From 4e9354fda88a25a2d5197cc7cf3f576f263aa49d Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 20 Aug 2014 20:27:04 +0000
Subject: [PATCH] in progress

---
 .../src/org/forester/archaeopteryx/AptxUtil.java   |   41 ++++++++++++++++++++
 .../org/forester/archaeopteryx/ControlPanel.java   |   32 +++++++++++++++
 2 files changed, 73 insertions(+)

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index e95283d..b2c3dd8 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -72,6 +72,7 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
@@ -135,6 +136,46 @@ public final class AptxUtil {
         return false;
     }
 
+    final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( n.getBranchData().isHasConfidences() ) {
+                final List<Confidence> c = n.getBranchData().getConfidences();
+                for( final Confidence confidence : c ) {
+                    if ( confidence.getStandardDeviation() > 0 ) {
+                        return true;
+                    }
+                }
+            }
+        }
+        return false;
+    }
+
+    final static public boolean isHasAtLeastOneNodeWithScientificName( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( n.getNodeData().isHasTaxonomy()
+                    && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+    final static public boolean isHasAtLeastOneNodeWithSequenceAnnotation( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( n.getNodeData().isHasSequence()
+                    && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAnnotations() ) ) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     final public static void launchWebBrowser( final URI uri,
                                                final boolean is_applet,
                                                final JApplet applet,
diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index e8ba350..27c6b99 100644
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -2298,6 +2298,38 @@ final class ControlPanel extends JPanel implements ActionListener {
 
     void setVisibilityOfX() {
         try {
+            if ( ( getCurrentTreePanel() != null ) && ( getCurrentTreePanel().getPhylogeny() != null ) ) {
+                if ( AptxUtil.isHasAtLeastOneBranchWithSupportSD( getCurrentTreePanel().getPhylogeny() ) ) {
+                    if ( getMainPanel().getMainFrame()._show_confidence_stddev_cbmi != null ) {
+                        getMainPanel().getMainFrame()._show_confidence_stddev_cbmi.setVisible( true );
+                    }
+                }
+                else {
+                    if ( getMainPanel().getMainFrame()._show_confidence_stddev_cbmi != null ) {
+                        getMainPanel().getMainFrame()._show_confidence_stddev_cbmi.setVisible( false );
+                    }
+                }
+                if ( AptxUtil.isHasAtLeastOneNodeWithScientificName( getCurrentTreePanel().getPhylogeny() ) ) {
+                    if ( getMainPanel().getMainFrame()._abbreviate_scientific_names != null ) {
+                        getMainPanel().getMainFrame()._abbreviate_scientific_names.setVisible( true );
+                    }
+                }
+                else {
+                    if ( getMainPanel().getMainFrame()._abbreviate_scientific_names != null ) {
+                        getMainPanel().getMainFrame()._abbreviate_scientific_names.setVisible( false );
+                    }
+                }
+                if ( AptxUtil.isHasAtLeastOneNodeWithSequenceAnnotation( getCurrentTreePanel().getPhylogeny() ) ) {
+                    if ( getMainPanel().getMainFrame()._show_annotation_ref_source != null ) {
+                        getMainPanel().getMainFrame()._show_annotation_ref_source.setVisible( true );
+                    }
+                }
+                else {
+                    if ( getMainPanel().getMainFrame()._show_annotation_ref_source != null ) {
+                        getMainPanel().getMainFrame()._show_annotation_ref_source.setVisible( false );
+                    }
+                }
+            }
             if ( isDrawPhylogram()
                     || ( ( getCurrentTreePanel() != null ) && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
                             .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) ) {
-- 
1.7.10.2