq.getName();
- c = getControlPanel().getSequenceColors().get( seq_name );
- if ( c == null ) {
- c = TreePanelUtil.calculateColorFromString( seq_name, false );
- getControlPanel().getSequenceColors().put( seq_name, c );
- }
- return c;
- }
- void checkForVectorProperties( final Phylogeny phy ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.getNodeData().getProperties() != null ) {
- final PropertiesMap pm = node.getNodeData().getProperties();
- final double[] vector = new double[ pm.getProperties().size() ];
- int counter = 0;
- for( final String ref : pm.getProperties().keySet() ) {
- if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
- final Property p = pm.getProperty( ref );
- final String value_str = p.getValue();
- final String index_str = ref
- .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
- double d = -100;
- try {
- d = Double.parseDouble( value_str );
- }
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
- + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
- return;
+ 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';
}
- int i = -1;
- try {
- i = Integer.parseInt( index_str );
+ else {
+ type = 'n';
}
- 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;
+ }
+ else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ if ( ForesterUtil
+ .seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ type = 'p';
}
- if ( i < 0 ) {
- JOptionPane.showMessageDialog( this,
- "Attempt to use negative index for vector data",
- "Problem with Vector Data",
- JOptionPane.ERROR_MESSAGE );
- return;
+ else {
+ type = 'n';
}
- 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 ] );
+ if ( type == '?' ) {
+ if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
+ type = 'p';
+ }
+ else {
+ type = 'n';
+ }
+ }
+ try {
+ Blast.openNcbiBlastWeb( query, type == 'n', this );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
}
- node.getNodeData().setVector( vector_l );
}
}
- if ( stats.getN() > 0 ) {
- _statistics_for_vector_data = stats;
- }
}
- void clearCurrentExternalNodesDataBuffer() {
- setCurrentExternalNodesDataBuffer( new StringBuilder() );
+ private final int calcDynamicHidingFactor() {
+ return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().getHeight() / ( 1.5 * getYdistance() ) ) );
+ }
+
+ final private int calcLengthOfLongestText() {
+ final StringBuilder sb = new StringBuilder();
+ if ( _ext_node_with_longest_txt_info != null ) {
+ nodeDataAsSB( _ext_node_with_longest_txt_info, sb );
+ if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) {
+ nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
+ }
+ }
+ return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
/**
- * Collapse the tree from the given node
- *
+ * Calculate the length of the distance between the given node and its
+ * parent.
+ *
* @param node
- * a PhylogenyNode
+ * @param ext_node_x
+ * @factor
+ * @return the distance value
*/
- final void collapse( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot collapse in unrooted display type",
- "Attempt to collapse in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- if ( !node.isExternal() && !node.isRoot() ) {
- final boolean collapse = !node.isCollapse();
- TreePanelUtil.collapseSubtree( node, collapse );
- updateSetOfCollapsedExternalNodes();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- calculateLongestExtNodeInfo();
- setNodeInPreorderToNull();
- _control_panel.displayedPhylogenyMightHaveChanged( true );
- resetPreferredSize();
- updateOvSizes();
- _main_panel.adjustJScrollPane();
- repaint();
+ final 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() );
}
- }
-
- final void collapseSpeciesSpecificSubtrees() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
+ else {
+ if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
+ return getXdistance();
+ }
+ return getXdistance() * factor;
}
- setWaitCursor();
- TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
- updateSetOfCollapsedExternalNodes();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- calculateLongestExtNodeInfo();
- setNodeInPreorderToNull();
- resetPreferredSize();
- _main_panel.adjustJScrollPane();
- setArrowCursor();
- repaint();
}
- final void colorRank( final String rank ) {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- setWaitCursor();
- AptxUtil.removeBranchColors( _phylogeny );
- final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
- if ( colorizations > 0 ) {
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
+ 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() );
}
- if ( _control_panel.getColorAccSpeciesCb() != null ) {
- _control_panel.getColorAccSpeciesCb().setSelected( false );
+ final String ann_str = sb.toString();
+ if ( !ForesterUtil.isEmpty( ann_str ) ) {
+ c = getControlPanel().getAnnotationColors().get( ann_str );
+ if ( c == null ) {
+ c = AptxUtil.calculateColorFromString( ann_str, false );
+ getControlPanel().getAnnotationColors().put( ann_str, c );
+ }
+ if ( c == null ) {
+ c = getTreeColorSet().getAnnotationColor();
+ }
}
-
- _options.setColorLabelsSameAsParentBranch( true );
- _control_panel.repaint();
}
- setArrowCursor();
- repaint();
- if ( colorizations > 0 ) {
- String msg = "Taxonomy colorization via " + rank + " completed:\n";
- if ( colorizations > 1 ) {
- msg += "colorized " + colorizations + " subtrees";
- }
- else {
- msg += "colorized one subtree";
+ return c;
+ }
+
+ final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( node.getDistanceToParent() < 0.0 ) {
+ return 0.0f;
}
- setEdited( true );
- JOptionPane.showMessageDialog( this,
- msg,
- "Taxonomy Colorization Completed (" + rank + ")",
- JOptionPane.INFORMATION_MESSAGE );
+ return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
}
else {
- String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
- msg += "Possible solutions (given that suitable taxonomic information is present):\n";
- msg += "select a different rank (e.g. phylum, genus, ...)\n";
- msg += " and/or\n";
- msg += "execute:\n";
- msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
- msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
- JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
+ if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
+ return getOvXDistance();
+ }
+ return getOvXDistance() * factor;
}
}
- final void confColor() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- setWaitCursor();
- AptxUtil.removeBranchColors( _phylogeny );
- TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
- }
- setArrowCursor();
- repaint();
+ final 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 void decreaseDomainStructureEvalueThreshold() {
- if ( _domain_structure_e_value_thr_exp > -20 ) {
- _domain_structure_e_value_thr_exp -= 1;
+ private void changeNodeFont( final PhylogenyNode node ) {
+ final FontChooser fc = new FontChooser();
+ Font f = null;
+ if ( ( node.getNodeData().getNodeVisualData() != null ) && !node.getNodeData().getNodeVisualData().isEmpty() ) {
+ f = node.getNodeData().getNodeVisualData().getFont();
}
- }
-
- /**
- * Find the node, if any, at the given location
- *
- * @param x
- * @param y
- * @return pointer to the node at x,y, null if not found
- */
- final PhylogenyNode findNode( final int x, final int y ) {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
- return null;
+ if ( f != null ) {
+ fc.setFont( f );
}
- final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
- for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
- && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
- && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
- && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
- && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
- return node;
+ else {
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ }
+ List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ nodes = getFoundNodesAsListOfPhylogenyNodes();
+ }
+ if ( !nodes.contains( node ) ) {
+ nodes.add( node );
+ }
+ final int count = nodes.size();
+ String title = "Change the font for ";
+ if ( count == 1 ) {
+ title += "one node";
+ }
+ else {
+ title += ( count + " nodes" );
+ }
+ fc.showDialog( this, title );
+ if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
+ for( final PhylogenyNode n : nodes ) {
+ if ( n.getNodeData().getNodeVisualData() == null ) {
+ n.getNodeData().setNodeVisualData( new NodeVisualData() );
+ }
+ final NodeVisualData vd = n.getNodeData().getNodeVisualData();
+ final Font ff = fc.getFont();
+ vd.setFontName( ff.getFamily().trim() );
+ int s = ff.getSize();
+ if ( s < 0 ) {
+ s = 0;
+ }
+ if ( s > Byte.MAX_VALUE ) {
+ s = Byte.MAX_VALUE;
+ }
+ vd.setFontSize( s );
+ vd.setFontStyle( ff.getStyle() );
+ }
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ getControlPanel().getUseVisualStylesCb().setSelected( true );
}
}
- return null;
- }
-
- final Configuration getConfiguration() {
- return _configuration;
- }
-
- final ControlPanel getControlPanel() {
- return _control_panel;
- }
-
- String getCurrentExternalNodesDataBufferAsString() {
- return _current_external_nodes_data_buffer.toString();
- }
-
- int getCurrentExternalNodesDataBufferChangeCounter() {
- return _current_external_nodes_data_buffer_change_counter;
- }
-
- final int getDomainStructureEvalueThreshold() {
- return _domain_structure_e_value_thr_exp;
+ setEdited( true );
+ repaint();
}
- final Set<Long> getFoundNodes0() {
- return _found_nodes_0;
+ final private void colorizeNodes( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
+ }
+ if ( node != null ) {
+ colorizeNodesHelper( c, node );
+ }
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode n : additional_nodes ) {
+ colorizeNodesHelper( c, n );
+ }
+ }
+ repaint();
}
- final Set<Long> getFoundNodes1() {
- return _found_nodes_1;
+ final private void colorizeSubtree( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
+ }
+ 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 an : additional_nodes ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
+ }
+ }
+ repaint();
}
- final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
- if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- return ( PhylogenyMethods.getBranchColorValue( node ) );
+ private void colorNodeFont( final PhylogenyNode node ) {
+ _color_chooser.setPreviewPanel( new JPanel() );
+ NodeColorizationActionListener al;
+ int count = 1;
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
+ count = additional_nodes.size();
+ if ( !additional_nodes.contains( node ) ) {
+ count++;
+ }
}
else {
- return ( getTreeColorSet().getBranchColor() );
+ al = new NodeColorizationActionListener( _color_chooser, node );
}
- }
-
- final int getLongestExtNodeInfo() {
- return _longest_ext_node_info;
- }
-
- final Options getOptions() {
- if ( _options == null ) {
- _options = getControlPanel().getOptions();
+ String title = "Change the (node and font) color for ";
+ if ( count == 1 ) {
+ title += "one node";
}
- return _options;
- }
-
- final Rectangle2D getOvRectangle() {
- return _ov_rectangle;
- }
-
- final Rectangle getOvVirtualRectangle() {
- return _ov_virtual_rectangle;
- }
-
- final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
- return _graphics_type;
- }
-
- final double getStartingAngle() {
- return _urt_starting_angle;
- }
-
- DescriptiveStatistics getStatisticsForExpressionValues() {
- return _statistics_for_vector_data;
+ else {
+ title += ( count + " nodes" );
+ }
+ final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null );
+ setEdited( true );
+ dialog.setVisible( true );
}
-
- final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
- if ( node.getNodeData().isHasTaxonomy() ) {
- return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
+ 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;
}
- // return non-colorized color
- return getTreeColorSet().getTaxonomyColor();
+ _color_chooser.setPreviewPanel( new JPanel() );
+ final SubtreeColorizationActionListener al;
+ final boolean color_found = getOptions().isColorAllFoundNodesWhenColoringSubtree();
+ if ( color_found && ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ 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 );
+ setEdited( true );
+ dialog.setVisible( true );
}
-
- final Color getSequenceBasedColor( final PhylogenyNode node ) {
- if ( node.getNodeData().isHasSequence() ) {
- return calculateSequenceBasedColor( node.getNodeData().getSequence() );
+ final private void copySubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
}
- // return non-colorized color
- return getTreeColorSet().getSequenceColor();
+ 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();
}
-
- /**
- * @return pointer to colorset for tree drawing
- */
- final TreeColorSet getTreeColorSet() {
- return getMainPanel().getTreeColorSet();
+ 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 File getTreeFile() {
- return _treefile;
+ 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 float getXcorrectionFactor() {
- return _x_correction_factor;
+ final private void cycleColors() {
+ getMainPanel().getTreeColorSet().cycleColorScheme();
+ for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
+ tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
+ }
}
- final float getXdistance() {
- return _x_distance;
+ final private void decreaseOvSize() {
+ if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
+ setOvMaxWidth( getOvMaxWidth() - 5 );
+ setOvMaxHeight( getOvMaxHeight() - 5 );
+ updateOvSettings();
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
}
- final float getYdistance() {
- return _y_distance;
- }
-
- final void increaseDomainStructureEvalueThreshold() {
- if ( _domain_structure_e_value_thr_exp < 3 ) {
- _domain_structure_e_value_thr_exp += 1;
+ final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
}
- }
-
- final void initNodeData() {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot delete entire tree",
+ "Attempt to delete entire tree",
+ JOptionPane.ERROR_MESSAGE );
return;
}
- double max_original_domain_structure_width = 0.0;
- for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
- if ( node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- RenderableDomainArchitecture rds = null;
- if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
- rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
- getConfiguration() );
- node.getNodeData().getSequence().setDomainArchitecture( rds );
- }
- else {
- rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
- }
- if ( getControlPanel().isShowDomainArchitectures() ) {
- final double dsw = rds.getOriginalSize().getWidth();
- if ( dsw > max_original_domain_structure_width ) {
- max_original_domain_structure_width = dsw;
- }
- }
- }
+ 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;
}
- if ( getControlPanel().isShowDomainArchitectures() ) {
- final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
- for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
- if ( node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
- .getSequence().getDomainArchitecture();
- rds.setRenderingFactorWidth( ds_factor_width );
- rds.setParameter( _domain_structure_e_value_thr_exp );
- }
- }
+ 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 boolean inOv( final MouseEvent e ) {
- return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
- && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
- && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
- + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
+ final 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 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 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 boolean isApplet() {
- return getMainPanel() instanceof MainPanelApplets;
+ 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 boolean isCanCollapse() {
- return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ 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 boolean isCanColorSubtree() {
- return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ 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 boolean isCanCopy() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
+ final private void drawOvalGradient( final float x,
+ final float y,
+ final float width,
+ final float heigth,
+ final Graphics2D g,
+ final Color color_1,
+ final Color color_2,
+ final Color color_border ) {
+ _ellipse.setFrame( x, y, width, heigth );
+ g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
+ g.fill( _ellipse );
+ if ( color_border != null ) {
+ g.setPaint( color_border );
+ g.draw( _ellipse );
+ }
}
- final boolean isCanCut( final PhylogenyNode node ) {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
- .isRoot() );
+ 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 boolean isCanDelete() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
+ 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 boolean isCanPaste() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
- && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
+ final private void drawRectGradient( final float x,
+ final float y,
+ final float width,
+ final float heigth,
+ final Graphics2D g,
+ final Color color_1,
+ final Color color_2,
+ final Color color_border ) {
+ _rectangle.setFrame( x, y, width, heigth );
+ g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
+ g.fill( _rectangle );
+ if ( color_border != null ) {
+ g.setPaint( color_border );
+ g.draw( _rectangle );
+ }
}
- final boolean isCanReroot() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
+ 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 boolean isCanSubtree( final PhylogenyNode node ) {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
- .isRoot() || ( _subtree_index > 0 ) ) );
+ 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 boolean isCurrentTreeIsSubtree() {
- return ( _subtree_index > 0 );
+ private final Color getColorForFoundNode( final PhylogenyNode n ) {
+ if ( isInCurrentExternalNodes( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor1();
+ }
+ else {
+ return getTreeColorSet().getFoundColor0and1();
+ }
}
- final boolean isEdited() {
- return _edited;
+ final private Set<Long> getCopiedAndPastedNodes() {
+ return getMainPanel().getCopiedAndPastedNodes();
}
- final boolean isInOvRect() {
- return _in_ov_rect;
+ final private Set<Long> getCurrentExternalNodes() {
+ return _current_external_nodes;
}
- final boolean isOvOn() {
- return _ov_on;
+ final private Phylogeny getCutOrCopiedTree() {
+ return getMainPanel().getCutOrCopiedTree();
}
- final boolean isPhyHasBranchLengths() {
- return _phy_has_branch_lengths;
+ private FontMetrics getFontMetricsForLargeDefaultFont() {
+ return getTreeFontSet().getFontMetricsLarge();
}
- final void midpointRoot() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- if ( !_phylogeny.isRerootable() ) {
- JOptionPane.showMessageDialog( this,
- "This is not rerootable",
- "Not rerootable",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- setNodeInPreorderToNull();
- setWaitCursor();
- PhylogenyMethods.midpointRoot( _phylogeny );
- resetNodeIdToDistToLeafMap();
- setArrowCursor();
- setEdited( true );
- repaint();
+ final private float getLastDragPointX() {
+ return _last_drag_point_x;
}
- final void mouseClicked( final MouseEvent e ) {
- if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
- final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
- final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
- double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
- * w_ratio;
- double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
- * h_ratio;
- if ( x < 0 ) {
- x = 0;
- }
- if ( y < 0 ) {
- y = 0;
- }
- final double max_x = getWidth() - getVisibleRect().width;
- final double max_y = getHeight() - getVisibleRect().height;
- if ( x > max_x ) {
- x = max_x;
- }
- if ( y > max_y ) {
- y = max_y;
- }
- getMainPanel().getCurrentScrollPane().getViewport()
- .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
- setInOvRect( true );
- repaint();
- }
- else {
- final PhylogenyNode node = findNode( e.getX(), e.getY() );
- if ( node != null ) {
- if ( !node.isRoot() && node.getParent().isCollapse() ) {
- return;
- }
- _highlight_node = node;
- // Check if shift key is down
- if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
- // Yes, so add to _found_nodes
- if ( getFoundNodes0() == null ) {
- setFoundNodes0( new HashSet<Long>() );
- }
- getFoundNodes0().add( node.getId() );
- // Check if control key is down
- }
- else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
- // Yes, so pop-up menu
- displayNodePopupMenu( node, e.getX(), e.getY() );
- // Handle unadorned click
- }
- else {
- // Check for right mouse button
- if ( e.getModifiers() == 4 ) {
- displayNodePopupMenu( node, e.getX(), e.getY() );
- }
- else {
- // if not in _found_nodes, clear _found_nodes
- handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
- }
- }
- }
- else {
- // no node was clicked
- _highlight_node = null;
- }
- }
- repaint();
+ final private float getLastDragPointY() {
+ return _last_drag_point_y;
}
- final void mouseDragInBrowserPanel( final MouseEvent e ) {
- setCursor( MOVE_CURSOR );
- final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
- scroll_position.x -= ( e.getX() - getLastDragPointX() );
- scroll_position.y -= ( e.getY() - getLastDragPointY() );
- if ( scroll_position.x < 0 ) {
- scroll_position.x = 0;
- }
- else {
- final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
- if ( scroll_position.x > max_x ) {
- scroll_position.x = max_x;
- }
- }
- if ( scroll_position.y < 0 ) {
- scroll_position.y = 0;
- }
- else {
- final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
- if ( scroll_position.y > max_y ) {
- scroll_position.y = max_y;
- }
- }
- if ( isOvOn() || getOptions().isShowScale() ) {
- repaint();
+ final private double getMaxDistanceToRoot() {
+ if ( _max_distance_to_root < 0 ) {
+ recalculateMaxDistanceToRoot();
}
- getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
+ return _max_distance_to_root;
}
- final void mouseDragInOvRectangle( final MouseEvent e ) {
- setCursor( HAND_CURSOR );
- final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
- final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
- final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
- double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
- double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
- scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
- scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
- if ( scroll_position.x <= 0 ) {
- scroll_position.x = 0;
- dx = 0;
- }
- else {
- final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
- if ( scroll_position.x >= max_x ) {
- dx = 0;
- scroll_position.x = max_x;
- }
- }
- if ( scroll_position.y <= 0 ) {
- dy = 0;
- scroll_position.y = 0;
- }
- else {
- final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
- if ( scroll_position.y >= max_y ) {
- dy = 0;
- scroll_position.y = max_y;
- }
- }
- repaint();
- getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
- setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
- setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
+ final private float getOvMaxHeight() {
+ return _ov_max_height;
}
- final void mouseMoved( final MouseEvent e ) {
- requestFocusInWindow();
- if ( _current_external_nodes != null ) {
- _current_external_nodes = null;
- repaint();
- }
- if ( getControlPanel().isNodeDescPopup() ) {
- if ( _node_desc_popup != null ) {
- _node_desc_popup.hide();
- _node_desc_popup = null;
- }
- }
- if ( getOptions().isShowOverview() && isOvOn() ) {
- if ( inOvVirtualRectangle( e ) ) {
- if ( !isInOvRect() ) {
- setInOvRect( true );
- repaint();
- }
- }
- else {
- if ( isInOvRect() ) {
- setInOvRect( false );
- repaint();
- }
- }
- }
- if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
- if ( !isInOv() ) {
- setInOv( true );
- }
- }
- else {
- if ( isInOv() ) {
- setInOv( false );
- }
- final PhylogenyNode node = findNode( e.getX(), e.getY() );
- if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
- if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
- for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
- addToCurrentExternalNodes( n.getId() );
- }
- setCursor( HAND_CURSOR );
- repaint();
- }
- else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
- setCursor( CUT_CURSOR );
- }
- else {
- setCursor( HAND_CURSOR );
- if ( getControlPanel().isNodeDescPopup() ) {
- showNodeDataPopup( e, node );
+ 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 List<Accession> getPdbAccs( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = new ArrayList<Accession>();
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
+ final SortedSet<Accession> cross_refs = seq.getCrossReferences();
+ for( final Accession acc : cross_refs ) {
+ if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
+ pdb_ids.add( acc );
}
}
}
- else {
- setCursor( ARROW_CURSOR );
- }
}
+ return pdb_ids;
}
- final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
- setCursor( ARROW_CURSOR );
+ final private double getScaleDistance() {
+ return _scale_distance;
}
- final void multiplyUrtFactor( final float f ) {
- _urt_factor *= f;
+ final private String getScaleLabel() {
+ return _scale_label;
}
- final JApplet obtainApplet() {
- return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ final private TreeFontSet getTreeFontSet() {
+ return getMainPanel().getTreeFontSet();
}
-
- final void paintBranchCircular( final PhylogenyNode p,
- final PhylogenyNode c,
- final Graphics2D g,
- final boolean radial_labels,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- final double angle = _urt_nodeid_angle_map.get( c.getId() );
- final double root_x = _root.getXcoord();
- final double root_y = _root.getYcoord();
- final double dx = root_x - p.getXcoord();
- final double dy = root_y - p.getYcoord();
- final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
- final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
- assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
- if ( ( c.isFirstChildNode() || c.isLastChildNode() )
- && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
- final double r2 = 2.0 * parent_radius;
- drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
- }
- drawLine( c.getXcoord(),
- c.getYcoord(),
- root_x + ( Math.cos( angle ) * parent_radius ),
- root_y + ( Math.sin( angle ) * parent_radius ),
- g );
- paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
- if ( c.isExternal() ) {
- final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c )
- || isInCurrentExternalNodes( c );
- if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
- && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
- return;
- }
- paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
- }
+
+ final public float getThreshold() {
+ return _partition_threshold;
}
- 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 );
+ 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 COLOR_NODE_FONT:
+ colorNodeFont( node );
+ break;
+ case CHANGE_NODE_FONT:
+ changeNodeFont( node );
+ break;
+ case OPEN_SEQ_WEB:
+ openSeqWeb( node );
+ break;
+ case BLAST:
+ blast( node );
+ break;
+ case OPEN_TAX_WEB:
+ openTaxWeb( node );
+ break;
+ case OPEN_PDB_WEB:
+ openPdbWeb( 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;
+ case UNCOLLAPSE_ALL:
+ uncollapseAll( node );
+ break;
+ case ORDER_SUBTREE:
+ orderSubtree( node );
+ break;
+ default:
+ throw new IllegalArgumentException( "unknown action: " + action );
}
- drawLine( c.getXSecondary(),
- c.getYSecondary(),
- root_x + ( Math.cos( angle ) * parent_radius ),
- root_y + ( Math.sin( angle ) * parent_radius ),
- g );
- if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
- g.setColor( getColorForFoundNode( c ) );
- drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary()
- - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
+ }
+
+ final 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 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() );
- }
+ final private void init() {
+ _color_chooser = new JColorChooser();
+ _rollover_popup = new JTextArea();
+ _rollover_popup.setFont( POPUP_FONT );
+ resetNodeIdToDistToLeafMap();
+ setTextAntialias();
+ setTreeFile( null );
+ setEdited( false );
+ initializeOvSettings();
+ resetDepthCollapseDepthValue();
+ resetRankCollapseRankValue();
+ 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;
}
- 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 );
+ return Blast.isContainsQueryForBlast( node );
}
- 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 );
+ final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
+ final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
+ if ( a != null ) {
+ return a.getValue();
}
- paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
+ return null;
}
- 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;
+ 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;
}
- if ( _control_panel.isShowSequenceRelations() ) {
- _query_sequence = _control_panel.getSelectedQuerySequence();
+ else {
+ return false;
}
- // 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 );
+ }
+
+ final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
+ return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
+ }
+
+ private boolean isInFoundNodes( final PhylogenyNode n ) {
+ return isInFoundNodes0( n ) || isInFoundNodes1( n );
+ }
+
+ final private boolean isInFoundNodes0( final PhylogenyNode node ) {
+ return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
+ }
+
+ final private boolean isInFoundNodes1( final PhylogenyNode node ) {
+ return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
+ }
+
+ final private boolean isInOv() {
+ return _in_ov;
+ }
+
+ final 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 void keyPressedCalls( final KeyEvent e ) {
+ if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
+ if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
+ if ( !isInOvRect() ) {
+ setInOvRect( true );
}
}
- 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 );
- }
+ else if ( isInOvRect() ) {
+ setInOvRect( false );
}
- 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 );
+ if ( e.isAltDown() ) {
+ if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
+ || ( e.getKeyCode() == KeyEvent.VK_C ) || ( e.getKeyCode() == KeyEvent.VK_BACK_SPACE ) ) {
+ getControlPanel().showWhole();
}
- else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
- _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
- .getDistanceToParent() * getXcorrectionFactor() ) ) );
+ else if ( e.isShiftDown()
+ && ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- else {
- _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
+ else if ( e.isShiftDown() && plusPressed( e.getKeyCode() ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- // 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 );
- }
+ else if ( e.getKeyCode() == KeyEvent.VK_O ) {
+ getControlPanel().orderPressed( this );
}
- 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();
- }
+ else if ( e.getKeyCode() == KeyEvent.VK_R ) {
+ getControlPanel().returnedToSuperTreePressed();
}
- //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 );
+ else if ( e.getKeyCode() == KeyEvent.VK_U ) {
+ getControlPanel().uncollapseAll( this );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
- 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 );
- }
+ else if ( e.getKeyCode() == KeyEvent.VK_UP ) {
+ getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
- if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
- paintPhylogenyLite( g );
+ else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
+ getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- if ( getControlPanel().getDynamicallyHideData() != null ) {
- getControlPanel().setDynamicHidingIsOn( false );
+ else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
+ getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
+ AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
