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.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.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 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 double TWO_PI = 2 * Math.PI;
- private final static int WIGGLE = 2;
- private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me
- 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 = 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 PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
- private PhylogenyNode _highlight_node = null;
- private boolean _in_ov = false;
- private boolean _in_ov_rect = false;
- private float _last_drag_point_x = 0;
- private float _last_drag_point_y = 0;
- private final Line2D _line = new Line2D.Float();
- private int _longest_ext_node_info = 0;
- private PhylogenyNode _ext_node_with_longest_txt_info = null;
- private MainPanel _main_panel = null;
- private double _max_distance_to_root = -1;
- private Popup _node_desc_popup;
- private int _node_frame_index = 0;
- private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
- private JPopupMenu _node_popup_menu = null;
- private JMenuItem _node_popup_menu_items[] = null;
- private PhylogenyNode[] _nodes_in_preorder = null;
- private Options _options = null;
- private float _ov_max_height = 0;
- private float _ov_max_width = 0;
- private boolean _ov_on = false;
- private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
- private final Rectangle _ov_virtual_rectangle = new Rectangle();
- private float _ov_x_correction_factor = 0.0f;
- private float _ov_x_distance = 0;
- private int _ov_x_position = 0;
- private float _ov_y_distance = 0;
- private int _ov_y_position = 0;
- private int _ov_y_start = 0;
- private final boolean _phy_has_branch_lengths;
- private Phylogeny _phylogeny = null;
- private final Path2D.Float _polygon = new Path2D.Float();
- private final StringBuffer _popup_buffer = new StringBuffer();
- private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
- private Sequence _query_sequence = null;
- private final Rectangle2D _rectangle = new Rectangle2D.Float();
- private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
- RenderingHints.VALUE_RENDER_DEFAULT );
- private JTextArea _rollover_popup;
- private PhylogenyNode _root;
- private final StringBuilder _sb = new StringBuilder();
- private double _scale_distance = 0.0;
- private String _scale_label = null;
- private DescriptiveStatistics _statistics_for_vector_data;
- private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
- private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
- private int _subtree_index = 0;
- private File _treefile = null;
- private float _urt_factor = 1;
- private float _urt_factor_ov = 1;
- final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
- final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
- private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
- private float _x_correction_factor = 0.0f;
- private float _x_distance = 0.0f;
- private float _y_distance = 0.0f;
- private int _length_of_longest_text;
- private int _longest_domain;
- private Map<String, AttributedString> _attributed_string_map = null;
+ 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
repaint();
}
}
- if ( e.isControlDown() ) {
+ if ( e.isControlDown() && e.isShiftDown() ) {
if ( notches < 0 ) {
getTreeFontSet().increaseFontSize();
}
updateOvSizes();
repaint();
}
+ else if ( e.isShiftDown() && e.isAltDown() ) {
+ if ( notches < 0 ) {
+ for( int i = 0; i < ( -notches ); ++i ) {
+ getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ }
+ else {
+ for( int i = 0; i < notches; ++i ) {
+ getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
+ AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ }
+ }
else if ( e.isShiftDown() ) {
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
@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
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() ) ) {
+ || ( 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 ) ) {
}
}
else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ if ( ForesterUtil
+ .seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
type = 'p';
}
else {
type = 'n';
}
}
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
try {
- Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
+ Blast.openNcbiBlastWeb( query, type == 'n', this );
}
catch ( final Exception e ) {
e.printStackTrace();
nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
}
}
-
return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
else {
al = new SubtreeColorizationActionListener( _color_chooser, node );
}
- final JDialog dialog = JColorChooser
- .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+ final JDialog dialog = JColorChooser.createDialog( this,
+ "Subtree colorization",
+ true,
+ _color_chooser,
+ al,
+ null );
setEdited( true );
dialog.setVisible( true );
}
g.draw( _arc );
}
- final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
+ final private void drawLine( final double x1,
+ final double y1,
+ final double x2,
+ final double y2,
+ final Graphics2D g ) {
if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
return;
}
}
}
- final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
+ 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 );
}
return _last_drag_point_y;
}
- final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
- if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
- final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
- _nodeid_dist_to_leaf.put( node.getId(), m );
- return m;
- }
- else {
- return _nodeid_dist_to_leaf.get( node.getId() );
- }
- }
-
final private double getMaxDistanceToRoot() {
if ( _max_distance_to_root < 0 ) {
recalculateMaxDistanceToRoot();
final private TreeFontSet getTreeFontSet() {
return getMainPanel().getTreeFontSet();
}
+
+ final public float getThreshold() {
+ return _partition_threshold;
+ }
final private float getUrtFactor() {
return _urt_factor;
sortDescendants( node );
break;
case GET_EXT_DESC_DATA:
- showExtDescNodeData( node );
+ showExtDescNodeData( node, '_' );
break;
case UNCOLLAPSE_ALL:
uncollapseAll( node );
}
final private void increaseOvSize() {
- if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
+ if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth()
+ / 2 ) )
&& ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
.getHeight() / 2 ) ) ) {
setOvMaxWidth( getOvMaxWidth() + 5 );
setTreeFile( null );
setEdited( false );
initializeOvSettings();
+ resetDepthCollapseDepthValue();
+ resetRankCollapseRankValue();
setStartingAngle( ( TWO_PI * 3 ) / 4 );
final ImageLoader il = new ImageLoader( this );
new Thread( il ).start();
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 ) ) );
+ && ( y >= ( getOvVirtualRectangle().y - 1 ) )
+ && ( y <= ( getOvVirtualRectangle().y + getOvVirtualRectangle().height + 1 ) ) );
}
final private boolean inOvVirtualRectangle( final MouseEvent e ) {
}
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() ) ) ) ) {
+ 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 {
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() ) ) );
+ || ( 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 ) ) );
+ || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) )
