From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Mon, 8 May 2023 14:23:35 +0000 (+0200)
Subject: JAL-3954 Create ParamDatastore builder for phmmer
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bbc8fc127287ad3a11f0b470d37d741ddca162ff;p=jalview.git

JAL-3954 Create ParamDatastore builder for phmmer
---

diff --git a/src/jalview/ws2/client/ebi/ParamStores.java b/src/jalview/ws2/client/ebi/ParamStores.java
new file mode 100644
index 0000000..ffd338d
--- /dev/null
+++ b/src/jalview/ws2/client/ebi/ParamStores.java
@@ -0,0 +1,285 @@
+package jalview.ws2.client.ebi;
+
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.simple.*;
+import jalview.ws2.params.SimpleParamDatastore;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+class ParamStores
+{
+  static final List<ArgumentI> phmmerParameters;
+
+  /**
+   * Set up phmmer parameters list.
+   */
+  static
+  {
+    var parameters = new ArrayList<ArgumentI>();
+    URL baseURL;
+    try
+    {
+      baseURL = new URL( "https://www.ebi.ac.uk/Tools/services/rest/hmmer3_phmmer/");
+    } catch (MalformedURLException e)
+    {
+      throw new ExceptionInInitializerError(e);
+    }
+    {
+      var builder = StringParameter.newBuilder();
+      builder.setName("cut-offs");
+      builder.setLabel("Cut-offs");
+      builder.setDescription("Set the method of controlling which target sequences match your query.");
+      builder.setRequired(true);
+      builder.setValue("E");
+      builder.setDefaultValue("E");
+      builder.setPossibleValues(List.of("E", "T"));
+      builder.setDisplayValues(List.of("E-values", "Bit scores"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("incE");
+      builder.setLabel("Significance E-values[Sequence]");
+      builder.setDescription("Significance E-values[Sequence]");
+      builder.setRequired(false);
+      builder.setValue(0.01);
+      builder.setDefaultValue(0.01);
+      builder.setMin(0.);
+      builder.setMax(10.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incE"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("incdomE");
+      builder.setLabel("Significance E-values[Hit]");
+      builder.setDescription("Significance E-values[Hit]");
+      builder.setRequired(false);
+      builder.setValue(0.03);
+      builder.setDefaultValue(0.03);
+      builder.setMin(0.);
+      builder.setMax(10.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incdomE"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("E");
+      builder.setLabel("Report E-values[Sequence]");
+      builder.setDescription("Report E-values[Sequence]");
+      builder.setRequired(false);
+      builder.setValue(1.0);
+      builder.setDefaultValue(1.0);
+      builder.setMin(0.);
+      builder.setMax(10.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/E"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("domE");
+      builder.setLabel("Report E-values[Hit]");
+      builder.setDescription("Report E-values[Hit]");
+      builder.setRequired(false);
+      builder.setValue(1.0);
+      builder.setDefaultValue(1.0);
+      builder.setMin(0.);
+      builder.setMax(10.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/domE"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("incT");
+      builder.setLabel("Significance bit scores[Sequence]");
+      builder.setDescription("Significance bit scores[Sequence]");
+      builder.setRequired(false);
+      builder.setValue(25.0);
+      builder.setDefaultValue(25.0);
+      builder.setMin(0.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incT"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("incdomT");
+      builder.setLabel("Significance bit scores[Hit]");
+      builder.setDescription("Significance bit scores[Hit]");
+      builder.setRequired(false);
+      builder.setValue(22.0);
+      builder.setDefaultValue(22.0);
+      builder.setMin(0.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incdomT"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("T");
+      builder.setLabel("Report bit scores[Sequence]");
+      builder.setDescription("Report bit scores[Sequence]");
+      builder.setRequired(false);
+      builder.setValue(7.0);
+      builder.setDefaultValue(7.0);
+      builder.setMin(0.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/T"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("domT");
+      builder.setLabel("Report bit scores[Hit]");
+      builder.setDescription("Report bit scores[Hit]");
+      builder.setRequired(false);
+      builder.setValue(5.0);
+      builder.setDefaultValue(5.0);
+      builder.setMin(0.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/domT"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("popen");
+      builder.setLabel("Gap Penalties[open]");
+      builder.setDescription("Gap Penalties[open]");
+      builder.setRequired(false);
+      builder.setValue(0.02);
+      builder.setDefaultValue(0.02);
+      builder.setMin(0.);
+      builder.setMax(0.5);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/popen"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("pextend");
