import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
+import org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence;
import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
import org.forester.archaeopteryx.tools.Blast;
import org.forester.archaeopteryx.tools.ImageLoader;
import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.DomainArchitecture;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.NodeData.NODE_DATA;
import org.forester.phylogeny.data.NodeVisualData;
public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
+ 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 );
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_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 = "posterior probability"; //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 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 final StringBuilder _sb = new StringBuilder();
private double _scale_distance = 0.0;
private String _scale_label = null;
- // expression values menu:
private DescriptiveStatistics _statistics_for_vector_data;
private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
private float _x_correction_factor = 0.0f;
private float _x_distance = 0.0f;
private float _y_distance = 0.0f;
+ private int _length_of_longest_text;
+ private int _longest_domain;
// private Image offscreenImage;
// private Graphics offscreenGraphics;
// private Dimension offscreenDimension;
calculateScaleDistance();
FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
- .getNumberOfDigitsAfterCommaForBranchLengthValues() );
+ .getNumberOfDigitsAfterCommaForBranchLengthValues() );
}
@Override
}
/**
- * Get a pointer to the phylogeny
- *
+ * Get a pointer to the phylogeny
+ *
* @return a pointer to the phylogeny
*/
public final Phylogeny getPhylogeny() {
/**
* Set a phylogeny tree.
- *
+ *
* @param t
* an instance of a Phylogeny
*/
/**
* Set parameters for printing the displayed tree
- *
+ *
*/
- final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
+ final void calcParametersForPainting( final int x, final int y ) {
// updateStyle(); not needed?
if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
initNodeData();
- if ( recalc_longest_ext_node_info ) {
- calculateLongestExtNodeInfo();
- if ( getOptions().isAllowFontSizeChange() ) {
- if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
- && ( getTreeFontSet().getLargeFont().getSize() > 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
- while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
- && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
- getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(),
- true );
- calculateLongestExtNodeInfo();
- }
- }
- else {
- while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
- && ( getTreeFontSet().getLargeFont().getSize() <= getTreeFontSet().getLargeFontMemory()
- .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) {
- getMainPanel().getTreeFontSet().increaseFontSize();
- calculateLongestExtNodeInfo();
- }
- }
+ calculateLongestExtNodeInfo();
+ if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
+ while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), true );
+ calculateLongestExtNodeInfo();
}
}
+ else {
+ 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 );
if ( ext_nodes == 1 ) {
_circ_max_depth = max_depth;
setUpUrtFactor();
//
- if ( getOptions().isAllowFontSizeChange() ) {
- if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- // int dynamic_hiding_factor = calcDynamicHidingFactor();
- // if ( dynamic_hiding_factor > 1 ) {
- // while ( dynamic_hiding_factor > 1
- // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
- // getTreeFontSet().decreaseFontSize( 1, true );
- // dynamic_hiding_factor = calcDynamicHidingFactor();
- // }
- // }
- // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
- // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
- // getTreeFontSet().increaseFontSize();
- // dynamic_hiding_factor = calcDynamicHidingFactor();
- // }
- // }
- }
+ if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ // int dynamic_hiding_factor = calcDynamicHidingFactor();
+ // if ( dynamic_hiding_factor > 1 ) {
+ // while ( dynamic_hiding_factor > 1
+ // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
+ // getTreeFontSet().decreaseFontSize( 1, true );
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
+ // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
+ // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
+ // getTreeFontSet().increaseFontSize();
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
}
//
}
return;
}
int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
- * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
+ * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
if ( max_length < 40 ) {
max_length = 40;
}
int longest = 30;
+ int longest_txt = 0;
+ _longest_domain = 0;
+ PhylogenyNode longest_txt_node = _phylogeny.getFirstExternalNode();
for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
int sum = 0;
if ( node.isCollapse() ) {
continue;
}
- if ( getControlPanel().isShowNodeNames() ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getName() + " " );
+ final StringBuilder sb = new StringBuilder();
+ nodeDataAsSB( node, sb );
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb );
}
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSequenceAcc()
- && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getSequence()
