import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
+import org.forester.archaeopteryx.tools.Blast;
+import org.forester.archaeopteryx.tools.ImageLoader;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
private final static int EURO_D = 10;
private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
private final static int MIN_ROOT_LENGTH = 3;
- private final static int BOX_SIZE = 4;
- private final static int HALF_BOX_SIZE = TreePanel.BOX_SIZE / 2;
private final static int MAX_SUBTREES = 100;
private final static int MAX_NODE_FRAMES = 10;
private final static int MOVE = 20;
private final static NumberFormat FORMATTER_CONFIDENCE;
private final static NumberFormat FORMATTER_BRANCH_LENGTH;
private final static int WIGGLE = 2;
- private final static int HALF_BOX_SIZE_PLUS_WIGGLE = HALF_BOX_SIZE + WIGGLE;
+ private final int _half_box_size_plus_wiggle;
private final static int LIMIT_FOR_HQ_RENDERING = 1000;
private final static int CONFIDENCE_LEFT_MARGIN = 4;
// TODO "rendering_hints" was static before. Need to make sure everything is OK with it not
private boolean _edited = false;
private Popup _node_desc_popup;
private JTextArea _rollover_popup;
+ private final int _box_size;
+ private final int _half_box_size;
//private final short _skip_counter = 0;
private final StringBuffer _popup_buffer = new StringBuffer();
final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
_configuration = configuration;
_phylogeny = t;
_phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
+ _box_size = tjp.getOptions().getDefaultNodeBoxSize();
+ _half_box_size = tjp.getOptions().getDefaultNodeBoxSize() / 2;
+ _half_box_size_plus_wiggle = _half_box_size + WIGGLE;
init();
// if ( !_phylogeny.isEmpty() ) {
_phylogeny.recalculateNumberOfExternalDescendants( true );
null,
options,
options[ 2 ] );
+ _nodes_in_preorder = null;
boolean node_only = true;
if ( r == 1 ) {
node_only = false;
g.fill( _rectangle );
}
+ //TODO FIXME
+ final private void drawRectGradient( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g,
+ final Color color_1,
+ final Color color_2,
+ final Color color_border ) {
+ _rectangle.setFrame( x, y, width, heigth );
+ g.setPaint( new GradientPaint( ( float ) x,
+ ( float ) y,
+ color_1,
+ ( float ) ( x + width ),
+ ( float ) ( y + heigth ),
+ color_2,
+ false ) );
+ g.fill( _rectangle );
+ if ( color_border != null ) {
+ g.setPaint( color_border );
+ g.draw( _rectangle );
+ }
+ }
+
+ //TODO FIXME
+ final private void drawOvalGradient( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g,
+ final Color color_1,
+ final Color color_2,
+ final Color color_border ) {
+ _ellipse.setFrame( x, y, width, heigth );
+ g.setPaint( new GradientPaint( ( float ) x,
+ ( float ) y,
+ color_1,
+ ( float ) ( x + width ),
+ ( float ) ( y + heigth ),
+ color_2,
+ false ) );
+ g.fill( _ellipse );
+ if ( color_border != null ) {
+ g.setPaint( color_border );
+ g.draw( _ellipse );
+ }
+ }
+
final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
JOptionPane.showMessageDialog( this,
"Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
- && ( ( node.getXcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= x )
- && ( ( node.getXcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= x )
- && ( ( node.getYcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= y )
- && ( ( node.getYcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= y ) ) {
+ && ( ( node.getXcoord() - _half_box_size_plus_wiggle ) <= x )
+ && ( ( node.getXcoord() + _half_box_size_plus_wiggle ) >= x )
+ && ( ( node.getYcoord() - _half_box_size_plus_wiggle ) <= y )
+ && ( ( node.getYcoord() + _half_box_size_plus_wiggle ) >= y ) ) {
return node;
}
}
*
* @return a pointer to the phylogeny
*/
- final Phylogeny getPhylogeny() {
+ public final Phylogeny getPhylogeny() {
return _phylogeny;
}
JOptionPane.WARNING_MESSAGE );
return;
}
+ _nodes_in_preorder = null;
setWaitCursor();
PhylogenyMethods.midpointRoot( _phylogeny );
resetNodeIdToDistToLeafMap();
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
boolean draw_vertical = true;
final PhylogenyNode parent = node.getParent();
- if ( ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
+ if ( ( ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE ) && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
.isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) )
&& ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
&& !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
.isDuplication() ) ) {
if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
&& ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( Math.abs( y2 - y1 ) <= TreePanel.HALF_BOX_SIZE ) {
+ if ( Math.abs( y2 - y1 ) <= _half_box_size ) {
draw_vertical = false;
}
else {
if ( y1 < y2 ) {
- y1 += TreePanel.HALF_BOX_SIZE;
+ y1 += _half_box_size;
}
else {
if ( !to_pdf ) {
- y1 -= TreePanel.HALF_BOX_SIZE + 1;
+ y1 -= _half_box_size + 1;
}
else {
- y1 -= TreePanel.HALF_BOX_SIZE;
+ y1 -= _half_box_size;
}
}
}
}
- if ( ( x2 - x1 ) <= TreePanel.HALF_BOX_SIZE ) {
+ if ( ( x2 - x1 ) <= _half_box_size ) {
draw_horizontal = false;
}
else if ( !draw_vertical ) {
- x1a += TreePanel.HALF_BOX_SIZE;
+ x1a += _half_box_size;
}
- if ( ( ( x2 - x1a ) > TreePanel.HALF_BOX_SIZE )
+ if ( ( ( x2 - x1a ) > _half_box_size )
&& !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
.isDuplication() ) ) {
- x2a -= TreePanel.HALF_BOX_SIZE;
+ x2a -= _half_box_size;
}
}
if ( draw_vertical ) {
g.draw( _arc );
}
}
- paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
+ //TODO new *****
+ if ( node.isExternal() ) {
+ //TODO new *****
+ paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
+ }
}
final void paintCircular( final Phylogeny phy,
_root = phy.getRoot();
_root.setXcoord( center_x );
_root.setYcoord( center_y );
- paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
double current_angle = starting_angle;
int i = 0;
current_angle += ( TWO_PI / _circ_num_ext_nodes );
}
paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
+ paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
}
final void paintCircularLite( final Phylogeny phy,
final boolean to_graphics_file ) {
if ( n.isExternal() ) {
if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
- System.out.println( "no " + n + ", fucker!" );//TODO
+ System.out.println( "no " + n + ", ERROR!" );//TODO
}
return _urt_nodeid_angle_map.get( n.getId() );
}
else {
d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- if ( d < BOX_SIZE ) {
- d = BOX_SIZE;
+ if ( d < _box_size ) {
+ d = _box_size;
}
_polygon.reset();
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - TreePanel.BOX_SIZE ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - _box_size ),
ForesterUtil.roundToInt( node.getYcoord() ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ),
ForesterUtil.roundToInt( node.getYcoord() - d ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ),
ForesterUtil.roundToInt( node.getYcoord() + d ) );
g.fillPolygon( _polygon );
paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
g.setColor( getTreeColorSet().getFoundColor() );
- g.fillRect( x - TreePanel.HALF_BOX_SIZE, y - TreePanel.HALF_BOX_SIZE, TreePanel.BOX_SIZE, TreePanel.BOX_SIZE );
+ g.fillRect( x - _half_box_size, y - _half_box_size, _box_size, _box_size );
}
final private void paintGainedAndLostCharacters( final Graphics2D g,
else {
assignGraphicsForNodeBoxWithColorForParentBranch( node, g );
}
- if ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file )
+ if ( ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE ) && !to_pdf && !to_graphics_file )
|| ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
if ( to_pdf || to_graphics_file ) {
if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
- drawOvalFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
+ //TODO FIXME
+ //drawOvalFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g );
+ drawOvalGradient( x - _half_box_size,
+ y - _half_box_size,
+ _box_size,
+ _box_size,
+ g,
+ Color.BLACK,
+ g.getColor(),
+ g.getColor() );
}
}
else {
- drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
+ //TODO FIXME
+ //drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
+ drawOvalGradient( x - _half_box_size,
+ y - _half_box_size,
+ _box_size,
+ _box_size,
+ g,
+ Color.BLACK,
+ g.getColor(),
+ g.getColor() );
}
}
}
&& node.getNodeData().isHasTaxonomy()
&& ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
.getUris().isEmpty() ) ) {
- x += drawTaxonomyImage( node.getXcoord() + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord(), node, g );
+ x += drawTaxonomyImage( node.getXcoord() + 2 + _half_box_size, node.getYcoord(), node, g );
}
if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
.isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
down_shift_factor = 1;
}
- final double pos_x = node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE;
+ final double pos_x = node.getXcoord() + x + 2 + _half_box_size;
final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
final String sb_str = _sb.toString();
// GUILHEM_BEG ______________
&& 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 + TreePanel.HALF_BOX_SIZE;
+ final double linePosX = node.getXcoord() + 2 + _half_box_size;