- final double angle = getStartingAngle();
- final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
- _dynamic_hiding_factor = 0;
- if ( getControlPanel().isDynamicallyHideData() ) {
- _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny()
- .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
+ else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
+ getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
+ AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
- if ( getControlPanel().getDynamicallyHideData() != null ) {
- if ( _dynamic_hiding_factor > 1 ) {
- getControlPanel().setDynamicHidingIsOn( true );
+ else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
+ getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
+ AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( plusPressed( e.getKeyCode() ) ) {
+ getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
+ AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ }
+ else {
+ if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
+ || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
+ final int d = 80;
+ int dx = 0;
+ int dy = -d;
+ if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
+ dy = d;
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
+ dx = -d;
+ dy = 0;
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
+ dx = d;
+ dy = 0;
+ }
+ final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
+ scroll_position.x = scroll_position.x + dx;
+ scroll_position.y = scroll_position.y + dy;
+ if ( scroll_position.x <= 0 ) {
+ scroll_position.x = 0;
}
else {
- getControlPanel().setDynamicHidingIsOn( false );
+ final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
+ if ( scroll_position.x >= max_x ) {
+ scroll_position.x = max_x;
+ }
}
- }
- 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 ( scroll_position.y <= 0 ) {
+ scroll_position.y = 0;
}
else {
- paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ 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 );
}
- if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
- g.setColor( getTreeColorSet().getOvColor() );
- paintUnrootedLite( _phylogeny.getRoot(),
- angle,
- angle + ( 2 * Math.PI ),
- g,
- ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
- paintOvRectangle( g );
- }
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
- final int d = radius + MOVE + getLongestExtNodeInfo();
- _dynamic_hiding_factor = 0;
- if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
- _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny()
- .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
- }
- if ( getControlPanel().getDynamicallyHideData() != null ) {
- if ( _dynamic_hiding_factor > 1 ) {
- getControlPanel().setDynamicHidingIsOn( true );
+ else 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 {
- getControlPanel().setDynamicHidingIsOn( 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 );
}
}
- 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 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 {
- y_scale = ( double ) getWidth() / getHeight();
- y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
+ getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
}
- _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 );
+ getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
+ repaint();
}
- }
- }
-
- 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;
+ 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();
}
}
- _node_frame_index = 0;
+ if ( e.getKeyCode() == KeyEvent.VK_HOME || e.getKeyCode() == KeyEvent.VK_ESCAPE ) {
+ getControlPanel().showWhole();
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_PAGE_UP ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_PAGE_DOWN ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ e.consume();
}
- /**
- * 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 ];
+ 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 {
+ _node_popup_menu_items[ i ].setEnabled( false );
+ }
}
- _node_frames[ _node_frame_index ] = null;
+ else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
+ final List<Accession> accs = getPdbAccs( node );
+ _node_popup_menu_items[ i ] = new JMenuItem( title );
+ if ( !ForesterUtil.isEmpty( accs ) ) {
+ if ( accs.size() == 1 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else if ( accs.size() == 2 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else if ( accs.size() == 3 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ }
+ else {
+ _node_popup_menu_items[ i ].setEnabled( false );
+ }
+ }
+ else if ( title.startsWith( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ]
+ .setText( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] + ": "
+ + getOptions().getExtDescNodeDataToReturn().toString() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
+ _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 );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.uncollapse_all ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanUncollapseAll( node ) );
+ }
+ _node_popup_menu_items[ i ].addActionListener( this );
+ _node_popup_menu.add( _node_popup_menu_items[ i ] );
}
}
- final void 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();
+ private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
+ if ( node != null ) {
+ if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getName() );
+ }
+ if ( node.getNodeData().isHasSequence() ) {
+ if ( getControlPanel().isShowSeqSymbols()
+ && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getSymbol() );
+ }
+ if ( getControlPanel().isShowGeneNames()
+ && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getGeneName() );
+ }
+ if ( getControlPanel().isShowSeqNames()
+ && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getName() );
+ }
+ if ( getControlPanel().isShowSequenceAcc()
+ && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
+ sb.append( node.getNodeData().getSequence().getAccession().getSource() );
+ sb.append( ":" );
+ }
+ sb.append( node.getNodeData().getSequence().getAccession().getValue() );
+ }
+ }
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( propertiesToString( node ) );
+ }
}
}
- final void resetNodeIdToDistToLeafMap() {
- _nodeid_dist_to_leaf = new HashMap<Long, Short>();
- }
-
- final void resetPreferredSize() {
- if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
- return;
+ private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
+ if ( _control_panel.isShowTaxonomyRank() && !ForesterUtil.isEmpty( taxonomy.getRank() ) ) {
+ sb.append( "[" );
+ sb.append( taxonomy.getRank() );
+ sb.append( "] " );
}
- 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() );
+ if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
+ sb.append( taxonomy.getTaxonomyCode() );
+ sb.append( " " );
}
- else {
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil.roundToInt( getXdistance()
- * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
+ if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
+ && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " (" );
+ sb.append( taxonomy.getCommonName() );
+ sb.append( ") " );
}
- else {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil.roundToInt( getXdistance()
- * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
+ else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
}
}
- setPreferredSize( new Dimension( x, y ) );
- }
-
- final void selectNode( final PhylogenyNode node ) {
- if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
- getFoundNodes0().remove( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
- if ( getFoundNodes0().size() < 1 ) {
- getControlPanel().searchReset0();
+ else if ( _control_panel.isShowTaxonomyScientificNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " " );
}
}
- else {
- getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
- getControlPanel().getSearchResetButton0().setEnabled( true );
- getControlPanel().getSearchResetButton0().setVisible( true );
- if ( getFoundNodes0() == null ) {
- setFoundNodes0( new HashSet<Long>() );
+ else if ( _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
}
- getFoundNodes0().add( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
}
}
- final void setArrowCursor() {
- setCursor( ARROW_CURSOR );
- repaint();
- }
-
- final void setControlPanel( final ControlPanel atv_control ) {
- _control_panel = atv_control;
- }
-
- void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
- increaseCurrentExternalNodesDataBufferChangeCounter();
- _current_external_nodes_data_buffer = sb;
- }
-
- final void setFoundNodes0( final Set<Long> found_nodes ) {
- _found_nodes_0 = found_nodes;
+ private final String obtainTitleForExtDescNodeData() {
+ return getOptions().getExtDescNodeDataToReturn().toString();
}
- final void setFoundNodes1( final Set<Long> found_nodes ) {
- _found_nodes_1 = found_nodes;
- }
-
- final void setInOvRect( final boolean in_ov_rect ) {
- _in_ov_rect = in_ov_rect;
- }
-
- final void setLargeFonts() {
- getTreeFontSet().largeFonts();
- }
-
- final void setLastMouseDragPointX( final float x ) {
- _last_drag_point_x = x;
- }
-
- final void setLastMouseDragPointY( final float y ) {
- _last_drag_point_y = y;
- }
-
- final void 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 );
- }
+ final private void openPdbWeb( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = getPdbAccs( node );
+ if ( ForesterUtil.isEmpty( pdb_ids ) ) {
+ cannotOpenBrowserWarningMessage( "PDB" );
+ return;
}
- 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 );
- //}
+ final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
+ if ( !ForesterUtil.isEmpty( uri_strs ) ) {
+ for( final String uri_str : uri_strs ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" );
+ }
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ }
}
else {
- _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
- _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
+ cannotOpenBrowserWarningMessage( "PDB" );
}
}
- final void setTinyFonts() {
- getTreeFontSet().tinyFonts();
- }
-
- final void setTreeFile( final File treefile ) {
- _treefile = treefile;
- }
-
- final void setXcorrectionFactor( final float f ) {
- _x_correction_factor = f;
- }
-
- final void setXdistance( final float x ) {
- _x_distance = x;
- }
-
- final void setYdistance( final float y ) {
- _y_distance = y;
- }
-
- final void sortDescendants( final PhylogenyNode node ) {
- if ( !node.isExternal() ) {
- DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
- if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
- .isShowTaxonomyCommonNames() ) ) {
- if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
- .isShowSeqSymbols() ) ) {
- pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
- }
- else if ( getControlPanel().isShowNodeNames() ) {
- pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
- }
+ final private void openSeqWeb( final PhylogenyNode node ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
+ cannotOpenBrowserWarningMessage( "sequence" );
+ return;
+ }
+ final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
+ if ( !ForesterUtil.isEmpty( uri_str ) ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" );
+ }
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
}
- PhylogenyMethods.sortNodeDescendents( node, pri );
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
}
- repaint();
+ else {
+ cannotOpenBrowserWarningMessage( "sequence" );
+ }
}
- 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 );
+ final private void openTaxWeb( final PhylogenyNode node ) {
+ if ( !isCanOpenTaxWeb( node ) ) {
+ cannotOpenBrowserWarningMessage( "taxonomic" );
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;
+ String uri_str = null;
+ final Taxonomy tax = node.getNodeData().getTaxonomy();
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
+ try {
+ uri_str = new URI( tax.getIdentifier().getValue() ).toString();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ uri_str = null;
+ e.printStackTrace();
+ }
}
- 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;
+ 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 = "http://www.uniprot.org/taxonomy/"
+ + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF_8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
- 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 ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ try {
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF_8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
- else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
- superTree();
+ else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ try {
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF_8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
- _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 );
+ else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
+ try {
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF_8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ }
+ if ( !ForesterUtil.isEmpty( uri_str ) ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ), "_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" );
}
- _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;
+ final private void paintBranchLength( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ g.setFont( getTreeFontSet().getSmallFont() );
+ if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) {
+ g.setColor( Color.BLACK );
}
- 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.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
- }
- setEdited( true );
- setArrowCursor();
- repaint();
- }
-
- final void updateOvSettings() {
- switch ( getOptions().getOvPlacement() ) {
- case LOWER_LEFT:
- setOvXPosition( OV_BORDER );
- setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
- setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
- break;
- case LOWER_RIGHT:
- setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
- setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
- setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
- break;
- case UPPER_RIGHT:
- setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
- setOvYPosition( OV_BORDER );
- setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
- break;
- default:
- setOvXPosition( OV_BORDER );
- setOvYPosition( OV_BORDER );
- setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
- break;
+ else {
+ g.setColor( getTreeColorSet().getBranchLengthColor() );
}
- }
-
- 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;
+ if ( !node.isRoot() ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
+ node.getParent().getXcoord() + EURO_D,
+ node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
+ g );
}
- 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 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
+ node.getParent().getXcoord() + ROUNDED_D,
+ node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
+ g );
}
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();
- }
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
+ node.getParent().getXcoord() + 3,
+ node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
+ g );
}
}
- }
-
- 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;
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
+ 3,
+ node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
+ g );
}
}
- private void abbreviateScientificName( final String sn, final StringBuilder sb ) {
- final String[] a = sn.split( "\\s+" );
- sb.append( a[ 0 ].substring( 0, 1 ) );
- sb.append( a[ 1 ].substring( 0, 2 ) );
- if ( a.length > 2 ) {
- for( int i = 2; i < a.length; i++ ) {
- sb.append( " " );
- sb.append( a[ i ] );
- }
+ final private void paintBranchLite( final Graphics2D g,
+ final float x1,
+ final float x2,
+ final float y1,
+ final float y2,
+ final PhylogenyNode node ) {
+ g.setColor( getTreeColorSet().getOvColor() );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
+ drawLine( x1, y1, x2, y2, g );
}
- }
-
- final private void addEmptyNode( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
+ _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
+ ( g ).draw( _quad_curve );
}
- final String label = createASimpleTextRepresentationOfANode( node );
- String msg = "";
- if ( ForesterUtil.isEmpty( label ) ) {
- msg = "How to add the new, empty node?";
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
+ final float dx = x2 - x1;
+ final float dy = y2 - y1;
+ _cubic_curve.setCurve( x1,
+ y1,
+ x1 + ( dx * 0.4f ),
+ y1 + ( dy * 0.2f ),
+ x1 + ( dx * 0.6f ),
+ y1 + ( dy * 0.8f ),
+ x2,
+ y2 );
+ ( g ).draw( _cubic_curve );
}
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;
+ final float x2a = x2;
+ final float x1a = x1;
+ // draw the vertical line
+ if ( node.isFirstChildNode() || node.isLastChildNode() ) {
+ drawLine( x1, y1, x1, y2, g );
}
- 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>();
+ // draw the horizontal line
+ drawLine( x1a, y2, x2a, y2, g );
}
- _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().getFoundColor0() );
+ /**
+ * Paint a branch which consists of a vertical and a horizontal bar
+ * @param is_ind_found_nodes
+ */
+ final private void paintBranchRectangular( final Graphics2D g,
+ final float x1,
+ final float x2,
+ final float y1,
+ final float y2,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
+ drawLine( x1, y1, x2, y2, g );
}
- else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
+ _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
+ g.draw( _quad_curve );
}
- else if ( to_pdf ) {
- g.setColor( getTreeColorSet().getBranchColorForPdf() );
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
+ final float dx = x2 - x1;
+ final float dy = y2 - y1;
+ _cubic_curve.setCurve( x1,
+ y1,
+ x1 + ( dx * 0.4f ),
+ y1 + ( dy * 0.2f ),
+ x1 + ( dx * 0.6f ),
+ y1 + ( dy * 0.8f ),
+ x2,
+ y2 );
+ g.draw( _cubic_curve );
}
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';
+ final float x2a = x2;
+ final float x1a = x1;
+ float y2_r = 0;
+ if ( node.isFirstChildNode() || node.isLastChildNode()
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
+ || ( 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 ) ) ) ) ) {
+ // Do nothing.
+ }
+ else {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ float x2c = x1 + EURO_D;
+ if ( x2c > x2a ) {
+ x2c = x2a;
}
+ drawLine( x1, y1, x2c, y2, g );
}
- else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- type = 'p';
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ if ( y2 > y1 ) {
+ y2_r = y2 - ROUNDED_D;
+ if ( y2_r < y1 ) {
+ y2_r = y1;
+ }
+ drawLine( x1, y1, x1, y2_r, g );
}
else {
- type = 'n';
+ y2_r = y2 + ROUNDED_D;
+ if ( y2_r > y1 ) {
+ y2_r = y1;
+ }
+ drawLine( x1, y1, x1, y2_r, g );
}
}
- }
- if ( type == '?' ) {
- if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
- type = 'p';
- }
else {
- type = 'n';
+ drawLine( x1, y1, x1, y2, g );
}
}
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
+ }
+ // draw the horizontal line
+ if ( !to_graphics_file && !to_pdf && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) )
+ || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
+ return;
+ }
+ float x1_r = 0;
+ if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawLine( x1_r, y2, x2a, y2, g );
+ }
}
- try {
- Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawLine( x1c, y2, x2a, y2, g );
+ }
}
- catch ( final Exception e ) {
- e.printStackTrace();
+ else {
+ drawLine( x1a, y2, x2a, y2, g );
}
- if ( Constants.ALLOW_DDBJ_BLAST ) {
- try {
- System.out.println( "trying: " + query );
- final Blast s = new Blast();
- s.ddbjBlast( query );
+ }
+ else {
+ final double w = PhylogenyMethods.getBranchWidthValue( node );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
}
- catch ( final Exception e ) {
- e.printStackTrace();
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
}
}
+ else {
+ drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ }
+ }
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
+ if ( x1_r > x2a ) {
+ x1_r = x2a;
+ }
+ if ( y2 > y2_r ) {
+ final double diff = y2 - y2_r;
+ _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
+ }
+ else {
+ _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
+ }
+ g.draw( _arc );
}
}
+ if ( node.isExternal() ) {
+ paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
+ }
}
- private final int calcDynamicHidingFactor() {
- return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().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;
+ final private double paintCirculars( final PhylogenyNode n,
+ final Phylogeny phy,
+ final float center_x,
+ final float center_y,
+ final double radius,
+ final boolean radial_labels,
+ final Graphics2D g,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
+ if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
+ System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
}
- return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
+ return _urt_nodeid_angle_map.get( n.getId() );
}
else {
- if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
- return getXdistance();
+ final List<PhylogenyNode> descs = n.getDescendants();
+ double sum = 0;
+ for( final PhylogenyNode desc : descs ) {
+ sum += paintCirculars( desc,
+ phy,
+ center_x,
+ center_y,
+ radius,
+ radial_labels,
+ g,
+ to_pdf,
+ to_graphics_file );
}
- 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() );
+ double r = 0;
+ if ( !n.isRoot() ) {
+ r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
}
- 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();
- }
+ 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 ) ) ) );
+ _urt_nodeid_angle_map.put( n.getId(), theta );
+ for( final PhylogenyNode desc : descs ) {
+ paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
}
+ return theta;
}
-
- 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() );
+ final private void paintCircularsLite( final PhylogenyNode n,
+ final Phylogeny phy,
+ final int center_x,
+ final int center_y,
+ final int radius,
+ final Graphics2D g ) {
+ if ( n.isExternal() ) {
+ return;
}
else {
- if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
- return getOvXDistance();
+ final List<PhylogenyNode> descs = n.getDescendants();
+ for( final PhylogenyNode desc : descs ) {
+ paintCircularsLite( desc, phy, center_x, center_y, radius, g );
+ }
+ float r = 0;
+ if ( !n.isRoot() ) {
+ 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 ) ) ) );
+ for( final PhylogenyNode desc : descs ) {
+ paintBranchCircularLite( n, desc, g );
}
- 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 );
- }
-
- private void changeNodeFont( final PhylogenyNode node ) {
- final FontChooser fc = new FontChooser();
- Font f = null;
- if ( ( node.getNodeData().getNodeVisualData() != null ) && !node.getNodeData().getNodeVisualData().isEmpty() ) {
- f = node.getNodeData().getNodeVisualData().getFont();
+ final private void paintCollapsedNode( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf,
+ final boolean is_in_found_nodes ) {
+ ////
+ //// TODO
+ ////
+ Color c = null;
+ int res[] = null;
+ if ( _found_nodes_0 != null || _found_nodes_1 != null ) {
+ res = calcFoundNodesInSubtree( node );
}
- if ( f != null ) {
- fc.setFont( f );
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ c = Color.BLACK;
+ }
+ //TODO
+ //FIXME
+ // else if ( is_in_found_nodes ) {
+ // c = getColorForFoundNode( node );
+ // }
+ // else if ( getControlPanel().isColorAccordingToSequence() ) {
+ // c = getSequenceBasedColor( node );
+ // }
+ // else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
+ // c = getTaxonomyBasedColor( node );
+ // }
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
+ && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ c = PhylogenyMethods.getBranchColorValue( node );
+ }
+ else if ( to_pdf ) {
+ g.setColor( getTreeColorSet().getBranchColorForPdf() );
}
else {
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ c = getTreeColorSet().getCollapseFillColor();
}
- fc.showDialog( this, "Select Font" );
- if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
- List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- nodes = getFoundNodesAsListOfPhylogenyNodes();
+ double d = node.getAllExternalDescendants().size();
+ float xxx;
+ double s = 0;
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( d > 1000 ) {
+ d = 0.75 * _y_distance;
}
- nodes.add( node );
- for( final PhylogenyNode n : nodes ) {
- if ( n.getNodeData().getNodeVisualData() == null ) {
- n.getNodeData().setNodeVisualData( new NodeVisualData() );
- }
- final NodeVisualData vd = n.getNodeData().getNodeVisualData();
- final Font ff = fc.getFont();
- vd.setFontName( ff.getFamily().trim() );
- int s = ff.getSize();
- if ( s < 0 ) {
- s = 0;
- }
- if ( s > Byte.MAX_VALUE ) {
- s = Byte.MAX_VALUE;
- }
- vd.setFontSize( s );
- vd.setFontStyle( ff.getStyle() );
- }
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- getControlPanel().getUseVisualStylesCb().setSelected( true );
- }
- }
- repaint();
- }
-
- final private void colorizeNodes( final Color c,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
- }
- if ( node != null ) {
- colorizeNodesHelper( c, node );
+ else {
+ d = 0.25 * Math.log10( d ) * _y_distance;
+ }
+ final float half_box_size = 0.5f * getOptions().getDefaultNodeShapeSize();
+ if ( d < half_box_size ) {
+ d = half_box_size;
+ }
+ _polygon.reset();
+ final float xx = node.getXcoord() - ( getOptions().getDefaultNodeShapeSize() );
+ xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
+ _polygon.moveTo( xxx, node.getYcoord() + 0.5 );
+ _polygon.lineTo( xxx, node.getYcoord() - 0.5 );
+ s = _options.isCollapsedWithAverageHeigh()
+ ? PhylogenyMethods.calculateAverageTreeHeight( node ) * _x_correction_factor : 1;
+ _polygon.lineTo( node.getXcoord() + s, node.getYcoord() - d );
+ _polygon.lineTo( node.getXcoord() + s, node.getYcoord() + d );
+ _polygon.closePath();
}
- if ( additional_nodes != null ) {
- for( final PhylogenyNode n : additional_nodes ) {
- colorizeNodesHelper( c, n );
+ else {
+ if ( d > 1000 ) {
+ d = _y_distance;
}
- }
- repaint();
- }
-
- final private void colorizeSubtree( final Color c,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
- }
- if ( node != null ) {
- for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ else {
+ d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- }
- if ( additional_nodes != null ) {
- for( final PhylogenyNode an : additional_nodes ) {
- for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
- }
+ final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
+ if ( d < box_size ) {
+ d = box_size;
}
+ final float xx = node.getXcoord() - ( 2 * box_size );
+ xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
+ _polygon.reset();
+ _polygon.moveTo( xxx, node.getYcoord() );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
+ _polygon.closePath();
}
- repaint();
- }
-
- private void colorNodeFont( final PhylogenyNode node ) {
- _color_chooser.setPreviewPanel( new JPanel() );
- NodeColorizationActionListener al;
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
- al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
- }
- else {
- al = new NodeColorizationActionListener( _color_chooser, node );
- }
- final JDialog dialog = JColorChooser.createDialog( this, "Node colorization", true, _color_chooser, al, null );
- dialog.setVisible( true );
- }
-
- 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 ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
- 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;
+ if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
+ g.setColor( c );
+ g.fill( _polygon );
}
- else {
- label = "";
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
+ g.setColor( getBackground() );
+ g.fill( _polygon );
+ g.setColor( c );
+ g.draw( _polygon );
}
- if ( !ForesterUtil.isEmpty( label ) ) {
- label = " [" + label + "]";
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ g.setPaint( new GradientPaint( xxx,
+ node.getYcoord(),
+ getBackground(),
+ node.getXcoord(),
+ ( float ) ( node.getYcoord() - d ),
+ c,
+ false ) );
+ g.fill( _polygon );
+ g.setPaint( c );
+ g.draw( _polygon );
}
- return label;
+ paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes, s );
}
- 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 private void paintConfidenceValues( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ final List<Confidence> confidences = node.getBranchData().getConfidences();
+ boolean not_first = false;
+ Collections.sort( confidences );
+ final StringBuilder sb = new StringBuilder();
+ for( final Confidence confidence : confidences ) {
+ if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE ) || ( !ForesterUtil.isEmpty( confidence.getType() )
+ && confidence.getType().equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) {
+ final double value = confidence.getValue();
+ if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ if ( value < getOptions().getMinConfidenceValue() ) {
+ return;
+ }
+ if ( not_first ) {
+ sb.append( "/" );
+ }
+ else {
+ not_first = true;
+ }
+ sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil
+ .round( value, getOptions().getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ if ( getOptions().isShowConfidenceStddev() ) {
+ if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ sb.append( "(" );
+ sb.append( FORMATTER_CONFIDENCE
+ .format( ForesterUtil.round( confidence.getStandardDeviation(),
+ getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ sb.append( ")" );
+ }
+ }
+ }
+ }
}
- 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;
+ if ( sb.length() > 0 ) {
+ final float parent_x = node.getParent().getXcoord();
+ float x = node.getXcoord();
+ g.setFont( getTreeFontSet().getSmallFont() );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ x += EURO_D;
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x += ROUNDED_D;
+ }
+ if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) {
+ g.setColor( Color.BLACK );
+ }
+ else {
+ g.setColor( getTreeColorSet().getConfidenceColor() );
+ }
+ final String conf_str = sb.toString();
+ TreePanel.drawString( conf_str,
+ parent_x + ( ( x - parent_x
+ - getTreeFontSet().getFontMetricsSmall().stringWidth( conf_str ) ) / 2 ),
+ ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
+ g );
}
- 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 paintGainedAndLostCharacters( final Graphics2D g,
+ final PhylogenyNode node,
+ final String gained,
+ final String lost ) {
+ if ( node.getParent() != null ) {
+ final float parent_x = node.getParent().getXcoord();
+ final float x = node.getXcoord();
+ g.setFont( getTreeFontSet().getLargeFont() );
+ g.setColor( getTreeColorSet().getGainedCharactersColor() );
+ if ( AptxConstants.SPECIAL_CUSTOM ) {
+ g.setColor( Color.BLUE );
+ }
+ TreePanel.drawString( gained,
+ parent_x + ( ( x - parent_x
+ - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
+ ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
+ g );
+ g.setColor( getTreeColorSet().getLostCharactersColor() );
+ TreePanel
+ .drawString( lost,
+ parent_x + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) )
+ / 2 ),
+ ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
+ g );
}
}
- final private void decreaseOvSize() {
- if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
- setOvMaxWidth( getOvMaxWidth() - 5 );
- setOvMaxHeight( getOvMaxHeight() - 5 );
- updateOvSettings();
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) {
+ final RenderableMsaSequence rs = RenderableMsaSequence
+ .createInstance( node.getNodeData().getSequence().getMolecularSequence(),
+ node.getNodeData().getSequence().getType(),
+ getConfiguration() );
+ if ( rs != null ) {
+ final int default_height = 8;
+ final float y = getYdistance();
+ final int h = ( y / 2 ) < default_height ? ForesterUtil.roundToInt( y * 2 ) : default_height;
+ rs.setRenderingHeight( h > 1 ? h : 1 );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
+ else {
+ rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
}
}
- final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
+ /**
+ * Draw a box at the indicated node.