- .getAccession().getValue()
- + " " );
- }
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getSequence().getName()
- + " " );
- }
- if ( getControlPanel().isShowSeqSymbols()
- && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getSequence()
- .getSymbol()
- + " " );
- }
- if ( getControlPanel().isShowGeneNames()
- && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getSequence()
- .getGeneName()
- + " " );
- }
- if ( getControlPanel().isShowAnnotation()
- && ( node.getNodeData().getSequence().getAnnotations() != null )
- && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( TreePanelUtil.createAnnotationString( node
- .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
- + " " );
- }
- if ( getControlPanel().isShowDomainArchitectures()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
- .getRenderingSize().getWidth();
- }
+ final int txt = sb.length();
+ if ( txt > longest_txt ) {
+ longest_txt = txt;
+ longest_txt_node = node;
}
- if ( node.getNodeData().isHasTaxonomy() ) {
- final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( tax.getTaxonomyCode() + " " );
- }
- if ( getControlPanel().isShowTaxonomyScientificNames()
- && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( tax.getScientificName() + " " );
- }
- if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( tax.getCommonName() + " ()" );
- }
+ boolean use_vis = false;
+ final Graphics2D g = ( Graphics2D ) getGraphics();
+ if ( getControlPanel().isUseVisualStyles() ) {
+ use_vis = setFont( g, node, false );
}
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( propertiesToString( node ).toString() );
+ if ( !use_vis ) {
+ sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
+ }
+ else {
+ sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() );
}
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
- .getGainedCharactersAsStringBuffer().toString() );
+ .getGainedCharactersAsStringBuffer().toString() );
+ }
+ if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
+ && ( node.getNodeData().getVector().size() > 0 ) ) {
+ if ( getConfiguration() != null ) {
+ sum += getConfiguration().getVectorDataWidth() + 10;
+ }
+ else {
+ sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10;
+ }
+ }
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ // FIXME
+ // TODO this might need some clean up
+ final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture();
+ sum += ( ( _domain_structure_width / ( ( RenderableDomainArchitecture ) d ).getOriginalSize()
+ .getWidth() ) * d.getTotalLength() ) + 10;
+ if ( d.getTotalLength() > _longest_domain ) {
+ _longest_domain = d.getTotalLength();
+ }
+ }
+ if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+ && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+ // FIXME
+ sum += RenderableMsaSequence.DEFAULT_WIDTH + 30;
}
if ( sum >= max_length ) {
- setLongestExtNodeInfo( max_length );
- return;
+ _longest_ext_node_info = max_length;
+ // return; //FIXME why?
}
if ( sum > longest ) {
longest = sum;
}
}
+ _ext_node_with_longest_txt_info = longest_txt_node;
if ( longest >= max_length ) {
- setLongestExtNodeInfo( max_length );
+ _longest_ext_node_info = max_length;
}
else {
- setLongestExtNodeInfo( longest );
+ _longest_ext_node_info = longest;
}
+ _length_of_longest_text = calcLengthOfLongestText();
}
final void calculateScaleDistance() {
}
if ( c == null ) {
if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- c = TreePanelUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
+ c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
}
else {
- c = TreePanelUtil.calculateColorFromString( tax.getScientificName(), true );
+ c = AptxUtil.calculateColorFromString( tax.getScientificName(), true );
getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
}
}
}
}
+ final Color calculateSequenceBasedColor( final Sequence seq ) {
+ if ( ForesterUtil.isEmpty( seq.getName() ) ) {
+ return getTreeColorSet().getSequenceColor();
+ }
+ Color c = null;
+ final String seq_name = seq.getName();
+ c = getControlPanel().getSequenceColors().get( seq_name );
+ if ( c == null ) {
+ c = AptxUtil.calculateColorFromString( seq_name, false );
+ getControlPanel().getSequenceColors().put( seq_name, c );
+ }
+ return c;
+ }
+
void checkForVectorProperties( final Phylogeny phy ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
}
catch ( final NumberFormatException e ) {
JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
- + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
+ + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
return;
}
int i = -1;
catch ( final NumberFormatException e ) {
JOptionPane.showMessageDialog( this,
"Could not parse \"" + index_str
- + "\" into index for vector data",
+ + "\" into index for vector data",
"Problem with Vector Data",
JOptionPane.ERROR_MESSAGE );
return;
/**
* Collapse the tree from the given node
- *
+ *
* @param node
* a PhylogenyNode
*/
_control_panel.getColorAccSpeciesCb().setSelected( false );
}
_options.setColorLabelsSameAsParentBranch( true );
+ if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) {
+ getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true );
+ }
_control_panel.repaint();
}
setArrowCursor();
/**
* Find the node, if any, at the given location
- *
+ *
* @param x
* @param y
* @return pointer to the node at x,y, null if not found
return _statistics_for_vector_data;
}
- /**
- * Find a color for this species name.
