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