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JAL-2629 can now choose number of jackhmmer iterations
[jalview.git]
/
src
/
jalview
/
hmmer
/
HmmerCommand.java
diff --git
a/src/jalview/hmmer/HmmerCommand.java
b/src/jalview/hmmer/HmmerCommand.java
index
6eb294f
..
b311b76
100644
(file)
--- a/
src/jalview/hmmer/HmmerCommand.java
+++ b/
src/jalview/hmmer/HmmerCommand.java
@@
-60,26
+60,40
@@
public abstract class HmmerCommand implements Runnable
static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
+ static final String NUMBER_OF_ITERATIONS = "label.number_of_iterations";
+
static final String TRIM_TERMINI_KEY = "label.trim_termini";
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 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 ARG_TRIM = "--trim";
+ static final String INCLUSION_THRESHOLD_KEY = "label.inclusion_threshold";
+
/**
* Constructor
*
/**
* Constructor
*
@@
-385,8
+399,8
@@
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
*/
*
* @return
*/