.getDefaultFontFamilyName(), Font.PLAIN, 9 );
final static Font js_font = new Font( Configuration
.getDefaultFontFamilyName(), Font.PLAIN, 9 );
- private static final String RETURN_TO_SUPER_TREE_TEXT = "Back to Super Tree";
+ private static final String RETURN_TO_SUPER_TREE_TEXT = "R";
private static final String SEARCH_TIP_TEXT = "Enter text to search for. Use ',' for logical OR and '+' for logical AND (not used in this manner for regular expression searches).";
private static final long serialVersionUID = -8463483932821545633L;
private NodeClickAction _action_when_node_clicked;
return getIsDrawPhylogramList().get( index );
}
- private void search0( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
+ private void search0( final MainPanel main_panel, final Phylogeny tree, String query_str ) {
getSearchFoundCountsLabel0().setVisible( true );
getSearchResetButton0().setEnabled( true );
getSearchResetButton0().setVisible( true );
String[] queries = null;
Set<Long> nodes = null;
+ query_str = query_str.replaceAll("\\s+", " " );
if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
queries = query_str.split( ",+" );
}
}
}
- private void search1( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
+ private void search1( final MainPanel main_panel, final Phylogeny tree, String query_str ) {
getSearchFoundCountsLabel1().setVisible( true );
getSearchResetButton1().setEnabled( true );
getSearchResetButton1().setVisible( true );
String[] queries = null;
Set<Long> nodes = null;
+ query_str = query_str.replaceAll("\\s+", " " );
if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
queries = query_str.split( ",+" );
}
_return_to_super_tree.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
_return_to_super_tree.setEnabled( true );
}
+
+ void activateButtonToUncollapseAll() {
+ _uncollapse_all.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
+ _uncollapse_all.setEnabled( true );
+ }
+
/**
* Add zoom and quick edit buttons. (Last modified 8/9/04)
final JPanel x_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
final JPanel y_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
final JPanel z_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
+ final JPanel o_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
if ( !getConfiguration().isUseNativeUI() ) {
x_panel.setBackground( getBackground() );
y_panel.setBackground( getBackground() );
z_panel.setBackground( getBackground() );
+ o_panel.setBackground( getBackground() );
}
add( _zoom_label = new JLabel( "Zoom:" ) );
customizeLabel( _zoom_label, getConfiguration() );
_zoom_in_y.setPreferredSize( new Dimension( 10, 10 ) );
_show_whole.setPreferredSize( new Dimension( 10, 10 ) );
_return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
+ _return_to_super_tree.setToolTipText( "return to the super-tree (if in sub-tree)" );
_return_to_super_tree.setEnabled( false );
- _order = new JButton( "Order Tree" );
- _uncollapse_all = new JButton( "Uncollapse All" );
+ _order = new JButton( "O" );
+ _order.setToolTipText( "order all" );
+ _uncollapse_all = new JButton( "U" );
+ _uncollapse_all.setToolTipText( "uncollapse all" );
addJButton( _zoom_in_y, x_panel );
addJButton( _zoom_out_x, y_panel );
addJButton( _show_whole, y_panel );
addJButton( _zoom_in_x, y_panel );
addJButton( _zoom_out_y, z_panel );
+
+ final JLabel spacer2 = new JLabel( "" );
+ add( spacer2 );
+ add( o_panel );
+ addJButton( _order, o_panel );
+ addJButton( _return_to_super_tree, o_panel );
+ addJButton( _uncollapse_all, o_panel );
+
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
setUpControlsForDomainStrucures();
}
if ( true ) {
setUpControlsForRankCollapse();
}
- final JLabel spacer2 = new JLabel( "" );
- add( spacer2 );
- addJButton( _return_to_super_tree, this );
- addJButton( _order, this );
- addJButton( _uncollapse_all, this );
+
final JLabel spacer3 = new JLabel( "" );
add( spacer3 );
setVisibilityOfDomainStrucureControls();
_return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
_return_to_super_tree.setEnabled( false );
}
+
+ void deactivateButtonToUncollapseAll() {
+ _uncollapse_all.setForeground( getConfiguration().getGuiButtonTextColor() );
+ _uncollapse_all.setEnabled( false );
+ }
+
void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
if ( ( _mainpanel != null )
updateDepthCollapseDepthDisplay();
updateRankCollapseRankDisplay();
getMainPanel().getControlPanel();
+ _mainpanel.getCurrentTreePanel().updateButtonToUncollapseAll();
_mainpanel.getCurrentTreePanel().calculateScaleDistance();
_mainpanel.getCurrentTreePanel().calcMaxDepth();
_mainpanel.adjustJScrollPane();
.setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel().getPhylogenyGraphicsType() );
}
getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
+ getMainPanel().getCurrentTreePanel().updateButtonToUncollapseAll();
getMainPanel().getControlPanel().search0();
getMainPanel().getControlPanel().search1();
getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
+ private static final BasicStroke STROKE_01_DASHED = new BasicStroke( 0.1f,
+ BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_ROUND,
+ 0,
+ new float[] {
+ 2.0f }, 0f );
+
+
+
