src/jalview/hmmer/HMMERParamStore.java

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