+ *
+ * @param x
+ * @param y
+ * @param node
+ * @param g
+ */
+ final private void paintNodeBox( final float x,
+ final float y,
+ final PhylogenyNode node,
+ final Graphics2D g,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ if ( node.isCollapse() ) {
return;
}
- if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
- JOptionPane.showMessageDialog( this,
- "Cannot delete entire tree",
- "Attempt to delete entire tree",
- JOptionPane.ERROR_MESSAGE );
- return;
+ // if this node should be highlighted, do so
+ if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
+ g.setColor( getTreeColorSet().getFoundColor0() );
+ drawOval( x - 8, y - 8, 16, 16, g );
+ drawOval( x - 9, y - 8, 17, 17, g );
+ drawOval( x - 9, y - 9, 18, 18, g );
}
- 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;
+ if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
+ || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
+ || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+ || ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
+ && ( node.getNodeData().getNodeVisualData() != null )
+ && ( !node.getNodeData().getNodeVisualData().isEmpty() ) )
+ || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null )
+ && ( ( node.getNodeData().getNodeVisualData().getNodeColor() != null )
+ || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
+ || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT )
+ || ( node.getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
+ || ( getControlPanel().isEvents() && node.isHasAssignedEvent()
+ && ( node.getNodeData().getEvent().isDuplication()
+ || node.getNodeData().getEvent().isSpeciation()
+ || node.getNodeData().getEvent().isSpeciationOrDuplication() ) ) ) {
+ NodeVisualData vis = null;
+ if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
+ && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) {
+ vis = node.getNodeData().getNodeVisualData();
+ }
+ float box_size = getOptions().getDefaultNodeShapeSize();
+ if ( ( vis != null ) && ( vis.getSize() != NodeVisualData.DEFAULT_SIZE ) ) {
+ box_size = vis.getSize();
+ }
+ final float half_box_size = box_size / 2.0f;
+ Color outline_color = null;
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ outline_color = Color.BLACK;
+ }
+ else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
+ outline_color = getColorForFoundNode( node );
+ }
+ else if ( vis != null ) {
+ if ( vis.getNodeColor() != null ) {
+ outline_color = vis.getNodeColor();
+ }
+ else if ( vis.getFontColor() != null ) {
+ outline_color = vis.getFontColor();
+ }
+ }
+ else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
+ final Event event = node.getNodeData().getEvent();
+ if ( event.isDuplication() ) {
+ outline_color = getTreeColorSet().getDuplicationBoxColor();
+ }
+ else if ( event.isSpeciation() ) {
+ outline_color = getTreeColorSet().getSpecBoxColor();
+ }
+ else if ( event.isSpeciationOrDuplication() ) {
+ outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
+ }
+ }
+ if ( outline_color == null ) {
+ outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
+ if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
+ outline_color = getTreeColorSet().getBranchColorForPdf();
+ }
+ }
+ NodeShape shape = null;
+ if ( vis != null ) {
+ if ( vis.getShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( vis.getShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ if ( shape == null ) {
+ if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ NodeFill fill = null;
+ if ( vis != null ) {
+ if ( vis.getFillType() == NodeFill.SOLID ) {
+ fill = NodeFill.SOLID;
+ }
+ else if ( vis.getFillType() == NodeFill.NONE ) {
+ fill = NodeFill.NONE;
+ }
+ else if ( vis.getFillType() == NodeFill.GRADIENT ) {
+ fill = NodeFill.GRADIENT;
+ }
+ }
+ if ( fill == null ) {
+ if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
+ fill = NodeFill.SOLID;
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ fill = NodeFill.NONE;
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ fill = NodeFill.GRADIENT;
+ }
+ }
+ Color vis_fill_color = null;
+ if ( ( vis != null ) && ( vis.getNodeColor() != null ) ) {
+ vis_fill_color = vis.getNodeColor();
+ }
+ if ( shape == NodeShape.CIRCLE ) {
+ if ( fill == NodeFill.GRADIENT ) {
+ drawOvalGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ to_pdf ? Color.WHITE : outline_color,
+ to_pdf ? outline_color : getBackground(),
+ outline_color );
+ }
+ else if ( fill == NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
+ }
+ drawOvalGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( fill == NodeVisualData.NodeFill.SOLID ) {
+ if ( vis_fill_color != null ) {
+ g.setColor( vis_fill_color );
+ }
+ else {
+ g.setColor( outline_color );
+ }
+ drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ }
+ }
+ else if ( shape == NodeVisualData.NodeShape.RECTANGLE ) {
+ if ( fill == NodeVisualData.NodeFill.GRADIENT ) {
+ drawRectGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ to_pdf ? Color.WHITE : outline_color,
+ to_pdf ? outline_color : getBackground(),
+ outline_color );
+ }
+ else if ( fill == NodeVisualData.NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
+ }
+ drawRectGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( fill == NodeVisualData.NodeFill.SOLID ) {
+ if ( vis_fill_color != null ) {
+ g.setColor( vis_fill_color );
+ }
+ else {
+ g.setColor( outline_color );
+ }
+ drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ }
+ }
}
- else if ( r != 0 ) {
- return;
+ }
+
+ final private int paintNodeData( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf,
+ final boolean is_in_found_nodes,
+ final double add ) {
+ if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
+ return 0;
}
- if ( node_only ) {
- PhylogenyMethods.removeNode( node, _phylogeny );
+ if ( getControlPanel().isWriteBranchLengthValues()
+ && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
+ && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
+ paintBranchLength( g, node, to_pdf, to_graphics_file );
}
- else {
- _phylogeny.deleteSubtree( node, true );
+ if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
+ return 0;
}
- _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;
+ if ( !getControlPanel().isShowExternalData() && ( node.isExternal() || node.isCollapse() ) ) {
+ return 0;
}
- _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 float x,
- final float y,
- final float width,
- final float heigth,
- final Graphics2D g,
- final Color color_1,
- final Color color_2,
- final Color color_border ) {
- _ellipse.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
- g.fill( _ellipse );
- if ( color_border != null ) {
- g.setPaint( color_border );
- g.draw( _ellipse );
+ _sb.setLength( 0 );
+ int x = 0;
+ if ( add > 0 ) {
+ x += add;
}
- }
-
- 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 float x,
- final float y,
- final float width,
- final float heigth,
- final Graphics2D g,
- final Color color_1,
- final Color color_2,
- final Color color_border ) {
- _rectangle.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
- g.fill( _rectangle );
- if ( color_border != null ) {
- g.setPaint( color_border );
- g.draw( _rectangle );
+ final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
+ if ( getControlPanel().isShowTaxonomyImages() && ( getImageMap() != null ) && !getImageMap().isEmpty()
+ && node.getNodeData().isHasTaxonomy() && ( ( node.getNodeData().getTaxonomy().getUris() != null )
+ && !node.getNodeData().getTaxonomy().getUris().isEmpty() ) ) {
+ x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
}
- }
-
- 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 );
- }
+ if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
+ || getControlPanel().isShowTaxonomyCommonNames() || getControlPanel().isShowTaxonomyRank() )
+ && node.getNodeData().isHasTaxonomy() ) {
+ x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
}
- 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;
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
+ final boolean saw_species = _sb.length() > 0;
+ _sb.setLength( 0 );
+ nodeDataAsSB( node, _sb );
+ if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
+ if ( ( _sb.length() == 0 ) && !saw_species ) {
+ if ( getOptions().isShowAbbreviatedLabelsForCollapsedNodes()
+ && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
+ || getControlPanel().isShowSeqNames() || getControlPanel().isShowNodeNames() ) ) {
+ final PhylogenyNode first = PhylogenyMethods.getFirstExternalNode( node );
+ final PhylogenyNode last = PhylogenyMethods.getLastExternalNode( node );
+ if ( getControlPanel().isShowTaxonomyCode() && first.getNodeData().isHasTaxonomy()
+ && last.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getTaxonomyCode() )
+ && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ addLabelForCollapsed( first.getNodeData().getTaxonomy().getTaxonomyCode(),
+ last.getNodeData().getTaxonomy().getTaxonomyCode(),
+ node.getAllExternalDescendants().size(),
+ node );
+ }
+ else if ( getControlPanel().isShowTaxonomyScientificNames() && first.getNodeData().isHasTaxonomy()
+ && last.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getScientificName() )
+ && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getScientificName() ) ) {
+ addLabelForCollapsed( first.getNodeData().getTaxonomy().getScientificName(),
+ last.getNodeData().getTaxonomy().getScientificName(),
+ node.getAllExternalDescendants().size(),
+ node );
+ }
+ else if ( getControlPanel().isShowSeqNames() && first.getNodeData().isHasSequence()
+ && last.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( first.getNodeData().getSequence().getName() )
+ && !ForesterUtil.isEmpty( last.getNodeData().getSequence().getName() ) ) {
+ addLabelForCollapsed( first.getNodeData().getSequence().getName(),
+ last.getNodeData().getSequence().getName(),
+ node.getAllExternalDescendants().size(),
+ node );
+ }
+ else if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( first.getName() )
+ && !ForesterUtil.isEmpty( last.getName() ) ) {
+ addLabelForCollapsed( first.getName(),
+ last.getName(),
+ node.getAllExternalDescendants().size(),
+ node );
+ }
+ }
+ }
+ else if ( ( _sb.length() > 0 ) || saw_species ) {
+ // _sb.setLength( 0 );
+ _sb.append( " [" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( "]" );
+ if ( _found_nodes_0 != null || _found_nodes_1 != null ) {
+ int[] res = calcFoundNodesInSubtree( node );
+ if ( res[ 0 ] > 0 ) {
+ _sb.append( " [" );
+ _sb.append( res[ 0 ] );
+ _sb.append( "/" );
+ _sb.append( res[ 1 ] );
+ _sb.append( "]" );
}
}
}
}
- 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 );
- }
-
- private final Color getColorForFoundNode( final PhylogenyNode n ) {
- if ( isInCurrentExternalNodes( n ) ) {
- return getTreeColorSet().getFoundColor0();
+ else {
+ // _sb.setLength( 0 );
}
- else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
- return getTreeColorSet().getFoundColor0();
+ // nodeDataAsSB( node, _sb );
+ final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
+ float down_shift_factor = 3.0f;
+ if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
+ down_shift_factor = 1;
}
- else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
- return getTreeColorSet().getFoundColor1();
+ float pos_x;
+ if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM
+ && ( node.isExternal() || node.isCollapse() ) ) {
+ pos_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x + ( 2 * TreePanel.MOVE ) + getXdistance()
+ + 3 );
}
else {
- return getTreeColorSet().getFoundColor0and1();
+ pos_x = node.getXcoord() + x + 2 + half_box_size;
}
- }
-
- final private Set<Long> getCopiedAndPastedNodes() {
- return getMainPanel().getCopiedAndPastedNodes();
- }
-
- final private Set<Long> getCurrentExternalNodes() {
- return _current_external_nodes;
- }
-
- final private Phylogeny getCutOrCopiedTree() {
- return getMainPanel().getCutOrCopiedTree();
- }
-
- private FontMetrics getFontMetricsForLargeDefaultFont() {
- return getTreeFontSet().getFontMetricsLarge();
- }
-
- private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
- final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
- if ( getFoundNodes0() != null ) {
- for( final Long id : getFoundNodes0() ) {
- additional_nodes.add( _phylogeny.getNode( id ) );
+ float pos_y;
+ if ( !using_visual_font ) {
+ pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) );
+ }
+ else {
+ pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
+ }
+ if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM
+ && ( node.isExternal() || node.isCollapse() ) ) {
+ drawConnection( node.getXcoord(), pos_x - x, node.getYcoord(), 5, 20, g, to_pdf );
+ if ( node.isCollapse() ) {
+ pos_x -= add;
}
}
- if ( getFoundNodes1() != null ) {
- for( final Long id : getFoundNodes1() ) {
- if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
- additional_nodes.add( _phylogeny.getNode( id ) );
+ final String sb_str = _sb.toString();
+ // GUILHEM_BEG ______________
+ if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
+ && ( _query_sequence != null ) ) {
+ x = paintSequenceRelation( g, node, x, half_box_size, pos_x, pos_y, sb_str );
+ }
+ // GUILHEM_END _____________
+ if ( sb_str.length() > 0 ) {
+ if ( !isAllowAttributedStrings() ) {
+ TreePanel.drawString( sb_str, pos_x, pos_y, g );
+ }
+ else {
+ drawStringX( sb_str, pos_x, pos_y, g );
+ }
+ }
+ if ( _sb.length() > 0 ) {
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
+ }
+ else {
+ x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
+ }
+ }
+ if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAnnotations() != null )
+ && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
+ final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else if ( getControlPanel().isColorAccordingToAnnotation() ) {
+ g.setColor( calculateColorForAnnotation( ann ) );
+ }
+ final String ann_str = TreePanelUtil.createAnnotationString( ann,
+ getOptions().isShowAnnotationRefSource() );
+ TreePanel.drawString( ann_str,
+ node.getXcoord() + x + 3 + half_box_size,
+ node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ),
+ g );
+ _sb.setLength( 0 );
+ _sb.append( ann_str );
+ if ( _sb.length() > 0 ) {
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
+ }
+ else {
+ x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
+ }
+ }
+ }
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
+ if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
+ && node.getNodeData().isHasBinaryCharacters() ) {
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else {
+ g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
+ }
+ if ( getControlPanel().isShowBinaryCharacters() ) {
+ TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
+ .toString(),
+ node.getXcoord() + x + 1 + half_box_size,
+ node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
+ / down_shift_factor ),
+ g );
+ paintGainedAndLostCharacters( g,
+ node,
+ node.getNodeData().getBinaryCharacters()
+ .getGainedCharactersAsStringBuffer().toString(),
+ node.getNodeData().getBinaryCharacters()
+ .getLostCharactersAsStringBuffer().toString() );
+ }
+ else {
+ TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
+ node.getXcoord() + x + 4 + half_box_size,
+ node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
+ / down_shift_factor ),
+ g );
+ paintGainedAndLostCharacters( g,
+ node,
+ "+" + node.getNodeData().getBinaryCharacters().getGainedCount(),
+ "-" + node.getNodeData().getBinaryCharacters().getLostCount() );
}
}
}
- return additional_nodes;
- }
-
- final private float getLastDragPointX() {
- return _last_drag_point_x;
- }
-
- final private float getLastDragPointY() {
- return _last_drag_point_y;
+ return x;
}
- 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() );
+ private final int paintSequenceRelation( final Graphics2D g,
+ final PhylogenyNode node,
+ int x,
+ final int half_box_size,
+ final float pos_x,
+ final float pos_y,
+ final String sb_str ) {
+ int nodeTextBoundsWidth = 0;
+ if ( sb_str.length() > 0 ) {
+ final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
+ nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
}
- }
-
- final private double getMaxDistanceToRoot() {
- if ( _max_distance_to_root < 0 ) {
- recalculateMaxDistanceToRoot();
+ if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
+ if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
+ g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
+ g.setColor( getTreeColorSet().getBackgroundColor() );
+ }
}
- 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 List<Accession> getPdbAccs( final PhylogenyNode node ) {
- final List<Accession> pdb_ids = new ArrayList<Accession>();
- if ( node.getNodeData().isHasSequence() ) {
- final Sequence seq = node.getNodeData().getSequence();
- if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
- final SortedSet<Accession> cross_refs = seq.getCrossReferences();
- for( final Accession acc : cross_refs ) {
- if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
- pdb_ids.add( acc );
+ else {
+ final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
+ for( final SequenceRelation seqRelation : seqRelations ) {
+ final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence )
+ || seqRelation.getRef1().isEqual( _query_sequence ) )
+ && seqRelation.getType()
+ .equals( getControlPanel().getSequenceRelationTypeBox().getSelectedItem() );
+ if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
+ final double linePosX = node.getXcoord() + 2 + half_box_size;
+ final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence()
+ || ( seqRelation.getConfidence() == null ) ) ? null
+ : " (" + seqRelation.getConfidence().getValue() + ")";
+ if ( sConfidence != null ) {
+ float confidenceX = pos_x;
+ if ( sb_str.length() > 0 ) {
+ confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
+ + CONFIDENCE_LEFT_MARGIN;
+ }
+ if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
+ final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
+ .getBounds().getWidth();
+ TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
+ x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
+ }
+ }
+ if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
+ {
+ if ( nodeTextBoundsWidth == 0 ) {
+ nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
+ }
+ else {
+ nodeTextBoundsWidth += 2;
+ }
+ g.drawLine( ( int ) linePosX + 1,
+ 3 + ( int ) pos_y,
+ ( int ) linePosX + x + nodeTextBoundsWidth,
+ 3 + ( int ) pos_y );
+ break;
}
}
}
}
- return pdb_ids;
- }
-
- 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 COLOR_NODE_FONT:
- colorNodeFont( node );
- break;
- case CHANGE_NODE_FONT:
- changeNodeFont( node );
- break;
- case OPEN_SEQ_WEB:
- openSeqWeb( node );
- break;
- case BLAST:
- blast( node );
- break;
- case OPEN_TAX_WEB:
- openTaxWeb( node );
- break;
- case OPEN_PDB_WEB:
- openPdbWeb( 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 ) {
- final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
- if ( a != null ) {
- return a.getValue();
- }
- return null;
+ return x;
}
- 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;
+ private final void drawConnection( final float x1,
+ final float x2,
+ final float y,
+ final int dist_left,
+ final int dist_right,
+ final Graphics2D g,
+ final boolean pdf ) {
+ if ( ( ( x1 + dist_left ) < ( x2 - dist_right ) ) ) {
+ final Stroke strok = g.getStroke();
+ Color col = null;
+ if ( strok == STROKE_005 ) {
+ g.setStroke( STROKE_001_DASHED );
+ }
+ else if ( strok == STROKE_01 ) {
+ g.setStroke( STROKE_005_DASHED );
+ }
+ else {
+ g.setStroke( STROKE_01_DASHED );
+ }
+ if ( pdf ) {
+ col = g.getColor();
+ g.setColor( lighter( col ) );
+ }
+ drawLine( x1 + dist_left, y, x2 - dist_right, y, g );
+ g.setStroke( strok );
+ if ( pdf ) {
+ g.setColor( col );
+ }
}
}
-
- final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
- return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
- }
-
- private boolean isInFoundNodes( final PhylogenyNode n ) {
- return isInFoundNodes0( n ) || isInFoundNodes1( n );
- }
-
- final private boolean isInFoundNodes0( final PhylogenyNode node ) {
- return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
- }
-
- final private boolean isInFoundNodes1( final PhylogenyNode node ) {
- return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
+
+ public static Color lighter( final Color color ) {
+ if ( ( color.getRed() == 0 ) && ( color.getGreen() == 0 ) && ( color.getBlue() == 0 ) ) {
+ return new Color( 200, 200, 200 );
+ }
+ else {
+ return color;
+ }
}
- final private boolean isInOv() {
- return _in_ov;
+ private final void addLabelForCollapsed( final String first,
+ final String last,
+ final int size,
+ final PhylogenyNode node ) {
+ _sb.append( first.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? first
+ : first.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) );
+ _sb.append( " ... " );
+ _sb.append( last.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? last
+ : last.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) );
+ _sb.append( " (" + size + ")" );
+ if ( _found_nodes_0 != null || _found_nodes_1 != null ) {
+ /////
+ /////
+ int[] res = calcFoundNodesInSubtree( node );
+ if ( res[ 0 ] > 0 ) {
+ _sb.append( " [" );
+ _sb.append( res[ 0 ] );
+ _sb.append( "/" );
+ _sb.append( res[ 1 ] );
+ _sb.append( "]" );
+ }
+ }
}
- final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
- int y_dist = 40;
- if ( getControlPanel().isShowTaxonomyImages() ) {
- y_dist = 40 + ( int ) getYdistance();
+ private final int[] calcFoundNodesInSubtree( final PhylogenyNode node ) {
+ final List<PhylogenyNode> all_descs = PhylogenyMethods.getAllDescendants( node );
+ int res[] = new int[ 2 ];
+ int found = 0;
+ int total = 0;
+ for( final PhylogenyNode desc : all_descs ) {
+ if ( desc.isHasNodeData() ) {
+ if ( ( _found_nodes_0 != null && _found_nodes_0.contains( desc.getId() ) )
+ || ( _found_nodes_1 != null && _found_nodes_1.contains( desc.getId() ) ) ) {
+ ++found;
+ }
+ ++total;
+ }
}
- return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
- || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
- .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
+ res[ 0 ] = found;
+ res[ 1 ] = total;
+ return res;
}
- 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 ) ) );
+ private final boolean isAllowAttributedStrings() {
+ return false;
}
- final private boolean isNonLinedUpCladogram() {
- return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
+ final private void paintNodeDataUnrootedCirc( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean to_graphics_file,
+ final boolean radial_labels,
+ final double ur_angle,
+ final boolean is_in_found_nodes ) {
+ if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
+ return;
+ }
+ _sb.setLength( 0 );
+ _sb.append( " " );
+ if ( node.getNodeData().isHasTaxonomy()
+ && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
+ || getControlPanel().isShowTaxonomyCommonNames() ) ) {
+ final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
+ if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
+ _sb.append( taxonomy.getTaxonomyCode() );
+ _sb.append( " " );
+ }
+ if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
+ && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ _sb.append( taxonomy.getScientificName() );
+ _sb.append( " (" );
+ _sb.append( taxonomy.getCommonName() );
+ _sb.append( ") " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ _sb.append( taxonomy.getScientificName() );
+ _sb.append( " " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ _sb.append( taxonomy.getCommonName() );
+ _sb.append( " " );
+ }
+ }
+ else if ( _control_panel.isShowTaxonomyScientificNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ _sb.append( taxonomy.getScientificName() );
+ _sb.append( " " );
+ }
+ }
+ else if ( _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ _sb.append( taxonomy.getCommonName() );
+ _sb.append( " " );
+ }
+ }
+ }
+ if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
+ _sb.append( " [" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( "]" );
+ }
+ if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ _sb.append( node.getName() );
+ }
+ if ( node.getNodeData().isHasSequence() ) {
+ if ( getControlPanel().isShowSequenceAcc()
+ && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
+ _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
+ _sb.append( ":" );
+ }
+ _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
+ }
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ _sb.append( node.getNodeData().getSequence().getName() );
+ }
+ }
+ //g.setFont( getTreeFontSet().getLargeFont() );
+ //if ( is_in_found_nodes ) {
+ // g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
+ // }
+ if ( _sb.length() > 1 ) {
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
+ final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
+ final String sb_str = _sb.toString();
+ double m = 0;
+ if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
+ m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
+ }
+ else {
+ m = ( float ) ( ur_angle % TWO_PI );
+ }
+ _at = g.getTransform();
+ boolean need_to_reset = false;
+ final float x_coord = node.getXcoord();
+ float y_coord;
+ if ( !using_visual_font ) {
+ y_coord = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / 3.0f );
+ }
+ else {
+ y_coord = node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / 3.0f );
+ }
+ if ( radial_labels ) {
+ need_to_reset = true;
+ boolean left = false;
+ if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
+ m -= PI;
+ left = true;
+ }
+ g.rotate( m, x_coord, node.getYcoord() );
+ if ( left ) {
+ if ( !using_visual_font ) {
+ g.translate( -( getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth() ),
+ 0 );
+ }
+ else {
+ g.translate( -( getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth() ), 0 );
+ }
+ }
+ }
+ else {
+ if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
+ need_to_reset = true;
+ if ( !using_visual_font ) {
+ g.translate( -getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth(), 0 );
+ }
+ else {
+ g.translate( -getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth(), 0 );
+ }
+ }
+ }
+ TreePanel.drawString( sb_str, x_coord, y_coord, g );
+ if ( need_to_reset ) {
+ g.setTransform( _at );
+ }
+ }
}
- final private boolean isUniformBranchLengthsForCladogram() {
- return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
+ final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
+ if ( node.isCollapse() ) {
+ return;
+ }
+ if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
+ g.setColor( getColorForFoundNode( node ) );
+ drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ node.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ g );
+ }
+ float new_x = 0;
+ if ( !node.isExternal() && !node.isCollapse() ) {
+ boolean first_child = true;
+ float y2 = 0.0f;
+ //final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode child_node = node.getChildNode( i );
+ final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
+ if ( first_child ) {
+ first_child = false;
+ y2 = node.getYSecondary() - ( getOvYDistance()
+ * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
+ }
+ else {
+ y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
+ }
+ final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
+ new_x = x2 + node.getXSecondary();
+ final float diff_y = node.getYSecondary() - y2;
+ final float diff_x = node.getXSecondary() - new_x;
+ if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
+ paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
+ }
+ child_node.setXSecondary( new_x );
+ child_node.setYSecondary( y2 );
+ y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
+ }
+ }
}
- final private void keyPressedCalls( final KeyEvent e ) {
- if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
- if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
- if ( !isInOvRect() ) {
- setInOvRect( true );
+ final private void paintNodeRectangular( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean dynamically_hide,
+ final int dynamic_hiding_factor,
+ final boolean to_graphics_file,
+ final boolean disallow_shortcutting ) {
+ final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
+ if ( node.isCollapse() ) {
+ if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
+ paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
+ }
+ return;
+ }
+ if ( node.isExternal() ) {
+ ++_external_node_index;
+ }
+ // Confidence values
+ if ( getControlPanel().isShowConfidenceValues() && !node.isExternal() && !node.isRoot()
+ && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
+ && node.getBranchData().isHasConfidences() ) {
+ paintConfidenceValues( g, node, to_pdf, to_graphics_file );
