revert to default turning off of anti-alias on apple macintosh.

[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 a615cb9..b874665 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -75,6 +75,7 @@ import org.forester.io.parsers.tol.TolParser;
 import org.forester.io.parsers.util.ParserUtils;
 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.Accession;
 import org.forester.phylogeny.data.BranchColor;
@@ -794,9 +795,8 @@ public final class AptxUtil {
                 desc.append( "\n" );
                 desc.append( "    Median: " + ForesterUtil.round( bs.median(), 6 ) );
                 desc.append( "\n" );
-                desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
-                desc.append( "\n" );
-                desc.append( "    SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
+                desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
+                        + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
                 desc.append( "\n" );
                 desc.append( "    Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
                 desc.append( "\n" );
@@ -815,9 +815,8 @@ public final class AptxUtil {
                 desc.append( "\n" );
                 desc.append( "    Median: " + ForesterUtil.round( ds.median(), 2 ) );
                 desc.append( "\n" );
-                desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
-                desc.append( "\n" );
-                desc.append( "    SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
+                desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) + " (stdev: "
+                        + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) + ")" );
                 desc.append( "\n" );
                 desc.append( "    Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
                 desc.append( "\n" );
@@ -852,11 +851,10 @@ public final class AptxUtil {
                         desc.append( "    Median: " + ForesterUtil.round( cs.median(), 6 ) );
                         desc.append( "\n" );
                         desc.append( "    Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
-                        desc.append( "\n" );
                         if ( cs.getN() > 2 ) {
-                            desc.append( "    SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
-                            desc.append( "\n" );
+                            desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
                         }
+                        desc.append( "\n" );
                         desc.append( "    Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
                         desc.append( "\n" );
                         desc.append( "    Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
@@ -920,17 +918,6 @@ public final class AptxUtil {
         return true;
     }
 
-    final static boolean isMac() {
-        try {
-            final String s = ForesterUtil.OS_NAME.toLowerCase();
-            return s.startsWith( "mac" );
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
-            return false;
-        }
-    }
-
     final static boolean isUsOrCanada() {
         try {
             if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
@@ -943,17 +930,6 @@ public final class AptxUtil {
         return false;
     }
 
-    final static boolean isWindows() {
-        try {
-            final String s = ForesterUtil.OS_NAME.toLowerCase();
-            return s.indexOf( "win" ) > -1;
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
-            return false;
-        }
-    }
-
     final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
                                                                       final ControlPanel atv_control,
                                                                       final Configuration configuration ) {
@@ -1061,6 +1037,7 @@ public final class AptxUtil {
         if ( midpoint_reroot ) {
             for( final Phylogeny phy : phys ) {
                 PhylogenyMethods.midpointRoot( phy );
+                PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
             }
         }
         return phys;
@@ -1298,7 +1275,7 @@ public final class AptxUtil {
         if ( os.toLowerCase().startsWith( "win" ) ) {
             Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
         }
-        else if ( isMac() ) {
+        else if ( ForesterUtil.isMac() ) {
             final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
             final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
             open_url.invoke( null, new Object[] { url } );