--- /dev/null
+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);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff