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
  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
  22 public class HMMERParamStore implements ParamDatastoreI
  23 {
  24
  25   String name;
  26
  27   List<WsParamSetI> presets = new ArrayList<>();
  28
  29   public HMMERParamStore(String name)
  30   {
  31     this.name = name;
  32   }
  33
  34   @Override
  35   public List<WsParamSetI> getPresets()
  36   {
  37     // TODO Auto-generated method stub
  38     return presets;
  39   }
  40
  41   @Override
  42   public WsParamSetI getPreset(String name)
  43   {
  44     // TODO Auto-generated method stub
  45     return null;
  46   }
  47
  48   @Override
  49   public List<ArgumentI> getServiceParameters()
  50   {
  51     List<ArgumentI> args = new ArrayList<>();
  52     if ("hmmsearch".equals(name))
  53     {
  54       args.add(new IntegerParameter(
  55               MessageManager.getString("label.number_of_results"),
  56               MessageManager
  57                       .getString("label.number_of_results_desc"),
  58               true, 100, 0, 100000));
  59       String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
  60       if (names != null && !names.isEmpty())
  61       {
  62         Collection<String> databases = new ArrayList<>();
  63         databases.add(MessageManager.getString("label.this_alignment"));
  64         Scanner nameScanner = new Scanner(names);
  65
  66         if (nameScanner.hasNext())
  67         {
  68           while (nameScanner.hasNext())
  69           {
  70             String next = nameScanner.next();
  71             if (next == "null")
  72             {
  73               Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
  74               Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
  75             }
  76             else
  77             {
  78               databases.add(next);
  79             }
  80           }
  81         }
  82         nameScanner.close();
  83         args.add(new Option(MessageManager.getString("label.database"),
  84                 MessageManager.getString("label.database_for_hmmsearch"),
  85                 true, MessageManager.getString("label.this_alignment"),
  86                 MessageManager.getString("label.this_alignment"), databases,
  87                 null));
  88       }
  89       args.add(new BooleanOption(
  90               MessageManager.getString("label.auto_align_seqs"),
  91               MessageManager.getString("label.auto_align_seqs_desc"),
  92               false, false, true, null));
  93       args.add(new BooleanOption(
  94               MessageManager.getString("label.use_accessions"),
  95               MessageManager.getString("label.use_accessions_desc"),
  96               false, false, true, null));
  97       args.add(new BooleanOption(
  98               MessageManager.getString("label.trim_termini"),
  99               MessageManager.getString("label.trim_termini_desc"), false,
 100               false, true, null));
 101       args.add(new LogarithmicParameter(
 102               MessageManager.getString("label.seq_e_value"),
 103               MessageManager.getString("label.seq_e_value_desc"), false,
 104               0.001d, -63d, 9d, 4d));
 105       /*
 106       args.add(new DoubleParameter(
 107               MessageManager.getString("label.seq_score"),
 108               MessageManager.getString("label.seq_score_desc"), false,
 109               0d, 0d, 10000d));
 110          */
 111       args.add(new LogarithmicParameter(
 112               MessageManager.getString("label.dom_e_value_desc"),
 113               MessageManager.getString("label.dom_e_value_desc"), false,
 114               0.001d, -63d, 9d, 4d));
 115       /*
 116       args.add(new DoubleParameter(
 117               MessageManager.getString("label.dom_score"),
 118               MessageManager.getString("label.dom_score_desc"), false, 0d,
 119               0d,
 120               10000d));
 121               */
 122     }
 123     if ("hmmalign".equals(name))
 124     {
 125       args.add(new BooleanOption(
 126               MessageManager.getString("label.trim_termini"),
 127               MessageManager.getString(
 128                       "label.trim_termini = Trim Non-Matching Termini_desc"),
 129               false, false, true, null));
 130
 131     }
 132     if ("hmmbuild".equals(name))
 133     {
 134       args.add(new BooleanOption(
 135               MessageManager.getString("label.trim_termini"),
 136               MessageManager.getString(
 137                       "label.trim_termini = Trim Non-Matching Termini_desc"),
 138               false, false, true, null));
 139
 140     }
 141     return args;
 142   }
 143
 144   @Override
 145   public boolean presetExists(String name)
 146   {
 147     // TODO Auto-generated method stub
 148     return false;
 149   }
 150
 151   @Override
 152   public void deletePreset(String name)
 153   {
 154     // TODO Auto-generated method stub
 155
 156   }
 157
 158   @Override
 159   public void storePreset(String presetName, String text,
 160           List<ArgumentI> jobParams)
 161   {
 162     // TODO Auto-generated method stub
 163
 164   }
 165
 166   @Override
 167   public void updatePreset(String oldName, String presetName, String text,
 168           List<ArgumentI> jobParams)
 169   {
 170     // TODO Auto-generated method stub
 171
 172   }
 173
 174   @Override
 175   public WsParamSetI parseServiceParameterFile(String name,
 176           String description, String[] serviceURL, String parameters)
 177           throws IOException
 178   {
 179     // TODO Auto-generated method stub
 180     return null;
 181   }
 182
 183   @Override
 184   public String generateServiceParameterFile(WsParamSetI pset)
 185           throws IOException
 186   {
 187     // TODO Auto-generated method stub
 188     return null;
 189   }
 190
 191 }