+ }
+ // Draw a line to root:
+ if ( node.isRoot() && _phylogeny.isRooted() ) {
+ paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
+ }
+ float new_x = 0;
+ float new_x_min = Float.MAX_VALUE;
+ float min_dist = 1.5f;
+ if ( !disallow_shortcutting ) {
+ if ( dynamic_hiding_factor > 4000 ) {
+ min_dist = 4;
+ }
+ else if ( dynamic_hiding_factor > 1000 ) {
+ min_dist = 3;
+ }
+ else if ( dynamic_hiding_factor > 100 ) {
+ min_dist = 2;
+ }
+ }
+ if ( !node.isExternal() && !node.isCollapse() ) {
+ boolean first_child = true;
+ float y2 = 0.0f;
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode child_node = node.getChildNode( i );
+ final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
+ if ( first_child ) {
+ first_child = false;
+ y2 = node.getYcoord() - ( _y_distance
+ * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
+ }
+ else {
+ y2 += _y_distance * child_node.getNumberOfExternalNodes();
+ }
+ final float x2 = calculateBranchLengthToParent( child_node, factor_x );
+ new_x = x2 + node.getXcoord();
+ if ( dynamically_hide && ( x2 < new_x_min ) ) {
+ new_x_min = x2;
+ }
+ final float diff_y = node.getYcoord() - y2;
+ final float diff_x = node.getXcoord() - new_x;
+ if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
+ || ( diff_x < -min_dist ) ) {
+ paintBranchRectangular( g,
+ node.getXcoord(),
+ new_x,
+ node.getYcoord(),
+ y2,
+ child_node,
+ to_pdf,
+ to_graphics_file );
}
+ child_node.setXcoord( new_x );
+ child_node.setYcoord( y2 );
+ y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- else if ( isInOvRect() ) {
- setInOvRect( false );
- }
+ paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
}
- 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 );
- }
+ if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+ && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+ paintMolecularSequences( g, node, to_pdf );
}
- 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 );
+ if ( dynamically_hide && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) )
+ || ( !node.isExternal() && ( ( new_x_min < 20 )
+ || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont()
+ .getHeight() ) ) ) ) ) {
+ return;
+ }
+ final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes, 0 );
+ paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf );
+ }
+
+ final private void paintNodeWithRenderableData( final int x,
+ final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf ) {
+ if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) {
+ return;
+ }
+ if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
+ return;
+ }
+ if ( ( !getControlPanel().isShowExternalData() && node.isExternal() ) ) {
+ return;
+ }
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) && ( node.getNodeData()
+ .getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
+ RenderableDomainArchitecture rds = null;
+ try {
+ rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
+ }
+ catch ( final ClassCastException cce ) {
+ cce.printStackTrace();
+ }
+ if ( rds != null ) {
+ final int default_height = 7;
+ float y = getYdistance();
+ if ( getControlPanel().isDynamicallyHideData() ) {
+ y = getTreeFontSet().getFontMetricsLarge().getHeight();
+ }
+ final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
+ rds.setRenderingHeight( h > 1 ? h : 2 );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( getOptions().isLineUpRendarableNodeData() ) {
+ if ( getOptions().isRightLineUpDomains() ) {
+ rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + _length_of_longest_text + 50 //TODO why plus 50?
+ + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ) ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
+ else {
+ rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + _length_of_longest_text + 50 ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
}
- else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
- getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ else {
+ rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
}
}
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;
+ if ( getOptions().isRightLineUpDomains() ) {
+ rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text )
+ - 20 ) + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
}
else {
- final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
- if ( scroll_position.y >= max_y ) {
- scroll_position.y = max_y;
- }
+ rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
}
- 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 );
+ }
+ if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
+ && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
+ final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
+ getStatisticsForExpressionValues(),
+ getConfiguration() );
+ if ( rv != null ) {
+ double domain_add = 0;
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ domain_add = _domain_structure_width + 10;
}
- }
- 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;
+ if ( getControlPanel().isDrawPhylogram() ) {
+ rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
}
else {
- getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
+ rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text
+ + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
}
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- if ( ae.getlabelDirectionCbmi() != null ) {
- ae.getlabelDirectionCbmi().setSelected( selected );
- }
+ }
+ }
+ //if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+ // && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+ // && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+ // paintMolecularSequences( g, node, to_pdf );
+ //}
+ }
+
+ final private void paintOvRectangle( final Graphics2D g ) {
+ final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
+ final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
+ final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
+ final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
+ final float width = getOvMaxWidth() / w_ratio;
+ final float height = getOvMaxHeight() / h_ratio;
+ final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
+ final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
+ g.setColor( getTreeColorSet().getFoundColor0() );
+ getOvRectangle().setRect( x, y, width, height );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
+ if ( ( width < 6 ) && ( height < 6 ) ) {
+ drawRectFilled( x, y, 6, 6, g );
+ getOvVirtualRectangle().setRect( x, y, 6, 6 );
+ }
+ else if ( width < 6 ) {
+ drawRectFilled( x, y, 6, height, g );
+ getOvVirtualRectangle().setRect( x, y, 6, height );
+ }
+ else if ( height < 6 ) {
+ drawRectFilled( x, y, width, 6, g );
+ getOvVirtualRectangle().setRect( x, y, width, 6 );
+ }
+ else {
+ drawRect( x, y, width, height, g );
+ if ( isInOvRect() ) {
+ drawRect( x + 1, y + 1, width - 2, height - 2, g );
+ }
+ getOvVirtualRectangle().setRect( x, y, width, height );
+ }
+ g.setStroke( s );
+ }
+
+ final private void paintPhylogenyLite( final Graphics2D g ) {
+ _phylogeny.getRoot().setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition()
+ + ( MOVE / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ) );
+ _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_05 );
+ for( final PhylogenyNode element : _nodes_in_preorder ) {
+ paintNodeLite( g, element );
+ }
+ g.setStroke( s );
+ paintOvRectangle( g );
+ }
+
+ /**
+ * Paint the root branch. (Differs from others because it will always be a
+ * single horizontal line).
+ * @param to_graphics_file
+ *
+ * @return new x1 value
+ */
+ final private void paintRootBranch( final Graphics2D g,
+ final float x1,
+ final float y1,
+ final PhylogenyNode root,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
+ float d = getXdistance();
+ if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
+ d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
+ }
+ if ( d < MIN_ROOT_LENGTH ) {
+ d = MIN_ROOT_LENGTH;
+ }
+ if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
+ drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
+ }
+ else {
+ final double w = PhylogenyMethods.getBranchWidthValue( root );
+ drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
+ }
+ paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
+ }
+
+ final private void paintScale( final Graphics2D g,
+ int x1,
+ int y1,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ x1 += MOVE;
+ final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
+ y1 -= 12;
+ final int y2 = y1 - 8;
+ final int y3 = y1 - 4;
+ g.setFont( getTreeFontSet().getSmallFont() );
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else {
+ g.setColor( getTreeColorSet().getBranchLengthColor() );
+ }
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
+ drawLine( x1, y1, x1, y2, g );
+ drawLine( x2, y1, x2, y2, g );
+ drawLine( x1, y3, x2, y3, g );
+ if ( getScaleLabel() != null ) {
+ g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
+ }
+ g.setStroke( s );
+ }
+
+ final private int paintTaxonomy( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean is_in_found_nodes,
+ final boolean to_pdf,
+ final boolean to_graphics_file,
+ final float x_shift ) {
+ final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
+ final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() );
+ float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
+ if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM
+ && node.isExternal() ) {
+ start_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift + ( 2 * TreePanel.MOVE ) + getXdistance()
+ + 3 );
+ }
+ float start_y;
+ if ( !using_visual_font ) {
+ start_y = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
+ / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
+ }
+ else {
+ start_y = node.getYcoord()
+ + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
+ }
+ _sb.setLength( 0 );
+ nodeTaxonomyDataAsSB( taxonomy, _sb );
+ final String label = _sb.toString();
+ /* GUILHEM_BEG */
+ if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
+ && ( node.getNodeData().isHasSequence() )
+ && node.getNodeData().getSequence().equals( _query_sequence ) ) {
+ // invert font color and background color to show that this is the query sequence
+ final Rectangle2D nodeTextBounds = new TextLayout( label,
+ g.getFont(),
+ new FontRenderContext( null, false, false ) )
+ .getBounds();
+ g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
+ g.setColor( getTreeColorSet().getBackgroundColor() );
+ }
+ /* GUILHEM_END */
+ TreePanel.drawString( label, start_x, start_y, g );
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ return getFontMetricsForLargeDefaultFont().stringWidth( label );
+ }
+ return getFontMetrics( g.getFont() ).stringWidth( label );
+ }
+
+ final private void paintUnrooted( final PhylogenyNode n,
+ final double low_angle,
+ final double high_angle,
+ final boolean radial_labels,
+ final Graphics2D g,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ if ( n.isRoot() ) {
+ n.setXcoord( getWidth() / 2 );
+ n.setYcoord( getHeight() / 2 );
+ }
+ if ( n.isExternal() ) {
+ paintNodeDataUnrootedCirc( g,
+ n,
+ to_pdf,
+ to_graphics_file,
+ radial_labels,
+ ( high_angle + low_angle ) / 2,
+ isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
+ return;
+ }
+ final float num_enclosed = n.getNumberOfExternalNodes();
+ final float x = n.getXcoord();
+ final float y = n.getYcoord();
+ double current_angle = low_angle;
+ // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
+ // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
+ // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
+ // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
+ for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode desc = n.getChildNode( i );
+ /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
+ // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
+ // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
+ // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
+ // continue;
+ // }
+ //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
+ // continue;
+ //}
+ //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
+ // continue;
+ // }
+ final int desc_num_enclosed = desc.getNumberOfExternalNodes();
+ final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
+ float length;
+ if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
+ if ( desc.getDistanceToParent() < 0 ) {
+ length = 0;
}
else {
- getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
+ length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
}
- 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();
+ else {
+ length = getUrtFactor();
}
- e.consume();
+ 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 );
+ }
+ if ( n.isRoot() ) {
+ paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
}
}
- 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 {
- _node_popup_menu_items[ i ].setEnabled( false );
- }
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
- final List<Accession> accs = getPdbAccs( node );
- _node_popup_menu_items[ i ] = new JMenuItem( title );
- if ( !ForesterUtil.isEmpty( accs ) ) {
- if ( accs.size() == 1 ) {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
- + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
- else if ( accs.size() == 2 ) {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
- + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
- else if ( accs.size() == 3 ) {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
- + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
- else {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
- + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
+ final private void paintUnrootedLite( final PhylogenyNode n,
+ final double low_angle,
+ final double high_angle,
+ 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 ) );
+ n.setXSecondary( x_pos );
+ n.setYSecondary( y_pos );
+ }
+ if ( n.isExternal() ) {
+ return;
+ }
+ final float num_enclosed = n.getNumberOfExternalNodes();
+ final float x = n.getXSecondary();
+ final float y = n.getYSecondary();
+ double current_angle = low_angle;
+ for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode desc = n.getChildNode( i );
+ final int desc_num_enclosed = desc.getNumberOfExternalNodes();
+ final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
+ float length;
+ if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
+ if ( desc.getDistanceToParent() < 0 ) {
+ length = 0;
}
else {
- _node_popup_menu_items[ i ].setEnabled( false );
- }
- //
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
- }
- 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;
+ length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
}
}
- 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 {
+ length = urt_ov_factor;
}
- else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
+ 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 ) || isInCurrentExternalNodes( desc ) ) {
+ g.setColor( getColorForFoundNode( desc ) );
+ drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ g );
+ g.setColor( getTreeColorSet().getOvColor() );
}
- _node_popup_menu_items[ i ].addActionListener( this );
- _node_popup_menu.add( _node_popup_menu_items[ i ] );
+ paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
+ current_angle += arc_size;
+ drawLine( x, y, new_x, new_y, g );
}
}
- private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
- if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
+ final private void pasteSubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
+ }
+ if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
+ JOptionPane.showMessageDialog( this,
+ "No tree in buffer (need to copy or cut a subtree first)",
+ "Attempt to paste with empty buffer",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ 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 + "?",
+ "Paste Subtree",
+ JOptionPane.CLOSED_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options,
+ options[ 2 ] );
+ boolean paste_as_sibling = true;
+ if ( r == 1 ) {
+ paste_as_sibling = false;
+ }
+ else if ( r != 0 ) {
+ return;
+ }
+ final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
+ buffer_phy.setAllNodesToNotCollapse();
+ PhylogenyMethods.preOrderReId( buffer_phy );
+ buffer_phy.setRooted( true );
+ boolean need_to_show_whole = false;
+ if ( paste_as_sibling ) {
+ if ( node.isRoot() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot paste sibling to root",
+ "Attempt to paste sibling to root",
+ JOptionPane.ERROR_MESSAGE );
+ return;
}
- sb.append( node.getName() );
+ buffer_phy.addAsSibling( node );
}
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- sb.append( node.getNodeData().getSequence().getSymbol() );
- }
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- sb.append( node.getNodeData().getSequence().getGeneName() );
- }
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- sb.append( node.getNodeData().getSequence().getName() );
+ else {
+ if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
+ need_to_show_whole = true;
+ _phylogeny = buffer_phy;
}
- if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
- sb.append( node.getNodeData().getSequence().getAccession().getSource() );
- sb.append( ":" );
- }
- sb.append( node.getNodeData().getSequence().getAccession().getValue() );
+ else {
+ buffer_phy.addAsChild( node );
}
}
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- sb.append( propertiesToString( 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();
}
+ repaint();
}
- private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
- if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
- sb.append( taxonomy.getTaxonomyCode() );
- sb.append( " " );
+ private final StringBuffer propertiesToString( final PhylogenyNode node ) {
+ return node.getNodeData().getProperties().asText();
+ }
+
+ private void setColor( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf,
+ final boolean is_in_found_nodes,
+ final Color default_color ) {
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
}
- if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
- && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName(), sb );
- }
- else {
- sb.append( taxonomy.getScientificName() );
- }
- sb.append( " (" );
- sb.append( taxonomy.getCommonName() );
- sb.append( ") " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName(), sb );
- }
- else {
- sb.append( taxonomy.getScientificName() );
- }
- sb.append( " " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- sb.append( taxonomy.getCommonName() );
- sb.append( " " );
- }
+ else if ( is_in_found_nodes ) {
+ g.setColor( getColorForFoundNode( node ) );
}
- else if ( _control_panel.isShowTaxonomyScientificNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName(), sb );
- }
- else {
- sb.append( taxonomy.getScientificName() );
- }
- sb.append( " " );
- }
+ else if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
+ && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
+ g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
}
- else if ( _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- sb.append( taxonomy.getCommonName() );
- sb.append( " " );
- }
+ else if ( getControlPanel().isColorAccordingToSequence() ) {
+ g.setColor( getSequenceBasedColor( node ) );
}
- }
-
- private final String obtainTitleForExtDescNodeData() {
- switch ( getOptions().getExtDescNodeDataToReturn() ) {
- case NODE_NAME:
- return "Node Names";
- case GENE_NAME:
- return "Gene Names";
- case SEQUENCE_NAME:
- return "Sequence Names";
- case SEQUENCE_SYMBOL:
- return "Sequence Symbols";
- case SEQUENCE_MOL_SEQ:
- return "Molecular Sequences";
- case SEQUENCE_MOL_SEQ_FASTA:
- return "Molecular Sequences (Fasta)";
- case SEQUENCE_ACC:
- return "Sequence Accessors";
- case TAXONOMY_SCIENTIFIC_NAME:
- return "Scientific Names";
- case TAXONOMY_CODE:
- return "Taxonomy Codes";
- case TAXONOMY_COMM0N_NAME:
- return "Taxonomy Common Names";
- case UNKNOWN:
- return "User Selected Data";
- default:
- throw new IllegalArgumentException( "unknown data element: "
- + getOptions().getExtDescNodeDataToReturn() );
+ else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
+ g.setColor( getTaxonomyBasedColor( node ) );
}
- }
-
- final private void openPdbWeb( final PhylogenyNode node ) {
- final List<Accession> pdb_ids = getPdbAccs( node );
- if ( ForesterUtil.isEmpty( pdb_ids ) ) {
- cannotOpenBrowserWarningMessage( "PDB" );
- return;
+ else if ( getControlPanel().isColorAccordingToAnnotation()
+ && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null )
+ && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
+ g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
}
- final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
- if ( !ForesterUtil.isEmpty( uri_strs ) ) {
- for( final String uri_str : uri_strs ) {
- try {
- AptxUtil.launchWebBrowser( new URI( uri_str ),
- isApplet(),
- isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
- }
- catch ( final IOException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- }
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
+ && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ }
+ else if ( to_pdf ) {
+ g.setColor( Color.BLACK );
}
else {
- cannotOpenBrowserWarningMessage( "PDB" );
+ g.setColor( default_color );
}
}
- final private void openSeqWeb( final PhylogenyNode node ) {
- if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
- cannotOpenBrowserWarningMessage( "sequence" );
- return;
- }
- final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
- if ( !ForesterUtil.isEmpty( uri_str ) ) {
- try {
- AptxUtil.launchWebBrowser( new URI( uri_str ),
- isApplet(),
- isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
- }
- catch ( final IOException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
+ getMainPanel().setCopiedAndPastedNodes( nodeIds );
+ }
+
+ final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
+ getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
+ }
+
+ private boolean setFont( final Graphics2D g, final PhylogenyNode node, final boolean is_in_found_nodes ) {
+ Font visual_font = null;
+ if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) {
+ visual_font = node.getNodeData().getNodeVisualData().getFont();
+ g.setFont( visual_font != null ? visual_font : getTreeFontSet().getLargeFont() );
}
else {
- cannotOpenBrowserWarningMessage( "sequence" );
+ g.setFont( getTreeFontSet().getLargeFont() );
+ }
+ if ( is_in_found_nodes ) {
+ g.setFont( g.getFont().deriveFont( Font.BOLD ) );
}
+ return visual_font != null;
}
- final private void openTaxWeb( final PhylogenyNode node ) {
- if ( !isCanOpenTaxWeb( node ) ) {
- cannotOpenBrowserWarningMessage( "taxonomic" );
- return;
- }
- String uri_str = null;
- final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
- && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
- try {
- uri_str = new URI( tax.getIdentifier().getValue() ).toString();
- }
- catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- uri_str = null;
- e.printStackTrace();
- }
+ final private void setInOv( final boolean in_ov ) {
+ _in_ov = in_ov;
+ }
+
+ final private void setOvMaxHeight( final float ov_max_height ) {
+ _ov_max_height = ov_max_height;
+ }
+
+ final private void setOvMaxWidth( final float ov_max_width ) {
+ _ov_max_width = ov_max_width;
+ }
+
+ final private void setOvXcorrectionFactor( final float f ) {
+ _ov_x_correction_factor = f;
+ }
+
+ final private void setOvXDistance( final float ov_x_distance ) {
+ _ov_x_distance = ov_x_distance;
+ }
+
+ final private void setOvXPosition( final int ov_x_position ) {
+ _ov_x_position = ov_x_position;
+ }
+
+ final private void setOvYDistance( final float ov_y_distance ) {
+ _ov_y_distance = ov_y_distance;
+ }
+
+ final private void setOvYPosition( final int ov_y_position ) {
+ _ov_y_position = ov_y_position;
+ }
+
+ final private void setOvYStart( final int ov_y_start ) {
+ _ov_y_start = ov_y_start;
+ }
+
+ final private void setScaleDistance( final double scale_distance ) {
+ _scale_distance = scale_distance;
+ }
+
+ final private void setScaleLabel( final String scale_label ) {
+ _scale_label = scale_label;
+ }
+
+ private final void setupStroke( final Graphics2D g ) {
+ if ( getYdistance() < 0.0001 ) {
+ g.setStroke( STROKE_0025 );
}
- 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 = "http://www.uniprot.org/taxonomy/"
- + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ if ( getYdistance() < 0.001 ) {
+ g.setStroke( STROKE_005 );
}
- else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- try {
- uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ else if ( getYdistance() < 0.01 ) {
+ g.setStroke( STROKE_01 );
}
- else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- try {
- uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ else if ( getYdistance() < 0.5 ) {
+ g.setStroke( STROKE_025 );
}
- else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- try {
- uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ else if ( getYdistance() < 1 ) {
+ g.setStroke( STROKE_05 );
}
- if ( !ForesterUtil.isEmpty( uri_str ) ) {
- try {
- 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 if ( getYdistance() < 2 ) {
+ g.setStroke( STROKE_075 );
+ }
+ else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) {
+ g.setStroke( STROKE_1 );
}
else {
- cannotOpenBrowserWarningMessage( "taxonomic" );
+ g.setStroke( STROKE_2 );
}
}
- final private void paintBranchLength( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- g.setFont( getTreeFontSet().getSmallFont() );
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ final private void setUpUrtFactor() {
+ final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
+ : getVisibleRect().height;
+ if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
+ setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
}
else {
- g.setColor( getTreeColorSet().getBranchLengthColor() );
- }
- if ( !node.isRoot() ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
+ final int max_depth = _circ_max_depth;
+ if ( max_depth > 0 ) {
+ setUrtFactor( d / ( 2 * max_depth ) );
}
else {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
+ setUrtFactor( d / 2 );
}
}
- else {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
- - getTreeFontSet().getSmallMaxDescent(), g );
- }
+ setUrtFactorOv( getUrtFactor() );
}
- final private void paintBranchLite( final Graphics2D g,
- final float x1,
- final float x2,
- final float y1,
- final float y2,
- final PhylogenyNode node ) {
- g.setColor( getTreeColorSet().getOvColor() );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
- drawLine( x1, y1, x2, y2, g );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
- _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
- ( g ).draw( _quad_curve );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
- final float dx = x2 - x1;
- final float dy = y2 - y1;
- _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
- + ( dy * 0.8f ), x2, y2 );
- ( g ).draw( _cubic_curve );
- }
- else {
- final float x2a = x2;
- final float x1a = x1;
- // draw the vertical line
- if ( node.isFirstChildNode() || node.isLastChildNode() ) {
- drawLine( x1, y1, x1, y2, g );
- }
- // draw the horizontal line
- drawLine( x1a, y2, x2a, y2, g );
- }
+ final private void setUrtFactor( final float urt_factor ) {
+ _urt_factor = urt_factor;
}
- /**
- * Paint a branch which consists of a vertical and a horizontal bar
- * @param is_ind_found_nodes
- */
- final private void paintBranchRectangular( final Graphics2D g,
- final float x1,
- final float x2,
- final float y1,
- final float y2,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
- drawLine( x1, y1, x2, y2, g );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
- _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
- g.draw( _quad_curve );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
- final float dx = x2 - x1;
- final float dy = y2 - y1;
- _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
- + ( dy * 0.8f ), x2, y2 );
- g.draw( _cubic_curve );
+ final private void setUrtFactorOv( final float urt_factor_ov ) {
+ _urt_factor_ov = urt_factor_ov;
+ }
+
+ private void showExtDescNodeData( final PhylogenyNode node, final char separator ) {
+ final List<String> data = new ArrayList<String>();
+ final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
+ if ( !nodes.contains( n ) ) {
+ nodes.add( n );
+ }
+ }
}
- else {
- final float x2a = x2;
- final float x1a = x1;
- float y2_r = 0;
- if ( node.isFirstChildNode() || node.isLastChildNode()
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
- || ( 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 ) ) ) ) ) {
- // Do nothing.