+ private static final BasicStroke STROKE_005_DASHED = new BasicStroke( 0.05f,
+ BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_ROUND,
+ 0,
+ new float[] {
+ 2.0f },
+ 0f );
+ private static final BasicStroke STROKE_001_DASHED = new BasicStroke( 0.01f,
+ BasicStroke.CAP_SQUARE,
+ BasicStroke.JOIN_ROUND,
+ 0,
+ new float[] {
+ 2.0f },
+ 0f );
private static final double TWO_PI = 2 * Math.PI;
private final static int WIGGLE = 2;
private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me
x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
}
setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
+ boolean saw_species = _sb.length() > 0;
+ _sb.setLength( 0 );
+ nodeDataAsSB( node, _sb );
if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- if ( _sb.length() == 0 ) {
+ if ( _sb.length() == 0 && !saw_species ) {
if ( getOptions().isShowAbbreviatedLabelsForCollapsedNodes()
&& ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
|| getControlPanel().isShowSeqNames() || getControlPanel().isShowNodeNames() ) ) {
&& last.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getTaxonomyCode() )
&& !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+
addLabelForCollapsed( first.getNodeData().getTaxonomy().getTaxonomyCode(),
last.getNodeData().getTaxonomy().getTaxonomyCode(),
node.getAllExternalDescendants().size() );
&& last.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getScientificName() )
&& !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getScientificName() ) ) {
- addLabelForCollapsed( first.getNodeData().getTaxonomy().getScientificName(),
+ addLabelForCollapsed( first.getNodeData().getTaxonomy().getScientificName(),
last.getNodeData().getTaxonomy().getScientificName(),
node.getAllExternalDescendants().size() );
}
}
}
}
- else if ( _sb.length() > 0 ) {
- _sb.setLength( 0 );
+ else if ( _sb.length() > 0 || saw_species ) {
+ // _sb.setLength( 0 );
_sb.append( " (" );
_sb.append( node.getAllExternalDescendants().size() );
_sb.append( ")" );
+
}
}
else {
- _sb.setLength( 0 );
+ // _sb.setLength( 0 );
}
- nodeDataAsSB( node, _sb );
+
+ // nodeDataAsSB( node, _sb );
+
final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
float down_shift_factor = 3.0f;
if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
down_shift_factor = 1;
}
- final float pos_x = node.getXcoord() + x + 2 + half_box_size;
+ float pos_x;
+ if ( getControlPanel().isDrawPhylogram() && getOptions().isAlignExtLabelsInPhylogram() && (node.isExternal() || node.isCollapse() ) ) {
+ pos_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x + ( 2 * TreePanel.MOVE ) + getXdistance()
+ + 3 );
+
+ }
+ else {
+ pos_x = node.getXcoord() + x + 2 + half_box_size;
+ }
float pos_y;
if ( !using_visual_font ) {
pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) );
else {
pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
}
+ if ( getControlPanel().isDrawPhylogram() && getOptions().isAlignExtLabelsInPhylogram() && (node.isExternal() || node.isCollapse() ) ) {
+ drawConnection( node.getXcoord(), pos_x - x, node.getYcoord(), 5, 20, g, to_pdf );
+ if ( node.isCollapse()) {
+ pos_x -= add;
+ }
+ }
final String sb_str = _sb.toString();
// GUILHEM_BEG ______________
if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
&& ( _query_sequence != null ) ) {
- int nodeTextBoundsWidth = 0;
- if ( sb_str.length() > 0 ) {
- final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
- nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
- }
- if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
- if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
- g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
- g.setColor( getTreeColorSet().getBackgroundColor() );
- }
- }
- else {
- final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
- for( final SequenceRelation seqRelation : seqRelations ) {
- final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence )
- || seqRelation.getRef1().isEqual( _query_sequence ) )
- && seqRelation.getType()
- .equals( getControlPanel().getSequenceRelationTypeBox().getSelectedItem() );
- if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
- final double linePosX = node.getXcoord() + 2 + half_box_size;
- final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence()
- || ( seqRelation.getConfidence() == null ) ) ? null
- : " (" + seqRelation.getConfidence().getValue() + ")";
- if ( sConfidence != null ) {
- float confidenceX = pos_x;
- if ( sb_str.length() > 0 ) {
- confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
- + CONFIDENCE_LEFT_MARGIN;
- }
- if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
- final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
- .getBounds().getWidth();
- TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
- x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
- }
- }
- if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
- {
- if ( nodeTextBoundsWidth == 0 ) {
- nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
- }
- else {
- nodeTextBoundsWidth += 2;
- }
- g.drawLine( ( int ) linePosX + 1,
- 3 + ( int ) pos_y,
- ( int ) linePosX + x + nodeTextBoundsWidth,
- 3 + ( int ) pos_y );
- break;
- }
- }
- }
- }
