JAL-2805 made needed color set methods public

[jalview.git] / forester / java / src / org / forester / application / surfacing.java

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index c35c98d..fc87a96 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -217,9 +217,9 @@ public class surfacing {
     final static private String                                     INPUT_GENOMES_FILE_OPTION                                                     = "genomes";
     final static private String                                     INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
     final static private String                                     SEQ_EXTRACT_OPTION                                                            = "prot_extract";
-    final static private String                                     PRG_VERSION                                                                   = "2.500";
-    final static private String                                     PRG_DATE                                                                      = "170323";
-    final static private String                                     E_MAIL                                                                        = "czmasek@burnham.org";
+    final static private String                                     PRG_VERSION                                                                   = "2.503";
+    final static private String                                     PRG_DATE                                                                      = "170518";
+    final static private String                                     E_MAIL                                                                        = "phyloxml@gmail.com";
     final static private String                                     WWW                                                                           = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
     final static private boolean                                    IGNORE_DUFS_DEFAULT                                                           = true;
     final static private boolean                                    IGNORE_COMBINATION_WITH_SAME_DEFAULLT                                         = false;
@@ -272,6 +272,7 @@ public class surfacing {
     public static final String                                      INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX        = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
     public static final String                                      INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
     private static final boolean                                    CALC_SIMILARITY_SCORES                                                        = false;
+    private static final String                                     SEPARATOR_FOR_DA                                                              = "--";
 
     @SuppressWarnings( "unchecked")
     public static void main( final String args[] ) {
@@ -1775,32 +1776,32 @@ public class surfacing {
         ForesterUtil
                 .programMessage( PRG_NAME,
                                  "Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file );
-        //
-        if ( true ) { //TODO
-            try {
-                MinimalDomainomeCalculator.calcOme( false,
-                                                    intrees[ 0 ],
-                                                    protein_lists_per_species,
-                                                    "---",
-                                                    1000,
-                                                    out_dir.toString() + "/" + output_file );
-            }
-            catch ( IOException e ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
-            }
+        final int LEVEL = 0;
+        try {
+            MinimalDomainomeCalculator.calc( false,
+                                             intrees[ 0 ],
+                                             LEVEL,
+                                             protein_lists_per_species,
+                                             SEPARATOR_FOR_DA,
+                                             -1,
+                                             out_dir.toString() + "/" + output_file,
+                                             true );
+        }
+        catch ( IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
         }
-        if ( true ) { //TODO
-            try {
-                MinimalDomainomeCalculator.calcOme( true,
-                                                    intrees[ 0 ],
-                                                    protein_lists_per_species,
-                                                    "---",
-                                                    1000,
-                                                    out_dir.toString() + "/" + output_file );
-            }
-            catch ( IOException e ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
-            }
+        try {
+            MinimalDomainomeCalculator.calc( true,
+                                             intrees[ 0 ],
+                                             LEVEL,
+                                             protein_lists_per_species,
+                                             SEPARATOR_FOR_DA,
+                                             -1,
+                                             out_dir.toString() + "/" + output_file,
+                                             true );
+        }
+        catch ( IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
         }
         if ( da_analysis ) {
             SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
@@ -2212,6 +2213,9 @@ public class surfacing {
                                  "Free memory       : " + free_memory + "MB, total memory: " + total_memory + "MB" );
         ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" );
         ForesterUtil.programMessage( PRG_NAME, surfacing.WWW );
+        ForesterUtil
+                .programMessage( PRG_NAME,
+                                 "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
         ForesterUtil.programMessage( PRG_NAME, "OK" );
         System.out.println();
     }
@@ -2307,5 +2311,11 @@ public class surfacing {
         System.out
                 .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" );
         System.out.println();
+        System.out
+                .println( "Example 3: surfacing -species_tree=master_tree.xml -no_eo -ie=1e-6 -mrel=0.5 -mo=10 -dufs -genomes=genomes.txt -out_dir=a605 -o=a605" );
+        System.out.println();
+        System.out
+                .println( "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
+        System.out.println();
     }
 }