+ || ( node.getXcoord() > ( getVisibleRect().getMaxX() + 20 ) ) );
}
final private boolean isNonLinedUpCladogram() {
return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
}
- final private boolean isUniformBranchLengthsForCladogram() {
- return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
- }
-
final private void keyPressedCalls( final KeyEvent e ) {
if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
setInOvRect( false );
}
}
- if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
+ if ( e.isAltDown() ) {
if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
- || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
- getMainPanel().getTreeFontSet().mediumFonts();
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ || ( e.getKeyCode() == KeyEvent.VK_C ) || ( e.getKeyCode() == KeyEvent.VK_BACK_SPACE ) ) {
+ getControlPanel().showWhole();
}
- else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
+ else if ( e.isShiftDown()
+ && ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) ) {
getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- else if ( plusPressed( e.getKeyCode() ) ) {
+ else if ( e.isShiftDown() && plusPressed( e.getKeyCode() ) ) {
getMainPanel().getTreeFontSet().increaseFontSize();
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- }
- else {
- if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
- || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
- getControlPanel().showWhole();
+ else if ( e.getKeyCode() == KeyEvent.VK_O ) {
+ getControlPanel().orderPressed( this );
}
- else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
- || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
- if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
- if ( e.getKeyCode() == KeyEvent.VK_UP ) {
- getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
- getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
- getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
- AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
- getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
- AptxConstants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- }
- else {
- final int d = 80;
- int dx = 0;
- int dy = -d;
- if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
- dy = d;
- }
- else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
- dx = -d;
- dy = 0;
- }
- else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
- dx = d;
- dy = 0;
- }
- final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
- scroll_position.x = scroll_position.x + dx;
- scroll_position.y = scroll_position.y + dy;
- if ( scroll_position.x <= 0 ) {
- scroll_position.x = 0;
- }
- else {
- final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
- if ( scroll_position.x >= max_x ) {
- scroll_position.x = max_x;
- }
- }
- if ( scroll_position.y <= 0 ) {
- scroll_position.y = 0;
- }
- else {
- final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
- if ( scroll_position.y >= max_y ) {
- scroll_position.y = max_y;
- }
- }
- repaint();
- getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
- }
+ else if ( e.getKeyCode() == KeyEvent.VK_R ) {
+ getControlPanel().returnedToSuperTreePressed();
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_U ) {
+ getControlPanel().uncollapseAll( this );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_UP ) {
+ getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
+ getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
+ getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
+ AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
+ getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
+ AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
+ }
+ else {
+ if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
+ || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
+ final int d = 80;
+ int dx = 0;
+ int dy = -d;
+ if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
+ dy = d;
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
+ dx = -d;
+ dy = 0;
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
+ dx = d;
+ dy = 0;
+ }
+ final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
+ scroll_position.x = scroll_position.x + dx;
+ scroll_position.y = scroll_position.y + dy;
+ if ( scroll_position.x <= 0 ) {
+ scroll_position.x = 0;
+ }
+ else {
+ final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
+ if ( scroll_position.x >= max_x ) {
+ scroll_position.x = max_x;
+ }
+ }
+ if ( scroll_position.y <= 0 ) {
+ scroll_position.y = 0;
+ }
+ else {
+ final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
+ if ( scroll_position.y >= max_y ) {
+ scroll_position.y = max_y;
+ }
+ }
+ repaint();
+ getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
+ }
else if ( e.getKeyCode() == KeyEvent.VK_S ) {
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
else {
getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
}
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- if ( ae.getlabelDirectionCbmi() != null ) {
- ae.getlabelDirectionCbmi().setSelected( selected );
- }
- }
- else {
- getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
- }
+ getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
repaint();
}
else if ( e.getKeyCode() == KeyEvent.VK_X ) {
else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
decreaseOvSize();
}
- e.consume();
}
+ if ( e.getKeyCode() == KeyEvent.VK_HOME || e.getKeyCode() == KeyEvent.VK_ESCAPE ) {
+ getControlPanel().showWhole();
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_PAGE_UP ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_PAGE_DOWN ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ e.consume();
}
final private void makePopupMenus( final PhylogenyNode node ) {
}
sb.append( node.getNodeData().getSequence().getGeneName() );
}
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( getControlPanel().isShowSeqNames()
+ && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
if ( sb.length() > 0 ) {
sb.append( " " );
}
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" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
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" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
- else if ( ( tax.getIdentifier() != null )
- && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ 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" ) ) ) {
+ && ( 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 );
}
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- AptxUtil.launchWebBrowser( new URI( uri_str ),
- isApplet(),
- isApplet() ? obtainApplet() : null,
- "_aptx_tax" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_tax" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
final boolean to_pdf,
final boolean to_graphics_file ) {
g.setFont( getTreeFontSet().getSmallFont() );
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) {
g.setColor( Color.BLACK );
}
else {
}
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 );
+ 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 );
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
+ node.getParent().getXcoord() + ROUNDED_D,
+ node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
+ g );
}
else {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
+ node.getParent().getXcoord() + 3,
