work for rrm project (ComPhy 2012 Moscow)

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 7f4bf60..2ef8817 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -270,7 +270,7 @@ public class surfacing {
     private static final String                               LOG_FILE_SUFFIX                                                               = "_log.txt";
     private static final String                               DATA_FILE_SUFFIX                                                              = "_domain_combination_data.txt";
     private static final String                               DATA_FILE_DESC                                                                = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN";
-    private static final INDIVIDUAL_SCORE_CUTOFF              INDIVIDUAL_SCORE_CUTOFF_DEFAULT                                               = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;
+    private static final INDIVIDUAL_SCORE_CUTOFF              INDIVIDUAL_SCORE_CUTOFF_DEFAULT                                               = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; //TODO look at me! change?
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX                          = "_indep_dc_gains_fitch_counts.txt";
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX                              = "_indep_dc_gains_fitch_lists.txt";
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX               = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";