JAL-2629 add simple jackhmmer functionality

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 57786e5..6cbe0c8 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -34,37 +34,6 @@ public class HMMSearch extends HmmerCommand
 {
   static final String HMMSEARCH = "hmmsearch";
 
-  /*
-   * constants for i18n lookup of passed parameter names
-   */
-  static final String DATABASE_KEY = "label.database";
-
-  static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
-
-  static final String USE_ACCESSIONS_KEY = "label.use_accessions";
-
-  static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
-
-  static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
-
-  static final String TRIM_TERMINI_KEY = "label.trim_termini";
-
-  static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
-
-  static final String CUTOFF_NONE = "None";
-
-  static final String CUTOFF_SCORE = "Score";
-
-  static final String CUTOFF_EVALUE = "E-Value";
-
-  static final String SEQ_EVALUE_KEY = "label.seq_evalue";
-
-  static final String DOM_EVALUE_KEY = "label.dom_evalue";
-
-  static final String SEQ_SCORE_KEY = "label.seq_score";
-
-  static final String DOM_SCORE_KEY = "label.dom_score";
-
   boolean realign = false;
 
   boolean trim = false;
@@ -104,7 +73,7 @@ public class HMMSearch extends HmmerCommand
 
     SequenceI hmmSeq = hmm.getConsensusSequence();
     long msgId = System.currentTimeMillis();
-    af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+    af.setProgressBar(MessageManager.getString("status.running_search"),
             msgId);
 
     try