+ node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
+ g );
}
}
else {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
- - getTreeFontSet().getSmallMaxDescent(), g );
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
+ 3,
+ node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
+ g );
}
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
final float dx = x2 - x1;
final float dy = y2 - y1;
- _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
- + ( dy * 0.8f ), x2, y2 );
+ _cubic_curve.setCurve( x1,
+ y1,
+ x1 + ( dx * 0.4f ),
+ y1 + ( dy * 0.2f ),
+ x1 + ( dx * 0.6f ),
+ y1 + ( dy * 0.8f ),
+ x2,
+ y2 );
( g ).draw( _cubic_curve );
}
else {
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
final float dx = x2 - x1;
final float dy = y2 - y1;
- _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
- + ( dy * 0.8f ), x2, y2 );
+ _cubic_curve.setCurve( x1,
+ y1,
+ x1 + ( dx * 0.4f ),
+ y1 + ( dy * 0.2f ),
+ x1 + ( dx * 0.6f ),
+ y1 + ( dy * 0.8f ),
+ x2,
+ y2 );
g.draw( _cubic_curve );
}
else {
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 ) ) ) ) ) {
+ 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 {
}
}
// draw the horizontal line
- if ( !to_graphics_file && !to_pdf
- && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
+ if ( !to_graphics_file && !to_pdf && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) )
+ || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
return;
}
float x1_r = 0;
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 ( ( 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 );
- }
+ //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 {
c = getTreeColorSet().getCollapseFillColor();
}
double d = node.getAllExternalDescendants().size();
- if ( d > 1000 ) {
- d = ( 3 * _y_distance ) / 3;
+ float xxx;
+ double s = 0;
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( d > 1000 ) {
+ d = 0.75 * _y_distance;
+ }
+ else {
+ d = 0.25 * Math.log10( d ) * _y_distance;
+ }
+ final float half_box_size = 0.5f * getOptions().getDefaultNodeShapeSize();
+ if ( d < half_box_size ) {
+ d = half_box_size;
+ }
+ _polygon.reset();
+ final float xx = node.getXcoord() - ( getOptions().getDefaultNodeShapeSize() );
+ xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
+ _polygon.moveTo( xxx, node.getYcoord() + 0.5 );
+ _polygon.lineTo( xxx, node.getYcoord() - 0.5 );
+ s = _options.isCollapsedWithAverageHeigh()
+ ? PhylogenyMethods.calculateAverageTreeHeight( node ) * _x_correction_factor : 1;
+ _polygon.lineTo( node.getXcoord() + s, node.getYcoord() - d );
+ _polygon.lineTo( node.getXcoord() + s, node.getYcoord() + d );
+ _polygon.closePath();
}
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 ( d > 1000 ) {
+ d = _y_distance;
+ }
+ else {
+ d = ( Math.log10( d ) * _y_distance ) / 2.5;
+ }
+ final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
+ if ( d < box_size ) {
+ d = box_size;
+ }
+ final float xx = node.getXcoord() - ( 2 * box_size );
+ xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
+ _polygon.reset();
+ _polygon.moveTo( xxx, node.getYcoord() );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
+ _polygon.closePath();
+ }
if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
g.setColor( c );
g.fill( _polygon );
g.draw( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
- .getYcoord() - d ), c, false ) );
+ g.setPaint( new GradientPaint( xxx,
+ node.getYcoord(),
+ getBackground(),
+ node.getXcoord(),
+ ( float ) ( node.getYcoord() - d ),
+ c,
+ false ) );
g.fill( _polygon );
g.setPaint( c );
g.draw( _polygon );
}
- paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
+ paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes, s );
}
final private void paintConfidenceValues( final Graphics2D g,
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 ) ) ) {
+ 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() ) {
else {
not_first = true;
}
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil
+ .round( value, getOptions().getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
if ( getOptions().isShowConfidenceStddev() ) {
if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
sb.append( "(" );
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
- .getStandardDeviation(), getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ sb.append( FORMATTER_CONFIDENCE
+ .format( ForesterUtil.round( confidence.getStandardDeviation(),
+ getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
sb.append( ")" );
}
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
x += ROUNDED_D;
}
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) {
g.setColor( Color.BLACK );
}
else {
}
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 );
+ parent_x + ( ( x - parent_x
+ - getTreeFontSet().getFontMetricsSmall().stringWidth( conf_str ) ) / 2 ),
+ ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
+ g );
}
}
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 );
+ 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 );
+ .drawString( lost,
+ parent_x + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) )
+ / 2 ),
+ ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
+ g );
}
}
private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) {
- final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
- .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
+ 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();
|| ( 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() ) ) ) {
+ && ( 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() ) ) {
}
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 );
+ 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();
}
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 );
+ 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();
final PhylogenyNode node,
final boolean to_graphics_file,
final boolean to_pdf,
- final boolean is_in_found_nodes ) {
+ final boolean is_in_found_nodes,
+ final double add ) {
if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
return 0;
}
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 ) ) {
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
+ && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
paintBranchLength( g, node, to_pdf, to_graphics_file );
}
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
return 0;
}
+ if ( !getControlPanel().isShowExternalData() && ( node.isExternal() || node.isCollapse() ) ) {
+ return 0;
+ }
_sb.setLength( 0 );
int x = 0;
+ if ( add > 0 ) {
+ x += add;
+ }
final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
- if ( getControlPanel().isShowTaxonomyImages()
- && ( getImageMap() != null )
- && !getImageMap().isEmpty()
- && node.getNodeData().isHasTaxonomy()
- && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
- .getUris().isEmpty() ) ) {
+ if ( getControlPanel().isShowTaxonomyImages() && ( getImageMap() != null ) && !getImageMap().isEmpty()
+ && node.getNodeData().isHasTaxonomy() && ( ( node.getNodeData().getTaxonomy().getUris() != null )
+ && !node.getNodeData().getTaxonomy().getUris().isEmpty() ) ) {
x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
}
- if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
- .isShowTaxonomyCommonNames() || getControlPanel().isShowTaxonomyRank() ) && node.getNodeData().isHasTaxonomy() ) {
