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