JAL-2629 partial refactoring of Hmmer command classes

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

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index a4bf8e4..af55dab 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -1,6 +1,5 @@
 package jalview.hmmer;
 
-
 import jalview.bin.Cache;
 import jalview.gui.Preferences;
 import jalview.util.MessageManager;
@@ -11,6 +10,7 @@ import jalview.ws.params.simple.BooleanOption;
 import jalview.ws.params.simple.IntegerParameter;
 import jalview.ws.params.simple.LogarithmicParameter;
 import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.StringParameter;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -18,7 +18,6 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Scanner;
 
-
 public class HMMERParamStore implements ParamDatastoreI
 {
 
@@ -60,7 +59,7 @@ public class HMMERParamStore implements ParamDatastoreI
     }
     if ("hmmbuild".equals(name))
     {
-
+      getHMMBuildParams(args);
 
     }
     return args;
@@ -116,8 +115,8 @@ public class HMMERParamStore implements ParamDatastoreI
             false, true, null));
     args.add(new LogarithmicParameter(
             MessageManager.getString("label.seq_e_value"),
-            MessageManager.getString("label.seq_e_value_desc"), false,
-            -3d, -37.92977945, 1d, 10d));
+            MessageManager.getString("label.seq_e_value_desc"), false, -3d,
+            -37.92977945, 1d, 10d));
     /*
     args.add(new DoubleParameter(
             MessageManager.getString("label.seq_score"),
@@ -126,8 +125,8 @@ public class HMMERParamStore implements ParamDatastoreI
        */
     args.add(new LogarithmicParameter(
             MessageManager.getString("label.dom_e_value_desc"),
-            MessageManager.getString("label.dom_e_value_desc"), false,
-            -3d, -37.92977945, 1d, 10d));
+            MessageManager.getString("label.dom_e_value_desc"), false, -3d,
+            -37.92977945, 1d, 10d));
     /*
     args.add(new DoubleParameter(
             MessageManager.getString("label.dom_score"),
@@ -141,11 +140,31 @@ public class HMMERParamStore implements ParamDatastoreI
   {
     args.add(new BooleanOption(
             MessageManager.getString("label.trim_termini"),
-            MessageManager.getString(
-                    "label.trim_termini = Trim Non-Matching Termini_desc"),
+            MessageManager.getString("label.trim_termini_desc"),
             false, false, true, null));
   }
 
+  private void getHMMBuildParams(List<ArgumentI> args)
+  {
+    args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
+            MessageManager.getString("label.hmm_name_desc"), true, ""));
+    args.add(new BooleanOption(
+            MessageManager.getString("label.use_reference"),
+            MessageManager.getString("label.use_reference_desc"), true,
+            true, true, null));
+
+    Collection<String> options = new ArrayList<>();
+    options.add(MessageManager.getString("label.alignment"));
+    options.add(MessageManager.getString("label.groups_and_alignment"));
+    options.add(MessageManager.getString("label.groups"));
+    options.add(MessageManager.getString("label.selected_group"));
+
+    args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
+            MessageManager.getString("label.hmmbuild_for_desc"), true,
+            MessageManager.getString("label.alignment"),
+            MessageManager.getString("label.alignment"), options, null));
+  }
+
   @Override
   public boolean presetExists(String name)
   {