From 226d82be9b70ce0c67b5b1055654d484073ea184 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 20 Aug 2014 02:48:23 +0000 Subject: [PATCH] clean up --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 68 ++++++++++++-------- .../src/org/forester/archaeopteryx/TreePanel.java | 65 ++++++++++--------- 2 files changed, 75 insertions(+), 58 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 71e58a5..77355ea 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -608,12 +608,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } ); if ( getConfiguration().isUseTabbedDisplay() ) { - AptxUtil.printAppletMessage( NAME, "using tabbed display" ); - AptxUtil.addPhylogeniesToTabs( phys, - new File( phys_url.getFile() ).getName(), - phys_url.toString(), - getConfiguration(), - getMainPanel() ); + try { + AptxUtil.printAppletMessage( NAME, "using tabbed display" ); + AptxUtil.addPhylogeniesToTabs( phys, + new File( phys_url.getFile() ).getName(), + phys_url.toString(), + getConfiguration(), + getMainPanel() ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, e.toString() ); + e.printStackTrace(); + } } else { AptxUtil.printAppletMessage( NAME, "not using tabbed display" ); @@ -623,28 +629,34 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() ); } - validate(); - setName( NAME ); - getMainPanel().getControlPanel().showWholeAll(); - getMainPanel().getControlPanel().showWhole(); - /* GUILHEM_BEG */ - getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems(); - for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny() - .getRelevantSequenceRelationTypes() ) { - getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type ); - } - final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE ); - if ( default_relation != null ) { - getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation ); - } - final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE ); - if ( default_sequence != null ) { - getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence ); - } - /* GUILHEM_END */ - System.gc(); - AptxUtil.printAppletMessage( NAME, "successfully initialized" ); - setVisible( true ); + try { + validate(); + setName( NAME ); + getMainPanel().getControlPanel().showWholeAll(); + getMainPanel().getControlPanel().showWhole(); + /* GUILHEM_BEG */ + getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems(); + for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny() + .getRelevantSequenceRelationTypes() ) { + getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().addItem( type ); + } + final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE ); + if ( default_relation != null ) { + getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().setSelectedItem( default_relation ); + } + final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE ); + if ( default_sequence != null ) { + getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence ); + } + /* GUILHEM_END */ + System.gc(); + AptxUtil.printAppletMessage( NAME, "successfully initialized" ); + setVisible( true ); + } + catch ( final Exception e ) { + ForesterUtil.printErrorMessage( NAME, e.toString() ); + e.printStackTrace(); + } } public void showTextFrame( final String s, final String title ) { diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index b94b97b..341a8cb 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -3426,47 +3426,52 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) { - if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { - if ( sb.length() > 0 ) { - sb.append( " " ); - } - sb.append( node.getName() ); - } - if ( node.getNodeData().isHasSequence() ) { - if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) { + if ( node != null ) { + if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) { if ( sb.length() > 0 ) { sb.append( " " ); } - sb.append( node.getNodeData().getSequence().getSymbol() ); + sb.append( node.getName() ); } - if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + if ( node.getNodeData().isHasSequence() ) { + if ( getControlPanel().isShowSeqSymbols() + && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getNodeData().getSequence().getSymbol() ); } - sb.append( node.getNodeData().getSequence().getGeneName() ); - } - if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + if ( getControlPanel().isShowGeneNames() + && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getNodeData().getSequence().getGeneName() ); + } + if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getNodeData().getSequence().getName() ); + } + if ( getControlPanel().isShowSequenceAcc() + && ( node.getNodeData().getSequence().getAccession() != null ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) { + sb.append( node.getNodeData().getSequence().getAccession().getSource() ); + sb.append( ":" ); + } + sb.append( node.getNodeData().getSequence().getAccession().getValue() ); } - sb.append( node.getNodeData().getSequence().getName() ); } - if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) { + if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { if ( sb.length() > 0 ) { sb.append( " " ); } - if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) { - sb.append( node.getNodeData().getSequence().getAccession().getSource() ); - sb.append( ":" ); - } - sb.append( node.getNodeData().getSequence().getAccession().getValue() ); - } - } - if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + sb.append( propertiesToString( node ) ); } - sb.append( propertiesToString( node ) ); } } -- 1.7.10.2