- *
- * @param species
- * @return the species color
- */
final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
- if ( node.getNodeData().isHasTaxonomy() ) {
+ if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) {
return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
}
// return non-colorized color
return getTreeColorSet().getTaxonomyColor();
}
- /**
- * @return pointer to colorset for tree drawing
- */
- final TreeColorSet getTreeColorSet() {
+ final Color getSequenceBasedColor( final PhylogenyNode node ) {
+ if ( node.getNodeData().isHasSequence() ) {
+ return calculateSequenceBasedColor( node.getNodeData().getSequence() );
+ }
+ // return non-colorized color
+ return getTreeColorSet().getSequenceColor();
+ }
+
+ public final TreeColorSet getTreeColorSet() {
return getMainPanel().getTreeColorSet();
}
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
- double max_original_domain_structure_width = 0.0;
+ double _max_original_domain_structure_width = 0.0;
for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
if ( node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
RenderableDomainArchitecture rds = null;
if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
- rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
- getConfiguration() );
+ if ( SPECIAL_DOMAIN_COLORING ) {
+ rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+ .getDomainArchitecture(), node.getName() );
+ }
+ else {
+ rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+ .getDomainArchitecture() );
+ }
node.getNodeData().getSequence().setDomainArchitecture( rds );
}
else {
}
if ( getControlPanel().isShowDomainArchitectures() ) {
final double dsw = rds.getOriginalSize().getWidth();
- if ( dsw > max_original_domain_structure_width ) {
- max_original_domain_structure_width = dsw;
+ if ( dsw > _max_original_domain_structure_width ) {
+ _max_original_domain_structure_width = dsw;
}
}
}
}
if ( getControlPanel().isShowDomainArchitectures() ) {
- final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
+ final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width );
for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
if ( node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
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 ) ) );
+ + 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 ) ) );
+ + getOvRectangle().getHeight() + 1 ) ) );
}
final boolean isApplet() {
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();
}
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 );
+ - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
}
}
else {
if ( !to_graphics_file ) {
g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
- + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
+ + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
g.fill( r );
}
else {
}
// 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 ) {
_nodes_in_preorder[ i++ ] = it.next();
}
}
- //final PhylogenyNodeIterator it;
- //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
- // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
- // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
- //}
+ final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 )
+ || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()
+ || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
+ || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() )
+ || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() )
+ || to_graphics_file || to_pdf;
for( final PhylogenyNode element : _nodes_in_preorder ) {
- paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()
- && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
+ paintNodeRectangular( g,
+ element,
+ to_pdf,
+ getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ),
+ dynamic_hiding_factor,
+ to_graphics_file,
+ disallow_shortcutting );
}
if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
if ( !( to_graphics_file || to_pdf ) ) {
y_pos + radius_ov,
( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
.getWidth() ) ) ),
- g );
+ g );
g.setTransform( _at );
paintOvRectangle( g );
}
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil
- .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
+ .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
}
else {
if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil.roundToInt( getXdistance()
- * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
+ * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
}
else {
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil.roundToInt( getXdistance()
- * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
+ * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
}
}
setPreferredSize( new Dimension( x, y ) );
_last_drag_point_y = y;
}
- final void setLongestExtNodeInfo( final int i ) {
- _longest_ext_node_info = i;
- }
-
final void setMediumFonts() {
getTreeFontSet().mediumFonts();
}
final void sortDescendants( final PhylogenyNode node ) {
if ( !node.isExternal() ) {
- DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
- if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
- .isShowTaxonomyCommonNames() ) ) {
- if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
- .isShowSeqSymbols() ) ) {
- pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
- }
- else if ( getControlPanel().isShowNodeNames() ) {
- pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
- }
+ DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+ if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
+ pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+ }
+ else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
+ || getControlPanel().isShowGeneNames() ) {
+ pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
PhylogenyMethods.sortNodeDescendents( node, pri );
setNodeInPreorderToNull();
}
}
- private void abbreviateScientificName( final String sn ) {
+ private void abbreviateScientificName( final String sn, final StringBuilder sb ) {
final String[] a = sn.split( "\\s+" );
- _sb.append( a[ 0 ].substring( 0, 1 ) );
- _sb.append( a[ 1 ].substring( 0, 2 ) );
+ sb.append( a[ 0 ].substring( 0, 1 ) );
+ sb.append( a[ 1 ].substring( 0, 2 ) );
if ( a.length > 2 ) {
for( int i = 2; i < a.length; i++ ) {
- _sb.append( " " );
- _sb.append( a[ i ] );
+ sb.append( " " );
+ sb.append( a[ i ] );
}
}
}
/**
* Calculate the length of the distance between the given node and its
* parent.
