From: Thomas <170013569@dundee.ac.uk>
Date: Fri, 12 Jul 2019 14:46:32 +0000 (+0100)
Subject: JAL-2629 can now choose number of jackhmmer iterations
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fmerge%2FJAL-3285_mchmmer_with_211_develop;p=jalview.git

JAL-2629 can now choose number of jackhmmer iterations
---

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 2c0fbb9..b627ac8 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1380,6 +1380,7 @@ label.executable_not_found = The ''{0}'' executable file was not found
 warn.command_failed = {0} failed
 label.invalid_folder = Invalid Folder
 label.number_of_results = Number of Results to Return
+label.number_of_iterations = Number of jackhmmer Iterations
 label.auto_align_seqs = Automatically Align Fetched Sequences
 label.new_returned = new sequences returned
 label.use_accessions = Return Accessions
@@ -1394,6 +1395,7 @@ label.inclusion_seq_score = Inclusion Sequence Score Threshold
 label.inclusion_dom_evalue = Inclusion Domain E-value Cut-off
 label.inclusion_dom_score = Inclusion Domain Score Threshold
 label.number_of_results_desc = The maximum number of hmmsearch results to display
+label.number_of_iterations_desc = The number of iterations jackhmmer will complete when searching for new sequences
 label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
 label.check_for_new_sequences_desc = Display number of new sequences returned from hmmsearch compared to the previous alignment 
 label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name
diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index be03ec5..df9ab55 100644
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -221,6 +221,10 @@ public final class HMMERParamStore implements ParamDatastoreI
 
     String database = MessageManager.getString("label.database");
     args.add(new FileParameter(database, "", false, "", ""));
+    args.add(new IntegerParameter(
+            MessageManager.getString(HMMSearch.NUMBER_OF_ITERATIONS),
+            MessageManager.getString("label.number_of_iterations_desc"),
+            true, 5, 1, 20));
     args.add(new RadioChoiceParameter(
             MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
             Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index f38be02..b311b76 100644
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -60,6 +60,8 @@ public abstract class HmmerCommand implements Runnable
 
   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 RETURN_N_NEW_SEQ = "label.check_for_new_sequences";
diff --git a/src/jalview/hmmer/Search.java b/src/jalview/hmmer/Search.java
index 5c7da7c..ceb79e5 100644
--- a/src/jalview/hmmer/Search.java
+++ b/src/jalview/hmmer/Search.java
@@ -329,6 +329,15 @@ public abstract class Search extends HmmerCommand
             searchAlignment = false;
           }
         }
+        else if (MessageManager.getString(NUMBER_OF_ITERATIONS)
+                .equals(name))
+        {
+          if (!arg.getValue().isEmpty())
+          {
+            args.add("-N");
+            args.add(arg.getValue());
+          }
+        }
       }
     }