private Set<Long> _current_external_nodes = null;
private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
private int _current_external_nodes_data_buffer_change_counter = 0;
- private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
- private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
+ private int _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 float _y_distance = 0.0f;
private int _length_of_longest_text;
private int _longest_domain;
- // private Image offscreenImage;
- // private Graphics offscreenGraphics;
- // private Dimension offscreenDimension;
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
calculateScaleDistance();
FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
- .getNumberOfDigitsAfterCommaForBranchLengthValues() );
+ .getNumberOfDigitsAfterCommaForBranchLengthValues() );
}
@Override
if ( e.isControlDown() ) {
if ( notches < 0 ) {
getTreeFontSet().increaseFontSize();
- getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
else {
getTreeFontSet().decreaseFontSize( 1, false );
- getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ resetPreferredSize();
+ updateOvSizes();
+ repaint();
}
else if ( e.isShiftDown() ) {
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
else {
if ( notches < 0 ) {
for( int i = 0; i < ( -notches ); ++i ) {
- getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
for( int i = 0; i < notches; ++i ) {
- getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
+ getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
if ( notches < 0 ) {
for( int i = 0; i < ( -notches ); ++i ) {
- getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
- getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
+ AptxConstants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
+ getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
else {
for( int i = 0; i < notches; ++i ) {
- getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
- Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
+ getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
+ AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
catch ( final Exception e ) {
e.printStackTrace();
}
- if ( Constants.ALLOW_DDBJ_BLAST ) {
- try {
- System.out.println( "trying: " + query );
- final Blast s = new Blast();
- s.ddbjBlast( query );
- }
- catch ( final Exception e ) {
- e.printStackTrace();
- }
- }
}
}
}
nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
}
}
+
return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
return;
}
_color_chooser.setPreviewPanel( new JPanel() );
- SubtreeColorizationActionListener al;
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final SubtreeColorizationActionListener al;
+ final boolean color_found = getOptions().isColorAllFoundNodesWhenColoringSubtree();
+ if ( color_found && ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) ) {
final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
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() {
|| ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
if ( e.getKeyCode() == KeyEvent.VK_UP ) {
- getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
- getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
- getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
- Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().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( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_FACTOR );
+ 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( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
- Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
+ AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( plusPressed( e.getKeyCode() ) ) {
- getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
+ AptxConstants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
else if ( e.getKeyCode() == KeyEvent.VK_S ) {
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() );
.equalsIgnoreCase( "uniprot" ) ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/"
- + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
+ + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
+ + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
+ + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
try {
uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
+ + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF_8 );
}
catch ( final UnsupportedEncodingException 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 {
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 {
not_first = true;
}
sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
if ( getOptions().isShowConfidenceStddev() ) {
if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
sb.append( "(" );
sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
- .getStandardDeviation(), getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ .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 );
}
}
final float x = node.getXcoord();
g.setFont( getTreeFontSet().getLargeFont() );
g.setColor( getTreeColorSet().getGainedCharactersColor() );
- if ( Constants.SPECIAL_CUSTOM ) {
+ 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 );
+ .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() );
+ .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
if ( rs != null ) {
final int default_height = 8;
final float y = getYdistance();
|| ( 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() ) ) ) {
+ .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 ( 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() ) {
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 ) {
}
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() ) {
&& !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:
&& !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 );
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 );
+ .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
}
else {
rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
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 );
+ + ( ( _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,
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 );
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() );
}
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() );
_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() );
setOvXDistance( ov_xdist );
final double height = _phylogeny.getHeight();
if ( height > 0 ) {
- final float corr = ( float ) ( ( x - 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_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
- * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
- if ( max_length < 40 ) {
- max_length = 40;
- }
+ 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;
+ }
int longest = 30;
int longest_txt = 0;
_longest_domain = 0;
}
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
sum += RenderableMsaSequence.DEFAULT_WIDTH + 30;
}
- if ( sum >= max_length ) {
- _longest_ext_node_info = max_length;
+ if ( sum >= max_possible_length ) {
+ _longest_ext_node_info = max_possible_length;
// return; //FIXME why?
}
if ( sum > longest ) {
}
}
_ext_node_with_longest_txt_info = longest_txt_node;
- if ( longest >= max_length ) {
- _longest_ext_node_info = max_length;
- }
- else {
- _longest_ext_node_info = longest;
- }
+ if ( longest >= max_possible_length ) {
+ _longest_ext_node_info = max_possible_length;
+ }
+ else {
+ _longest_ext_node_info = longest;
+ }
_length_of_longest_text = calcLengthOfLongestText();
}
}
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;
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 );
}
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 ) {
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 ) );
git://source.jalview.org / jalview.git / blobdiff