+ 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 );
}
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 ) {
- _sb.setLength( 0 );
- _sb.append( " (" );
+ if ( ( _sb.length() == 0 ) && !saw_species ) {
+ if ( getOptions().isShowAbbreviatedLabelsForCollapsedNodes()
+ && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
+ || getControlPanel().isShowSeqNames() || getControlPanel().isShowNodeNames() ) ) {
+ final PhylogenyNode first = PhylogenyMethods.getFirstExternalNode( node );
+ final PhylogenyNode last = PhylogenyMethods.getLastExternalNode( node );
+ if ( getControlPanel().isShowTaxonomyCode() && first.getNodeData().isHasTaxonomy()
+ && last.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getTaxonomyCode() )
+ && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ addLabelForCollapsed( first.getNodeData().getTaxonomy().getTaxonomyCode(),
+ last.getNodeData().getTaxonomy().getTaxonomyCode(),
+ node.getAllExternalDescendants().size(),
+ node );
+ }
+ else if ( getControlPanel().isShowTaxonomyScientificNames() && first.getNodeData().isHasTaxonomy()
+ && last.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getScientificName() )
+ && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getScientificName() ) ) {
+ addLabelForCollapsed( first.getNodeData().getTaxonomy().getScientificName(),
+ last.getNodeData().getTaxonomy().getScientificName(),
+ node.getAllExternalDescendants().size(),
+ node );
+ }
+ else if ( getControlPanel().isShowSeqNames() && first.getNodeData().isHasSequence()
+ && last.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( first.getNodeData().getSequence().getName() )
+ && !ForesterUtil.isEmpty( last.getNodeData().getSequence().getName() ) ) {
+ addLabelForCollapsed( first.getNodeData().getSequence().getName(),
+ last.getNodeData().getSequence().getName(),
+ node.getAllExternalDescendants().size(),
+ node );
+ }
+ else if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( first.getName() )
+ && !ForesterUtil.isEmpty( last.getName() ) ) {
+ addLabelForCollapsed( first.getName(),
+ last.getName(),
+ node.getAllExternalDescendants().size(),
+ node );
+ }
+ }
+ }
+ else if ( ( _sb.length() > 0 ) || saw_species ) {
+ // _sb.setLength( 0 );
+ _sb.append( " [" );
_sb.append( node.getAllExternalDescendants().size() );
- _sb.append( ")" );
+ _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( "]" );
+ }
+ }
}
}
else {
- _sb.setLength( 0 );
+ // _sb.setLength( 0 );
}
- nodeDataAsSB( node, _sb );
+ // 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 float pos_x = node.getXcoord() + x + 2 + half_box_size;
+ float pos_x;
+ if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM
+ && ( node.isExternal() || node.isCollapse() ) ) {
+ pos_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x + ( 2 * TreePanel.MOVE ) + getXdistance()
+ + 3 );
+ }
+ else {
+ pos_x = node.getXcoord() + x + 2 + half_box_size;
+ }
float pos_y;
if ( !using_visual_font ) {
pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) );
else {
pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
}
+ if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM
+ && ( node.isExternal() || node.isCollapse() ) ) {
+ drawConnection( node.getXcoord(), pos_x - x, node.getYcoord(), 5, 20, g, to_pdf );
+ if ( node.isCollapse() ) {
+ pos_x -= add;
+ }
+ }
final String sb_str = _sb.toString();
// GUILHEM_BEG ______________
if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
&& ( _query_sequence != null ) ) {
- int nodeTextBoundsWidth = 0;
- if ( sb_str.length() > 0 ) {
- final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
- nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
- }
- if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
- if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
- g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
- g.setColor( getTreeColorSet().getBackgroundColor() );
- }
- }
- 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;
- }
- }
- }
- }
+ 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 );
drawStringX( sb_str, pos_x, pos_y, g );
}
}
- // GUILHEM_END _____________
if ( _sb.length() > 0 ) {
if ( !using_visual_font && !is_in_found_nodes ) {
x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
else 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 );
+ 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 ( 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() );
+ .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() );
+ TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
+ node.getXcoord() + x + 4 + half_box_size,
+ node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
+ / down_shift_factor ),
+ g );
+ paintGainedAndLostCharacters( g,
+ node,
+ "+" + node.getNodeData().getBinaryCharacters().getGainedCount(),
+ "-" + node.getNodeData().getBinaryCharacters().getLostCount() );
}
}
}
return x;
}
+ private final int paintSequenceRelation( final Graphics2D g,
+ final PhylogenyNode node,
+ int x,
+ final int half_box_size,
+ final float pos_x,
+ final float pos_y,
+ final String sb_str ) {
+ int nodeTextBoundsWidth = 0;
+ if ( sb_str.length() > 0 ) {
+ final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
+ nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
+ }
+ if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
+ if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
+ g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
+ g.setColor( getTreeColorSet().getBackgroundColor() );
+ }
+ }
+ 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 x;
+ }
+
+ private final void drawConnection( final float x1,
+ final float x2,
+ final float y,
+ final int dist_left,
+ final int dist_right,
+ final Graphics2D g,
+ final boolean pdf ) {
+ if ( ( ( x1 + dist_left ) < ( x2 - dist_right ) ) ) {
+ final Stroke strok = g.getStroke();
+ Color col = null;
+ if ( strok == STROKE_005 ) {
+ g.setStroke( STROKE_001_DASHED );
+ }
+ else if ( strok == STROKE_01 ) {
+ g.setStroke( STROKE_005_DASHED );
+ }
+ else {
+ g.setStroke( STROKE_01_DASHED );
+ }
+ if ( pdf ) {
+ col = g.getColor();
+ g.setColor( lighter( col ) );
+ }
+ drawLine( x1 + dist_left, y, x2 - dist_right, y, g );
+ g.setStroke( strok );
+ if ( pdf ) {
+ g.setColor( col );
+ }
+ }
+ }
+
+ public static Color lighter( final Color color ) {
+ if ( ( color.getRed() == 0 ) && ( color.getGreen() == 0 ) && ( color.getBlue() == 0 ) ) {
+ return new Color( 200, 200, 200 );
+ }
+ else {
+ return color;
+ }
+ }
+
+ private final void addLabelForCollapsed( final String first,
+ final String last,
+ final int size,
+ final PhylogenyNode node ) {
+ _sb.append( first.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? first
+ : first.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) );
+ _sb.append( " ... " );
+ _sb.append( last.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? last
+ : last.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) );
+ _sb.append( " (" + size + ")" );
+ if ( _found_nodes_0 != null || _found_nodes_1 != null ) {
+ /////
+ /////
+ int[] res = calcFoundNodesInSubtree( node );
+ if ( res[ 0 ] > 0 ) {
+ _sb.append( " [" );
+ _sb.append( res[ 0 ] );
+ _sb.append( "/" );
+ _sb.append( res[ 1 ] );
+ _sb.append( "]" );
+ }
+ }
+ }
+
+ private final int[] calcFoundNodesInSubtree( final PhylogenyNode node ) {
