JAL-2629 adjust parameter min and max to better suit HMMER ranges

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

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 1bfc72f..ab33c95 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -1,6 +1,8 @@
 package jalview.hmmer;
 
 
+import jalview.bin.Cache;
+import jalview.gui.Preferences;
 import jalview.util.MessageManager;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
@@ -8,10 +10,13 @@ import jalview.ws.params.WsParamSetI;
 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 java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
+import java.util.Scanner;
 
 
 public class HMMERParamStore implements ParamDatastoreI
@@ -46,66 +51,101 @@ public class HMMERParamStore implements ParamDatastoreI
     List<ArgumentI> args = new ArrayList<>();
     if ("hmmsearch".equals(name))
     {
-      args.add(new IntegerParameter(
-              MessageManager.getString("label.number_of_results"),
-              MessageManager
-                      .getString("label.number_of_results_desc"),
-              true, 100, 0, 100000));
-      args.add(new BooleanOption(
-              MessageManager.getString("label.auto_align_seqs"),
-              MessageManager.getString("label.auto_align_seqs_desc"),
-              false, false, true, null));
-      args.add(new BooleanOption(
-              MessageManager.getString("label.use_accessions"),
-              MessageManager.getString("label.use_accessions_desc"),
-              false, false, true, null));
-      args.add(new BooleanOption(
-              MessageManager.getString("label.trim_termini"),
-              MessageManager.getString("label.trim_termini_desc"), false,
-              false, true, null));
-      args.add(new LogarithmicParameter(
-              MessageManager.getString("label.seq_e_value"),
-              MessageManager.getString("label.seq_e_value_desc"), false,
-              0.001d, -63d, 9d, 4d));
-      /*
-      args.add(new DoubleParameter(
-              MessageManager.getString("label.seq_score"),
-              MessageManager.getString("label.seq_score_desc"), false,
-              0d, 0d, 10000d));
-         */
-      args.add(new LogarithmicParameter(
-              MessageManager.getString("label.dom_e_value_desc"),
-              MessageManager.getString("label.dom_e_value_desc"), false,
-              0.001d, -63d, 9d, 4d));
-      /*
-      args.add(new DoubleParameter(
-              MessageManager.getString("label.dom_score"),
-              MessageManager.getString("label.dom_score_desc"), false, 0d,
-              0d,
-              10000d));
-              */
+      getHMMSearchParams(args);
     }
     if ("hmmalign".equals(name))
     {
-      args.add(new BooleanOption(
-              MessageManager.getString("label.trim_termini"),
-              MessageManager.getString(
-                      "label.trim_termini = Trim Non-Matching Termini_desc"),
-              false, false, true, null));
+      getHMMAlignParams(args);
 
     }
     if ("hmmbuild".equals(name))
     {
-      args.add(new BooleanOption(
-              MessageManager.getString("label.trim_termini"),
-              MessageManager.getString(
-                      "label.trim_termini = Trim Non-Matching Termini_desc"),
-              false, false, true, null));
+
 
     }
     return args;
   }
 
+  private void getHMMSearchParams(List<ArgumentI> args)
+  {
+    args.add(new IntegerParameter(
+            MessageManager.getString("label.number_of_results"),
+            MessageManager.getString("label.number_of_results_desc"), true,
+            100, 0, 100000));
+    String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+    if (names != null && !names.isEmpty())
+    {
+      Collection<String> databases = new ArrayList<>();
+      databases.add(MessageManager.getString("label.this_alignment"));
+      Scanner nameScanner = new Scanner(names);
+
+      if (nameScanner.hasNext())
+      {
+        while (nameScanner.hasNext())
+        {
+          String next = nameScanner.next();
+          if (next == "null")
+          {
+            Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+            Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+          }
+          else
+          {
+            databases.add(next);
+          }
+        }
+      }
+      nameScanner.close();
+      args.add(new Option(MessageManager.getString("label.database"),
+              MessageManager.getString("label.database_for_hmmsearch"),
+              true, MessageManager.getString("label.this_alignment"),
+              MessageManager.getString("label.this_alignment"), databases,
+              null));
+    }
+    args.add(new BooleanOption(
+            MessageManager.getString("label.auto_align_seqs"),
+            MessageManager.getString("label.auto_align_seqs_desc"), false,
+            false, true, null));
+    args.add(new BooleanOption(
+            MessageManager.getString("label.use_accessions"),
+            MessageManager.getString("label.use_accessions_desc"), false,
+            false, true, null));
+    args.add(new BooleanOption(
+            MessageManager.getString("label.trim_termini"),
+            MessageManager.getString("label.trim_termini_desc"), false,
+            false, true, null));
+    args.add(new LogarithmicParameter(
+            MessageManager.getString("label.seq_e_value"),
+            MessageManager.getString("label.seq_e_value_desc"), false,
+            -9.96578, -126d, 3.3219d, 2d));
+    /*
+    args.add(new DoubleParameter(
+            MessageManager.getString("label.seq_score"),
+            MessageManager.getString("label.seq_score_desc"), false,
+            0d, 0d, 10000d));
+       */
+    args.add(new LogarithmicParameter(
+            MessageManager.getString("label.dom_e_value_desc"),
+            MessageManager.getString("label.dom_e_value_desc"), false,
+            -9.96578, -126d, 3.3219d, 2d));
+    /*
+    args.add(new DoubleParameter(
+            MessageManager.getString("label.dom_score"),
+            MessageManager.getString("label.dom_score_desc"), false, 0d,
+            0d,
+            10000d));
+            */
+  }
+
+  private void getHMMAlignParams(List<ArgumentI> args)
+  {
+    args.add(new BooleanOption(
+            MessageManager.getString("label.trim_termini"),
+            MessageManager.getString(
+                    "label.trim_termini = Trim Non-Matching Termini_desc"),
+            false, false, true, null));
+  }
+
   @Override
   public boolean presetExists(String name)
   {