+ for( final PhylogenyNode n : nodes ) {
+ switch ( getOptions().getExtDescNodeDataToReturn() ) {
+ case NODE_NAME:
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ data.add( n.getName() );
+ }
+ break;
+ case SEQUENCE_NAME:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ data.add( n.getNodeData().getSequence().getName() );
+ }
+ break;
+ case GENE_NAME:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ data.add( n.getNodeData().getSequence().getGeneName() );
+ }
+ break;
+ case SEQUENCE_SYMBOL:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+ data.add( n.getNodeData().getSequence().getSymbol() );
+ }
+ break;
+ case SEQUENCE_MOL_SEQ_FASTA:
+ final StringBuilder sb = new StringBuilder();
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+ final StringBuilder ann = new StringBuilder();
+ if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( n.getName() ) ) {
+ ann.append( n.getName() );
+ ann.append( separator );
+ }
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( getControlPanel().isShowTaxonomyCode()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ ann.append( separator );
+ }
+ if ( getControlPanel().isShowTaxonomyScientificNames()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ ann.append( n.getNodeData().getTaxonomy().getScientificName() );
+ ann.append( separator );
+ }
+ if ( getControlPanel().isShowTaxonomyCommonNames()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ ann.append( n.getNodeData().getTaxonomy().getCommonName() );
+ ann.append( separator );
+ }
+ }
+ if ( getControlPanel().isShowSeqSymbols()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+ ann.append( n.getNodeData().getSequence().getSymbol() );
+ ann.append( separator );
+ }
+ if ( getControlPanel().isShowSeqNames()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ ann.append( n.getNodeData().getSequence().getName() );
+ ann.append( separator );
+ }
+ if ( getControlPanel().isShowGeneNames()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ ann.append( n.getNodeData().getSequence().getGeneName() );
+ ann.append( separator );
+ }
+ if ( getControlPanel().isShowSequenceAcc()
+ && n.getNodeData().getSequence().getAccession() != null ) {
+ ann.append( n.getNodeData().getSequence().getAccession().asText() );
+ ann.append( separator );
+ }
+
+ final String ann_str;
+ if ( ann.length() > 0 && ann.charAt( ann.length() - 1 ) == separator ) {
+ ann_str = ann.substring( 0, ann.length() - 1 );
+ }
+ else {
+ ann_str = ann.toString();
+ }
+ sb.append( SequenceWriter.toFasta( ann_str,
+ n.getNodeData().getSequence().getMolecularSequence(),
+ 60 ) );
+ data.add( sb.toString() );
+ }
+ break;
+ case SEQUENCE_ACC:
+ if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
+ data.add( n.getNodeData().getSequence().getAccession().toString() );
+ }
+ break;
+ case TAXONOMY_SCIENTIFIC_NAME:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getScientificName() );
+ }
+ break;
+ case TAXONOMY_CODE:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ break;
+ case DOMAINS_ALL:
+ case DOMAINS_COLLAPSED_PER_PROTEIN:
+ if ( n.getNodeData().isHasSequence()
+ && ( n.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ final DomainArchitecture da = n.getNodeData().getSequence().getDomainArchitecture();
+ final Set<String> s = new HashSet<String>();
+ for( int i = 0; i < da.getDomains().size(); ++i ) {
+ final ProteinDomain d = da.getDomain( i );
+ if ( d.getConfidence() <= Math.pow( 10, getDomainStructureEvalueThresholdExp() ) ) {
+ final String name = d.getName();
+ if ( !( s.contains( name ) ) ) {
+ data.add( name );
+ if ( getOptions()
+ .getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) {
+ s.add( name );
+ }
+ }
+ }
+ }
+ }
+ break;
+ case SEQ_ANNOTATIONS:
+ if ( n.getNodeData().isHasSequence() ) {
+ if ( n.getNodeData().isHasSequence()
+ && ( n.getNodeData().getSequence().getAnnotations() != null ) ) {
+ final SortedSet<Annotation> a = n.getNodeData().getSequence().getAnnotations();
+ for( int i = 0; i < a.size(); ++i ) {
+ data.add( n.getNodeData().getSequence().getAnnotation( i ).toString() );
+ }
+ }
+ }
+ break;
+ case GO_TERM_IDS:
+ if ( n.getNodeData().isHasSequence() ) {
+ if ( n.getNodeData().isHasSequence()
+ && ( n.getNodeData().getSequence().getAnnotations() != null ) ) {
+ final SortedSet<Annotation> a = n.getNodeData().getSequence().getAnnotations();
+ for( int i = 0; i < a.size(); ++i ) {
+ final Annotation ann = n.getNodeData().getSequence().getAnnotation( i );
+ final String ref = ann.getRef();
+ if ( ref.toUpperCase().startsWith( "GO:" ) ) {
+ data.add( ref );
+ }
+ }
+ }
+ }
+ break;
+ case UNKNOWN:
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
+ break;
+ default:
+ throw new IllegalArgumentException( "unknown data element: "
+ + getOptions().getExtDescNodeDataToReturn() );
+ }
+ } // for loop
+ final StringBuilder sb = new StringBuilder();
+ final int size = TreePanelUtil.nodeDataIntoStringBuffer( data, getOptions(), sb );
+ if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
+ || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
+ if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+ System.out.println( sb );
+ }
+ if ( sb.length() < 1 ) {
+ clearCurrentExternalNodesDataBuffer();
+ }
+ else {
+ setCurrentExternalNodesDataBuffer( sb );
+ }
+ }
+ else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
+ if ( sb.length() < 1 ) {
+ TreePanelUtil.showInformationMessage( this,
+ "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
+ "Descendants of selected node do not contain selected data" );
+ clearCurrentExternalNodesDataBuffer();
+ }
+ else {
+ setCurrentExternalNodesDataBuffer( sb );
+ String title;
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() ) + " for " + data.size() + " nodes, unique entries: "
+ + size;
}
else {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- float x2c = x1 + EURO_D;
- if ( x2c > x2a ) {
- x2c = x2a;
+ title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() ) + " for " + data.size() + "/"
+ + node.getNumberOfExternalNodes() + " external descendats of node " + node
+ + ", unique entries: " + size;
+ }
+ final String s = sb.toString().trim();
+ getMainPanel().getMainFrame().showTextFrame( s, title );
+ }
+ }
+ }
+
+ final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
+ try {
+ if ( ( node.getName().length() > 0 )
+ || ( node.getNodeData().isHasTaxonomy()
+ && !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()
+ && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
+ lines++;
+ boolean enc_data = false;
+ final Taxonomy tax = node.getNodeData().getTaxonomy();
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ _popup_buffer.append( "[" );
+ _popup_buffer.append( tax.getTaxonomyCode() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " " );
}
- drawLine( x1, y1, x2c, y2, g );
+ _popup_buffer.append( tax.getScientificName() );
+ enc_data = true;
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- if ( y2 > y1 ) {
- y2_r = y2 - ROUNDED_D;
- if ( y2_r < y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
+ if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " (" );
}
else {
- y2_r = y2 + ROUNDED_D;
- if ( y2_r > y1 ) {
- y2_r = y1;
+ _popup_buffer.append( "(" );
+ }
+ _popup_buffer.append( tax.getCommonName() );
+ _popup_buffer.append( ")" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " (" );
+ }
+ else {
+ _popup_buffer.append( "(" );
+ }
+ _popup_buffer.append( tax.getAuthority() );
+ _popup_buffer.append( ")" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " [" );
+ }
+ else {
+ _popup_buffer.append( "[" );
+ }
+ _popup_buffer.append( tax.getRank() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( tax.getSynonyms().size() > 0 ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " " );
+ }
+ _popup_buffer.append( "[" );
+ int counter = 1;
+ for( final String syn : tax.getSynonyms() ) {
+ if ( !ForesterUtil.isEmpty( syn ) ) {
+ enc_data = true;
+ _popup_buffer.append( syn );
+ if ( counter < tax.getSynonyms().size() ) {
+ _popup_buffer.append( ", " );
+ }
}
- drawLine( x1, y1, x1, y2_r, g );
+ counter++;
}
+ _popup_buffer.append( "]" );
}
- else {
- drawLine( x1, y1, x1, y2, g );
+ if ( !enc_data ) {
+ if ( ( tax.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
+ if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
+ _popup_buffer.append( "[" );
+ _popup_buffer.append( tax.getIdentifier().getProvider() );
+ _popup_buffer.append( "] " );
+ }
+ _popup_buffer.append( tax.getIdentifier().getValue() );
+ }
}
}
- }
- // draw the horizontal line
- if ( !to_graphics_file && !to_pdf
- && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
- return;
- }
- float x1_r = 0;
- if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawLine( x1_r, y2, x2a, y2, g );
+ if ( node.getNodeData().isHasSequence()
+ && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
+ lines++;
+ boolean enc_data = false;
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
}
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawLine( x1c, y2, x2a, y2, g );
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( seq.getAccession() != null ) {
+ _popup_buffer.append( "[" );
+ if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
+ _popup_buffer.append( seq.getAccession().getSource() );
+ _popup_buffer.append( ":" );
+ }
+ _popup_buffer.append( seq.getAccession().getValue() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
}
- }
- else {
- drawLine( x1a, y2, x2a, y2, g );
- }
- }
- else {
- final double w = PhylogenyMethods.getBranchWidthValue( node );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
+ if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " [" );
+ }
+ else {
+ _popup_buffer.append( "[" );
+ }
+ _popup_buffer.append( seq.getSymbol() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " [" );
+ }
+ else {
+ _popup_buffer.append( "[" );
+ }
+ _popup_buffer.append( seq.getGeneName() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " " );
+ }
+ _popup_buffer.append( seq.getName() );
}
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
+ if ( node.getNodeData().isHasDate() ) {
+ lines++;
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
}
+ _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
}
- else {
- drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ if ( node.getNodeData().isHasDistribution() ) {
+ lines++;
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
+ }
+ _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
}
- }
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( x1_r > x2a ) {
- x1_r = x2a;
+ if ( node.getBranchData().isHasConfidences() ) {
+ final List<Confidence> confs = node.getBranchData().getConfidences();
+ for( final Confidence confidence : confs ) {
+ lines++;
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
+ _popup_buffer.append( "[" );
+ _popup_buffer.append( confidence.getType() );
+ _popup_buffer.append( "] " );
+ }
+ _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
+ getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ _popup_buffer.append( " (sd=" );
+ _popup_buffer.append( FORMATTER_CONFIDENCE
+ .format( ForesterUtil.round( confidence.getStandardDeviation(),
+ getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ _popup_buffer.append( ")" );
+ }
+ }
}
- if ( y2 > y2_r ) {
- final double diff = y2 - y2_r;
- _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
+ if ( node.getNodeData().isHasProperties() ) {
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
+ }
+ _popup_buffer.append( node.getNodeData().getProperties().asText() );
}
- else {
- _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
+ if ( _popup_buffer.length() > 0 ) {
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _rollover_popup
+ .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
+ _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
+ if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
+ }
+ else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
+ }
+ else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
+ }
+ else {
+ _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
+ }
+ }
+ else {
+ _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
+ }
+ _rollover_popup.setText( _popup_buffer.toString() );
+ _node_desc_popup = PopupFactory.getSharedInstance()
+ .getPopup( null,
+ _rollover_popup,
+ e.getLocationOnScreen().x + 10,
+ e.getLocationOnScreen().y - ( lines * 20 ) );
+ _node_desc_popup.show();
}
- g.draw( _arc );
}
}
- if ( node.isExternal() ) {
- paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
+ catch ( final Exception ex ) {
+ // Do nothing.
}
}
- final private double paintCirculars( final PhylogenyNode n,
- final Phylogeny phy,
- final float center_x,
- final float center_y,
- final double radius,
- final boolean radial_labels,
- final Graphics2D g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
- if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
- System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
- }
- return _urt_nodeid_angle_map.get( n.getId() );
+ final private void showNodeEditFrame( final PhylogenyNode n ) {
+ if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
+ // pop up edit box for single node
+ _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
+ _node_frame_index++;
}
else {
- final List<PhylogenyNode> descs = n.getDescendants();
- double sum = 0;
- for( final PhylogenyNode desc : descs ) {
- sum += paintCirculars( desc,
- phy,
- center_x,
- center_y,
- radius,
- radial_labels,
- g,
- to_pdf,
- to_graphics_file );
- }
- double r = 0;
- if ( !n.isRoot() ) {
- 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 ) ) ) );
- _urt_nodeid_angle_map.put( n.getId(), theta );
- for( final PhylogenyNode desc : descs ) {
- paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
- }
- return theta;
+ JOptionPane.showMessageDialog( this, "too many node windows are open" );
}
}
- final private void paintCircularsLite( final PhylogenyNode n,
- final Phylogeny phy,
- final int center_x,
- final int center_y,
- final int radius,
- final Graphics2D g ) {
- if ( n.isExternal() ) {
- return;
+ final private void showNodeFrame( final PhylogenyNode n ) {
+ if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
+ // pop up edit box for single node
+ _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
+ _node_frame_index++;
}
else {
- final List<PhylogenyNode> descs = n.getDescendants();
- for( final PhylogenyNode desc : descs ) {
- paintCircularsLite( desc, phy, center_x, center_y, radius, g );
- }
- float r = 0;
- if ( !n.isRoot() ) {
- 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 ) ) ) );
- for( final PhylogenyNode desc : descs ) {
- paintBranchCircularLite( n, desc, g );
- }
+ JOptionPane.showMessageDialog( this, "too many node windows are open" );
}
}
- final private void paintCollapsedNode( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf,
- final boolean is_in_found_nodes ) {
- Color c = null;
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- c = Color.BLACK;
- }
- else if ( is_in_found_nodes ) {
- c = getColorForFoundNode( node );
- }
- else if ( getControlPanel().isColorAccordingToSequence() ) {
- c = getSequenceBasedColor( node );
- }
- else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- c = getTaxonomyBasedColor( node );
- }
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
- && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- c = PhylogenyMethods.getBranchColorValue( node );
+ final private void switchDisplaygetPhylogenyGraphicsType() {
+ switch ( getPhylogenyGraphicsType() ) {
+ case RECTANGULAR:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
+ break;
+ case EURO_STYLE:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
+ break;
+ case ROUNDED:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
+ break;
+ case CURVED:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
+ break;
+ case TRIANGULAR:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
+ break;
+ case CONVEX:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ break;
+ case UNROOTED:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ break;
+ case CIRCULAR:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ break;
+ default:
+ throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
}
- else {
- c = getTreeColorSet().getCollapseFillColor();
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ getControlPanel().getDynamicallyHideData().setEnabled( false );
+ }
+ else {
+ getControlPanel().getDynamicallyHideData().setEnabled( true );
+ }
}
- double d = node.getAllExternalDescendants().size();
- if ( d > 1000 ) {
- d = ( 3 * _y_distance ) / 3;
+ if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ getControlPanel().setDrawPhylogramEnabled( true );
}
else {
- d = ( Math.log10( d ) * _y_distance ) / 2.5;
- }
- final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
- if ( d < box_size ) {
- d = box_size;
- }
- final float xx = node.getXcoord() - ( 2 * box_size );
- final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
- _polygon.reset();
- _polygon.moveTo( xxx, node.getYcoord() );
- _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
- _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
- _polygon.closePath();
- if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
- g.setColor( c );
- g.fill( _polygon );
- }
- else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
- g.setColor( getBackground() );
- g.fill( _polygon );
- g.setColor( c );
- g.draw( _polygon );
+ getControlPanel().setDrawPhylogramEnabled( false );
}
- else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
- .getYcoord() - d ), c, false ) );
- g.fill( _polygon );
- g.setPaint( c );
- g.draw( _polygon );
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
+ }
+
+ final void calcMaxDepth() {
+ if ( _phylogeny != null ) {
+ _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
}
- paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
- final private void paintConfidenceValues( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- final List<Confidence> confidences = node.getBranchData().getConfidences();
- boolean not_first = false;
- Collections.sort( confidences );
- final StringBuilder sb = new StringBuilder();
- for( final Confidence confidence : confidences ) {
- final double value = confidence.getValue();
- if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- if ( value < getOptions().getMinConfidenceValue() ) {
- return;
+ /**
+ * Set parameters for printing the displayed tree
+ *
+ */
+ final void calcParametersForPainting( final int x, final int y ) {
+ // updateStyle(); not needed?
+ if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
+ initNodeData();
+ calculateLongestExtNodeInfo();
+ if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
+ while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), true );
+ calculateLongestExtNodeInfo();
}
- if ( not_first ) {
- sb.append( "/" );
+ }
+ else {
+ while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) ) && ( getTreeFontSet().getLargeFont()
+ .getSize() <= ( getTreeFontSet().getLargeFontMemory().getSize()
+ - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ calculateLongestExtNodeInfo();
}
- else {
- not_first = true;
- }
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- if ( getOptions().isShowConfidenceStddev() ) {
- if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- sb.append( "(" );
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
- getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- sb.append( ")" );
- }
+ }
+ //_length_of_longest_text = calcLengthOfLongestText();
+ int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
+ final int max_depth = PhylogenyMethods.calculateMaxDepthConsiderCollapsed( _phylogeny ) + 1;
+ if ( ext_nodes == 1 ) {
+ ext_nodes = max_depth;
+ if ( ext_nodes < 1 ) {
+ ext_nodes = 1;
}
}
- }
- if ( sb.length() > 0 ) {
- final float parent_x = node.getParent().getXcoord();
- float x = node.getXcoord();
- g.setFont( getTreeFontSet().getSmallFont() );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- x += EURO_D;
+ updateOvSizes();
+ float xdist = 0;
+ float ov_xdist = 0;
+ if ( !isNonLinedUpCladogram() ) {
+ xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
+ ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x += ROUNDED_D;
+ else {
+ xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
+ ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
}
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
+ if ( xdist < 0.0 ) {
+ xdist = 0.0f;
+ }
+ if ( ov_xdist < 0.0 ) {
+ ov_xdist = 0.0f;
+ }
+ if ( ydist < 0.0 ) {
+ ydist = 0.0f;
+ }
+ setXdistance( xdist );
+ setYdistance( ydist );
+ setOvXDistance( ov_xdist );
+ final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() );
+ //final double height = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ if ( height > 0 ) {
+ final float corr = ( float ) ( ( x - ( 2.0 * TreePanel.MOVE ) - getLongestExtNodeInfo()
+ - getXdistance() ) / height );
+ setXcorrectionFactor( corr > 0 ? corr : 0 );
+ final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
+ setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
}
else {
- g.setColor( getTreeColorSet().getConfidenceColor() );
+ setXcorrectionFactor( 0 );
+ setOvXcorrectionFactor( 0 );
}
- final String conf_str = sb.toString();
- TreePanel.drawString( conf_str,
- parent_x
- + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall()
- .stringWidth( conf_str ) ) / 2 ),
- ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
- g );
- }
- }
-
- final private void paintGainedAndLostCharacters( final Graphics2D g,
- final PhylogenyNode node,
- final String gained,
- final String lost ) {
- if ( node.getParent() != null ) {
- final float parent_x = node.getParent().getXcoord();
- final float x = node.getXcoord();
- g.setFont( getTreeFontSet().getLargeFont() );
- g.setColor( getTreeColorSet().getGainedCharactersColor() );
- if ( Constants.SPECIAL_CUSTOM ) {
- g.setColor( Color.BLUE );
+ _circ_max_depth = max_depth;
+ setUpUrtFactor();
+ //
+ if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ // int dynamic_hiding_factor = calcDynamicHidingFactor();
+ // if ( dynamic_hiding_factor > 1 ) {
+ // while ( dynamic_hiding_factor > 1
+ // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
+ // getTreeFontSet().decreaseFontSize( 1, true );
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
+ // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
+ // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
+ // getTreeFontSet().increaseFontSize();
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
}
- TreePanel
- .drawString( gained,
- parent_x
- + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
- ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
- g );
- g.setColor( getTreeColorSet().getLostCharactersColor() );
- TreePanel
- .drawString( lost,
- parent_x
- + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ),
- ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
- g );
+ //
}
}
- /**
- * Draw a box at the indicated node.