+ x = paintSequenceRelation( g, node, x, half_box_size, pos_x, pos_y, sb_str );
}
+ // GUILHEM_END _____________
if ( sb_str.length() > 0 ) {
if ( !isAllowAttributedStrings() ) {
TreePanel.drawString( sb_str, pos_x, pos_y, g );
drawStringX( sb_str, pos_x, pos_y, g );
}
}
- // GUILHEM_END _____________
+
if ( _sb.length() > 0 ) {
if ( !using_visual_font && !is_in_found_nodes ) {
x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
return x;
}
+ private final int paintSequenceRelation( final Graphics2D g,
+ final PhylogenyNode node,
+ int x,
+ final int half_box_size,
+ float pos_x,
+ float pos_y,
+ final String sb_str ) {
+ int nodeTextBoundsWidth = 0;
+ if ( sb_str.length() > 0 ) {
+ final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
+ nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
+ }
+ if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
+ if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
+ g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
+ g.setColor( getTreeColorSet().getBackgroundColor() );
+ }
+ }
+ else {
+ final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
+ for( final SequenceRelation seqRelation : seqRelations ) {
+ final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence )
+ || seqRelation.getRef1().isEqual( _query_sequence ) )
+ && seqRelation.getType()
+ .equals( getControlPanel().getSequenceRelationTypeBox().getSelectedItem() );
+ if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
+ final double linePosX = node.getXcoord() + 2 + half_box_size;
+ final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence()
+ || ( seqRelation.getConfidence() == null ) ) ? null
+ : " (" + seqRelation.getConfidence().getValue() + ")";
+ if ( sConfidence != null ) {
+ float confidenceX = pos_x;
+ if ( sb_str.length() > 0 ) {
+ confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
+ + CONFIDENCE_LEFT_MARGIN;
+ }
+ if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
+ final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
+ .getBounds().getWidth();
+ TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
+ x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
+ }
+ }
+ if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
+ {
+ if ( nodeTextBoundsWidth == 0 ) {
+ nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
+ }
+ else {
+ nodeTextBoundsWidth += 2;
+ }
+ g.drawLine( ( int ) linePosX + 1,
+ 3 + ( int ) pos_y,
+ ( int ) linePosX + x + nodeTextBoundsWidth,
+ 3 + ( int ) pos_y );
+ break;
+ }
+ }
+ }
+ }
+ return x;
+ }
+
+ private final void drawConnection( final float x1,
+ final float x2,
+ final float y,
+ final int dist_left,
+ final int dist_right,
+ final Graphics2D g,
+ final boolean pdf ) {
+ if ( ( ( x1 + dist_left ) < ( x2 - dist_right ) ) ) {
+ final Stroke strok = g.getStroke();
+ Color col = null;
+ if ( strok == STROKE_005 ) {
+ g.setStroke( STROKE_001_DASHED );
+ }
+ else if ( strok == STROKE_01 ) {
+ g.setStroke( STROKE_005_DASHED );
+ }
+ else {
+ g.setStroke( STROKE_01_DASHED );
+ }
+ if ( pdf ) {
+ col = g.getColor();
+ g.setColor( lighter( col ) );
+ }
+ drawLine( x1 + dist_left, y, x2 - dist_right, y, g );
+ g.setStroke( strok );
+ if ( pdf ) {
+ g.setColor( col );
+ }
+ }
+ }
+
+ public static Color lighter( final Color color ) {
+ if ( ( color.getRed() == 0 ) && ( color.getGreen() == 0 ) && ( color.getBlue() == 0 ) ) {
+ return new Color( 200, 200, 200 );
+ }
+ else {
+ return color;
+ }
+ }
+
private final void addLabelForCollapsed( final String first, final String last, final int size ) {
_sb.append( first.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? first
: first.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) );
final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() );
- final float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
+ float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
+ if ( getControlPanel().isDrawPhylogram() && getOptions().isAlignExtLabelsInPhylogram() && node.isExternal() ) {
+ start_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift + ( 2 * TreePanel.MOVE ) + getXdistance()
+ + 3 );
+ }
float start_y;
if ( !using_visual_font ) {
start_y = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
setYdistance( ydist );
setOvXDistance( ov_xdist );
final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() );
+ //final double height = PhylogenyMethods.calculateMaxDepth( _phylogeny );
if ( height > 0 ) {
final float corr = ( float ) ( ( x - ( 2.0 * TreePanel.MOVE ) - getLongestExtNodeInfo()
- getXdistance() ) / height );
final void recalculateMaxDistanceToRoot() {
_max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
+ if ( getPhylogeny().getRoot().getDistanceToParent() > 0 ) {
+ _max_distance_to_root += getPhylogeny().getRoot().getDistanceToParent();
+ }
}
/**
getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
}
}
+
+ final void updateButtonToUncollapseAll() {
+ if ( PhylogenyMethods.isHasCollapsedNodes(_phylogeny) ) {
+ getControlPanel().activateButtonToUncollapseAll();
+ }
+ else {
+ getControlPanel().deactivateButtonToUncollapseAll();
+ }
+ }
final void zoomInDomainStructure() {
if ( _domain_structure_width < 2000 ) {
git://source.jalview.org / jalview.git / commitdiff