+ final List<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;
+ }
+ }
+ res[ 0 ] = found;
+ res[ 1 ] = total;
+ return res;
+ }
+
private final boolean isAllowAttributedStrings() {
return false;
}
_sb.setLength( 0 );
_sb.append( " " );
if ( node.getNodeData().isHasTaxonomy()
- && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
- .isShowTaxonomyCommonNames() ) ) {
+ && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
+ || getControlPanel().isShowTaxonomyCommonNames() ) ) {
final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
_sb.append( taxonomy.getTaxonomyCode() );
_sb.append( node.getName() );
}
if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+ if ( getControlPanel().isShowSequenceAcc()
+ && ( node.getNodeData().getSequence().getAccession() != null ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
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 );
+ drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ node.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ g );
}
float new_x = 0;
if ( !node.isExternal() && !node.isCollapse() ) {
boolean first_child = true;
float y2 = 0.0f;
- final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
+ //final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
final PhylogenyNode child_node = node.getChildNode( i );
- int factor_x;
- if ( !isUniformBranchLengthsForCladogram() ) {
- factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
- }
- else {
- factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
- }
+ final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
if ( first_child ) {
first_child = false;
- y2 = node.getYSecondary()
- - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
- .getNumberOfExternalNodes() ) );
+ y2 = node.getYSecondary() - ( getOvYDistance()
+ * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
}
else {
y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
++_external_node_index;
}
// Confidence values
- if ( getControlPanel().isShowConfidenceValues()
- && !node.isExternal()
- && !node.isRoot()
+ if ( getControlPanel().isShowConfidenceValues() && !node.isExternal() && !node.isRoot()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && node.getBranchData().isHasConfidences() ) {
+ || ( 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.isExternal() && !node.isCollapse() ) {
boolean first_child = true;
float y2 = 0.0f;
- final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
final PhylogenyNode child_node = node.getChildNode( i );
- int factor_x;
- if ( !isUniformBranchLengthsForCladogram() ) {
- factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
- }
- else {
- factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
- }
+ final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
if ( first_child ) {
first_child = false;
- y2 = node.getYcoord()
- - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
+ y2 = node.getYcoord() - ( _y_distance
+ * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
}
else {
y2 += _y_distance * child_node.getNumberOfExternalNodes();
&& ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
paintMolecularSequences( g, node, to_pdf );
}
- 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()
+ 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 );
+ 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 );
}
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 ) ) {
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) && ( node.getNodeData()
+ .getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
RenderableDomainArchitecture rds = null;
try {
rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
if ( getOptions().isLineUpRendarableNodeData() ) {
if ( getOptions().isRightLineUpDomains() ) {
rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
- + _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds
- .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
+ + _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 ),
+ rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + _length_of_longest_text + 50 ),
node.getYcoord() - ( h / 2.0f ),
g,
this,
}
else {
if ( getOptions().isRightLineUpDomains() ) {
- rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) - 20 )
- + ( ( _longest_domain - rds.getTotalLength() ) * rds
- .getRenderingFactorWidth() ),
- node.getYcoord() - ( h / 2.0f ),
- g,
- this,
- to_pdf );
+ rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text )
+ - 20 ) + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
}
else {
rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
}
else {
- rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + domain_add ),
- node.getYcoord() - 3,
- g,
- this,
- to_pdf );
+ rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text
+ + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
}
}
}
//if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
// && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
// && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
- // paintMolecularSequences( g, node, to_pdf );
+ // paintMolecularSequences( g, node, to_pdf );
//}
}
}
final private void paintPhylogenyLite( final Graphics2D g ) {
- _phylogeny
- .getRoot()
- .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
- .getWidth() ) ) ) );
+ _phylogeny.getRoot().setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition()
+ + ( MOVE / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ) );
_phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
final Stroke s = g.getStroke();
g.setStroke( STROKE_05 );
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_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 ) );
+ start_y = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
+ / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
}
else {
start_y = node.getYcoord()
final String label = _sb.toString();
/* GUILHEM_BEG */
if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
- && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
+ && ( 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();
+ 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() );
}
}
private final StringBuffer propertiesToString( final PhylogenyNode node ) {
- final PropertiesMap properties = node.getNodeData().getProperties();
- final StringBuffer sb = new StringBuffer();
- boolean first = true;
- for( final String ref : properties.getPropertyRefs() ) {
- if ( first ) {
- first = false;
- }
- else {
- sb.append( " " );
- }
- final Property p = properties.getProperty( ref );
- sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
- sb.append( "=" );
- sb.append( p.getValue() );
- if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
- }
- }
- return sb;
+ return node.getNodeData().getProperties().asText();
}
private void setColor( final Graphics2D g,
g.setColor( getTaxonomyBasedColor( node ) );
}
else if ( getControlPanel().isColorAccordingToAnnotation()
- && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
- .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
+ && ( 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()
_urt_factor_ov = urt_factor_ov;
}
- private void showExtDescNodeData( final PhylogenyNode node ) {
+ 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 ) ) {
