in progress

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 42883c6..b795c3e 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -36,7 +36,6 @@ import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Map.Entry;
 import java.util.Set;
 import java.util.SortedMap;
 import java.util.SortedSet;
@@ -232,8 +231,8 @@ public class surfacing {
     final static private String                               INPUT_SPECIES_TREE_OPTION                                              = "species_tree";
     final static private String                               SEQ_EXTRACT_OPTION                                                     = "prot_extract";
     final static private char                                 SEPARATOR_FOR_INPUT_VALUES                                             = '#';
-    final static private String                               PRG_VERSION                                                            = "2.100";
-    final static private String                               PRG_DATE                                                               = "2011.06.17";
+    final static private String                               PRG_VERSION                                                            = "2.200";
+    final static private String                               PRG_DATE                                                               = "2011.10.18";
     final static private String                               E_MAIL                                                                 = "czmasek@burnham.org";
     final static private String                               WWW                                                                    = "www.phylosoft.org/forester/applications/surfacing";
     final static private boolean                              IGNORE_DUFS_DEFAULT                                                    = true;
@@ -1727,14 +1726,8 @@ public class surfacing {
         final SortedSet<String> domains_which_are_always_single = new TreeSet<String>();
         final SortedSet<String> domains_which_are_sometimes_single_sometimes_not = new TreeSet<String>();
         final SortedSet<String> domains_which_never_single = new TreeSet<String>();
-        final BufferedWriter domains_which_are_always_single_writer = null;
-        final BufferedWriter domains_which_are_sometimes_single_sometimes_not_writer = null;
-        final BufferedWriter domains_which_never_single_writer = null;
-        BufferedWriter all_genomes_domains_per_potein_histo_writer = null;
         BufferedWriter domains_per_potein_stats_writer = null;
         try {
-            all_genomes_domains_per_potein_histo_writer = new BufferedWriter( new FileWriter( out_dir
-                    + ForesterUtil.FILE_SEPARATOR + output_file + "__all_genomes_domains_per_potein_histo.txt" ) );
             domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
                     + output_file + "__domains_per_potein_stats.txt" ) );
             domains_per_potein_stats_writer.write( "Genome" );
@@ -1990,16 +1983,18 @@ public class surfacing {
             domains_per_potein_stats_writer.write( "\n" );
             domains_per_potein_stats_writer.flush();
             domains_per_potein_stats_writer.close();
-            for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
-                all_genomes_domains_per_potein_histo_writer.write( entry.getKey() + "\t" + entry.getValue() + "\n" );
-            }
-            all_genomes_domains_per_potein_histo_writer.flush();
-            all_genomes_domains_per_potein_histo_writer.close();
+            ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+                    + "__all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" );
+            ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+                    + "__domains_always_single_.txt" ), domains_which_are_always_single, "\n" );
+            ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+                    + "__domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" );
+            ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+                    + "__domains_always_combined.txt" ), domains_which_never_single, "\n" );
         }
         catch ( final IOException e2 ) {
             ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
         }
-        //
         if ( query_domains_writer_ary != null ) {
             for( int j = 0; j < query_domain_ids_array.length; j++ ) {
                 try {

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 78b01ea..5af580b 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -38,6 +38,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.StringReader;
+import java.io.Writer;
 import java.math.BigDecimal;
 import java.net.URL;
 import java.text.DateFormat;
@@ -47,10 +48,12 @@ import java.text.NumberFormat;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Set;
 import java.util.SortedMap;
 import java.util.SortedSet;
@@ -220,6 +223,27 @@ public final class ForesterUtil {
         return s.replaceAll( "[\\s]+", " " );
     }
 
+    final public static void collection2file( final File file, final Collection<?> data, final String separator )
+            throws IOException {
+        final Writer writer = new BufferedWriter( new FileWriter( file ) );
+        collection2writer( writer, data, separator );
+        writer.close();
+    }
+
+    final public static void collection2writer( final Writer writer, final Collection<?> data, final String separator )
+            throws IOException {
+        boolean first = true;
+        for( final Object object : data ) {
+            if ( !first ) {
+                writer.write( separator );
+            }
+            else {
+                first = false;
+            }
+            writer.write( object.toString() );
+        }
+    }
+
     final public static String colorToHex( final Color color ) {
         final String rgb = Integer.toHexString( color.getRGB() );
         return rgb.substring( 2, rgb.length() );
@@ -536,6 +560,33 @@ public final class ForesterUtil {
         return map;
     }
 
+    final public static void map2file( final File file,
+                                       final Map<?, ?> data,
+                                       final String entry_separator,
+                                       final String data_separator ) throws IOException {
+        final Writer writer = new BufferedWriter( new FileWriter( file ) );
+        map2writer( writer, data, entry_separator, data_separator );
+        writer.close();
+    }
+
+    final public static void map2writer( final Writer writer,
+                                         final Map<?, ?> data,
+                                         final String entry_separator,
+                                         final String data_separator ) throws IOException {
+        for( final Entry<?, ?> entry : data.entrySet() ) {
+            boolean first = true;
+            if ( !first ) {
+                writer.write( data_separator );
+            }
+            else {
+                first = false;
+            }
+            writer.write( entry.getKey().toString() );
+            writer.write( entry_separator );
+            writer.write( entry.getValue().toString() );
+        }
+    }
+
     final public static StringBuffer mapToStringBuffer( final Map map, final String key_value_separator ) {
         final StringBuffer sb = new StringBuffer();
         for( final Iterator iter = map.keySet().iterator(); iter.hasNext(); ) {
@@ -772,6 +823,10 @@ public final class ForesterUtil {
         return str.split( regex );
     }
 
+    final public static String stringArrayToString( final String[] a ) {
+        return stringArrayToString( a, ", " );
+    }
+
     final public static String stringArrayToString( final String[] a, final String separator ) {
         final StringBuilder sb = new StringBuilder();
         if ( ( a != null ) && ( a.length > 0 ) ) {
@@ -783,6 +838,18 @@ public final class ForesterUtil {
         return sb.toString();
     }
 
+    final public static String[] stringListToArray( final List<String> list ) {
+        if ( list != null ) {
+            final String[] str = new String[ list.size() ];
+            int i = 0;
+            for( final String l : list ) {
+                str[ i++ ] = l;
+            }
+            return str;
+        }
+        return null;
+    }
+
     final public static String stringListToString( final List<String> l, final String separator ) {
         final StringBuilder sb = new StringBuilder();
         if ( ( l != null ) && ( l.size() > 0 ) ) {
@@ -794,10 +861,6 @@ public final class ForesterUtil {
         return sb.toString();
     }
 
-    final public static String stringArrayToString( final String[] a ) {
-        return stringArrayToString( a, ", " );
-    }
-
     final public static String[] stringSetToArray( final Set<String> strings ) {
         final String[] str_array = new String[ strings.size() ];
         int i = 0;
@@ -807,18 +870,6 @@ public final class ForesterUtil {
         return str_array;
     }
 
-    final public static String[] stringListToArray( final List<String> list ) {
-        if ( list != null ) {
-            final String[] str = new String[ list.size() ];
-            int i = 0;
-            for( final String l : list ) {
-                str[ i++ ] = l;
-            }
-            return str;
-        }
-        return null;
-    }
-
     final public static void unexpectedFatalError( final String prg_name, final Exception e ) {
         System.err.println();
         System.err.println( "[" + prg_name