src/jalview/ws2/client/ebi/ParamStores.java

   1 package jalview.ws2.client.ebi;
   2
   3 import jalview.ws.params.ArgumentI;
   4 import jalview.ws.params.ParamDatastoreI;
   5 import jalview.ws.params.ParamManager;
   6 import jalview.ws.params.simple.*;
   7 import jalview.ws2.params.SimpleParamDatastore;
   8
   9 import java.net.MalformedURLException;
  10 import java.net.URL;
  11 import java.util.ArrayList;
  12 import java.util.Collections;
  13 import java.util.List;
  14
  15 class ParamStores
  16 {
  17   static final List<ArgumentI> phmmerParameters;
  18
  19   /**
  20    * Set up phmmer parameters list.
  21    */
  22   static
  23   {
  24     var parameters = new ArrayList<ArgumentI>();
  25     URL baseURL;
  26     try
  27     {
  28       baseURL = new URL( "https://www.ebi.ac.uk/Tools/services/rest/hmmer3_phmmer/");
  29     } catch (MalformedURLException e)
  30     {
  31       throw new ExceptionInInitializerError(e);
  32     }
  33     {
  34       var builder = StringParameter.newBuilder();
  35       builder.setName("cut-offs");
  36       builder.setLabel("Cut-offs");
  37       builder.setDescription("Set the method of controlling which target sequences match your query.");
  38       builder.setRequired(true);
  39       builder.setValue("E");
  40       builder.setDefaultValue("E");
  41       builder.setPossibleValues(List.of("E", "T"));
  42       builder.setDisplayValues(List.of("E-values", "Bit scores"));
  43       parameters.add(builder.build());
  44     }
  45     {
  46       var builder = DoubleParameter.newBuilder();
  47       builder.setName("incE");
  48       builder.setLabel("Significance E-values[Sequence]");
  49       builder.setDescription("Significance E-values[Sequence]");
  50       builder.setRequired(false);
  51       builder.setValue(0.01);
  52       builder.setDefaultValue(0.01);
  53       builder.setMin(0.);
  54       builder.setMax(10.);
  55       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incE"));
  56       parameters.add(builder.build());
  57     }
  58     {
  59       var builder = DoubleParameter.newBuilder();
  60       builder.setName("incdomE");
  61       builder.setLabel("Significance E-values[Hit]");
  62       builder.setDescription("Significance E-values[Hit]");
  63       builder.setRequired(false);
  64       builder.setValue(0.03);
  65       builder.setDefaultValue(0.03);
  66       builder.setMin(0.);
  67       builder.setMax(10.);
  68       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incdomE"));
  69       parameters.add(builder.build());
  70     }
  71     {
  72       var builder = DoubleParameter.newBuilder();
  73       builder.setName("E");
  74       builder.setLabel("Report E-values[Sequence]");
  75       builder.setDescription("Report E-values[Sequence]");
  76       builder.setRequired(false);
  77       builder.setValue(1.0);
  78       builder.setDefaultValue(1.0);
  79       builder.setMin(0.);
  80       builder.setMax(10.);
  81       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/E"));
  82       parameters.add(builder.build());
  83     }
  84     {
  85       var builder = DoubleParameter.newBuilder();
  86       builder.setName("domE");
  87       builder.setLabel("Report E-values[Hit]");
  88       builder.setDescription("Report E-values[Hit]");
  89       builder.setRequired(false);
  90       builder.setValue(1.0);
  91       builder.setDefaultValue(1.0);
  92       builder.setMin(0.);
  93       builder.setMax(10.);
  94       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/domE"));
  95       parameters.add(builder.build());
  96     }
  97     {
  98       var builder = DoubleParameter.newBuilder();
  99       builder.setName("incT");
 100       builder.setLabel("Significance bit scores[Sequence]");
 101       builder.setDescription("Significance bit scores[Sequence]");
 102       builder.setRequired(false);
 103       builder.setValue(25.0);
 104       builder.setDefaultValue(25.0);
 105       builder.setMin(0.);
 106       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incT"));
 107       parameters.add(builder.build());
 108     }
 109     {
 110       var builder = DoubleParameter.newBuilder();
 111       builder.setName("incdomT");
 112       builder.setLabel("Significance bit scores[Hit]");
 113       builder.setDescription("Significance bit scores[Hit]");
 114       builder.setRequired(false);
 115       builder.setValue(22.0);
 116       builder.setDefaultValue(22.0);
 117       builder.setMin(0.);
 118       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/incdomT"));
 119       parameters.add(builder.build());
 120     }
 121     {
 122       var builder = DoubleParameter.newBuilder();
 123       builder.setName("T");
 124       builder.setLabel("Report bit scores[Sequence]");
 125       builder.setDescription("Report bit scores[Sequence]");
 126       builder.setRequired(false);
 127       builder.setValue(7.0);
 128       builder.setDefaultValue(7.0);
 129       builder.setMin(0.);
 130       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/T"));
 131       parameters.add(builder.build());
 132     }
 133     {
 134       var builder = DoubleParameter.newBuilder();
 135       builder.setName("domT");
 136       builder.setLabel("Report bit scores[Hit]");
 137       builder.setDescription("Report bit scores[Hit]");
 138       builder.setRequired(false);
 139       builder.setValue(5.0);
 140       builder.setDefaultValue(5.0);
 141       builder.setMin(0.);
 142       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/domT"));
 143       parameters.add(builder.build());
 144     }
 145     {
 146       var builder = DoubleParameter.newBuilder();
 147       builder.setName("popen");
 148       builder.setLabel("Gap Penalties[open]");
 149       builder.setDescription("Gap Penalties[open]");
 150       builder.setRequired(false);
 151       builder.setValue(0.02);
 152       builder.setDefaultValue(0.02);
