From: cmzmasek Date: Thu, 6 Oct 2016 23:27:29 +0000 (-0700) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f4c563596b6968fd343fdab7fa32b54431a17f2e;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 03f5590..501877f 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -289,25 +289,10 @@ final class ControlPanel extends JPanel implements ActionListener { showWhole(); } else if ( e.getSource() == _return_to_super_tree ) { - _mainpanel.getCurrentTreePanel().superTree(); - showWhole(); + returnedToSuperTreePressed(); } else if ( e.getSource() == _order ) { - DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; - if ( isShowTaxonomyScientificNames() || isShowTaxonomyCode() ) { - pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; - } - else if ( isShowSeqNames() || isShowSeqSymbols() || isShowGeneNames() ) { - pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; - } - PhylogenyMethods.orderAppearanceX( tp.getPhylogeny().getRoot(), true, pri ); - tp.setNodeInPreorderToNull(); - tp.getPhylogeny().externalNodesHaveChanged(); - tp.getPhylogeny().clearHashIdToNodeMap(); - tp.getPhylogeny().recalculateNumberOfExternalDescendants( true ); - tp.resetNodeIdToDistToLeafMap(); - tp.setEdited( true ); - displayedPhylogenyMightHaveChanged( true ); + orderPressed( tp ); } else if ( e.getSource() == _uncollapse_all ) { uncollapseAll( tp ); @@ -406,6 +391,31 @@ final class ControlPanel extends JPanel implements ActionListener { } } + void orderPressed( final TreePanel tp ) { + DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; + if ( isShowTaxonomyScientificNames() || isShowTaxonomyCode() ) { + pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; + } + else if ( isShowSeqNames() || isShowSeqSymbols() || isShowGeneNames() ) { + pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; + } + PhylogenyMethods.orderAppearanceX( tp.getPhylogeny().getRoot(), true, pri ); + tp.setNodeInPreorderToNull(); + tp.getPhylogeny().externalNodesHaveChanged(); + tp.getPhylogeny().clearHashIdToNodeMap(); + tp.getPhylogeny().recalculateNumberOfExternalDescendants( true ); + tp.resetNodeIdToDistToLeafMap(); + tp.setEdited( true ); + displayedPhylogenyMightHaveChanged( true ); + } + + void returnedToSuperTreePressed() { + if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { + _mainpanel.getCurrentTreePanel().superTree(); + showWhole(); + } + } + public JCheckBox getColorAccSequenceCb() { return _color_acc_sequence; } @@ -637,7 +647,7 @@ final class ControlPanel extends JPanel implements ActionListener { getSearchResetButton0().setVisible( true ); String[] queries = null; Set nodes = null; - query_str = query_str.replaceAll("\\s+", " " ); + query_str = query_str.replaceAll( "\\s+", " " ); if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) { queries = query_str.split( ",+" ); } @@ -705,7 +715,7 @@ final class ControlPanel extends JPanel implements ActionListener { getSearchResetButton1().setVisible( true ); String[] queries = null; Set nodes = null; - query_str = query_str.replaceAll("\\s+", " " ); + query_str = query_str.replaceAll( "\\s+", " " ); if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) { queries = query_str.split( ",+" ); } @@ -1202,12 +1212,11 @@ final class ControlPanel extends JPanel implements ActionListener { _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) @@ -1242,11 +1251,11 @@ final class ControlPanel extends JPanel implements ActionListener { _zoom_in_y = new TypomaticJButton( "Y+" ); _zoom_out_y = new TypomaticJButton( "Y-" ); _show_whole = new JButton( "F" ); - _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [F or Home]" ); - _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+cursor-right]" ); - _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+cursor-up]" ); - _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+cursor-left]" ); - _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+cursor-down]" ); + _show_whole.setToolTipText( "fit and center to display [Alt+C or Home]" ); + _zoom_in_x.setToolTipText( "zoom in horizontally [Alt+Right or Shift+Alt+mousewheel]" ); + _zoom_in_y.setToolTipText( "zoom in vertically [Alt+Up or Shift+mousewheel]" ); + _zoom_out_x.setToolTipText( "zoom out horizontally [Alt+Left or Shift+Alt+mousewheel]" ); + _zoom_out_y.setToolTipText( "zoom out vertically [Alt+Down or Shift+mousewheel]" ); if ( getConfiguration().isUseNativeUI() && ForesterUtil.isMac() ) { _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) ); _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) ); @@ -1259,25 +1268,23 @@ final class ControlPanel extends JPanel implements ActionListener { _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.setToolTipText( "return to the super-tree (if in sub-tree) [Alt+R]" ); _return_to_super_tree.setEnabled( false ); _order = new JButton( "O" ); - _order.setToolTipText( "order all" ); + _order.setToolTipText( "order all [Alt+O]" ); _uncollapse_all = new JButton( "U" ); - _uncollapse_all.setToolTipText( "uncollapse all" ); + _uncollapse_all.setToolTipText( "uncollapse all [Alt+U]" ); 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(); } @@ -1287,7 +1294,6 @@ final class ControlPanel