- *
- * @param x
- * @param y
- * @param node
- * @param g
- */
- final private void paintNodeBox( final float x,
- final float y,
- final PhylogenyNode node,
- final Graphics2D g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- if ( node.isCollapse() ) {
+ final void calculateLongestExtNodeInfo() {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
- // if this node should be highlighted, do so
- if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
- g.setColor( getTreeColorSet().getFoundColor0() );
- drawOval( x - 8, y - 8, 16, 16, g );
- drawOval( x - 9, y - 8, 17, 17, g );
- drawOval( x - 9, y - 9, 18, 18, g );
+ int max_possible_length = ForesterUtil
+ .roundToInt( ( getSize().getWidth() - ( 2 * MOVE ) ) * AptxConstants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
+ if ( max_possible_length < 20 ) {
+ max_possible_length = 20;
}
- if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
- || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
- || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
- || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
- .getNodeData().getNodeVisualData().getNodeColor() != null )
- || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
- || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node
- .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
- || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
- .isDuplication()
- || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
- .isSpeciationOrDuplication() ) ) ) {
- NodeVisualData vis = null;
- if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
- && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) {
- vis = node.getNodeData().getNodeVisualData();
+ int longest = 30;
+ int longest_txt = 0;
+ _longest_domain = 0;
+ PhylogenyNode longest_txt_node = _phylogeny.getFirstExternalNode();
+ for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
+ int sum = 0;
+ if ( node.isCollapse() ) {
+ continue;
}
- float box_size = getOptions().getDefaultNodeShapeSize();
- if ( ( vis != null ) && ( vis.getSize() != NodeVisualData.DEFAULT_SIZE ) ) {
- box_size = vis.getSize();
+ final StringBuilder sb = new StringBuilder();
+ nodeDataAsSB( node, sb );
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb );
}
- final float half_box_size = box_size / 2.0f;
- Color outline_color = null;
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- outline_color = Color.BLACK;
+ final int txt = sb.length();
+ if ( txt > longest_txt ) {
+ longest_txt = txt;
+ longest_txt_node = node;
}
- else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
- outline_color = getColorForFoundNode( node );
+ boolean use_vis = false;
+ final Graphics2D g = ( Graphics2D ) getGraphics();
+ if ( g != null && getControlPanel().isUseVisualStyles() ) {
+ use_vis = setFont( g, node, false );
}
- else if ( vis != null ) {
- if ( vis.getNodeColor() != null ) {
- outline_color = vis.getNodeColor();
- }
- else if ( vis.getFontColor() != null ) {
- outline_color = vis.getFontColor();
- }
+ if ( !use_vis ) {
+ sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
- else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
- final Event event = node.getNodeData().getEvent();
- if ( event.isDuplication() ) {
- outline_color = getTreeColorSet().getDuplicationBoxColor();
- }
- else if ( event.isSpeciation() ) {
- outline_color = getTreeColorSet().getSpecBoxColor();
- }
- else if ( event.isSpeciationOrDuplication() ) {
- outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
- }
+ else {
+ sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() );
}
- if ( outline_color == null ) {
- outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
- if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
- outline_color = getTreeColorSet().getBranchColorForPdf();
- }
+ if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
+ sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
+ .getGainedCharactersAsStringBuffer().toString() );
}
- NodeShape shape = null;
- if ( vis != null ) {
- if ( vis.getShape() == NodeShape.CIRCLE ) {
- shape = NodeShape.CIRCLE;
+ if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
+ && ( node.getNodeData().getVector().size() > 0 ) ) {
+ if ( getConfiguration() != null ) {
+ sum += getConfiguration().getVectorDataWidth() + 10;
}
- else if ( vis.getShape() == NodeShape.RECTANGLE ) {
- shape = NodeShape.RECTANGLE;
+ else {
+ sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10;
}
}
- if ( shape == null ) {
- if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
- shape = NodeShape.CIRCLE;
- }
- else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) {
- shape = NodeShape.RECTANGLE;
- }
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ // FIXME
+ // TODO this might need some clean up
+ final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture();
+ sum += ( ( _domain_structure_width
+ / ( ( RenderableDomainArchitecture ) d ).getOriginalSize().getWidth() ) * d.getTotalLength() )
+ + 10;
+ if ( d.getTotalLength() > _longest_domain ) {
+ _longest_domain = d.getTotalLength();
+ }
+ }
+ if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+ && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+ // FIXME
+ sum += RenderableMsaSequence.DEFAULT_WIDTH + 30;
+ }
+ if ( sum >= max_possible_length ) {
+ _longest_ext_node_info = max_possible_length;
+ // return; //FIXME why?
}
- NodeFill fill = null;
- if ( vis != null ) {
- if ( vis.getFillType() == NodeFill.SOLID ) {
- fill = NodeFill.SOLID;
- }
- else if ( vis.getFillType() == NodeFill.NONE ) {
- fill = NodeFill.NONE;
- }
- else if ( vis.getFillType() == NodeFill.GRADIENT ) {
- fill = NodeFill.GRADIENT;
- }
+ if ( sum > longest ) {
+ longest = sum;
}
- if ( fill == null ) {
- if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
- fill = NodeFill.SOLID;
- }
- else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
- fill = NodeFill.NONE;
- }
- else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- fill = NodeFill.GRADIENT;
- }
+ }
+ _ext_node_with_longest_txt_info = longest_txt_node;
+ if ( longest >= max_possible_length ) {
+ _longest_ext_node_info = max_possible_length;
+ }
+ else {
+ _longest_ext_node_info = longest;
+ }
+ _length_of_longest_text = calcLengthOfLongestText();
+ }
+
+ final void calculateScaleDistance() {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ return;
+ }
+ final double height = getMaxDistanceToRoot();
+ if ( height > 0 ) {
+ if ( ( height <= 0.5 ) ) {
+ setScaleDistance( 0.01 );
}
- Color vis_fill_color = null;
- if ( ( vis != null ) && ( vis.getNodeColor() != null ) ) {
- vis_fill_color = vis.getNodeColor();
+ else if ( height <= 5.0 ) {
+ setScaleDistance( 0.1 );
}
- if ( shape == NodeShape.CIRCLE ) {
- if ( fill == NodeFill.GRADIENT ) {
- drawOvalGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
- : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
+ else if ( height <= 50.0 ) {
+ setScaleDistance( 1 );
+ }
+ else if ( height <= 500.0 ) {
+ setScaleDistance( 10 );
+ }
+ else {
+ setScaleDistance( 100 );
+ }
+ }
+ else {
+ setScaleDistance( 0.0 );
+ }
+ String scale_label = String.valueOf( getScaleDistance() );
+ if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
+ scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
+ }
+ setScaleLabel( scale_label );
+ }
+
+ final Color calculateSequenceBasedColor( final Sequence seq ) {
+ if ( ForesterUtil.isEmpty( seq.getName() ) ) {
+ return getTreeColorSet().getSequenceColor();
+ }
+ Color c = null;
+ final String seq_name = seq.getName();
+ c = getControlPanel().getSequenceColors().get( seq_name );
+ if ( c == null ) {
+ c = AptxUtil.calculateColorFromString( seq_name, false );
+ getControlPanel().getSequenceColors().put( seq_name, c );
+ }
+ return c;
+ }
+
+ final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
+ if ( getOptions().isColorByTaxonomicGroup() ) {
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ boolean ex = false;
+ String group = null;
+ try {
+ group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
}
- else if ( fill == NodeFill.NONE ) {
- Color background = getBackground();
- if ( to_pdf ) {
- background = Color.WHITE;
- }
- drawOvalGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- background,
- background,
- outline_color );
+ catch ( final Exception e ) {
+ ex = true;
}
- else if ( fill == NodeVisualData.NodeFill.SOLID ) {
- if ( vis_fill_color != null ) {
- g.setColor( vis_fill_color );
- }
- else {
- g.setColor( outline_color );
+ if ( !ex && !ForesterUtil.isEmpty( group ) ) {
+ final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ if ( c != null ) {
+ return c;
}
- drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
- else if ( shape == NodeVisualData.NodeShape.RECTANGLE ) {
- if ( fill == NodeVisualData.NodeFill.GRADIENT ) {
- drawRectGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
- : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
- }
- else if ( fill == NodeVisualData.NodeFill.NONE ) {
- Color background = getBackground();
- if ( to_pdf ) {
- background = Color.WHITE;
- }
- drawRectGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- background,
- background,
- outline_color );
+ return getTreeColorSet().getTaxonomyColor();
+ }
+ else {
+ if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ return getTreeColorSet().getTaxonomyColor();
+ }
+ Color c = null;
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
+ }
+ if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
+ }
+ if ( c == null ) {
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
+ getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
}
- else if ( fill == NodeVisualData.NodeFill.SOLID ) {
- if ( vis_fill_color != null ) {
- g.setColor( vis_fill_color );
- }
- else {
- g.setColor( outline_color );
- }
- drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ else {
+ c = AptxUtil.calculateColorFromString( tax.getScientificName(), true );
+ getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
}
}
+ return c;
+ }
+ }
+
+ void clearCurrentExternalNodesDataBuffer() {
+ setCurrentExternalNodesDataBuffer( new StringBuilder() );
+ }
+
+ /**
+ * Collapse the tree from the given node
+ *
+ * @param node
+ * a PhylogenyNode
+ */
+ final void collapse( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot collapse in unrooted display type",
+ "Attempt to collapse in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ if ( !node.isExternal() && !node.isRoot() ) {
+ final boolean collapse = !node.isCollapse();
+ TreePanelUtil.collapseSubtree( node, collapse );
+ updateSetOfCollapsedExternalNodes();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ calculateLongestExtNodeInfo();
+ setNodeInPreorderToNull();
+ _control_panel.displayedPhylogenyMightHaveChanged( true );
+ resetPreferredSize();
+ updateOvSizes();
+ _main_panel.adjustJScrollPane();
+ repaint();
}
}
- final private int paintNodeData( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf,
- final boolean is_in_found_nodes ) {
- if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
- return 0;
+ final void uncollapseAll( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot uncollapse in unrooted display type",
+ "Attempt to uncollapse in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
}
- if ( getOptions().isShowBranchLengthValues()
- && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
- paintBranchLength( g, node, to_pdf, to_graphics_file );
+ if ( !node.isExternal() ) {
+ TreePanelUtil.uncollapseSubtree( node );
+ updateSetOfCollapsedExternalNodes();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ calculateLongestExtNodeInfo();
+ setNodeInPreorderToNull();
+ _control_panel.displayedPhylogenyMightHaveChanged( true );
+ resetPreferredSize();
+ updateOvSizes();
+ _main_panel.adjustJScrollPane();
+ repaint();
}
- if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
- return 0;
+ }
+
+ final void collapseSpeciesSpecificSubtrees() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
}
- _sb.setLength( 0 );
- int x = 0;
- final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
- if ( getControlPanel().isShowTaxonomyImages()
- && ( getImageMap() != null )
- && !getImageMap().isEmpty()
- && node.getNodeData().isHasTaxonomy()
- && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
- .getUris().isEmpty() ) ) {
- x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
+ setWaitCursor();
+ TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+ updateSetOfCollapsedExternalNodes();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ calculateLongestExtNodeInfo();
+ setNodeInPreorderToNull();
+ resetPreferredSize();
+ resetDepthCollapseDepthValue();
+ resetRankCollapseRankValue();
+ _main_panel.adjustJScrollPane();
+ getControlPanel().showWhole();
+ setArrowCursor();
+ }
+
+ final void colorRank( final String rank ) {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
}
- if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
- .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
- x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
+ setWaitCursor();
+ AptxUtil.removeBranchColors( _phylogeny );
+ final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ if ( colorizations > 0 ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
+ }
+ if ( _control_panel.getColorAccSpeciesCb() != null ) {
+ _control_panel.getColorAccSpeciesCb().setSelected( false );
+ }
+ _options.setColorLabelsSameAsParentBranch( true );
+ if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) {
+ getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true );
+ }
+ _control_panel.repaint();
}
- setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
- if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- if ( _sb.length() > 0 ) {
- _sb.setLength( 0 );
- _sb.append( " (" );
- _sb.append( node.getAllExternalDescendants().size() );
- _sb.append( ")" );
+ setArrowCursor();
+ repaint();
+ if ( colorizations > 0 ) {
+ String msg = "Taxonomy colorization via " + rank + " completed:\n";
+ if ( colorizations > 1 ) {
+ msg += "colorized " + colorizations + " subtrees";
+ }
+ else {
+ msg += "colorized one subtree";
}
+ setEdited( true );
+ JOptionPane.showMessageDialog( this,
+ msg,
+ "Taxonomy Rank-Colorization Completed (" + rank + ")",
+ JOptionPane.INFORMATION_MESSAGE );
}
else {
- _sb.setLength( 0 );
+ String msg = "Could not taxonomy rank-colorize any subtree via " + rank + ".\n";
+ msg += "Possible solutions (given that suitable taxonomic information is present):\n";
+ msg += "select a different rank (e.g. phylum, genus, ...)\n";
+ msg += " and/or\n";
+ msg += "execute:\n";
+ msg += "1. \"" + MainFrame.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
+ msg += "2. \"" + MainFrame.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
+ JOptionPane.showMessageDialog( this,
+ msg,
+ "Taxonomy Rank-Colorization Failed",
+ JOptionPane.WARNING_MESSAGE );
}
- nodeDataAsSB( node, _sb );
- final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
- float down_shift_factor = 3.0f;
- if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
- down_shift_factor = 1;
+ }
+
+ final void confColor() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
}
- final float pos_x = node.getXcoord() + x + 2 + half_box_size;
- float pos_y;
- if ( !using_visual_font ) {
- pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) );
+ setWaitCursor();
+ AptxUtil.removeBranchColors( _phylogeny );
+ TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
- else {
- pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
+ setArrowCursor();
+ repaint();
+ }
+
+ final void decreaseDomainStructureEvalueThresholdExp() {
+ if ( _domain_structure_e_value_thr_exp > -20 ) {
+ _domain_structure_e_value_thr_exp -= 1;
}
- final String sb_str = _sb.toString();
- // GUILHEM_BEG ______________
- if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
- && ( _query_sequence != null ) ) {
- int nodeTextBoundsWidth = 0;
- if ( sb_str.length() > 0 ) {
- final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
- nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
+ }
+
+ /**
+ * Find the node, if any, at the given location
+ *
+ * @param x
+ * @param y
+ * @return pointer to the node at x,y, null if not found
+ */
+ public final PhylogenyNode findNode( final int x, final int y ) {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ return null;
+ }
+ final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
+ for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
+ && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
+ && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
+ && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
+ && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
+ return node;
}
- if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
- if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
- g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
- g.setColor( getTreeColorSet().getBackgroundColor() );
+ }
+ return null;
+ }
+
+ final Configuration getConfiguration() {
+ return _configuration;
+ }
+
+ final ControlPanel getControlPanel() {
+ return _control_panel;
+ }
+
+ String getCurrentExternalNodesDataBufferAsString() {
+ return _current_external_nodes_data_buffer.toString();
+ }
+
+ int getCurrentExternalNodesDataBufferChangeCounter() {
+ return _current_external_nodes_data_buffer_change_counter;
+ }
+
+ final int getDomainStructureEvalueThresholdExp() {
+ return _domain_structure_e_value_thr_exp;
+ }
+
+ public final Set<Long> getFoundNodes0() {
+ return _found_nodes_0;
+ }
+
+ public final Set<Long> getFoundNodes1() {
+ return _found_nodes_1;
+ }
+
+ public List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ if ( getFoundNodes0() != null ) {
+ for( final Long id : getFoundNodes0() ) {
+ final PhylogenyNode n = _phylogeny.getNode( id );
+ if ( n != null ) {
+ additional_nodes.add( n );
}
}
- else {
- final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
- for( final SequenceRelation seqRelation : seqRelations ) {
- final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
- .getRef1().isEqual( _query_sequence ) )
- && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
- .getSelectedItem() );
- if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
- final double linePosX = node.getXcoord() + 2 + half_box_size;
- final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
- .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
- + ")";
- if ( sConfidence != null ) {
- float confidenceX = pos_x;
- if ( sb_str.length() > 0 ) {
- confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
- + CONFIDENCE_LEFT_MARGIN;
- }
- if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
- final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
- .getBounds().getWidth();
- TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
- x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
- }
- }
- if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
- {
- if ( nodeTextBoundsWidth == 0 ) {
- nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
- }
- else {
- nodeTextBoundsWidth += 2;
- }
- g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
- + nodeTextBoundsWidth, 3 + ( int ) pos_y );
- break;
- }
+ }
+ if ( getFoundNodes1() != null ) {
+ for( final Long id : getFoundNodes1() ) {
+ if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
+ final PhylogenyNode n = _phylogeny.getNode( id );
+ if ( n != null ) {
+ additional_nodes.add( n );
}
}
}
}
- if ( sb_str.length() > 0 ) {
- TreePanel.drawString( sb_str, pos_x, pos_y, g );
+ return additional_nodes;
+ }
+
+ final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
+ if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ return ( PhylogenyMethods.getBranchColorValue( node ) );
}
- // GUILHEM_END _____________
- if ( _sb.length() > 0 ) {
- if ( !using_visual_font && !is_in_found_nodes ) {
- x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
- }
- else {
- x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
- }
+ else {
+ return ( getTreeColorSet().getBranchColor() );
}
- if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAnnotations() != null )
- && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
- final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else if ( getControlPanel().isColorAccordingToAnnotation() ) {
- g.setColor( calculateColorForAnnotation( ann ) );
- }
- final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
- TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
- _sb.setLength( 0 );
- _sb.append( ann_str );
- if ( _sb.length() > 0 ) {
- if ( !using_visual_font && !is_in_found_nodes ) {
- x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
- }
- else {
- x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
- }
- }
+ }
+
+ final int getLongestExtNodeInfo() {
+ return _longest_ext_node_info;
+ }
+
+ final Options getOptions() {
+ if ( _options == null ) {
+ _options = getControlPanel().getOptions();
+ }
+ return _options;
+ }
+
+ final Rectangle2D getOvRectangle() {
+ return _ov_rectangle;
+ }
+
+ final Rectangle getOvVirtualRectangle() {
+ return _ov_virtual_rectangle;
+ }
+
+ final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
+ return _graphics_type;
+ }
+
+ final Color getSequenceBasedColor( final PhylogenyNode node ) {
+ if ( node.getNodeData().isHasSequence() ) {
+ return calculateSequenceBasedColor( node.getNodeData().getSequence() );
}
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
- && node.getNodeData().isHasBinaryCharacters() ) {
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else {
- g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
- }
- if ( getControlPanel().isShowBinaryCharacters() ) {
- TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
- .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
- paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
- .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
- .getLostCharactersAsStringBuffer().toString() );
- }
- else {
- TreePanel
- .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
- node.getXcoord() + x + 4 + half_box_size,
- node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ),
- g );
- paintGainedAndLostCharacters( g, node, "+"
- + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
- + node.getNodeData().getBinaryCharacters().getLostCount() );
- }
- }
+ // return non-colorized color
+ return getTreeColorSet().getSequenceColor();
+ }
+
+ final double getStartingAngle() {
+ return _urt_starting_angle;
+ }
+
+ DescriptiveStatistics getStatisticsForExpressionValues() {
+ return _statistics_for_vector_data;
+ }
+
+ final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
+ if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) {
+ return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
}
- return x;
+ // return non-colorized color
+ return getTreeColorSet().getTaxonomyColor();
}
- final private void paintNodeDataUnrootedCirc( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean to_graphics_file,
- final boolean radial_labels,
- final double ur_angle,
- final boolean is_in_found_nodes ) {
- if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
+ public final File getTreeFile() {
+ return _treefile;
+ }
+
+ final float getXcorrectionFactor() {
+ return _x_correction_factor;
+ }
+
+ final float getXdistance() {
+ return _x_distance;
+ }
+
+ final float getYdistance() {
+ return _y_distance;
+ }
+
+ final void increaseDomainStructureEvalueThresholdExp() {
+ if ( _domain_structure_e_value_thr_exp < 3 ) {
+ _domain_structure_e_value_thr_exp += 1;
+ }
+ }
+
+ final void initNodeData() {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
- _sb.setLength( 0 );
- _sb.append( " " );
- if ( node.getNodeData().isHasTaxonomy()
- && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
- .isShowTaxonomyCommonNames() ) ) {
- final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
- if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
- _sb.append( taxonomy.getTaxonomyCode() );
- _sb.append( " " );
- }
- if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
- && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getScientificName() );
- _sb.append( " (" );
- _sb.append( taxonomy.getCommonName() );
- _sb.append( ") " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- _sb.append( taxonomy.getScientificName() );
- _sb.append( " " );
+ double _max_original_domain_structure_width = 0.0;
+ for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
+ if ( node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ RenderableDomainArchitecture rds = null;
+ if ( !( node.getNodeData().getSequence()
+ .getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
+ if ( SPECIAL_DOMAIN_COLORING ) {
+ rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+ .getDomainArchitecture(), node.getName() );
+ }
+ else {
+ rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+ .getDomainArchitecture() );
+ }
+ node.getNodeData().getSequence().setDomainArchitecture( rds );
}
- else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getCommonName() );
- _sb.append( " " );
+ else {
+ rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
}
- }
- else if ( _control_panel.isShowTaxonomyScientificNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- _sb.append( taxonomy.getScientificName() );
- _sb.append( " " );
+ if ( getControlPanel().isShowDomainArchitectures() ) {
+ final double dsw = rds.getOriginalSize().getWidth();
+ if ( dsw > _max_original_domain_structure_width ) {
+ _max_original_domain_structure_width = dsw;
+ }
}
}
- else if ( _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getCommonName() );
- _sb.append( " " );
+ }
+ if ( getControlPanel().isShowDomainArchitectures() ) {
+ final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width );
+ for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
+ if ( node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
+ .getSequence().getDomainArchitecture();
+ rds.setRenderingFactorWidth( ds_factor_width );
+ rds.setParameter( _domain_structure_e_value_thr_exp );
}
}
}
- if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- _sb.append( " [" );
- _sb.append( node.getAllExternalDescendants().size() );
- _sb.append( "]" );
+ }
+
+ final boolean inOv( final MouseEvent e ) {
+ return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
+ && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
+ && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) )
+ && ( e.getY() < ( ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
+ }
+
+ final boolean inOvRectangle( final MouseEvent e ) {
+ return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
+ && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
+ && ( e.getY() >= ( getOvRectangle().getY() - 1 ) )
+ && ( e.getY() <= ( getOvRectangle().getY() + getOvRectangle().getHeight() + 1 ) ) );
+ }
+
+ final boolean isCanCollapse() {
+ return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ }
+
+ final boolean isCanUncollapseAll( final PhylogenyNode node ) {
+ if ( node.isExternal() || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
+ return false;
}
- if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getName() );
+ if ( node.isCollapse() ) {
+ return true;
}
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
- _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
- _sb.append( ":" );
- }
- _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
- }
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getNodeData().getSequence().getName() );
+ final PhylogenyNodeIterator it = new PreorderTreeIterator( node );
+ while ( it.hasNext() ) {
+ if ( it.next().isCollapse() ) {
+ return true;
}
}
- //g.setFont( getTreeFontSet().getLargeFont() );
- //if ( is_in_found_nodes ) {
- // g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
- // }
- if ( _sb.length() > 1 ) {
- setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
- final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
- final String sb_str = _sb.toString();
- double m = 0;
- if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
+ return false;
+ }
+
+ final boolean isCanColorSubtree() {
+ return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ }
+
+ final boolean isCanCopy() {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
+ }
+
+ final boolean isCanCut( final PhylogenyNode node ) {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
+ && !node.isRoot() );
+ }
+
+ final boolean isCanDelete() {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
+ }
+
+ final boolean isCanPaste() {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
+ && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
+ }
+
+ final boolean isCanReroot() {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
+ }
+
+ final boolean isCanSubtree( final PhylogenyNode node ) {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal()
+ && ( !node.isRoot() || ( _subtree_index > 0 ) ) );
+ }
+
+ public final boolean isCurrentTreeIsSubtree() {
+ return ( _subtree_index > 0 );
+ }
+
+ final boolean isEdited() {
+ return _edited;
+ }
+
+ final boolean isInOvRect() {
+ return _in_ov_rect;
+ }
+
+ final boolean isOvOn() {
+ return _ov_on;
+ }
+
+ final boolean isPhyHasBranchLengths() {
+ return _phy_has_branch_lengths;
+ }
+
+ final void midpointRoot() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ if ( !_phylogeny.isRerootable() ) {
+ JOptionPane.showMessageDialog( this,
+ "This is not rerootable",
+ "Not rerootable",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ setNodeInPreorderToNull();
+ setWaitCursor();
+ PhylogenyMethods.midpointRoot( _phylogeny );
+ resetNodeIdToDistToLeafMap();
+ setArrowCursor();
+ setEdited( true );
+ repaint();
+ }
+
+ final void mouseClicked( final MouseEvent e ) {
+ if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
+ final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
+ final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
+ double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
+ * w_ratio;
+ double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
+ * h_ratio;
+ if ( x < 0 ) {
+ x = 0;
}
- else {
- m = ( float ) ( ur_angle % TWO_PI );
+ if ( y < 0 ) {
+ y = 0;
}
- _at = g.getTransform();
- boolean need_to_reset = false;
- final float x_coord = node.getXcoord();
- float y_coord;
- if ( !using_visual_font ) {
- y_coord = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / 3.0f );
+ final double max_x = getWidth() - getVisibleRect().width;
+ final double max_y = getHeight() - getVisibleRect().height;
+ if ( x > max_x ) {
+ x = max_x;
}
- else {
- y_coord = node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / 3.0f );
+ if ( y > max_y ) {
+ y = max_y;
}
- if ( radial_labels ) {
- need_to_reset = true;
- boolean left = false;
- if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
- m -= PI;
- left = true;
+ getMainPanel().getCurrentScrollPane().getViewport()
+ .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
+ setInOvRect( true );
+ repaint();
+ }
+ else {
+ final PhylogenyNode node = findNode( e.getX(), e.getY() );
+ if ( node != null ) {
+ if ( !node.isRoot() && node.getParent().isCollapse() ) {
+ return;
}
- g.rotate( m, x_coord, node.getYcoord() );
- if ( left ) {
- if ( !using_visual_font ) {
- g.translate( -( getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth() ),
- 0 );
- }
- else {
- g.translate( -( getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth() ), 0 );
+ _highlight_node = node;
+ // Check if shift key is down
+ if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
+ // Yes, so add to _found_nodes
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
}
+ getFoundNodes0().add( node.getId() );
+ // Check if control key is down
}
- }
- else {
- if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
- need_to_reset = true;
- if ( !using_visual_font ) {
- g.translate( -getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth(), 0 );
+ else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
+ // Yes, so pop-up menu
+ displayNodePopupMenu( node, e.getX(), e.getY() );
+ // Handle unadorned click
+ }
+ else {
+ // Check for right mouse button
+ if ( e.getModifiers() == 4 ) {
+ displayNodePopupMenu( node, e.getX(), e.getY() );
}
else {
- g.translate( -getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth(), 0 );
+ // if not in _found_nodes, clear _found_nodes
+ handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
}
}
}
- TreePanel.drawString( sb_str, x_coord, y_coord, g );
- if ( need_to_reset ) {
- g.setTransform( _at );
- }
- }
- }
+ else {
+ // no node was clicked so partition tree instead
+ _highlight_node = null;
+
+ _clicked_x = e.getX();
+ if (!getPhylogeny().isEmpty()) {
+
+ PhylogenyNode furthestNode = PhylogenyMethods.calculateNodeWithMaxDistanceToRoot( _phylogeny );
+ _furthest_node_x = furthestNode.getXcoord();
+ _root_x = _phylogeny.getRoot().getXcoord();
+
+ // don't bother if 0 distance tree or clicked x lies outside of tree
+ if (_furthest_node_x != _root_x && !(_clicked_x < _root_x || _clicked_x > _furthest_node_x))
+ {
+ _partition_tree = true;
- final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
- if ( node.isCollapse() ) {
- if ( !node.isRoot() && !node.getParent().isCollapse() ) {
- paintCollapsedNode( g, node, false, false, false );
- }
- return;
- }
- if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
- g.setColor( getColorForFoundNode( node ) );
- drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary()
- - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
- }
- float new_x = 0;
- if ( !node.isExternal() && !node.isCollapse() ) {
- boolean first_child = true;
- float y2 = 0.0f;
- final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode child_node = node.getChildNode( i );
- int factor_x;
- if ( !isUniformBranchLengthsForCladogram() ) {
- factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
- }
- else {
- factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
- }
- if ( first_child ) {
- first_child = false;
- y2 = node.getYSecondary()
- - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
- .getNumberOfExternalNodes() ) );
- }
- else {
- y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
}
- final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
- new_x = x2 + node.getXSecondary();
- final float diff_y = node.getYSecondary() - y2;
- final float diff_x = node.getXSecondary() - new_x;
- if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
- paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
+
+
+ }
}
- child_node.setXSecondary( new_x );
- child_node.setYSecondary( y2 );
- y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
}
- }
+ repaint();
}
- final private void paintNodeRectangular( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean dynamically_hide,
- final int dynamic_hiding_factor,
- final boolean to_graphics_file ) {
- final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
- if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
- paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
+ final void mouseDragInBrowserPanel( final MouseEvent e ) {
+ setCursor( MOVE_CURSOR );
+ final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
+ scroll_position.x -= ( e.getX() - getLastDragPointX() );
+ scroll_position.y -= ( e.getY() - getLastDragPointY() );
+ if ( scroll_position.x < 0 ) {
+ scroll_position.x = 0;
+ }
+ else {
+ final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
+ if ( scroll_position.x > max_x ) {
+ scroll_position.x = max_x;
}
- return;
}
- if ( node.isExternal() ) {
- ++_external_node_index;
+ if ( scroll_position.y < 0 ) {
+ scroll_position.y = 0;
}
- // Confidence values
- if ( getControlPanel().isShowConfidenceValues()
- && !node.isExternal()
- && !node.isRoot()
- && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && node.getBranchData().isHasConfidences() ) {
- paintConfidenceValues( g, node, to_pdf, to_graphics_file );
+ else {
+ final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
+ if ( scroll_position.y > max_y ) {
+ scroll_position.y = max_y;
+ }
}
- // Draw a line to root:
- if ( node.isRoot() && _phylogeny.isRooted() ) {
- paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
+ if ( isOvOn() || getOptions().isShowScale() ) {
+ repaint();
}
- float new_x = 0;
- float new_x_min = Float.MAX_VALUE;
- final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
- float min_dist = 1.5f;
- if ( !disallow_shortcutting ) {
- // System.out.println( dynamic_hiding_factor );
- if ( dynamic_hiding_factor > 4000 ) {
- min_dist = 4;
- }
- else if ( dynamic_hiding_factor > 1000 ) {
- min_dist = 3;
- }
- else if ( dynamic_hiding_factor > 100 ) {
- min_dist = 2;
- }
+ getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
+ }
+
+ final void mouseDragInOvRectangle( final MouseEvent e ) {
+ setCursor( HAND_CURSOR );
+ final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
+ final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
+ final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
+ double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
+ double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
+ scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
+ scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
+ if ( scroll_position.x <= 0 ) {
+ scroll_position.x = 0;
+ dx = 0;
}
- if ( !node.isExternal() && !node.isCollapse() ) {
- boolean first_child = true;
- float y2 = 0.0f;
- final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode child_node = node.getChildNode( i );
- int factor_x;
- if ( !isUniformBranchLengthsForCladogram() ) {
- factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
- }
- else {
- factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
- }
- if ( first_child ) {
- first_child = false;
- y2 = node.getYcoord()
- - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
- }
- else {
- y2 += _y_distance * child_node.getNumberOfExternalNodes();
- }
- final float x2 = calculateBranchLengthToParent( child_node, factor_x );
- new_x = x2 + node.getXcoord();
- if ( dynamically_hide && ( x2 < new_x_min ) ) {
- new_x_min = x2;
- }
- final float diff_y = node.getYcoord() - y2;
- final float diff_x = node.getXcoord() - new_x;
- if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
- || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
- paintBranchRectangular( g,
- node.getXcoord(),
- new_x,
- node.getYcoord(),
- y2,
- child_node,
- to_pdf,
- to_graphics_file );
- }
- child_node.setXcoord( new_x );
- child_node.setYcoord( y2 );
- y2 += _y_distance * child_node.getNumberOfExternalNodes();
+ else {
+ final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
+ if ( scroll_position.x >= max_x ) {
+ dx = 0;
+ scroll_position.x = max_x;
}
- paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
}
- if ( dynamically_hide
- && !is_in_found_nodes
- && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
- .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont()
- .getHeight() ) ) ) ) ) {
- return;
+ if ( scroll_position.y <= 0 ) {
+ dy = 0;
+ scroll_position.y = 0;
}
- final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
- paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf );
+ else {
+ final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
+ if ( scroll_position.y >= max_y ) {
+ dy = 0;
+ scroll_position.y = max_y;
+ }
+ }
+ repaint();
+ getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
+ setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
+ setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
}
- final private void paintNodeWithRenderableData( final int x,
- final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf ) {
- if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
- return;
+ final void mouseMoved( final MouseEvent e ) {
+ requestFocusInWindow();
+ if ( _current_external_nodes != null ) {
+ _current_external_nodes = null;
+ repaint();
}
- if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
- return;
+ if ( getControlPanel().isNodeDescPopup() ) {
+ if ( _node_desc_popup != null ) {
+ _node_desc_popup.hide();
+ _node_desc_popup = null;
+ }
}
- 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 ( getOptions().isShowOverview() && isOvOn() ) {
+ if ( inOvVirtualRectangle( e ) ) {
+ if ( !isInOvRect() ) {
+ setInOvRect( true );
+ repaint();
}
- if ( rds != null ) {
- rds.setRenderingHeight( 6 );
- rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
+ }
+ else {
+ if ( isInOvRect() ) {
+ setInOvRect( false );
+ repaint();
}
}
}
- //////////////
- 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 xx = 0;
- PhylogenyNode my_node = node;
- if ( !getControlPanel().isDrawPhylogram() ) {
- my_node = getPhylogeny().getFirstExternalNode();
+ if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
+ if ( !isInOv() ) {
+ setInOv( true );
+ }
+ }
+ else {
+ if ( isInOv() ) {
+ setInOv( false );
+ }
+ final PhylogenyNode node = findNode( e.getX(), e.getY() );
+ if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
+ if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
+ for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
+ addToCurrentExternalNodes( n.getId() );
+ }
+ setCursor( HAND_CURSOR );
+ repaint();
}
- if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
- xx += getFontMetricsForLargeDefaultFont()
- .stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
+ 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 );
}
- if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
- xx += getFontMetricsForLargeDefaultFont().stringWidth( my_node.getName() + " " );
+ else {
+ setCursor( HAND_CURSOR );
+ if ( getControlPanel().isNodeDescPopup() ) {
+ showNodeDataPopup( e, node );
+ }
}
- rv.render( my_node.getXcoord() + xx, node.getYcoord() - 5, g, this, to_pdf );
+ }
+ else {
+ setCursor( ARROW_CURSOR );
}
}
- //////////////
}
- final private void paintOvRectangle( final Graphics2D g ) {
- final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
- final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
- final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
- final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
- final float width = getOvMaxWidth() / w_ratio;
- final float height = getOvMaxHeight() / h_ratio;
- final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
- final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
- g.setColor( getTreeColorSet().getFoundColor0() );
- getOvRectangle().setRect( x, y, width, height );
- final Stroke s = g.getStroke();
- g.setStroke( STROKE_1 );
- if ( ( width < 6 ) && ( height < 6 ) ) {
- drawRectFilled( x, y, 6, 6, g );
- getOvVirtualRectangle().setRect( x, y, 6, 6 );
- }
- else if ( width < 6 ) {
- drawRectFilled( x, y, 6, height, g );
- getOvVirtualRectangle().setRect( x, y, 6, height );
- }
- else if ( height < 6 ) {
- drawRectFilled( x, y, width, 6, g );
- getOvVirtualRectangle().setRect( x, y, width, 6 );
- }
- else {
- drawRect( x, y, width, height, g );
- if ( isInOvRect() ) {
- drawRect( x + 1, y + 1, width - 2, height - 2, g );
- }
- getOvVirtualRectangle().setRect( x, y, width, height );
- }
- g.setStroke( s );
+ final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
+ setCursor( ARROW_CURSOR );
}
- final private void paintPhylogenyLite( final Graphics2D g ) {
- _phylogeny
- .getRoot()
- .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
- .getWidth() ) ) ) );
- _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
- final Stroke s = g.getStroke();
- g.setStroke( STROKE_05 );
- for( final PhylogenyNode element : _nodes_in_preorder ) {
- paintNodeLite( g, element );
- }
- g.setStroke( s );
- paintOvRectangle( g );
+ final void multiplyUrtFactor( final float f ) {
+ _urt_factor *= f;
}
- /**
- * Paint the root branch. (Differs from others because it will always be a
- * single horizontal line).
- * @param to_graphics_file
- *
- * @return new x1 value
- */
- final private void paintRootBranch( final Graphics2D g,
- final float x1,
- final float y1,
- final PhylogenyNode root,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
- float d = getXdistance();
- if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
- d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
+ 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 );
}
- if ( d < MIN_ROOT_LENGTH ) {
- d = MIN_ROOT_LENGTH;
+ drawLine( c.getXcoord(),
+ c.getYcoord(),
+ root_x + ( Math.cos( angle ) * parent_radius ),
+ root_y + ( Math.sin( angle ) * parent_radius ),
+ g );
+ paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
+ if ( c.isExternal() ) {
+ final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c )
+ || isInCurrentExternalNodes( c );
+ if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
+ && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
+ return;
+ }
+ paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
}
- if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
- drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
+ }
+
+ 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 );
}
- else {
- final double w = PhylogenyMethods.getBranchWidthValue( root );
- drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
+ drawLine( c.getXSecondary(),
+ c.getYSecondary(),
+ root_x + ( Math.cos( angle ) * parent_radius ),
+ root_y + ( Math.sin( angle ) * parent_radius ),
+ g );
+ if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
+ g.setColor( getColorForFoundNode( c ) );
+ drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ c.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ g );
}
- paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
}
- final private void paintScale( final Graphics2D g,
- int x1,
- int y1,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- x1 += MOVE;
- final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
- y1 -= 12;
- final int y2 = y1 - 8;
- final int y3 = y1 - 4;
- g.setFont( getTreeFontSet().getSmallFont() );
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else {
- g.setColor( getTreeColorSet().getBranchLengthColor() );
+ 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() );
+ }
}
- 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 );
+ paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
+ paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file );
+ }
+
+ final void paintCircularLite( final Phylogeny phy,
+ final double starting_angle,
+ final int center_x,
+ final int center_y,
+ final int radius,
+ final Graphics2D g ) {
+ final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
+ _root = phy.getRoot();
+ _root.setXSecondary( center_x );
+ _root.setYSecondary( center_y );
+ double current_angle = starting_angle;
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
+ n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
+ _urt_nodeid_angle_map.put( n.getId(), current_angle );
+ current_angle += ( TWO_PI / circ_num_ext_nodes );
}
- g.setStroke( s );
+ paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
}
- final private int paintTaxonomy( final Graphics2D g,
- final PhylogenyNode node,
- final boolean is_in_found_nodes,
- final boolean to_pdf,
- final boolean to_graphics_file,
- final float x_shift ) {
- final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
- final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
- setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() );
- final float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
- float start_y;
- if ( !using_visual_font ) {
- start_y = node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / ( node.getNumberOfDescendants() == 1 ? 1
- : 3.0f ) );
- }
- else {
- start_y = node.getYcoord()
- + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
- }
- _sb.setLength( 0 );
- nodeTaxonomyDataAsSB( taxonomy, _sb );
- final String label = _sb.toString();
- /* GUILHEM_BEG */
- if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
- && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
- // invert font color and background color to show that this is the query sequence
- final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
- false,
- false ) )
- .getBounds();
- g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
- g.setColor( getTreeColorSet().getBackgroundColor() );
- }
- /* GUILHEM_END */
- TreePanel.drawString( label, start_x, start_y, g );
- if ( !using_visual_font && !is_in_found_nodes ) {
- return getFontMetricsForLargeDefaultFont().stringWidth( label );
- }
- return getFontMetrics( g.getFont() ).stringWidth( label );
+ public final void paintFile( final Graphics2D g,
+ final boolean to_pdf,
+ final int graphics_file_width,
+ final int graphics_file_height,
+ final int graphics_file_x,
+ final int graphics_file_y ) {
+ paintPhylogeny(g,to_pdf,true,graphics_file_width,graphics_file_height,graphics_file_x,graphics_file_y);
}
+ 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 ) {
- final private void paintUnrooted( final PhylogenyNode n,
- final double low_angle,
- final double high_angle,
- final boolean radial_labels,
- final Graphics2D g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- if ( n.isRoot() ) {
- n.setXcoord( getWidth() / 2 );
- n.setYcoord( getHeight() / 2 );
- }
- if ( n.isExternal() ) {
- paintNodeDataUnrootedCirc( g,
- n,
- to_pdf,
- to_graphics_file,
- radial_labels,
- ( high_angle + low_angle ) / 2,
- isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
- final float num_enclosed = n.getNumberOfExternalNodes();
- final float x = n.getXcoord();
- final float y = n.getYcoord();
- double current_angle = low_angle;
- // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
- // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
- // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
- // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
- for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode desc = n.getChildNode( i );
- /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
- // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
- // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
- // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
- // continue;
- // }
- //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
- // continue;
- //}
- //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
- // continue;
- // }
- final int desc_num_enclosed = desc.getNumberOfExternalNodes();
- final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
- float length;
- if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
- if ( desc.getDistanceToParent() < 0 ) {
- length = 0;
+ 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 {
- length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
+ if ( getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.WHITE );
+ }
+ g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
}
}
else {
- length = getUrtFactor();
+ 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 );
+ }
}
- 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 );
+ setupStroke( g );
}
- if ( n.isRoot() ) {
- paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
+ else {
+ g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
}
- }
-
- final private void paintUnrootedLite( final PhylogenyNode n,
- final double low_angle,
- final double high_angle,
- 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 ) );
- n.setXSecondary( x_pos );
- n.setYSecondary( y_pos );
+ if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ _external_node_index = 0;
+ // Position starting X of tree
+ if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/ ) {
+ _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
+ }
+ else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
+ _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE
+ + ( _phylogeny.getRoot().getDistanceToParent() * getXcorrectionFactor() ) ) );
+ }
+ else {
+ _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
+ }
+ // Position starting Y of tree
+ _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
+ + ( TreePanel.MOVE / 2.0f ) );
+ final int dynamic_hiding_factor = calcDynamicHidingFactor();
+ if ( getControlPanel().isDynamicallyHideData() ) {
+ if ( dynamic_hiding_factor > 1 ) {
+ getControlPanel().setDynamicHidingIsOn( true );
+ }
+ else {
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ }
+ if ( _nodes_in_preorder == null ) {
+ _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
+ int i = 0;
+ for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
+ _nodes_in_preorder[ i++ ] = it.next();
+ }
+ }
+ final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 )
+ /* || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()*/ //TODO check if this is really not needed.