if ( n.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
final StringBuilder ann = new StringBuilder();
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( n.getName() ) ) {
ann.append( n.getName() );
- ann.append( "|" );
+ ann.append( separator );
}
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
- ann.append( "SYM=" );
+ 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( "|" );
+ ann.append( separator );
}
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- ann.append( "NAME=" );
+ if ( getControlPanel().isShowSeqNames()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
ann.append( n.getNodeData().getSequence().getName() );
- ann.append( "|" );
+ ann.append( separator );
}
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
- ann.append( "GN=" );
+ if ( getControlPanel().isShowGeneNames()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
ann.append( n.getNodeData().getSequence().getGeneName() );
- ann.append( "|" );
+ ann.append( separator );
}
- if ( n.getNodeData().getSequence().getAccession() != null ) {
- ann.append( "ACC=" );
+ if ( getControlPanel().isShowSequenceAcc()
+ && n.getNodeData().getSequence().getAccession() != null ) {
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( "|" );
- }
+ ann.append( separator );
}
- String ann_str;
- if ( ann.charAt( ann.length() - 1 ) == '|' ) {
+
+ 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 ) );
+ sb.append( SequenceWriter.toFasta( ann_str,
+ n.getNodeData().getSequence().getMolecularSequence(),
+ 60 ) );
data.add( sb.toString() );
}
break;
final String name = d.getName();
if ( !( s.contains( name ) ) ) {
data.add( name );
- if ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) {
+ if ( getOptions()
+ .getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) {
s.add( name );
}
}
}
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" );
+ TreePanelUtil.showInformationMessage( this,
+ "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
+ "Descendants of selected node do not contain selected data" );
clearCurrentExternalNodesDataBuffer();
}
else {
String title;
if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() )
- + " for "
- + data.size()
- + " nodes, unique entries: "
+ : obtainTitleForExtDescNodeData() ) + " for " + data.size() + " nodes, unique entries: "
+ size;
}
else {
title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() )
- + " for "
- + data.size()
- + "/"
- + node.getNumberOfExternalNodes()
- + " external descendats of node "
- + node
+ : 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 );
- }
+ 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() ) {
+ || ( 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 ) {
_popup_buffer.append( "]" );
}
if ( !enc_data ) {
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
+ if ( ( tax.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
_popup_buffer.append( "[" );
_popup_buffer.append( tax.getIdentifier().getProvider() );
_popup_buffer.append( confidence.getType() );
_popup_buffer.append( "] " );
}
- _popup_buffer
- .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
- getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
+ getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
_popup_buffer.append( " (sd=" );
- _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
- .getStandardDeviation(), getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ _popup_buffer.append( 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() ) {
+ if ( _popup_buffer.length() > 0 ) {
_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() ) );
- }
}
+ _popup_buffer.append( node.getNodeData().getProperties().asText() );
}
if ( _popup_buffer.length() > 0 ) {
if ( !getConfiguration().isUseNativeUI() ) {
_rollover_popup
- .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
+ .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
_rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
_rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
_rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
}
_rollover_popup.setText( _popup_buffer.toString() );
- _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
- _rollover_popup,
- e.getLocationOnScreen().x + 10,
- e.getLocationOnScreen().y
- - ( lines * 20 ) );
+ _node_desc_popup = PopupFactory.getSharedInstance()
+ .getPopup( null,
+ _rollover_popup,
+ e.getLocationOnScreen().x + 10,
+ e.getLocationOnScreen().y - ( lines * 20 ) );
_node_desc_popup.show();
}
}
else {
getControlPanel().setDrawPhylogramEnabled( false );
}
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
- }
- else {
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
- }
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
}
final void calcMaxDepth() {
calculateLongestExtNodeInfo();
if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
&& ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
- while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
+ 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 ) ) ) {
+ while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) ) && ( getTreeFontSet().getLargeFont()
+ .getSize() <= ( getTreeFontSet().getLargeFontMemory().getSize()
+ - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
getMainPanel().getTreeFontSet().increaseFontSize();
calculateLongestExtNodeInfo();
}
}
//_length_of_longest_text = calcLengthOfLongestText();
int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
- final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ final int max_depth = PhylogenyMethods.calculateMaxDepthConsiderCollapsed( _phylogeny ) + 1;
if ( ext_nodes == 1 ) {
ext_nodes = max_depth;
if ( ext_nodes < 1 ) {
updateOvSizes();
float xdist = 0;
float ov_xdist = 0;
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
+ if ( !isNonLinedUpCladogram() ) {
xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
}
setXdistance( xdist );
setYdistance( ydist );
setOvXDistance( ov_xdist );
- final double height = _phylogeny.getHeight();
+ 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 );
+ 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 );
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
- int max_possible_length = ForesterUtil.roundToInt( ( getSize().getWidth() - 2 * MOVE )
- * AptxConstants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
+ 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;
- }
+ max_possible_length = 20;
+ }
int longest = 30;
int longest_txt = 0;
_longest_domain = 0;
}
boolean use_vis = false;
final Graphics2D g = ( Graphics2D ) getGraphics();
- if ( getControlPanel().isUseVisualStyles() ) {
+ if ( g != null && getControlPanel().isUseVisualStyles() ) {
use_vis = setFont( g, node, false );
}
if ( !use_vis ) {
}
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
- .getGainedCharactersAsStringBuffer().toString() );
+ .getGainedCharactersAsStringBuffer().toString() );
}
if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
&& ( node.getNodeData().getVector().size() > 0 ) ) {
// 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;
+ sum += ( ( _domain_structure_width
+ / ( ( RenderableDomainArchitecture ) d ).getOriginalSize().getWidth() ) * d.getTotalLength() )
+ + 10;
if ( d.getTotalLength() > _longest_domain ) {
_longest_domain = d.getTotalLength();
}
}
}
_ext_node_with_longest_txt_info = longest_txt_node;
