From 5c7ed97187f95fffe2bf97b5d7b5fec206e79ecc Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 30 May 2018 12:16:32 +0100
Subject: [PATCH] JAL-3005 JAL-2629 file chooser argument for HMM search
 database

---
 resources/lang/Messages.properties     |    1 +
 resources/lang/Messages_es.properties  |    1 +
 src/jalview/hmmer/HMMERParamStore.java |   22 ++++++++++++++++------
 src/jalview/hmmer/HMMSearch.java       |   18 ++++++++++++++++--
 4 files changed, 34 insertions(+), 8 deletions(-)

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 4a5059e..c25cda8 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1421,3 +1421,4 @@ label.groups_and_alignment = All groups and alignment
 label.groups = All groups
 label.selected_group = Selected group
 label.use_info_for_height = Use Information Content as Letter Height
+action.search = Search
\ No newline at end of file
diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index e0e0a4a..eb217bd 100644
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1362,3 +1362,4 @@ label.most_bound_molecules = M
 label.most_polymer_residues = Más Residuos de Polímeros
 label.cached_structures = Estructuras en Caché
 label.free_text_search = Búsqueda de texto libre
+action.search = Buscar
\ No newline at end of file
diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 00cae85..452097b 100644
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -10,9 +10,11 @@ import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.params.simple.BooleanOption;
 import jalview.ws.params.simple.DoubleParameter;
+import jalview.ws.params.simple.FileParameter;
 import jalview.ws.params.simple.IntegerParameter;
 import jalview.ws.params.simple.LogarithmicParameter;
 import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.RadioChoiceParameter;
 import jalview.ws.params.simple.StringParameter;
 
 import java.io.File;
@@ -104,7 +106,7 @@ public final class HMMERParamStore implements ParamDatastoreI
     args.add(new BooleanOption(
             MessageManager.getString(HMMSearch.AUTO_ALIGN_SEQS_KEY),
             MessageManager.getString("label.auto_align_seqs_desc"), false,
-            false, true, null));
+            false, false, null));
     args.add(new BooleanOption(
             MessageManager.getString(HMMSearch.USE_ACCESSIONS_KEY),
             MessageManager.getString("label.use_accessions_desc"), false,
@@ -119,18 +121,26 @@ public final class HMMERParamStore implements ParamDatastoreI
      */
     addChoiceOfHmm(args);
 
-    addChoiceOfDatabase(args);
-
+    // addChoiceOfDatabase(args);
+
+    String thisAlignment = MessageManager
+            .getString(HMMSearch.THIS_ALIGNMENT_KEY);
+    String database = MessageManager.getString("label.database");
+    args.add(new RadioChoiceParameter(
+            MessageManager.getString("action.search"), null,
+            Arrays.asList(thisAlignment,
+                    database),
+            thisAlignment));
+    args.add(new FileParameter(database, "", false, "", ""));
     args.add(new IntegerParameter(
             MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
             MessageManager.getString("label.number_of_results_desc"), true,
             100, 0, 100000));
-    args.add(new StringParameter(
+    args.add(new RadioChoiceParameter(
             MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
-            true, HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_NONE,
             Arrays.asList(HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_EVALUE,
                     HMMSearch.CUTOFF_SCORE),
-            null));
+            HMMSearch.CUTOFF_EVALUE));
     args.add(new LogarithmicParameter(
             MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
             MessageManager.getString("label.seq_e_value_desc"), false, 1D,
diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index a58b949..6cda421 100644
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -195,6 +195,7 @@ public class HMMSearch extends HmmerCommand
     String seqScoreCutoff = null;
     String domScoreCutoff = null;
     databaseName = "Alignment";
+    boolean searchAlignment = false;
 
     if (params != null)
     {
@@ -206,6 +207,18 @@ public class HMMSearch extends HmmerCommand
         {
           seqsToReturn = Integer.parseInt(arg.getValue());
         }
+        else if (MessageManager.getString("action.search").equals(name))
+        {
+          searchAlignment = arg.getValue().equals(
+                  MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
+        }
+        else if (MessageManager.getString(DATABASE_KEY).equals(name))
+        {
+          dbPath = arg.getValue();
+          int pos = dbPath.lastIndexOf(File.separator);
+          databaseName = dbPath.substring(pos + 1);
+          databaseFile = new File(dbPath);
+        }
         else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
                 .equals(name))
         {
@@ -280,8 +293,9 @@ public class HMMSearch extends HmmerCommand
       args.add(domScoreCutoff);
     }
 
-    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
-            .equals(dbPath))
+//    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
+//            .equals(dbPath))
+      if (searchAlignment)
     {
       /*
        * no external database specified for search, so
-- 
1.7.10.2