+ || to_graphics_file || to_pdf;
+ for( final PhylogenyNode element : _nodes_in_preorder ) {
+ paintNodeRectangular( g,
+ element,
+ to_pdf,
+ getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ),
+ dynamic_hiding_factor,
+ to_graphics_file,
+ disallow_shortcutting );
+ }
+ if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
+ if ( !( to_graphics_file || to_pdf ) ) {
+ paintScale( g,
+ getVisibleRect().x,
+ getVisibleRect().y + getVisibleRect().height,
+ to_pdf,
+ to_graphics_file );
+ }
+ else {
+ paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ }
+ }
+ if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
+ paintPhylogenyLite( g );
+ }
}
- if ( n.isExternal() ) {
- return;
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ final double angle = getStartingAngle();
+ final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
+ _dynamic_hiding_factor = 0;
+ if ( getControlPanel().isDynamicallyHideData() ) {
+ _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5
+ * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
+ }
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ if ( _dynamic_hiding_factor > 1 ) {
+ getControlPanel().setDynamicHidingIsOn( true );
+ }
+ else {
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ }
+ paintUnrooted( _phylogeny.getRoot(),
+ angle,
+ ( float ) ( angle + ( 2 * Math.PI ) ),
+ radial_labels,
+ g,
+ to_pdf,
+ to_graphics_file );
+ if ( getOptions().isShowScale() ) {
+ if ( !( to_graphics_file || to_pdf ) ) {
+ paintScale( g,
+ getVisibleRect().x,
+ getVisibleRect().y + getVisibleRect().height,
+ to_pdf,
+ to_graphics_file );
+ }
+ else {
+ paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ }
+ }
+ if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
+ g.setColor( getTreeColorSet().getOvColor() );
+ paintUnrootedLite( _phylogeny.getRoot(),
+ angle,
+ angle + ( 2 * Math.PI ),
+ g,
+ ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
+ paintOvRectangle( g );
+ }
}
- final float num_enclosed = n.getNumberOfExternalNodes();
- final float x = n.getXSecondary();
- final float y = n.getYSecondary();
- double current_angle = low_angle;
- for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode desc = n.getChildNode( i );
- final int desc_num_enclosed = desc.getNumberOfExternalNodes();
- final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
- float length;
- if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
- if ( desc.getDistanceToParent() < 0 ) {
- length = 0;
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
+ final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() )
+ / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
+ final int d = radius + MOVE + getLongestExtNodeInfo();
+ _dynamic_hiding_factor = 0;
+ if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
+ _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5
+ * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
+ }
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ if ( _dynamic_hiding_factor > 1 ) {
+ getControlPanel().setDynamicHidingIsOn( true );
}
else {
- length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
+ getControlPanel().setDynamicHidingIsOn( false );
}
}
- else {
- length = urt_ov_factor;
+ 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 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 ) || isInCurrentExternalNodes( desc ) ) {
- g.setColor( getColorForFoundNode( desc ) );
- drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
- desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
- OVERVIEW_FOUND_NODE_BOX_SIZE,
- OVERVIEW_FOUND_NODE_BOX_SIZE,
- g );
- g.setColor( getTreeColorSet().getOvColor() );
+
+
+ }
+ if (_partition_tree) {
+ g.setColor( Color.BLACK );
+ _partition_threshold = (_clicked_x - _root_x) / (_furthest_node_x - _root_x);
+ drawLine( _clicked_x, 0, _clicked_x, getHeight(),g);
+ _partition_tree = false;
+ }
+ }
+
+
+ final void recalculateMaxDistanceToRoot() {
+ _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
+ if ( getPhylogeny().getRoot().getDistanceToParent() > 0 ) {
+ _max_distance_to_root += getPhylogeny().getRoot().getDistanceToParent();
+ }
+ }
+
+ /**
+ * Remove all edit-node frames
+ */
+ final void removeAllEditNodeJFrames() {
+ for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
+ if ( _node_frames[ i ] != null ) {
+ _node_frames[ i ].dispose();
+ _node_frames[ i ] = null;
}
- paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
- current_angle += arc_size;
- drawLine( x, y, new_x, new_y, g );
}
+ _node_frame_index = 0;
}
- final private void pasteSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
+ /**
+ * 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;
}
- if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
+ }
+
+ final void reRoot( final PhylogenyNode node ) {
+ if ( !getPhylogeny().isRerootable() ) {
JOptionPane.showMessageDialog( this,
- "No tree in buffer (need to copy or cut a subtree first)",
- "Attempt to paste with empty buffer",
- JOptionPane.ERROR_MESSAGE );
+ "This is not rerootable",
+ "Not rerootable",
+ JOptionPane.WARNING_MESSAGE );
return;
}
- 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 + "?",
- "Paste Subtree",
- JOptionPane.CLOSED_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[ 2 ] );
- boolean paste_as_sibling = true;
- if ( r == 1 ) {
- paste_as_sibling = false;
- }
- else if ( r != 0 ) {
+ 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;
}
- final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
- buffer_phy.setAllNodesToNotCollapse();
- PhylogenyMethods.preOrderReId( buffer_phy );
- buffer_phy.setRooted( true );
- boolean need_to_show_whole = false;
- if ( paste_as_sibling ) {
- if ( node.isRoot() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot paste sibling to root",
- "Attempt to paste sibling to root",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- buffer_phy.addAsSibling( node );
- }
- else {
- if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
- need_to_show_whole = true;
- _phylogeny = buffer_phy;
- }
- 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 );
+ getPhylogeny().reRoot( node );
+ getPhylogeny().recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
+ setNodeInPreorderToNull();
+ resetPreferredSize();
+ getMainPanel().adjustJScrollPane();
setEdited( true );
- if ( need_to_show_whole ) {
+ repaint();
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
getControlPanel().showWhole();
}
- repaint();
}
- private final StringBuffer propertiesToString( final PhylogenyNode node ) {
- final PropertiesMap properties = node.getNodeData().getProperties();
- final StringBuffer sb = new StringBuffer();
- boolean first = true;
- for( final String ref : properties.getPropertyRefs() ) {
- if ( first ) {
- first = false;
+ 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().calculateHeight( !_options.isCollapsedWithAverageHeigh() ) )
+ + getXdistance() );
+ }
+ else {
+ if ( !isNonLinedUpCladogram() ) {
+ x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil
+ .roundToInt( getXdistance() * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
}
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() ) );
+ x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil
+ .roundToInt( getXdistance() * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
}
}
- return sb;
+ setPreferredSize( new Dimension( x, y ) );
}
- private void setColor( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf,
- final boolean is_in_found_nodes,
- final Color default_color ) {
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else if ( is_in_found_nodes ) {
- g.setColor( getColorForFoundNode( node ) );
- }
- else if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
- && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
- g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
- }
- else if ( getControlPanel().isColorAccordingToSequence() ) {
- g.setColor( getSequenceBasedColor( node ) );
- }
- else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- g.setColor( getTaxonomyBasedColor( node ) );
- }
- else if ( getControlPanel().isColorAccordingToAnnotation()
- && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
- .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
- g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
- }
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
- && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
- }
- else if ( to_pdf ) {
- g.setColor( Color.BLACK );
+ final void selectNode( final PhylogenyNode node ) {
+ if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
+ getFoundNodes0().remove( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
+ if ( getFoundNodes0().size() < 1 ) {
+ getControlPanel().searchReset0();
+ }
}
else {
- g.setColor( default_color );
+ getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
+ getControlPanel().getSearchResetButton0().setEnabled( true );
+ getControlPanel().getSearchResetButton0().setVisible( true );
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
+ }
+ getFoundNodes0().add( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
}
}
- final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
- getMainPanel().setCopiedAndPastedNodes( nodeIds );
+ final void setArrowCursor() {
+ setCursor( ARROW_CURSOR );
+ repaint();
}
- final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
- getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
+ final void setControlPanel( final ControlPanel atv_control ) {
+ _control_panel = atv_control;
}
- private boolean setFont( final Graphics2D g, final PhylogenyNode node, final boolean is_in_found_nodes ) {
- Font visual_font = null;
- if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) {
- visual_font = node.getNodeData().getNodeVisualData().getFont();
- g.setFont( visual_font != null ? visual_font : getTreeFontSet().getLargeFont() );
- }
- else {
- g.setFont( getTreeFontSet().getLargeFont() );
- }
- if ( is_in_found_nodes ) {
- g.setFont( g.getFont().deriveFont( Font.BOLD ) );
- }
- return visual_font != null;
+ void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
+ increaseCurrentExternalNodesDataBufferChangeCounter();
+ _current_external_nodes_data_buffer = sb;
+ }
+
+ public final void setFoundNodes0( final Set<Long> found_nodes ) {
+ _found_nodes_0 = found_nodes;
}
- final private void setInOv( final boolean in_ov ) {
- _in_ov = in_ov;
+ public final void setFoundNodes1( final Set<Long> found_nodes ) {
+ _found_nodes_1 = found_nodes;
}
- final private void setOvMaxHeight( final float ov_max_height ) {
- _ov_max_height = ov_max_height;
+ final void setInOvRect( final boolean in_ov_rect ) {
+ _in_ov_rect = in_ov_rect;
}
- final private void setOvMaxWidth( final float ov_max_width ) {
- _ov_max_width = ov_max_width;
+ final void setLargeFonts() {
+ getTreeFontSet().largeFonts();
}
- final private void setOvXcorrectionFactor( final float f ) {
- _ov_x_correction_factor = f;
+ final void setLastMouseDragPointX( final float x ) {
+ _last_drag_point_x = x;
}
- final private void setOvXDistance( final float ov_x_distance ) {
- _ov_x_distance = ov_x_distance;
+ final void setLastMouseDragPointY( final float y ) {
+ _last_drag_point_y = y;
}
- final private void setOvXPosition( final int ov_x_position ) {
- _ov_x_position = ov_x_position;
+ final void setMediumFonts() {
+ getTreeFontSet().mediumFonts();
}
- final private void setOvYDistance( final float ov_y_distance ) {
- _ov_y_distance = ov_y_distance;
+ final void setNodeInPreorderToNull() {
+ _nodes_in_preorder = null;
}
- final private void setOvYPosition( final int ov_y_position ) {
- _ov_y_position = ov_y_position;
+ final void setOvOn( final boolean ov_on ) {
+ _ov_on = ov_on;
}
- final private void setOvYStart( final int ov_y_start ) {
- _ov_y_start = ov_y_start;
+ 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;
+ final void setSmallFonts() {
+ getTreeFontSet().smallFonts();
}
- final private void setScaleLabel( final String scale_label ) {
- _scale_label = scale_label;
+ final void setStartingAngle( final double starting_angle ) {
+ _urt_starting_angle = starting_angle;
}
- private final void setupStroke( final Graphics2D g ) {
- if ( getYdistance() < 0.001 ) {
- g.setStroke( STROKE_005 );
- }
- else if ( getYdistance() < 0.01 ) {
- g.setStroke( STROKE_01 );
- }
- else if ( getYdistance() < 0.5 ) {
- g.setStroke( STROKE_025 );
- }
- else if ( getYdistance() < 1 ) {
- g.setStroke( STROKE_05 );
- }
- else if ( getYdistance() < 2 ) {
- g.setStroke( STROKE_075 );
- }
- else if ( getYdistance() < 20 ) {
- g.setStroke( STROKE_1 );
- }
- else {
- g.setStroke( STROKE_2 );
- }
+ void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
+ _statistics_for_vector_data = statistics_for_expression_values;
}
- final private void setUpUrtFactor() {
- final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
- : getVisibleRect().height;
- if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
- setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
- }
- else {
- final int max_depth = _circ_max_depth;
- if ( max_depth > 0 ) {
- setUrtFactor( d / ( 2 * max_depth ) );
+ 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 {
- setUrtFactor( d / 2 );
+ _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
}
}
- setUrtFactorOv( getUrtFactor() );
+ 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 private void setUrtFactor( final float urt_factor ) {
- _urt_factor = urt_factor;
+ final void setTinyFonts() {
+ getTreeFontSet().tinyFonts();
}
- final private void setUrtFactorOv( final float urt_factor_ov ) {
- _urt_factor_ov = urt_factor_ov;
+ public final void setTreeFile( final File treefile ) {
+ _treefile = treefile;
}
- private void showExtDescNodeData( final PhylogenyNode node ) {
- final List<String> data = new ArrayList<String>();
- final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
- if ( !nodes.contains( n ) ) {
- nodes.add( n );
- }
- }
- }
- for( final PhylogenyNode n : nodes ) {
- switch ( getOptions().getExtDescNodeDataToReturn() ) {
- case NODE_NAME:
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- data.add( n.getName() );
- }
- break;
- case SEQUENCE_NAME:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- data.add( n.getNodeData().getSequence().getName() );
- }
- break;
- case GENE_NAME:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
- data.add( n.getNodeData().getSequence().getGeneName() );
- }
- break;
- case SEQUENCE_SYMBOL:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
- data.add( n.getNodeData().getSequence().getSymbol() );
- }
- break;
- case SEQUENCE_MOL_SEQ:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
- data.add( n.getNodeData().getSequence().getMolecularSequence() );
- }
- break;
- case SEQUENCE_MOL_SEQ_FASTA:
- final StringBuilder sb = new StringBuilder();
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
- final StringBuilder ann = new StringBuilder();
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- ann.append( n.getName() );
- ann.append( "|" );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
- ann.append( "SYM=" );
- ann.append( n.getNodeData().getSequence().getSymbol() );
- ann.append( "|" );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- ann.append( "NAME=" );
- ann.append( n.getNodeData().getSequence().getName() );
- ann.append( "|" );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
- ann.append( "GN=" );
- ann.append( n.getNodeData().getSequence().getGeneName() );
- ann.append( "|" );
- }
- if ( n.getNodeData().getSequence().getAccession() != null ) {
- ann.append( "ACC=" );
- ann.append( n.getNodeData().getSequence().getAccession().asText() );
- ann.append( "|" );
- }
- if ( n.getNodeData().isHasTaxonomy() ) {
- if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- ann.append( "TAXID=" );
- ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
- ann.append( "|" );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- ann.append( "SN=" );
- ann.append( n.getNodeData().getTaxonomy().getScientificName() );
- ann.append( "|" );
- }
- }
- String ann_str;
- if ( ann.charAt( ann.length() - 1 ) == '|' ) {
- ann_str = ann.substring( 0, ann.length() - 1 );
- }
- else {
- ann_str = ann.toString();
- }
- sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
- .getMolecularSequence(), 60 ) );
- data.add( sb.toString() );
- }
- break;
- case SEQUENCE_ACC:
- if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
- data.add( n.getNodeData().getSequence().getAccession().toString() );
- }
- break;
- case TAXONOMY_SCIENTIFIC_NAME:
- if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- data.add( n.getNodeData().getTaxonomy().getScientificName() );
- }
- break;
- case TAXONOMY_COMM0N_NAME:
- if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
- data.add( n.getNodeData().getTaxonomy().getCommonName() );
- }
- break;
- case TAXONOMY_CODE:
- if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
- }
- break;
- case UNKNOWN:
- TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
- break;
- default:
- throw new IllegalArgumentException( "unknown data element: "
- + getOptions().getExtDescNodeDataToReturn() );
- }
- } // for loop
- final StringBuilder sb = new StringBuilder();
- final int size = TreePanelUtil.makeSB( data, getOptions(), sb );
- if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
- || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
- if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
- System.out.println( sb );
- }
- if ( sb.length() < 1 ) {
- clearCurrentExternalNodesDataBuffer();
+ final void setXcorrectionFactor( final float f ) {
+ _x_correction_factor = f;
+ }
+
+ final void setXdistance( final float x ) {
+ _x_distance = x;
+ }
+
+ final void setYdistance( final float y ) {
+ _y_distance = y;
+ }
+
+ final void sortDescendants( final PhylogenyNode node ) {
+ if ( !node.isExternal() ) {
+ DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+ if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
+ pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
}
- else {
- setCurrentExternalNodesDataBuffer( sb );
+ else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
+ || getControlPanel().isShowGeneNames() ) {
+ pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
+ PhylogenyMethods.sortNodeDescendents( node, pri );
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ }
+ repaint();
+ }
+
+ final void subTree( final PhylogenyNode node ) {
+ 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;
}
- else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
- if ( sb.length() < 1 ) {
- TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
- + ")", "Descendants of selected node do not contain selected data" );
- clearCurrentExternalNodesDataBuffer();
- }
- else {
- setCurrentExternalNodesDataBuffer( sb );
- String title;
- if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
- title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() )
- + " for "
- + data.size()
- + " nodes, unique entries: "
- + size;
- }
- else {
- title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() )
- + " for "
- + data.size()
- + "/"
- + node.getNumberOfExternalNodes()
- + " external descendats of node "
- + node
- + ", unique entries: " + size;
- }
- final String s = sb.toString().trim();
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- ae.showTextFrame( s, title );
- }
- else {
- getMainPanel().getMainFrame().showTextFrame( s, title );
- }
+ 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 );
+ if ( _phylogeny.getRoot().isCollapse() ) {
+ _phylogeny.getRoot().setCollapse( false );
}
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ updateSubSuperTreeButton();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ resetRankCollapseRankValue();
+ resetDepthCollapseDepthValue();
+ getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
+ getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay();
+ getMainPanel().getControlPanel().updateRankCollapseRankDisplay();
}
+ else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
+ superTree();
+ }
+ _main_panel.getControlPanel().showWhole();
+ repaint();
}
- final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
- try {
- if ( ( node.getName().length() > 0 )
- || ( 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()
- && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
- lines++;
- boolean enc_data = false;
- final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- _popup_buffer.append( "[" );
- _popup_buffer.append( tax.getTaxonomyCode() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " " );
- }
- _popup_buffer.append( tax.getScientificName() );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " (" );
- }
- else {
- _popup_buffer.append( "(" );
- }
- _popup_buffer.append( tax.getCommonName() );
- _popup_buffer.append( ")" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " (" );
- }
- else {
- _popup_buffer.append( "(" );
- }
- _popup_buffer.append( tax.getAuthority() );
- _popup_buffer.append( ")" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " [" );
- }
- else {
- _popup_buffer.append( "[" );
- }
- _popup_buffer.append( tax.getRank() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( tax.getSynonyms().size() > 0 ) {
- if ( enc_data ) {
- _popup_buffer.append( " " );
- }
- _popup_buffer.append( "[" );
- int counter = 1;
- for( final String syn : tax.getSynonyms() ) {
- if ( !ForesterUtil.isEmpty( syn ) ) {
- enc_data = true;
- _popup_buffer.append( syn );
- if ( counter < tax.getSynonyms().size() ) {
- _popup_buffer.append( ", " );
- }
- }
- counter++;
- }
- _popup_buffer.append( "]" );
- }
- if ( !enc_data ) {
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
- if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
- _popup_buffer.append( "[" );
- _popup_buffer.append( tax.getIdentifier().getProvider() );
- _popup_buffer.append( "] " );
- }
- _popup_buffer.append( tax.getIdentifier().getValue() );
- }
- }
- }
- if ( node.getNodeData().isHasSequence()
- && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
- lines++;
- boolean enc_data = false;
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- final Sequence seq = node.getNodeData().getSequence();
- if ( seq.getAccession() != null ) {
- _popup_buffer.append( "[" );
- if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
- _popup_buffer.append( seq.getAccession().getSource() );
- _popup_buffer.append( ":" );
- }
- _popup_buffer.append( seq.getAccession().getValue() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " [" );
- }
- else {
- _popup_buffer.append( "[" );
- }
- _popup_buffer.append( seq.getSymbol() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " [" );
- }
- else {
- _popup_buffer.append( "[" );
- }
- _popup_buffer.append( seq.getGeneName() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " " );
- }
- _popup_buffer.append( seq.getName() );
- }
- }
- if ( node.getNodeData().isHasDate() ) {
- lines++;
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
- }
- if ( node.getNodeData().isHasDistribution() ) {
- lines++;
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
- }
- if ( node.getBranchData().isHasConfidences() ) {
- final List<Confidence> confs = node.getBranchData().getConfidences();
- for( final Confidence confidence : confs ) {
- lines++;
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
- _popup_buffer.append( "[" );
- _popup_buffer.append( confidence.getType() );
- _popup_buffer.append( "] " );
- }
- _popup_buffer
- .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
- getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- _popup_buffer.append( " (sd=" );
- _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
- .getStandardDeviation(), getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- _popup_buffer.append( ")" );
- }
- }
- }
- if ( node.getNodeData().isHasProperties() ) {
- final PropertiesMap properties = node.getNodeData().getProperties();
- for( final String ref : properties.getPropertyRefs() ) {
- _popup_buffer.append( "\n" );
- final Property p = properties.getProperty( ref );
- _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
- _popup_buffer.append( "=" );
- _popup_buffer.append( p.getValue() );
- if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
- }
- }
- }
- if ( _popup_buffer.length() > 0 ) {
- if ( !getConfiguration().isUseNativeUI() ) {
- _rollover_popup
- .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
- _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
- if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
- }
- else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
- }
- else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
- }
- else {
- _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
- }
- }
- else {
- _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
- }
- _rollover_popup.setText( _popup_buffer.toString() );
- _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
- _rollover_popup,
- e.getLocationOnScreen().x + 10,
- e.getLocationOnScreen().y
- - ( lines * 20 ) );
- _node_desc_popup.show();
- }
- }
+ 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 );
}
- catch ( final Exception ex ) {
- // Do nothing.
+ _sub_phylogenies[ _subtree_index ] = null;
+ _sub_phylogenies_temp_roots[ _subtree_index ] = null;
+ _phylogeny = _sub_phylogenies[ --_subtree_index ];
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ resetRankCollapseRankValue();
+ resetDepthCollapseDepthValue();
+ getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
+ getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay();
+ getMainPanel().getControlPanel().updateRankCollapseRankDisplay();
+ updateSubSuperTreeButton();
+ }
+
+ final void orderSubtree( final PhylogenyNode node ) {
+ if ( node.isExternal() ) {
+ return;
+ }
+ DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+ if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
+ pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
}
+ else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
+ || getControlPanel().isShowGeneNames() ) {
+ pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
+ }
+ PhylogenyMethods.orderAppearanceX( node, true, pri );
+ setNodeInPreorderToNull();
+ getPhylogeny().externalNodesHaveChanged();
+ getPhylogeny().clearHashIdToNodeMap();
+ getPhylogeny().recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ repaint();
}
- final private void showNodeEditFrame( final PhylogenyNode n ) {
- if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
- // pop up edit box for single node
- _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
- _node_frame_index++;
+ final void swap( final PhylogenyNode node ) {
+ if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
+ return;
}
- else {
- JOptionPane.showMessageDialog( this, "too many node windows are open" );
+ 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 private void showNodeFrame( final PhylogenyNode n ) {
- if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
- // pop up edit box for single node
- _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
- _node_frame_index++;
+ final void taxColor() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
}
- else {
- JOptionPane.showMessageDialog( this, "too many node windows are open" );
+ setWaitCursor();
+ TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
+ setEdited( true );
+ setArrowCursor();
+ repaint();
}
- final private void switchDisplaygetPhylogenyGraphicsType() {
- switch ( getPhylogenyGraphicsType() ) {
- case RECTANGULAR:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
- break;
- case EURO_STYLE:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
- break;
- case ROUNDED:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
- break;
- case CURVED:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
- break;
- case TRIANGULAR:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
- break;
- case CONVEX:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ 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 UNROOTED:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ 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 CIRCULAR:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ case UPPER_RIGHT:
+ setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
+ setOvYPosition( OV_BORDER );
+ setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
break;
default:
- throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
+ setOvXPosition( OV_BORDER );
+ setOvYPosition( OV_BORDER );
+ setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
+ break;
}
- if ( getControlPanel().getDynamicallyHideData() != null ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- getControlPanel().getDynamicallyHideData().setEnabled( false );
+ }
+
+ 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() ) {
+ ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
}
else {
- getControlPanel().getDynamicallyHideData().setEnabled( true );
+ 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.calculateHeight( !_options.isCollapsedWithAverageHeigh() );
+ if ( height > 0 ) {
+ final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
+ setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
+ }
+ else {
+ setOvXcorrectionFactor( 0 );
}
}
- if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- getControlPanel().setDrawPhylogramEnabled( true );
+ 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().setDrawPhylogramEnabled( false );
+ getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
}
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
+ }
+
+ final void updateButtonToUncollapseAll() {
+ if ( PhylogenyMethods.isHasCollapsedNodes( _phylogeny ) ) {
+ getControlPanel().activateButtonToUncollapseAll();
}
else {
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
+ getControlPanel().deactivateButtonToUncollapseAll();
+ }
+ }
+
+ 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;
}
}
g.drawString( str, x, y );
}
- final private static boolean plusPressed( final int key_code ) {
- return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
- || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
+ final private void drawStringX( final String str, final float x, final float y, final Graphics2D g ) {
+ //TODO
+ //FIXME
+ if ( getAttributedStringMap() == null /*&& getAttributedStringMap().containsKey(str) */ ) {
+ final AttributedString as = new AttributedString( str );
+ //Font plainFont = new Font("Times New Roman", Font.PLAIN, 24);
+ as.addAttribute( TextAttribute.FONT, g.getFont() );
+ as.addAttribute( TextAttribute.UNDERLINE, TextAttribute.UNDERLINE_ON, 1, 3 );
+ as.addAttribute( TextAttribute.SUPERSCRIPT, TextAttribute.SUPERSCRIPT_SUPER, 3, 4 );
+ as.addAttribute( TextAttribute.FOREGROUND, Color.BLUE, 1, 2 );
+ as.addAttribute( TextAttribute.FOREGROUND, Color.PINK, 3, 5 );
+ as.addAttribute( TextAttribute.STRIKETHROUGH, TextAttribute.STRIKETHROUGH_ON, 2, 4 );
+ g.drawString( as.getIterator(), x, y );
+ }
+ else {
+ g.drawString( str, x, y );
+ }
}
- final private class NodeColorizationActionListener implements ActionListener {
+ private final Map<String, AttributedString> getAttributedStringMap() {
+ return _attributed_string_map;
+ }
- List<PhylogenyNode> _additional_nodes = null;
- JColorChooser _chooser = null;
- PhylogenyNode _node = null;
+ private final void setAttributedStringMap( final Map<String, AttributedString> attributed_string_map ) {
+ _attributed_string_map = attributed_string_map;
+ }
- NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
- _chooser = chooser;
- _node = node;
- }
+ 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 ) );
+ }
- NodeColorizationActionListener( final JColorChooser chooser,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _chooser = chooser;
- _node = node;
- _additional_nodes = additional_nodes;
+ public void decreaseDepthCollapseLevel() {
+ if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) {
+ if ( _depth_collapse_level <= 1 ) {
+ _depth_collapse_level = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ uncollapseAll();
+ }
+ else {
+ --_depth_collapse_level;
+ PhylogenyMethods.collapseToDepth( _phylogeny, _depth_collapse_level );
+ }
}
+ }
- @Override
- public void actionPerformed( final ActionEvent e ) {
- final Color c = _chooser.getColor();
- if ( c != null ) {
- colorizeNodes( c, _node, _additional_nodes );
+ public void increaseDepthCollapseLevel() {
+ if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) {
+ final int max = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ if ( _depth_collapse_level >= max ) {
+ _depth_collapse_level = 1;
+ }
+ else {
+ ++_depth_collapse_level;
}
+ PhylogenyMethods.collapseToDepth( _phylogeny, _depth_collapse_level );
}
}
- final private class SubtreeColorizationActionListener implements ActionListener {
-
- List<PhylogenyNode> _additional_nodes = null;
- JColorChooser _chooser = null;
- PhylogenyNode _node = null;
+ public void decreaseRankCollapseLevel() {
+ if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) {
+ final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( _phylogeny );
+ if ( ranks.length > 1 ) {
+ if ( _rank_collapse_level <= 0 ) {
+ _rank_collapse_level = ranks.length - 1;
+ uncollapseAll();
+ }
+ else {
+ --_rank_collapse_level;
+ PhylogenyMethods.collapseToRank( _phylogeny,
+ mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) );
+ }
+ }
+ }
+ }
- SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
- _chooser = chooser;
- _node = node;
+ public void increaseRankCollapseLevel() {
+ if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) {
+ final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( _phylogeny );
+ if ( ranks.length > 1 ) {
+ if ( _rank_collapse_level >= ( ranks.length - 1 ) ) {
+ _rank_collapse_level = 0;
+ PhylogenyMethods.collapseToRank( _phylogeny,
+ mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) );
+ }
+ else if ( _rank_collapse_level == ( ranks.length - 2 ) ) {
+ ++_rank_collapse_level;
+ uncollapseAll();
+ }
+ else {
+ ++_rank_collapse_level;
+ PhylogenyMethods.collapseToRank( _phylogeny,
+ mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) );
+ }
+ }
}
+ }
- SubtreeColorizationActionListener( final JColorChooser chooser,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _chooser = chooser;
- _node = node;
- _additional_nodes = additional_nodes;
+ private final static int mapToAbsoluteRankLevel( final String present_ranks_sorted[],
+ final int rank_collapse_level ) {
+ final String rank_str = present_ranks_sorted[ rank_collapse_level ];
+ if ( !TaxonomyUtil.RANK_TO_INT.containsKey( rank_str ) ) {
+ throw new IllegalStateException( "unexpected exception: cannot find rank " + rank_str );
}
+ return TaxonomyUtil.RANK_TO_INT.get( rank_str );
+ }
- @Override
- public void actionPerformed( final ActionEvent e ) {
- final Color c = _chooser.getColor();
- if ( c != null ) {
- colorizeSubtree( c, _node, _additional_nodes );
- }
+ private final void uncollapseAll() {
+ final PhylogenyNodeIterator it = new PreorderTreeIterator( _phylogeny );
+ while ( it.hasNext() ) {
+ it.next().setCollapse( false );
}
}
+
+ final int resetDepthCollapseDepthValue() {
+ return _depth_collapse_level = -1;
+ }
+
+ final int getDepthCollapseDepthValue() {
+ return _depth_collapse_level;
+ }
+
+ final void setDepthCollapseDepthValue( final int depth_collapse_level ) {
+ _depth_collapse_level = depth_collapse_level;
+ }
+
+ final int resetRankCollapseRankValue() {
+ return _rank_collapse_level = -1;
+ }
+
+ final int getRankCollapseRankValue() {
+ return _rank_collapse_level;
+ }
+
+ final void setRankCollapseRankValue( final int rank_collapse_level ) {
+ _rank_collapse_level = rank_collapse_level;
+ }
}
git://source.jalview.org / jalview.git / blobdiff