From 37e4406efc1bc2a613a3229ae105677e9e9c3f62 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 20 Aug 2014 02:20:06 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java | 2 ++ forester/java/src/org/forester/archaeopteryx/Configuration.java | 2 +- forester/java/src/org/forester/archaeopteryx/MainFrame.java | 2 +- forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java | 2 ++ forester/java/src/org/forester/archaeopteryx/TreePanel.java | 3 ++- 5 files changed, 8 insertions(+), 3 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index ece59e5..71e58a5 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -822,6 +822,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); + customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); + customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); _jmenubar.add( _options_jmenu ); } diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 5debb52..5df336a 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -93,7 +93,7 @@ public final class Configuration { { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" }, { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" }, - { "Branch Widths", "display", "no" }, { "Protein Domains", "display", "no" }, + { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" }, { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" }, { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index ef2ebcb..b64958b 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -126,7 +126,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values"; static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information"; static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures"; - static final String LINE_UP_RENDERABLE_DATA = "Line Up Node Diagrams"; + static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)"; JMenuBar _jmenubar; JMenu _file_jmenu; JMenu _tools_menu; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index 6e6db91..389b626 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -282,6 +282,8 @@ public final class MainFrameApplet extends MainFrame { customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); + customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); + customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); _jmenubar.add( _options_jmenu ); } diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index a4c7821..b94b97b 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -4778,7 +4778,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) + && ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { RenderableDomainArchitecture rds = null; try { rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); -- 1.7.10.2