domain + go output work begins

[jalview.git] / forester / java / src / org / forester / archaeopteryx / AptxUtil.java

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index e95283d..3ac6c56 100644 (file)
--- 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;
@@ -111,8 +112,8 @@ public final class AptxUtil {
 
     /**
      * Returns true if at least one branch has a length larger than zero.
-     * 
-     * 
+     *
+     *
      * @param phy
      */
     final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
@@ -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,
@@ -230,7 +271,7 @@ public final class AptxUtil {
                                                                          final ControlPanel ac,
                                                                          final GraphicsExportType type,
                                                                          final Options options ) throws IOException {
-        tree_panel.calcParametersForPainting( width, height, true );
+        tree_panel.calcParametersForPainting( width, height );
         tree_panel.resetPreferredSize();
         tree_panel.repaint();
         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
@@ -531,8 +572,8 @@ public final class AptxUtil {
 
     /**
      * Exits with -1.
-     * 
-     * 
+     *
+     *
      * @param message
      *            to message to be printed
      */
@@ -760,7 +801,7 @@ public final class AptxUtil {
             if ( options.isGraphicsExportVisibleOnly() ) {
                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
             }
-            tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
+            tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() );
             tree_panel.resetPreferredSize();
             tree_panel.repaint();
         }
@@ -825,7 +866,7 @@ public final class AptxUtil {
             if ( options.isGraphicsExportVisibleOnly() ) {
                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
             }
-            tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
+            tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() );
             tree_panel.resetPreferredSize();
             tree_panel.repaint();
         }