- if ( longest >= max_possible_length ) {
+ if ( longest >= max_possible_length ) {
_longest_ext_node_info = max_possible_length;
- }
- else {
- _longest_ext_node_info = longest;
- }
+ }
+ else {
+ _longest_ext_node_info = longest;
+ }
_length_of_longest_text = calcLengthOfLongestText();
}
}
}
- void checkForVectorProperties( final Phylogeny phy ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.getNodeData().getProperties() != null ) {
- final PropertiesMap pm = node.getNodeData().getProperties();
- final double[] vector = new double[ pm.getProperties().size() ];
- int counter = 0;
- for( final String ref : pm.getProperties().keySet() ) {
- if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
- final Property p = pm.getProperty( ref );
- final String value_str = p.getValue();
- final String index_str = ref
- .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
- double d = -100;
- try {
- d = Double.parseDouble( value_str );
- }
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
- + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
- return;
- }
- int i = -1;
- try {
- i = Integer.parseInt( index_str );
- }
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this,
- "Could not parse \"" + index_str
- + "\" into index for vector data",
- "Problem with Vector Data",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( i < 0 ) {
- JOptionPane.showMessageDialog( this,
- "Attempt to use negative index for vector data",
- "Problem with Vector Data",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- vector[ i ] = d;
- ++counter;
- stats.addValue( d );
- }
- }
- final List<Double> vector_l = new ArrayList<Double>( counter );
- for( int i = 0; i < counter; ++i ) {
- vector_l.add( vector[ i ] );
- }
- node.getNodeData().setVector( vector_l );
- }
- }
- if ( stats.getN() > 0 ) {
- _statistics_for_vector_data = stats;
- }
- }
-
void clearCurrentExternalNodesDataBuffer() {
setCurrentExternalNodesDataBuffer( new StringBuilder() );
}
repaint();
}
}
-
+
final void uncollapseAll( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
JOptionPane.showMessageDialog( this,
return;
}
if ( !node.isExternal() ) {
- TreePanelUtil.uncollapseSubtree( node);
+ TreePanelUtil.uncollapseSubtree( node );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
setNodeInPreorderToNull();
resetPreferredSize();
+ resetDepthCollapseDepthValue();
+ resetRankCollapseRankValue();
_main_panel.adjustJScrollPane();
+ getControlPanel().showWhole();
setArrowCursor();
- repaint();
}
- final void collapseByTaxonomicRank( final String rank ) {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- setWaitCursor();
-
- final int collapsed = TreePanelUtil.collapseByTaxonomicRank( _phylogeny, rank, this );
-
- setArrowCursor();
- repaint();
- if ( collapsed > 0 ) {
- String msg = "Collapsing via " + rank + " completed:\n";
- if ( collapsed > 1 ) {
- msg += "collapsed " + collapsed + " subtrees";
- }
- else {
- msg += "collapsed one subtree";
- }
- setEdited( true );
- JOptionPane.showMessageDialog( this,
- msg,
- "Taxonomy Rank-Collapsing Completed (" + rank + ")",
- JOptionPane.INFORMATION_MESSAGE );
- }
- else {
- String msg = "Could not taxonomy rank-collapse 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 Rank-Collapsing Failed", JOptionPane.WARNING_MESSAGE );
- }
- }
-
-
-
final void colorRank( final String rank ) {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
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 Rank-Colorization Failed", JOptionPane.WARNING_MESSAGE );
+ 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 );
}
}
* @param y
* @return pointer to the node at x,y, null if not found
*/
- final PhylogenyNode findNode( final int x, final int y ) {
+ public final PhylogenyNode findNode( final int x, final int y ) {
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return null;
}
return _domain_structure_e_value_thr_exp;
}
- final Set<Long> getFoundNodes0() {
+ public final Set<Long> getFoundNodes0() {
return _found_nodes_0;
}
- final Set<Long> getFoundNodes1() {
+ public final Set<Long> getFoundNodes1() {
return _found_nodes_1;
}
- List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+ public List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
if ( getFoundNodes0() != null ) {
for( final Long id : getFoundNodes0() ) {
return getTreeColorSet().getTaxonomyColor();
}
- final File getTreeFile() {
+ public final File getTreeFile() {
return _treefile;
}
if ( node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
RenderableDomainArchitecture rds = null;
- if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
+ if ( !( node.getNodeData().getSequence()
+ .getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
if ( SPECIAL_DOMAIN_COLORING ) {
rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
- .getDomainArchitecture(), node.getName() );
+ .getDomainArchitecture(), node.getName() );
}
else {
rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
- .getDomainArchitecture() );
+ .getDomainArchitecture() );
}
node.getNodeData().getSequence().setDomainArchitecture( rds );
}
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 ) ) );
+ && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) )
+ && ( e.getY() < ( ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
}
final boolean inOvRectangle( final MouseEvent e ) {
return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
&& ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
- && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
- + getOvRectangle().getHeight() + 1 ) ) );
- }
-
- final boolean isApplet() {
- return getMainPanel() instanceof MainPanelApplets;
+ && ( 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 ) {
+ if ( node.isExternal() || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
return false;
}
if ( node.isCollapse() ) {
}
return false;
}
-
+
final boolean isCanColorSubtree() {
return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
}
final boolean isCanCut( final PhylogenyNode node ) {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
- .isRoot() );
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
+ && !node.isRoot() );
}
final boolean isCanDelete() {
}
final boolean isCanSubtree( final PhylogenyNode node ) {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
- .isRoot() || ( _subtree_index > 0 ) ) );
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal()
+ && ( !node.isRoot() || ( _subtree_index > 0 ) ) );
}
- final boolean isCurrentTreeIsSubtree() {
+ public final boolean isCurrentTreeIsSubtree() {
return ( _subtree_index > 0 );
}
y = max_y;
}
getMainPanel().getCurrentScrollPane().getViewport()
- .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
+ .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
setInOvRect( true );
repaint();
}
}
}
else {
- // no node was clicked
+ // 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;
+
+ }
+
+
}
+ }
+ }
repaint();
}
_urt_factor *= f;
}
- final JApplet obtainApplet() {
- return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- }
-
final void paintBranchCircular( final PhylogenyNode p,
final PhylogenyNode c,
final Graphics2D g,
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 );
+ 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 );
}
}
paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
