From d71ba6a18b95b463e53869ae1738cc84d51f495f Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 21 Sep 2012 19:20:46 +0000 Subject: [PATCH] fixed error when dsiplaying domains and species --- .../src/org/forester/archaeopteryx/Constants.java | 2 +- .../src/org/forester/archaeopteryx/TreePanel.java | 83 ++++++++++---------- 2 files changed, 43 insertions(+), 42 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index ed9dea5..70244b5 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -43,7 +43,7 @@ public final class Constants { public final static boolean ALLOW_DDBJ_BLAST = false; public final static String PRG_NAME = "Archaeopteryx"; final static String VERSION = "0.973"; - final static String PRG_DATE = "120907"; + final static String PRG_DATE = "120921"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Verdana", "Tahoma", "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 6fba312..d256cce 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -227,7 +227,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 private Sequence _query_sequence = null; private final FontRenderContext _frc = new FontRenderContext( null, false, @@ -3206,28 +3205,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee .getLostCharactersAsStringBuffer().toString() ); } else { - if ( DRAW_MEAN_COUNTS && node.isInternal() ) { - final List ec = node.getAllExternalDescendants(); - double sum = 0; - int count = 0; - for( final PhylogenyNode phylogenyNode : ec ) { - count++; - if ( phylogenyNode.getNodeData().getBinaryCharacters() != null ) { - sum += phylogenyNode.getNodeData().getBinaryCharacters().getPresentCount(); - } - } - final double mean = ForesterUtil.round( sum / count, 1 ); - TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " [" - + mean + "]", node.getXcoord() + x + 4 + half_box_size, node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); - } - else { - TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), - node.getXcoord() + x + 4 + half_box_size, - node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), - g ); - } + TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), + node.getXcoord() + x + 4 + half_box_size, + node.getYcoord() + + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), + g ); paintGainedAndLostCharacters( g, node, "+" + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" + node.getNodeData().getBinaryCharacters().getLostCount() ); @@ -3620,26 +3602,45 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( rds != null ) { rds.setRenderingHeight( 6 ); int x = 0; - if ( getControlPanel().isShowTaxonomyCode() - && ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( node ) ) ) ) { - x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " ); - } - if ( getControlPanel().isShowGeneNames() - && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " ); - } - if ( getControlPanel().isShowGeneSymbols() - && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) { - x += getTreeFontSet()._fm_large - .stringWidth( node.getNodeData().getSequence().getSymbol() + " " ); + if ( node.getNodeData().isHasTaxonomy() ) { + if ( getControlPanel().isShowTaxonomyCode() + && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { + x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy() + .getTaxonomyCode() + + " " ); + } + if ( getControlPanel().isShowTaxonomyScientificNames() + && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) { + x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy() + .getScientificName() + + " " ); + } + if ( getControlPanel().isShowTaxonomyCommonNames() + && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) { + x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy() + .getCommonName() + + " " ); + } } - if ( getControlPanel().isShowSequenceAcc() - && ( node.getNodeData().getSequence().getAccession() != null ) ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession() - .toString() - + " " ); + if ( node.getNodeData().isHasSequence() ) { + if ( getControlPanel().isShowGeneNames() + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + + " " ); + } + if ( getControlPanel().isShowGeneSymbols() + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + + " " ); + } + if ( getControlPanel().isShowSequenceAcc() + && ( node.getNodeData().getSequence().getAccession() != null ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence() + .getAccession().toString() + + " " ); + } } - if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { + if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) { x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " ); } rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf ); -- 1.7.10.2