extends JPanel implements ActionListener { if ( true ) { setUpControlsForRankCollapse(); } - final JLabel spacer3 = new JLabel( "" ); add( spacer3 ); setVisibilityOfDomainStrucureControls(); @@ -1499,12 +1505,11 @@ final class ControlPanel extends JPanel implements ActionListener { _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() ); _return_to_super_tree.setEnabled( false ); } - - void deactivateButtonToUncollapseAll() { + + void deactivateButtonToUncollapseAll() { _uncollapse_all.setForeground( getConfiguration().getGuiButtonTextColor() ); _uncollapse_all.setEnabled( false ); } - void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) { if ( ( _mainpanel != null ) @@ -2629,8 +2634,6 @@ final class ControlPanel extends JPanel implements ActionListener { } final void updateRankCollapseRankDisplay() { - - if ( _rank_collapse_depth_tf != null ) { final String r = obtainRankCollapseDepthValue(); if ( r.equals( "off" ) ) { diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 4961579..a07d472 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -239,15 +239,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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, + private static final BasicStroke STROKE_01_DASHED = new BasicStroke( 0.1f, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_ROUND, 0, new float[] { - 2.0f }, 0f ); - - - + 2.0f }, + 0f ); private static final BasicStroke STROKE_005_DASHED = new BasicStroke( 0.05f, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_ROUND, @@ -454,7 +452,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } } - if ( e.isControlDown() ) { + if ( e.isControlDown() && e.isShiftDown() ) { if ( notches < 0 ) { getTreeFontSet().increaseFontSize(); } @@ -466,6 +464,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee updateOvSizes(); repaint(); } + else if ( e.isShiftDown() && e.isAltDown() ) { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + else { + for( int i = 0; i < notches; ++i ) { + getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + } else if ( e.isShiftDown() ) { if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { @@ -1584,89 +1597,47 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setInOvRect( false ); } } - if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) { + if ( e.isAltDown() ) { if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) - || ( e.getKeyCode() == KeyEvent.VK_F ) ) { - getMainPanel().getTreeFontSet().mediumFonts(); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + || ( e.getKeyCode() == KeyEvent.VK_C ) || ( e.getKeyCode() == KeyEvent.VK_BACK_SPACE ) ) { + getControlPanel().showWhole(); } - else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { + else if ( e.isShiftDown() + && ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) ) { getMainPanel().getTreeFontSet().decreaseFontSize( 1, false ); getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); } - else if ( plusPressed( e.getKeyCode() ) ) { + else if ( e.isShiftDown() && plusPressed( e.getKeyCode() ) ) { getMainPanel().getTreeFontSet().increaseFontSize(); getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); } - } - else { - if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) - || ( e.getKeyCode() == KeyEvent.VK_F ) ) { - getControlPanel().showWhole(); + else if ( e.getKeyCode() == KeyEvent.VK_O ) { + getControlPanel().orderPressed( this ); } - else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN ) - || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) { - if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) { - if ( e.getKeyCode() == KeyEvent.VK_UP ) { - getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { - getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { - getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, - AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { - getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, - AptxConstants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - else { - final int d = 80; - int dx = 0; - int dy = -d; - if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { - dy = d; - } - else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { - dx = -d; - dy = 0; - } - else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { - dx = d; - dy = 0; - } - final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); - scroll_position.x = scroll_position.x + dx; - scroll_position.y = scroll_position.y + dy; - if ( scroll_position.x <= 0 ) { - scroll_position.x = 0; - } - else { - final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); - if ( scroll_position.x >= max_x ) { - scroll_position.x = max_x; - } - } - if ( scroll_position.y <= 0 ) { - scroll_position.y = 0; - } - else { - final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); - if ( scroll_position.y >= max_y ) { - scroll_position.y = max_y; - } - } - repaint(); - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); - } + else if ( e.getKeyCode() == KeyEvent.VK_R ) { + getControlPanel().returnedToSuperTreePressed(); + } + else if ( e.getKeyCode() == KeyEvent.VK_U ) { + getControlPanel().uncollapseAll( this ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_UP ) { + getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { + getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { + getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { + getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, + AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); } else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); @@ -1680,6 +1651,50 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); } + } + else { + if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN ) + || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) { + final int d = 80; + int dx = 0; + int dy = -d; + if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { + dy = d; + } + else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { + dx = -d; + dy = 0; + } + else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { + dx = d; + dy = 0; + } + final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); + scroll_position.x = scroll_position.x + dx; + scroll_position.y = scroll_position.y + dy; + if ( scroll_position.x <= 0 ) { + scroll_position.x = 0; + } + else { + final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); + if ( scroll_position.x >= max_x ) { + scroll_position.x = max_x; + } + } + if ( scroll_position.y <= 0 ) { + scroll_position.y = 0; + } + else { + final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); + if ( scroll_position.y >= max_y ) { + scroll_position.y = max_y; + } + } + repaint(); + getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); + } else if ( e.getKeyCode() == KeyEvent.VK_S ) { if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { @@ -1706,16 +1721,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - if ( ae.getlabelDirectionCbmi() != null ) { - ae.getlabelDirectionCbmi().setSelected( selected ); - } - } - else { - getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected ); - } + getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected ); repaint(); } else if ( e.getKeyCode() == KeyEvent.VK_X ) { @@ -1736,8 +1742,19 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) { decreaseOvSize(); } - e.consume(); } + if ( e.getKeyCode() == KeyEvent.VK_HOME ) { + getControlPanel().showWhole(); + } + else if ( e.getKeyCode() == KeyEvent.VK_PAGE_UP ) { + getMainPanel().getTreeFontSet().increaseFontSize(); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + else if ( e.getKeyCode() == KeyEvent.VK_PAGE_DOWN ) { + getMainPanel().getTreeFontSet().decreaseFontSize( 1, false ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + e.consume(); } final private void makePopupMenus( final PhylogenyNode node ) { @@ -2850,11 +2867,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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; + final boolean saw_species = _sb.length() > 0; _sb.setLength( 0 ); nodeDataAsSB( node, _sb ); if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) { - if ( _sb.length() == 0 && !saw_species ) { + if ( ( _sb.length() == 0 ) && !saw_species ) { if ( getOptions().isShowAbbreviatedLabelsForCollapsedNodes() && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowSeqNames() || getControlPanel().isShowNodeNames() ) ) { @@ -2864,7 +2881,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && 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() ); @@ -2873,7 +2889,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && 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() ); } @@ -2893,31 +2909,28 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } } - else if ( _sb.length() > 0 || saw_species ) { - // _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; } float pos_x; - if ( getControlPanel().isDrawPhylogram() && getOptions().isAlignExtLabelsInPhylogram() && (node.isExternal() || node.isCollapse() ) ) { + 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; @@ -2929,9 +2942,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) ); } - if ( getControlPanel().isDrawPhylogram() && getOptions().isAlignExtLabelsInPhylogram() && (node.isExternal() || node.isCollapse() ) ) { + 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()) { + if ( node.isCollapse() ) { pos_x -= add; } } @@ -2950,7 +2964,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee drawStringX( sb_str, pos_x, pos_y, g ); } } - if ( _sb.length() > 0 ) { if ( !using_visual_font && !is_in_found_nodes ) { x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5; @@ -3029,12 +3042,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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 ) { + final PhylogenyNode node, + int x, + final int half_box_size, + final float pos_x, + final float pos_y, + final String sb_str ) { int nodeTextBoundsWidth = 0; if ( sb_str.length() > 0 ) { final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how... @@ -6400,9 +6413,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getControlPanel().activateButtonToReturnToSuperTree( _subtree_index ); } } - + final void updateButtonToUncollapseAll() { - if ( PhylogenyMethods.isHasCollapsedNodes(_phylogeny) ) { + if ( PhylogenyMethods.isHasCollapsedNodes( _phylogeny ) ) { getControlPanel().activateButtonToUncollapseAll(); } else {