- *
+ *
* @param node
* @param ext_node_x
* @factor
if ( !ForesterUtil.isEmpty( ann_str ) ) {
c = getControlPanel().getAnnotationColors().get( ann_str );
if ( c == null ) {
- c = TreePanelUtil.calculateColorFromString( ann_str, false );
+ c = AptxUtil.calculateColorFromString( ann_str, false );
getControlPanel().getAnnotationColors().put( ann_str, c );
}
if ( c == null ) {
else {
fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
}
- fc.showDialog( this, "Select Font" );
- if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
- List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- nodes = getFoundNodesAsListOfPhylogenyNodes();
- }
+ List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ nodes = getFoundNodesAsListOfPhylogenyNodes();
+ }
+ if ( !nodes.contains( node ) ) {
nodes.add( node );
+ }
+ final int count = nodes.size();
+ String title = "Change the font for ";
+ if ( count == 1 ) {
+ title += "one node";
+ }
+ else {
+ title += ( count + " nodes" );
+ }
+ fc.showDialog( this, title );
+ if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
for( final PhylogenyNode n : nodes ) {
if ( n.getNodeData().getNodeVisualData() == null ) {
n.getNodeData().setNodeVisualData( new NodeVisualData() );
getControlPanel().getUseVisualStylesCb().setSelected( true );
}
}
+ setEdited( true );
repaint();
}
+ private void colorNodeFont( final PhylogenyNode node ) {
+ _color_chooser.setPreviewPanel( new JPanel() );
+ NodeColorizationActionListener al;
+ int count = 1;
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
+ count = additional_nodes.size();
+ if ( !additional_nodes.contains( node ) ) {
+ count++;
+ }
+ }
+ else {
+ al = new NodeColorizationActionListener( _color_chooser, node );
+ }
+ String title = "Change the (node and font) color for ";
+ if ( count == 1 ) {
+ title += "one node";
+ }
+ else {
+ title += ( count + " nodes" );
+ }
+ final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null );
+ setEdited( true );
+ dialog.setVisible( true );
+ }
+
final private void colorizeNodes( final Color c,
final PhylogenyNode node,
final List<PhylogenyNode> additional_nodes ) {
}
}
if ( additional_nodes != null ) {
- for( final PhylogenyNode n : additional_nodes ) {
- n.getBranchData().setBranchColor( new BranchColor( c ) );
+ for( final PhylogenyNode an : additional_nodes ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
}
}
repaint();
}
- private void colorNodeFont( final PhylogenyNode node ) {
- _color_chooser.setPreviewPanel( new JPanel() );
- NodeColorizationActionListener al;
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
- al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
- }
- else {
- al = new NodeColorizationActionListener( _color_chooser, node );
- }
- final JDialog dialog = JColorChooser.createDialog( this, "Node colorization", true, _color_chooser, al, null );
- dialog.setVisible( true );
- }
-
final private void colorSubtree( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
JOptionPane.showMessageDialog( this,
}
final JDialog dialog = JColorChooser
.createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+ setEdited( true );
dialog.setVisible( true );
}
g.fill( _ellipse );
}
- final private void drawOvalGradient( final double x,
- final double y,
- final double width,
- final double heigth,
+ final private void drawOvalGradient( final float x,
+ final float y,
+ final float width,
+ final float heigth,
final Graphics2D g,
final Color color_1,
final Color color_2,
final Color color_border ) {
_ellipse.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint( ( float ) x,
- ( float ) y,
- color_1,
- ( float ) ( x + width ),
- ( float ) ( y + heigth ),
- color_2,
- false ) );
+ g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
g.fill( _ellipse );
if ( color_border != null ) {
g.setPaint( color_border );
g.fill( _rectangle );
}
- final private void drawRectGradient( final double x,
- final double y,
- final double width,
- final double heigth,
+ final private void drawRectGradient( final float x,
+ final float y,
+ final float width,
+ final float heigth,
final Graphics2D g,
final Color color_1,
final Color color_2,
final Color color_border ) {
_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.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
g.fill( _rectangle );
if ( color_border != null ) {
g.setPaint( color_border );
return getTreeFontSet().getFontMetricsLarge();
}
- private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+ List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
if ( getFoundNodes0() != null ) {
for( final Long id : getFoundNodes0() ) {
- additional_nodes.add( _phylogeny.getNode( id ) );
+ final PhylogenyNode n = _phylogeny.getNode( id );
+ if ( n != null ) {
+ additional_nodes.add( n );
+ }
}
}
if ( getFoundNodes1() != null ) {
for( final Long id : getFoundNodes1() ) {
if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
- additional_nodes.add( _phylogeny.getNode( id ) );
+ final PhylogenyNode n = _phylogeny.getNode( id );
+ if ( n != null ) {
+ additional_nodes.add( n );
+ }
}
}
}
return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
&& ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
&& ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
- + getOvVirtualRectangle().height + 1 ) ) );
+ + getOvVirtualRectangle().height + 1 ) ) );
}
final private boolean inOvVirtualRectangle( final MouseEvent e ) {
&& ( ( !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() ) ) ) ) {
+ .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+ .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
return true;
}
else {
}
return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
|| ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