}
+ 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_height,
final int graphics_file_x,
final int graphics_file_y ) {
+
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
}
else {
if ( !to_graphics_file ) {
- g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
- + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
+ g.setPaint( new GradientPaint( r.x,
+ r.y,
+ getTreeColorSet().getBackgroundColor(),
+ r.x,
+ r.y + r.height,
+ getTreeColorSet().getBackgroundColorGradientBottom() ) );
g.fill( r );
}
else {
&& ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
_external_node_index = 0;
// Position starting X of tree
- if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
+ 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() ) ) );
+ _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 ) );
+ + ( TreePanel.MOVE / 2.0f ) );
final int dynamic_hiding_factor = calcDynamicHidingFactor();
if ( getControlPanel().isDynamicallyHideData() ) {
if ( dynamic_hiding_factor > 1 ) {
}
}
final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 )
- || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()
- || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
- || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() )
- || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() )
+ /* || 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,
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 ) );
+ _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5
+ * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
}
if ( getControlPanel().getDynamicallyHideData() != null ) {
if ( _dynamic_hiding_factor > 1 ) {
}
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
+ 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 ) );
+ _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5
+ * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
}
if ( getControlPanel().getDynamicallyHideData() != null ) {
if ( _dynamic_hiding_factor > 1 ) {
getStartingAngle(),
x_pos + radius_ov,
y_pos + radius_ov,
- ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
- .getWidth() ) ) ),
- g );
+ ( int ) ( radius_ov - ( getLongestExtNodeInfo()
+ / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ),
+ g );
g.setTransform( _at );
paintOvRectangle( g );
}
- }
+
+
+ }
+ 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();
+ }
}
/**
y = TreePanel.MOVE
+ ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
if ( getControlPanel().isDrawPhylogram() ) {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil
- .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
-
+ x = TreePanel.MOVE + getLongestExtNodeInfo()
+ + ForesterUtil.roundToInt( ( getXcorrectionFactor()
+ * getPhylogeny().calculateHeight( !_options.isCollapsedWithAverageHeigh() ) )
+ + getXdistance() );
}
else {
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil.roundToInt( getXdistance()
- * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
+ if ( !isNonLinedUpCladogram() ) {
+ x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil
+ .roundToInt( getXdistance() * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
}
else {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil.roundToInt( getXdistance()
- * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
+ x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil
+ .roundToInt( getXdistance() * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
}
}
setPreferredSize( new Dimension( x, y ) );
_current_external_nodes_data_buffer = sb;
}
- final void setFoundNodes0( final Set<Long> found_nodes ) {
+ public final void setFoundNodes0( final Set<Long> found_nodes ) {
_found_nodes_0 = found_nodes;
}
- final void setFoundNodes1( final Set<Long> found_nodes ) {
+ public final void setFoundNodes1( final Set<Long> found_nodes ) {
_found_nodes_1 = found_nodes;
}
getTreeFontSet().tinyFonts();
}
- final void setTreeFile( final File treefile ) {
+ public final void setTreeFile( final File treefile ) {
_treefile = treefile;
}
_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();
_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();
}
if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
}
- else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols() || getControlPanel().isShowGeneNames() ) {
+ else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
+ || getControlPanel().isShowGeneNames() ) {
pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
PhylogenyMethods.orderAppearanceX( node, true, pri );
-
setNodeInPreorderToNull();
getPhylogeny().externalNodesHaveChanged();
getPhylogeny().clearHashIdToNodeMap();
getControlPanel().displayedPhylogenyMightHaveChanged( true );
repaint();
}
-
+
final void swap( final PhylogenyNode node ) {
if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
return;
}
final void updateOvSizes() {
- if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
+ if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) )
+ || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
setOvOn( true );
float l = getLongestExtNodeInfo();
final float w_ratio = getOvMaxWidth() / getWidth();
final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
float ov_xdist = 0;
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
+ if ( !isNonLinedUpCladogram() ) {
ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
}
else {
ydist = 0.0f;
}
setOvXDistance( ov_xdist );
- final double height = _phylogeny.getHeight();
+ final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() );
if ( height > 0 ) {
final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
}
}
+ final void updateButtonToUncollapseAll() {
+ if ( PhylogenyMethods.isHasCollapsedNodes( _phylogeny ) ) {
+ getControlPanel().activateButtonToUncollapseAll();
+ }
+ else {
+ getControlPanel().deactivateButtonToUncollapseAll();
+ }
+ }
+
final void zoomInDomainStructure() {
if ( _domain_structure_width < 2000 ) {
_domain_structure_width *= 1.2;
final private static void drawString( final String str, final float x, final float y, final Graphics2D g ) {
g.drawString( str, x, y );
}
-
-
+
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);
+ 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);
+ 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 );
}
}
-
private final Map<String, AttributedString> getAttributedStringMap() {
- return _attributed_string_map ;
+ return _attributed_string_map;
}
-
+
private final void setAttributedStringMap( final Map<String, AttributedString> attributed_string_map ) {
_attributed_string_map = attributed_string_map;
}
final private static boolean plusPressed( final int key_code ) {
return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
- || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
+ || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON )
+ || ( key_code == KeyEvent.VK_1 ) );
+ }
+
+ 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 );
+ }
+ }
+ }
+
+ 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 );
+ }
+ }
+
+ 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 ) );
+ }
+ }
+ }
+ }
+
+ 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 ) );
+ }
+ }
+ }
+ }
+
+ 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 );
+ }
+
+ 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