Update spike branch to latest (HMMSearch file chooser arg)

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

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 00cae85..452097b 100644 (file)
--- 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,