JAL-2629 hmmer searches now read domain rather than full scores

[jalview.git] / src / jalview / hmmer / HmmerCommand.java

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index 6eb294f..f38be02 100644 (file)
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -62,24 +62,36 @@ public abstract class HmmerCommand implements Runnable
 
   static final String TRIM_TERMINI_KEY = "label.trim_termini";
 
+  static final String RETURN_N_NEW_SEQ = "label.check_for_new_sequences";
+
   static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
 
-  static final String CUTOFF_NONE = "None";
+  static final String CUTOFF_NONE = "label.default";
+
+  static final String CUTOFF_SCORE = "label.score";
+
+  static final String CUTOFF_EVALUE = "label.evalue";
+
+  static final String REPORTING_SEQ_EVALUE_KEY = "label.reporting_seq_evalue";
 
-  static final String CUTOFF_SCORE = "Score";
+  static final String REPORTING_DOM_EVALUE_KEY = "label.reporting_dom_evalue";
 
-  static final String CUTOFF_EVALUE = "E-Value";
+  static final String REPORTING_SEQ_SCORE_KEY = "label.reporting_seq_score";
 
-  static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+  static final String REPORTING_DOM_SCORE_KEY = "label.reporting_dom_score";
 
-  static final String DOM_EVALUE_KEY = "label.dom_evalue";
+  static final String INCLUSION_SEQ_EVALUE_KEY = "label.inclusion_seq_evalue";
 
-  static final String SEQ_SCORE_KEY = "label.seq_score";
+  static final String INCLUSION_DOM_EVALUE_KEY = "label.inclusion_dom_evalue";
 
-  static final String DOM_SCORE_KEY = "label.dom_score";
+  static final String INCLUSION_SEQ_SCORE_KEY = "label.inclusion_seq_score";
+
+  static final String INCLUSION_DOM_SCORE_KEY = "label.inclusion_dom_score";
 
   static final String ARG_TRIM = "--trim";
 
+  static final String INCLUSION_THRESHOLD_KEY = "label.inclusion_threshold";
+
   /**
    * Constructor
    * 
@@ -385,8 +397,8 @@ public abstract class HmmerCommand implements Runnable
   }
 
   /**
-   * Answers the HMM profile for the profile sequence the user selected (default
-   * is just the first HMM sequence in the alignment)
+   * Answers the query sequence the user selected (default is just the first
+   * sequence in the alignment)
    * 
    * @return
    */