 153       builder.setMin(0.);
 154       builder.setMax(0.5);
 155       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/popen"));
 156       parameters.add(builder.build());
 157     }
 158     {
 159       var builder = DoubleParameter.newBuilder();
 160       builder.setName("pextend");
 161       builder.setLabel("Gap Penalties[extend]");
 162       builder.setDescription("Gap Penalties[extend]");
 163       builder.setRequired(false);
 164       builder.setValue(0.4);
 165       builder.setDefaultValue(0.4);
 166       builder.setMin(0.);
 167       builder.setMax(1.);
 168       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/pextend"));
 169       parameters.add(builder.build());
 170     }
 171     {
 172       var builder = StringParameter.newBuilder();
 173       builder.setName("mx");
 174       builder.setLabel("Gap Penalties[Substitution scoring matrix]");
 175       builder.setDescription("Gap Penalties[Substitution scoring matrix]");
 176       builder.setRequired(false);
 177       builder.setValue("BLOSUM62");
 178       builder.setDefaultValue("BLOSUM62");
 179       builder.setPossibleValues(List.of("BLOSUM45", "BLOSUM62", "BLOSUM90", "PAM30", "PAM70"));
 180       builder.setDisplayValues(List.of("BLOSUM45", "BLOSUM62", "BLOSUM90", "PAM30", "PAM70"));
 181       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/mx"));
 182       parameters.add(builder.build());
 183     }
 184     {
 185       var builder = BooleanOption.newBuilder();
 186       builder.setName("nobias");
 187       builder.setLabel("No bias filter");
 188       builder.setDescription(
 189               "The '--nobias' option turns off (bypasses) the biased composition filter which is on by default.");
 190       builder.setRequired(false);
 191       builder.setValue(false);
 192       builder.setDefaultValue(false);
 193       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/nobias"));
 194       parameters.add(builder.build());
 195     }
 196     {
 197       var builder = BooleanOption.newBuilder();
 198       builder.setName("compressedout");
 199       builder.setLabel("Compressed Output");
 200       builder.setDescription(
 201               "By default it runs hmm2c plus post-processing (default output), whereas with compressedout, it gets compressed output only.");
 202       builder.setRequired(false);
 203       builder.setValue(false);
 204       builder.setDefaultValue(false);
 205       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/compressedout"));
 206       parameters.add(builder.build());
 207     }
 208     {
 209       var builder = BooleanOption.newBuilder();
 210       builder.setName("alignView");
 211       builder.setLabel("Output Alignment");
 212       builder.setDescription("Output alignment in result");
 213       builder.setRequired(false);
 214       builder.setValue(true);
 215       builder.setDefaultValue(true);
 216       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/alignView"));
 217       parameters.add(builder.build());
 218     }
 219     {
 220       var builder = StringParameter.newBuilder();
 221       builder.setName("database");
 222       builder.setLabel("Sequence Database");
 223       builder.setDescription("Sequence Database Selection");
 224       builder.setRequired(true);
 225       builder.setValue("uniprotkb");
 226       builder.setDefaultValue("uniprotkb");
 227       builder.setPossibleValues(List.of("swissprot", "uniprotrefprot", "uniprotkb", "pdb", "rp75", "rp55", "rp35", "rp15", "ensembl", "merops", "qfo", "chembl"));
 228       builder.setDisplayValues(List.of("SwissProt", "Reference Proteomes", "UniProtKB", "PDB", "rp75", "rp55", "rp35", "rp15", "Ensembl", "MEROPS", "Quest for Orthologs", "ChEMBL"));
 229       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/database"));
 230       parameters.add(builder.build());
 231     }
 232     {
 233       var builder = DoubleParameter.newBuilder();
 234       builder.setName("evalue");
 235       builder.setLabel("Expectation Value Threshold");
 236       builder.setDescription(
 237               "Expectation value cut-off for reporting target profiles in the per-target output.");
 238       builder.setRequired(false);
 239       builder.setValue(0.01);
 240       builder.setDefaultValue(0.01);
 241       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/evalue"));
 242       parameters.add(builder.build());
 243     }
 244 //    {
 245 //      var builder = StringParameter.newBuilder();
 246 //      builder.setName("sequence");
 247 //      builder.setLabel("Input Sequence");
 248 //      builder.setDescription(
 249 //              "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.");
 250 //      builder.setRequired(false);
 251 //
 252 //      builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/sequence"));
 253 //      parameters.add(builder.build());
 254 //    }
 255     {
 256       var builder = IntegerParameter.newBuilder();
 257       builder.setName("nhits");
 258       builder.setLabel("Number of Hits Displayed");
 259       builder.setDescription("Number of hits to be displayed.");
 260       builder.setRequired(false);
 261       builder.setValue(100);
 262       builder.setDefaultValue(100);
 263       builder.setDetailsUrl(resolveURL(baseURL, "parameterdetails/nhits"));
 264       parameters.add(builder.build());
 265     }
 266     phmmerParameters = Collections.unmodifiableList(parameters);
 267   }
 268
 269   private static URL resolveURL(URL base, String spec)
 270   {
 271     try
 272     {
 273       return new URL(base, spec);
 274     } catch (MalformedURLException e)
 275     {
 276       throw new ExceptionInInitializerError(e);
 277     }
 278   }
 279
 280   public static ParamDatastoreI newPhmmerDatastore(URL url, ParamManager manager)
 281   {
 282     return new SimpleParamDatastore(url, phmmerParameters,
 283             Collections.emptyList(), manager);
 284   }
 285 }