- .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
+ .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 ) ) );
+ .getMaxX() + 20 ) ) );
}
final private boolean isNonLinedUpCladogram() {
}
}
+ private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
+ if ( node != null ) {
+ if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getName() );
+ }
+ if ( node.getNodeData().isHasSequence() ) {
+ if ( getControlPanel().isShowSeqSymbols()
+ && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getSymbol() );
+ }
+ if ( getControlPanel().isShowGeneNames()
+ && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getGeneName() );
+ }
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getName() );
+ }
+ if ( getControlPanel().isShowSequenceAcc()
+ && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
+ sb.append( node.getNodeData().getSequence().getAccession().getSource() );
+ sb.append( ":" );
+ }
+ sb.append( node.getNodeData().getSequence().getAccession().getValue() );
+ }
+ }
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( propertiesToString( node ) );
+ }
+ }
+ }
+
+ private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
+ if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
+ sb.append( taxonomy.getTaxonomyCode() );
+ sb.append( " " );
+ }
+ if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
+ && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " (" );
+ sb.append( taxonomy.getCommonName() );
+ sb.append( ") " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
+ }
+ }
+ else if ( _control_panel.isShowTaxonomyScientificNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " " );
+ }
+ }
+ else if ( _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
+ }
+ }
+ }
+
private final String obtainTitleForExtDescNodeData() {
switch ( getOptions().getExtDescNodeDataToReturn() ) {
case NODE_NAME:
AptxUtil.launchWebBrowser( new URI( uri_str ),
isApplet(),
isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
+ "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
AptxUtil.launchWebBrowser( new URI( uri_str ),
isApplet(),
isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
+ "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
AptxUtil.launchWebBrowser( new URI( uri_str ),
isApplet(),
isApplet() ? obtainApplet() : null,
- "_aptx_tax" );
+ "_aptx_tax" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
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 );
+ .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 );
+ .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 );
+ .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
}
else {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
- - getTreeFontSet().getSmallMaxDescent(), g );
+ - getTreeFontSet().getSmallMaxDescent(), g );
}
}
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 );
+ + ( dy * 0.8f ), x2, y2 );
( g ).draw( _cubic_curve );
}
else {
/**
* Paint a branch which consists of a vertical and a horizontal bar
- * @param is_ind_found_nodes
+ * @param is_ind_found_nodes
*/
final private void paintBranchRectangular( final Graphics2D g,
final float x1,
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 );
+ + ( dy * 0.8f ), x2, y2 );
g.draw( _cubic_curve );
}
else {
else if ( is_in_found_nodes ) {
c = getColorForFoundNode( node );
}
+ else if ( getControlPanel().isColorAccordingToSequence() ) {
+ c = getSequenceBasedColor( node );
+ }
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
c = getTaxonomyBasedColor( node );
}
d = box_size;
}
final float xx = node.getXcoord() - ( 2 * box_size );
- final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
+ 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 );
Collections.sort( confidences );
final StringBuilder sb = new StringBuilder();
for( final Confidence confidence : confidences ) {
- final double value = confidence.getValue();
- if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- if ( value < getOptions().getMinConfidenceValue() ) {
- return;
- }
- if ( not_first ) {
- sb.append( "/" );
- }
- else {
- not_first = true;
- }
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- if ( getOptions().isShowConfidenceStddev() ) {
- if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- sb.append( "(" );
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
- getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- sb.append( ")" );
+ if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE )
+ || ( !ForesterUtil.isEmpty( confidence.getType() ) && confidence.getType()
+ .equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) {
+ final double value = confidence.getValue();
+ if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ if ( value < getOptions().getMinConfidenceValue() ) {
+ return;
+ }
+ if ( not_first ) {
+ sb.append( "/" );
+ }
+ else {
+ not_first = true;
+ }
+ sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ if ( getOptions().isShowConfidenceStddev() ) {
+ if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ sb.append( "(" );
+ sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
+ .getStandardDeviation(), getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ sb.append( ")" );
+ }
}
}
}
final String 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 );
+ + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall()
+ .stringWidth( conf_str ) ) / 2 ),
+ ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
+ g );
}
}
g.setColor( Color.BLUE );
}
TreePanel
- .drawString( gained,
- parent_x
- + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
- ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
- g );
+ .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 );
}
}
/**
* Draw a box at the indicated node.
- *
+ *
* @param x
* @param y
* @param node
* @param g
*/
- final private void paintNodeBox( final double x,
- final double y,
+ final private void paintNodeBox( final float x,
+ final float y,
final PhylogenyNode node,
final Graphics2D g,
final boolean to_pdf,
if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
|| ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
|| ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
- || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
- .isDuplication()
- || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
- .isSpeciationOrDuplication() ) ) ) {
- final double box_size = getOptions().getDefaultNodeShapeSize();
- final double half_box_size = box_size / 2.0;
+ || ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
+ && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData()
+ .getNodeVisualData().isEmpty() ) )
+ || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
+ .getNodeData().getNodeVisualData().getNodeColor() != null )
+ || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
+ || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node
+ .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
+ || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
+ .isDuplication()
+ || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) ) ) {
+ NodeVisualData vis = null;
+ if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
+ && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) {
+ vis = node.getNodeData().getNodeVisualData();
+ }
+ float box_size = getOptions().getDefaultNodeShapeSize();
+ if ( ( vis != null ) && ( vis.getSize() != NodeVisualData.DEFAULT_SIZE ) ) {
+ box_size = vis.getSize();
+ }
+ final float half_box_size = box_size / 2.0f;
Color outline_color = null;
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
outline_color = Color.BLACK;
else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
outline_color = getColorForFoundNode( node );
}
+ else if ( vis != null ) {
+ if ( vis.getNodeColor() != null ) {
+ outline_color = vis.getNodeColor();
+ }
+ else if ( vis.getFontColor() != null ) {
+ outline_color = vis.getFontColor();
+ }
+ }
else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
}
}
- else {
+ if ( outline_color == null ) {
outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
outline_color = getTreeColorSet().getBranchColorForPdf();
}
}
- if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ NodeShape shape = null;
+ if ( vis != null ) {
+ if ( vis.getShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( vis.getShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ if ( shape == null ) {
+ if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ NodeFill fill = null;
+ if ( vis != null ) {
+ if ( vis.getFillType() == NodeFill.SOLID ) {
+ fill = NodeFill.SOLID;
+ }
+ else if ( vis.getFillType() == NodeFill.NONE ) {
+ fill = NodeFill.NONE;
+ }
+ else if ( vis.getFillType() == NodeFill.GRADIENT ) {
+ fill = NodeFill.GRADIENT;
+ }
+ }
+ if ( fill == null ) {
+ if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
+ fill = NodeFill.SOLID;
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ fill = NodeFill.NONE;
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ fill = NodeFill.GRADIENT;
+ }
+ }
+ Color vis_fill_color = null;
+ if ( ( vis != null ) && ( vis.getNodeColor() != null ) ) {
+ vis_fill_color = vis.getNodeColor();
+ }
+ if ( shape == NodeShape.CIRCLE ) {
+ if ( fill == NodeFill.GRADIENT ) {
drawOvalGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
: outline_color, to_pdf ? outline_color : getBackground(), outline_color );
}
- else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ else if ( fill == NodeFill.NONE ) {
Color background = getBackground();
if ( to_pdf ) {
background = Color.WHITE;
background,
outline_color );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
- g.setColor( outline_color );
+ else if ( fill == NodeVisualData.NodeFill.SOLID ) {
+ if ( vis_fill_color != null ) {
+ g.setColor( vis_fill_color );
+ }
+ else {
+ g.setColor( outline_color );
+ }
drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
- else if ( getOptions().getDefaultNodeShape() == NodeVisualData.NodeShape.RECTANGLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.GRADIENT ) {
+ else if ( shape == NodeVisualData.NodeShape.RECTANGLE ) {
+ if ( fill == NodeVisualData.NodeFill.GRADIENT ) {
drawRectGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
: outline_color, to_pdf ? outline_color : getBackground(), outline_color );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
+ else if ( fill == NodeVisualData.NodeFill.NONE ) {
Color background = getBackground();
if ( to_pdf ) {
background = Color.WHITE;
background,
outline_color );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
- g.setColor( outline_color );
+ else if ( fill == NodeVisualData.NodeFill.SOLID ) {
+ if ( vis_fill_color != null ) {
+ g.setColor( vis_fill_color );
+ }
+ else {
+ g.setColor( outline_color );
+ }
drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
return 0;
}
- if ( getOptions().isShowBranchLengthValues()
+ 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 ) ) {
+ && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
paintBranchLength( g, node, to_pdf, to_graphics_file );
}
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
else {
_sb.setLength( 0 );
}
- if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getName() );