+      builder.setLabel("Gap Penalties[extend]");
+      builder.setDescription("Gap Penalties[extend]");
+      builder.setRequired(false);
+      builder.setValue(0.4);
+      builder.setDefaultValue(0.4);
+      builder.setMin(0.);
+      builder.setMax(1.);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/pextend"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = StringParameter.newBuilder();
+      builder.setName("mx");
+      builder.setLabel("Gap Penalties[Substitution scoring matrix]");
+      builder.setDescription("Gap Penalties[Substitution scoring matrix]");
+      builder.setRequired(false);
+      builder.setValue("BLOSUM62");
+      builder.setDefaultValue("BLOSUM62");
+      builder.setPossibleValues(List.of("BLOSUM45", "BLOSUM62", "BLOSUM90", "PAM30", "PAM70"));
+      builder.setDisplayValues(List.of("BLOSUM45", "BLOSUM62", "BLOSUM90", "PAM30", "PAM70"));
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/mx"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = BooleanOption.newBuilder();
+      builder.setName("nobias");
+      builder.setLabel("No bias filter");
+      builder.setDescription(
+              "The '--nobias' option turns off (bypasses) the biased composition filter which is on by default.");
+      builder.setRequired(false);
+      builder.setValue(false);
+      builder.setDefaultValue(false);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/nobias"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = BooleanOption.newBuilder();
+      builder.setName("compressedout");
+      builder.setLabel("Compressed Output");
+      builder.setDescription(
+              "By default it runs hmm2c plus post-processing (default output), whereas with compressedout, it gets compressed output only.");
+      builder.setRequired(false);
+      builder.setValue(false);
+      builder.setDefaultValue(false);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/compressedout"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = BooleanOption.newBuilder();
+      builder.setName("alignView");
+      builder.setLabel("Output Alignment");
+      builder.setDescription("Output alignment in result");
+      builder.setRequired(false);
+      builder.setValue(true);
+      builder.setDefaultValue(true);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/alignView"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = StringParameter.newBuilder();
+      builder.setName("database");
+      builder.setLabel("Sequence Database");
+      builder.setDescription("Sequence Database Selection");
+      builder.setRequired(true);
+      builder.setValue("uniprotkb");
+      builder.setDefaultValue("uniprotkb");
+      builder.setPossibleValues(List.of("swissprot", "uniprotrefprot", "uniprotkb", "pdb", "rp75", "rp55", "rp35", "rp15", "ensembl", "merops", "qfo", "chembl"));
+      builder.setDisplayValues(List.of("SwissProt", "Reference Proteomes", "UniProtKB", "PDB", "rp75", "rp55", "rp35", "rp15", "Ensembl", "MEROPS", "Quest for Orthologs", "ChEMBL"));
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/database"));
+      parameters.add(builder.build());
+    }
+    {
+      var builder = DoubleParameter.newBuilder();
+      builder.setName("evalue");
+      builder.setLabel("Expectation Value Threshold");
+      builder.setDescription(
+              "Expectation value cut-off for reporting target profiles in the per-target output.");
+      builder.setRequired(false);
+      builder.setValue(0.01);
+      builder.setDefaultValue(0.01);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/evalue"));
+      parameters.add(builder.build());
+    }
+//    {
+//      var builder = StringParameter.newBuilder();
+//      builder.setName("sequence");
+//      builder.setLabel("Input Sequence");
+//      builder.setDescription(
+//              "The input sequence can be entered directly into this form. The sequence can be be in FASTA or UniProtKB/Swiss-Prot format. A partially formatted sequence is not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.");
+//      builder.setRequired(false);
+//
+//      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/sequence"));
+//      parameters.add(builder.build());
+//    }
+    {
+      var builder = IntegerParameter.newBuilder();
+      builder.setName("nhits");
+      builder.setLabel("Number of Hits Displayed");
+      builder.setDescription("Number of hits to be displayed.");
+      builder.setRequired(false);
+      builder.setValue(100);
+      builder.setDefaultValue(100);
+      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/nhits"));
+      parameters.add(builder.build());
+    }
+    phmmerParameters = Collections.unmodifiableList(parameters);
+  }
+
+  private static URL resolveURL(URL base, String spec)
+  {
+    try
+    {
+      return new URL(base, spec);
+    } catch (MalformedURLException e)
+    {
+      throw new ExceptionInInitializerError(e);
+    }
+  }
+  
+  public static ParamDatastoreI newPhmmerDatastore(URL url, ParamManager manager)
+  {
+    return new SimpleParamDatastore(url, phmmerParameters,
+            Collections.emptyList(), manager);
+  }
+}