final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
.getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
+ ")";
g.setColor( calculateColorForAnnotation( ann ) );
}
final String ann_str = ann.asSimpleText().toString();
- TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+ TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + _half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
_sb.append( ann_str );
}
if ( getControlPanel().isShowBinaryCharacters() ) {
TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
- .toString(), node.getXcoord() + x + 1 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+ .toString(), node.getXcoord() + x + 1 + _half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
}
final double mean = ForesterUtil.round( sum / count, 1 );
TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " ["
- + mean + "]", node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+ + mean + "]", node.getXcoord() + x + 4 + _half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
}
else {
TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
- node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE,
+ node.getXcoord() + x + 4 + _half_box_size,
node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
g );
child_node.setYcoord( y2 );
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
+ //TODO new *****
+ paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
+ //TODO new *****
}
if ( dynamically_hide
&& !is_in_found_nodes
if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) {
x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
}
+ if ( getControlPanel().isShowGeneNames() ) {
+ x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
+ }
+ if ( getControlPanel().isShowGeneSymbols() ) {
+ x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
+ }
+ if ( getControlPanel().isShowSequenceAcc() ) {
+ x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
+ .toString()
+ + " " );
+ }
if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
}
else {
g.setColor( getTreeColorSet().getTaxonomyColor() );
}
- final double start_x = node.getXcoord() + 3 + TreePanel.HALF_BOX_SIZE + x_shift;
+ final double start_x = node.getXcoord() + 3 + _half_box_size + x_shift;
final double start_y = node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
_sb.setLength( 0 );
if ( n.isRoot() ) {
n.setXcoord( getWidth() / 2 );
n.setYcoord( getHeight() / 2 );
- paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
}
if ( n.isExternal() ) {
paintNodeDataUnrootedCirc( g,
final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
desc.setXcoord( new_x );
desc.setYcoord( new_y );
- paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
current_angle += arc_size;
assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
drawLine( x, y, new_x, new_y, g );
+ paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
+ }
+ if ( n.isRoot() ) {
+ paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
}
}
setPreferredSize( new Dimension( x, y ) );
}
- final void setArrowCursor() {
+ public final void setArrowCursor() {
setCursor( ARROW_CURSOR );
repaint();
}
getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
}
- final void setEdited( final boolean edited ) {
+ public final void setEdited( final boolean edited ) {
_edited = edited;
}
* @param t
* an instance of a Phylogeny
*/
- final void setTree( final Phylogeny t ) {
+ public final void setTree( final Phylogeny t ) {
+ _nodes_in_preorder = null;
_phylogeny = t;
}
_urt_factor_ov = urt_factor_ov;
}
- final void setWaitCursor() {
+ public final void setWaitCursor() {
setCursor( WAIT_CURSOR );
repaint();
}
JOptionPane.WARNING_MESSAGE );
return;
}
+ _nodes_in_preorder = null;
if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
_sub_phylogenies[ _subtree_index ] = _phylogeny;
_sub_phylogenies_temp_roots[ _subtree_index ] = node;
}
final void superTree() {
+ _nodes_in_preorder = null;
final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
for( final PhylogenyNode n : temp_root.getDescendants() ) {
n.setParent( temp_root );
final void swap( final PhylogenyNode node ) {
if ( !node.isExternal() ) {
_phylogeny.swapChildren( node );
+ _nodes_in_preorder = null;
}
repaint();
}
}
}
- synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
+ public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
getMainPanel().setImageMap( image_map );
}
- synchronized Hashtable<String, BufferedImage> getImageMap() {
+ public synchronized Hashtable<String, BufferedImage> getImageMap() {
return getMainPanel().getImageMap();
}
}
git://source.jalview.org / jalview.git / blobdiff