- }
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getNodeData().getSequence().getSymbol() );
- }
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getNodeData().getSequence().getGeneName() );
- }
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getNodeData().getSequence().getName() );
- }
- if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
- _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
- _sb.append( ":" );
- }
- _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
- }
- }
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( propertiesToString( node ) );
- }
+ 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 ) ) {
final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
.getRef1().isEqual( _query_sequence ) )
&& seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
- .getSelectedItem() );
+ .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
+ 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();
+ .getBounds().getWidth();
TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
}
nodeTextBoundsWidth += 2;
}
g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
- + nodeTextBoundsWidth, 3 + ( int ) pos_y );
+ + nodeTextBoundsWidth, 3 + ( int ) pos_y );
break;
}
}
}
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 );
+ + ( 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 );
+ .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() );
+ .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 );
+ .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() );
+ + node.getNodeData().getBinaryCharacters().getLostCount() );
}
}
}
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 );
+ - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
}
float new_x = 0;
if ( !node.isExternal() && !node.isCollapse() ) {
final boolean to_pdf,
final boolean dynamically_hide,
final int dynamic_hiding_factor,
- final boolean to_graphics_file ) {
+ final boolean to_graphics_file,
+ final boolean disallow_shortcutting ) {
final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
if ( node.isCollapse() ) {
if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
&& !node.isRoot()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && node.getBranchData().isHasConfidences() ) {
+ && node.getBranchData().isHasConfidences() ) {
paintConfidenceValues( g, node, to_pdf, to_graphics_file );
}
// Draw a line to root:
}
float new_x = 0;
float new_x_min = Float.MAX_VALUE;
- final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
float min_dist = 1.5f;
if ( !disallow_shortcutting ) {
- // System.out.println( dynamic_hiding_factor );
if ( dynamic_hiding_factor > 4000 ) {
min_dist = 4;
}
final float diff_y = node.getYcoord() - y2;
final float diff_x = node.getXcoord() - new_x;
if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
- || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
+ || ( diff_x < -min_dist ) ) {
paintBranchRectangular( g,
node.getXcoord(),
new_x,
&& !is_in_found_nodes
&& ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
.isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont()
- .getHeight() ) ) ) ) ) {
+ .getHeight() ) ) ) ) ) {
return;
}
final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
final PhylogenyNode node,
final boolean to_graphics_file,
final boolean to_pdf ) {
- if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
+ if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) {
return;
}
if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
return;
}
if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null )
+ && ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
RenderableDomainArchitecture rds = null;
- if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
- try {
- rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
- }
- catch ( final ClassCastException cce ) {
- cce.printStackTrace();
+ try {
+ rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
+ }
+ catch ( final ClassCastException cce ) {
+ cce.printStackTrace();
+ }
+ if ( rds != null ) {
+ final int default_height = 7;
+ float y = getYdistance();
+ if ( getControlPanel().isDynamicallyHideData() ) {
+ y = getTreeFontSet().getFontMetricsLarge().getHeight();
+ }
+ final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
+ rds.setRenderingHeight( h > 1 ? h : 2 );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( getOptions().isLineUpRendarableNodeData() ) {
+ if ( getOptions().isRightLineUpDomains() ) {
+ rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + _length_of_longest_text + ( ( _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 ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
+ }
+ else {
+ rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
+ }
}
- if ( rds != null ) {
- rds.setRenderingHeight( 6 );
- rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
+ 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 );
+ }
+ else {
+ rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
}
}
}
- //////////////
if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
&& ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
getStatisticsForExpressionValues(),
getConfiguration() );
if ( rv != null ) {
- int xx = 0;
- PhylogenyNode my_node = node;
- if ( !getControlPanel().isDrawPhylogram() ) {
- my_node = getPhylogeny().getFirstExternalNode();
+ double domain_add = 0;
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ domain_add = _domain_structure_width + 10;
