work on data buffer for aLeaves MAFFT suite + clean up

[jalview.git] / forester / java / src / org / forester / util / ForesterUtil.java

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 9d9570d..336c887 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -61,6 +61,11 @@ import java.util.TreeMap;
 import java.util.TreeSet;
 import java.util.regex.Pattern;
 
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Distribution;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+
 public final class ForesterUtil {
 
     public final static String       FILE_SEPARATOR                   = System.getProperty( "file.separator" );
@@ -90,6 +95,30 @@ public final class ForesterUtil {
     private ForesterUtil() {
     }
 
+    public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
+        if ( !node.getNodeData().isHasTaxonomy() ) {
+            node.getNodeData().setTaxonomy( new Taxonomy() );
+        }
+    }
+
+    public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
+        if ( !node.getNodeData().isHasSequence() ) {
+            node.getNodeData().setSequence( new Sequence() );
+        }
+    }
+
+    final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
+        if ( !node.getNodeData().isHasDistribution() ) {
+            node.getNodeData().setDistribution( new Distribution( "" ) );
+        }
+    }
+
+    final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
+        if ( !node.getNodeData().isHasDate() ) {
+            node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
+        }
+    }
+
     final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
         if ( sb.length() > 0 ) {
             sb.append( separator );
@@ -742,7 +771,7 @@ public final class ForesterUtil {
     }
 
     final public static void printErrorMessage( final String prg_name, final String message ) {
-        System.out.println( "[" + prg_name + "] > error: " + message );
+        System.err.println( "[" + prg_name + "] > error: " + message );
     }
 
     final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) {
@@ -926,7 +955,7 @@ public final class ForesterUtil {
     final public static void unexpectedFatalError( final String prg_name, final Exception e ) {
         System.err.println();
         System.err.println( "[" + prg_name
-                + "] > unexpected error (Should not have occured! Please contact program author(s).)" );
+                + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
         e.printStackTrace( System.err );
         System.err.println();
         System.exit( -1 );
@@ -935,7 +964,7 @@ public final class ForesterUtil {
     final public static void unexpectedFatalError( final String prg_name, final String message ) {
         System.err.println();
         System.err.println( "[" + prg_name
-                + "] > unexpected error. Should not have occured! Please contact program author(s)." );
+                + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
         System.err.println( message );
         System.err.println();
         System.exit( -1 );
@@ -944,7 +973,7 @@ public final class ForesterUtil {
     final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) {
         System.err.println();
         System.err.println( "[" + prg_name
-                + "] > unexpected error. Should not have occured! Please contact program author(s)." );
+                + "] > Unexpected error. Should not have occured! Please contact program author(s)." );
         System.err.println( message );
         e.printStackTrace( System.err );
         System.err.println();