src/jalview/hmmer/HMMERParamStore.java

   1 package jalview.hmmer;
   2
   3 import jalview.bin.Cache;
   4 import jalview.gui.Preferences;
   5 import jalview.util.MessageManager;
   6 import jalview.ws.params.ArgumentI;
   7 import jalview.ws.params.ParamDatastoreI;
   8 import jalview.ws.params.WsParamSetI;
   9 import jalview.ws.params.simple.BooleanOption;
  10 import jalview.ws.params.simple.IntegerParameter;
  11 import jalview.ws.params.simple.LogarithmicParameter;
  12 import jalview.ws.params.simple.Option;
  13 import jalview.ws.params.simple.StringParameter;
  14
  15 import java.io.IOException;
  16 import java.util.ArrayList;
  17 import java.util.Collection;
  18 import java.util.List;
  19 import java.util.Scanner;
  20
  21 public final class HMMERParamStore implements ParamDatastoreI
  22 {
  23   private static final String HMMBUILD = "hmmbuild";
  24
  25   private static final String HMMALIGN = "hmmalign";
  26
  27   private static final String HMMSEARCH = "hmmsearch";
  28
  29   String name;
  30
  31   List<WsParamSetI> presets = new ArrayList<>();
  32
  33   private HMMERParamStore(String nam)
  34   {
  35     this.name = nam;
  36   }
  37
  38   public static HMMERParamStore forBuild()
  39   {
  40     return new HMMERParamStore(HMMBUILD);
  41   }
  42
  43   public static HMMERParamStore forAlign()
  44   {
  45     return new HMMERParamStore(HMMALIGN);
  46   }
  47
  48   public static HMMERParamStore forSearch()
  49   {
  50     return new HMMERParamStore(HMMSEARCH);
  51   }
  52
  53   @Override
  54   public List<WsParamSetI> getPresets()
  55   {
  56     return presets;
  57   }
  58
  59   @Override
  60   public WsParamSetI getPreset(String nam)
  61   {
  62     return null;
  63   }
  64
  65   @Override
  66   public List<ArgumentI> getServiceParameters()
  67   {
  68     List<ArgumentI> args = new ArrayList<>();
  69     switch (name)
  70     {
  71     case HMMSEARCH:
  72       getHMMSearchParams(args);
  73       break;
  74     case HMMALIGN:
  75       getHMMAlignParams(args);
  76       break;
  77     case HMMBUILD:
  78       getHMMBuildParams(args);
  79       break;
  80     default:
  81     }
  82
  83     return args;
  84   }
  85
  86   private void getHMMSearchParams(List<ArgumentI> args)
  87   {
  88     args.add(new IntegerParameter(
  89             MessageManager.getString("label.number_of_results"),
  90             MessageManager.getString("label.number_of_results_desc"), true,
  91             100, 0, 100000));
  92     String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
  93     if (names != null && !names.isEmpty())
  94     {
  95       Collection<String> databases = new ArrayList<>();
  96       databases.add(MessageManager.getString("label.this_alignment"));
  97       Scanner nameScanner = new Scanner(names);
  98
  99       if (nameScanner.hasNext())
 100       {
 101         while (nameScanner.hasNext())
 102         {
 103           String next = nameScanner.next();
 104           if ("null".equals(next))
 105           {
 106             Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
 107             Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
 108           }
 109           else
 110           {
 111             databases.add(next);
 112           }
 113         }
 114       }
 115       nameScanner.close();
 116       args.add(new Option(MessageManager.getString("label.database"),
 117               MessageManager.getString("label.database_for_hmmsearch"),
 118               true, MessageManager.getString("label.this_alignment"),
 119               MessageManager.getString("label.this_alignment"), databases,
 120               null));
 121     }
 122     args.add(new BooleanOption(
 123             MessageManager.getString("label.auto_align_seqs"),
 124             MessageManager.getString("label.auto_align_seqs_desc"), false,
 125             false, true, null));
 126     args.add(new BooleanOption(
 127             MessageManager.getString("label.use_accessions"),
 128             MessageManager.getString("label.use_accessions_desc"), false,
 129             false, true, null));
 130     args.add(new BooleanOption(
 131             MessageManager.getString("label.trim_termini"),
 132             MessageManager.getString("label.trim_termini_desc"), false,
 133             false, true, null));
 134     args.add(new LogarithmicParameter(
 135             MessageManager.getString("label.seq_e_value"),
 136             MessageManager.getString("label.seq_e_value_desc"), false, -3d,
 137             -37.92977945, 1d, 10d));
 138     /*
 139     args.add(new DoubleParameter(
 140             MessageManager.getString("label.seq_score"),
 141             MessageManager.getString("label.seq_score_desc"), false,
 142             0d, 0d, 10000d));
 143        */
 144     args.add(new LogarithmicParameter(
 145             MessageManager.getString("label.dom_e_value_desc"),
 146             MessageManager.getString("label.dom_e_value_desc"), false, -3d,
 147             -37.92977945, 1d, 10d));
 148     /*
 149     args.add(new DoubleParameter(
 150             MessageManager.getString("label.dom_score"),
 151             MessageManager.getString("label.dom_score_desc"), false, 0d,
 152             0d,
 153             10000d));
 154             */
 155   }
 156
 157   private void getHMMAlignParams(List<ArgumentI> args)
 158   {
 159     args.add(new BooleanOption(
 160             MessageManager.getString("label.trim_termini"),
 161             MessageManager.getString("label.trim_termini_desc"),
 162             false, false, true, null));
 163   }
 164
 165   private void getHMMBuildParams(List<ArgumentI> args)
 166   {
 167     args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
 168             MessageManager.getString("label.hmm_name_desc"), true, ""));
 169     // todo only enable Use Reference Annotation if RF is present
 170     args.add(new BooleanOption(
 171             MessageManager.getString("label.use_reference"),
 172             MessageManager.getString("label.use_reference_desc"), true,
 173             true, true, null));
 174
 175     Collection<String> options = new ArrayList<>();
 176     options.add(MessageManager.getString("label.alignment"));
 177     options.add(MessageManager.getString("label.groups_and_alignment"));
 178     options.add(MessageManager.getString("label.groups"));
 179     options.add(MessageManager.getString("label.selected_group"));
 180
 181     args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
 182             MessageManager.getString("label.hmmbuild_for_desc"), true,
 183             MessageManager.getString("label.alignment"),
 184             MessageManager.getString("label.alignment"), options, null));
 185   }
 186
 187   @Override
 188   public boolean presetExists(String forName)
 189   {
 190     return false;
 191   }
 192
 193   @Override
 194   public void deletePreset(String forName)
 195   {
 196   }
 197
 198   @Override
 199   public void storePreset(String presetName, String text,
 200           List<ArgumentI> jobParams)
 201   {
 202   }
 203
 204   @Override
 205   public void updatePreset(String oldName, String presetName, String text,
 206           List<ArgumentI> jobParams)
 207   {
 208   }
 209
 210   @Override
 211   public WsParamSetI parseServiceParameterFile(String forName,
 212           String description, String[] serviceURL, String parameters)
 213           throws IOException
 214   {
 215     return null;
 216   }
 217
 218   @Override
 219   public String generateServiceParameterFile(WsParamSetI pset)
 220           throws IOException
 221   {
 222     return null;
 223   }
 224
 225 }