}
- if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
- xx += getFontMetricsForLargeDefaultFont()
- .stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
}
- if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
- xx += getFontMetricsForLargeDefaultFont().stringWidth( my_node.getName() + " " );
+ else {
+ 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() ) ) ) {
+ final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
+ .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
+ if ( rs != null ) {
+ final int default_height = 7;
+ float y = getYdistance();
+ if ( getControlPanel().isDynamicallyHideData() ) {
+ y = getTreeFontSet().getFontMetricsLarge().getHeight();
+ }
+ final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
+ rs.setRenderingHeight( h > 1 ? h : 2 );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
+ else {
+ rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
}
- rv.render( my_node.getXcoord() + xx, node.getYcoord() - 5, g, this, to_pdf );
}
}
- //////////////
+ }
+
+ final private int calcLengthOfLongestText() {
+ final StringBuilder sb = new StringBuilder();
+ if ( _ext_node_with_longest_txt_info != null ) {
+ nodeDataAsSB( _ext_node_with_longest_txt_info, sb );
+ if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) {
+ nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
+ }
+ }
+ return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
final private void paintOvRectangle( final Graphics2D g ) {
final private void paintPhylogenyLite( final Graphics2D g ) {
_phylogeny
- .getRoot()
- .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
- .getWidth() ) ) ) );
+ .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 );
/**
* Paint the root branch. (Differs from others because it will always be a
* single horizontal line).
- * @param to_graphics_file
- *
+ * @param to_graphics_file
+ *
* @return new x1 value
*/
final private void paintRootBranch( final Graphics2D g,
+ ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
}
_sb.setLength( 0 );
- if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
- _sb.append( taxonomy.getTaxonomyCode() );
- _sb.append( " " );
- }
- if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
- && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName() );
- }
- else {
- _sb.append( taxonomy.getScientificName() );
- }
- _sb.append( " (" );
- _sb.append( taxonomy.getCommonName() );
- _sb.append( ") " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName() );
- }
- else {
- _sb.append( taxonomy.getScientificName() );
- }
- _sb.append( " " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getCommonName() );
- _sb.append( " " );
- }
- }
- else if ( _control_panel.isShowTaxonomyScientificNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName() );
- }
- else {
- _sb.append( taxonomy.getScientificName() );
- }
- _sb.append( " " );
- }
- }
- else if ( _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getCommonName() );
- _sb.append( " " );
- }
- }
+ nodeTaxonomyDataAsSB( taxonomy, _sb );
final String label = _sb.toString();
/* GUILHEM_BEG */
if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
false,
false ) )
- .getBounds();
+ .getBounds();
g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
g.setColor( getTreeColorSet().getBackgroundColor() );
}
&& ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
}
+ else if ( getControlPanel().isColorAccordingToSequence() ) {
+ g.setColor( getSequenceBasedColor( node ) );
+ }
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
}
private final void setupStroke( final Graphics2D g ) {
+ if ( getYdistance() < 0.0001 ) {
+ g.setStroke( STROKE_0025 );
+ }
if ( getYdistance() < 0.001 ) {
g.setStroke( STROKE_005 );
}
else if ( getYdistance() < 2 ) {
g.setStroke( STROKE_075 );
}
- else if ( getYdistance() < 20 ) {
+ else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) {
g.setStroke( STROKE_1 );
}
else {
ann_str = ann.toString();
}
sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
- .getMolecularSequence(), 60 ) );
+ .getMolecularSequence(), 60 ) );
data.add( sb.toString() );
}
break;
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" );
+ + ")", "Descendants of selected node do not contain selected data" );
clearCurrentExternalNodesDataBuffer();
}
else {
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() ) {
+ .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( "] " );
}
_popup_buffer
- .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
- getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ .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() ) ) );
+ .getStandardDeviation(), getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
_popup_buffer.append( ")" );
}
}
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() );
else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
_rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
}
- else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
- }
else {
_rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
}
_rollover_popup,
e.getLocationOnScreen().x + 10,
e.getLocationOnScreen().y
- - ( lines * 20 ) );
+ - ( lines * 20 ) );
_node_desc_popup.show();
}
}
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
+ .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
}
else {
getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
git://source.jalview.org / jalview.git / blobdiff