X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=c020b28de7b0b599f4c5fdfad2b4f2e25fd6c541;hb=775c5ac0371ef0cfc3c4f34a2719903fa228e9e0;hp=7c40d10eed7d712e48438b28b53cb808560c5240;hpb=ccf4c584032d16ed0ed8d0678f01305887724f96;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 7c40d10..c020b28 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -5,7 +5,7 @@ // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved -// +// // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either @@ -15,7 +15,7 @@ // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. -// +// // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA @@ -125,16 +125,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private static final float HALF_PI = ( float ) ( Math.PI / 2.0 ); private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 ); private static final short OV_BORDER = 10; - final static Cursor CUT_CURSOR = Cursor - .getPredefinedCursor( Cursor.CROSSHAIR_CURSOR ); - final static Cursor MOVE_CURSOR = Cursor - .getPredefinedCursor( Cursor.MOVE_CURSOR ); - final static Cursor ARROW_CURSOR = Cursor - .getPredefinedCursor( Cursor.DEFAULT_CURSOR ); - final static Cursor HAND_CURSOR = Cursor - .getPredefinedCursor( Cursor.HAND_CURSOR ); - final static Cursor WAIT_CURSOR = Cursor - .getPredefinedCursor( Cursor.WAIT_CURSOR ); + final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR ); + final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR ); + final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR ); + final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR ); + final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR ); private final static long serialVersionUID = -978349745916505029L; private final static int EURO_D = 10; private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node"; @@ -222,8 +217,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private JTextArea _rollover_popup; //private final short _skip_counter = 0; private final StringBuffer _popup_buffer = new StringBuffer(); - final private static Font POPUP_FONT = new Font( Configuration - .getDefaultFontFamilyName(), + final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 12 ); private static final boolean DRAW_MEAN_COUNTS = true; //TODO remove me later @@ -2138,8 +2132,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final double r2 = 2.0 * parent_radius; drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); } - drawLine( c.getXcoord(), c.getYcoord(), root_x + ( Math.cos( angle ) * parent_radius ), root_y - + ( Math.sin( angle ) * parent_radius ), g ); + drawLine( c.getXcoord(), + c.getYcoord(), + root_x + ( Math.cos( angle ) * parent_radius ), + root_y + ( Math.sin( angle ) * parent_radius ), + g ); paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c ) ); if ( c.isExternal() ) { final boolean is_in_found_nodes = isInFoundNodes( c ); @@ -2164,8 +2161,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final double r2 = 2.0 * parent_radius; drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); } - drawLine( c.getXSecondary(), c.getYSecondary(), root_x + ( Math.cos( angle ) * parent_radius ), root_y - + ( Math.sin( angle ) * parent_radius ), g ); + drawLine( c.getXSecondary(), + c.getYSecondary(), + root_x + ( Math.cos( angle ) * parent_radius ), + root_y + ( Math.sin( angle ) * parent_radius ), + g ); if ( isInFoundNodes( c ) ) { g.setColor( getTreeColorSet().getFoundColor() ); drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g ); @@ -2186,13 +2186,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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()._small_max_descent, g ); + .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g ); } else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() - + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g ); + .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g ); } else { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() @@ -2277,8 +2275,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee boolean draw_vertical = true; final PhylogenyNode parent = node.getParent(); if ( ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file ) || ( ( getControlPanel() - .isEvents() ) - && ( parent != null ) && parent.isHasAssignedEvent() ) ) + .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) ) && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) ) && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent .isDuplication() ) ) { @@ -2561,12 +2558,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee d = BOX_SIZE; } _polygon.reset(); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - TreePanel.BOX_SIZE ), ForesterUtil - .roundToInt( node.getYcoord() ) ); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), ForesterUtil - .roundToInt( node.getYcoord() - d ) ); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), ForesterUtil - .roundToInt( node.getYcoord() + d ) ); + _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - TreePanel.BOX_SIZE ), + ForesterUtil.roundToInt( node.getYcoord() ) ); + _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), + ForesterUtil.roundToInt( node.getYcoord() - d ) ); + _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), + ForesterUtil.roundToInt( node.getYcoord() + d ) ); g.fillPolygon( _polygon ); paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); } @@ -2649,9 +2646,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.setColor( getTreeColorSet().getConfidenceColor() ); } TreePanel - .drawString( conf_str, parent_x - + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ), ( node - .getYcoord() + getTreeFontSet()._small_max_ascent ) - 1, g ); + .drawString( conf_str, + parent_x + + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ), + ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1, + g ); } } @@ -2673,9 +2672,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.setColor( Color.BLUE ); } TreePanel - .drawString( gained, parent_x - + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ), ( node - .getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ), g ); + .drawString( gained, + parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ), + ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ), + g ); g.setColor( getTreeColorSet().getLostCharactersColor() ); TreePanel.drawString( lost, parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ), @@ -2772,8 +2772,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee x += drawTaxonomyImage( node.getXcoord() + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord(), node, g ); } if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel() - .isShowTaxonomyCommonNames() ) - && node.getNodeData().isHasTaxonomy() ) { + .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) { x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x ); } if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { @@ -2967,10 +2966,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); } else { - TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), node - .getXcoord() - + x + 4 + TreePanel.HALF_BOX_SIZE, node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); + TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), + node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE, + node.getYcoord() + + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), + g ); } paintGainedAndLostCharacters( g, node, "+" + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" @@ -3006,8 +3006,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final int x_w = ( int ) ( x + ws + 0.5 ); final int y_h = ( int ) ( my_y + hs + 0.5 ); if ( ( x_w - x > 7 ) && ( y_h - my_y > 7 ) ) { - g.drawImage( bi, ( int ) ( x + 0.5 + offset ), ( int ) ( my_y + 0.5 ), x_w, y_h, 0, 0, bi - .getWidth(), bi.getHeight(), null ); + g.drawImage( bi, + ( int ) ( x + 0.5 + offset ), + ( int ) ( my_y + 0.5 ), + x_w, + y_h, + 0, + 0, + bi.getWidth(), + bi.getHeight(), + null ); ws += 8; } else { @@ -4488,9 +4496,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _popup_buffer.append( confidence.getType() ); _popup_buffer.append( "] " ); } - _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil - .round( confidence.getValue(), getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + _popup_buffer + .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); } } if ( _popup_buffer.length() > 0 ) {