+package jalview.hmmer;
+
+
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.LogarithmicParameter;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+
+public class HMMERParamStore implements ParamDatastoreI
+{
+
+ String name;
+
+ List<WsParamSetI> presets = new ArrayList<>();
+
+ public HMMERParamStore(String name)
+ {
+ this.name = name;
+ }
+
+ @Override
+ public List<WsParamSetI> getPresets()
+ {
+ // TODO Auto-generated method stub
+ return presets;
+ }
+
+ @Override
+ public WsParamSetI getPreset(String name)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public List<ArgumentI> getServiceParameters()
+ {
+ List<ArgumentI> args = new ArrayList<>();
+ if ("hmmsearch".equals(name))
+ {
+ args.add(new IntegerParameter(
+ MessageManager.getString("label.number_of_results"),
+ MessageManager
+ .getString("label.number_of_results_desc"),
+ true, 100, 0, 100000));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.auto_align_seqs"),
+ MessageManager.getString("label.auto_align_seqs_desc"),
+ false, false, true, null));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.use_accessions"),
+ MessageManager.getString("label.use_accessions_desc"),
+ false, false, true, null));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"), false,
+ false, true, null));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString("label.seq_e_value"),
+ MessageManager.getString("label.seq_e_value_desc"), false,
+ 0.001d, -63d, 9d, 4d));
+ /*
+ args.add(new DoubleParameter(
+ MessageManager.getString("label.seq_score"),
+ MessageManager.getString("label.seq_score_desc"), false,
+ 0d, 0d, 10000d));
+ */
+ args.add(new LogarithmicParameter(
+ MessageManager.getString("label.dom_e_value_desc"),
+ MessageManager.getString("label.dom_e_value_desc"), false,
+ 0.001d, -63d, 9d, 4d));
+ /*
+ args.add(new DoubleParameter(
+ MessageManager.getString("label.dom_score"),
+ MessageManager.getString("label.dom_score_desc"), false, 0d,
+ 0d,
+ 10000d));
+ */
+ }
+ if ("hmmalign".equals(name))
+ {
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString(
+ "label.trim_termini = Trim Non-Matching Termini_desc"),
+ false, false, true, null));
+
+ }
+ if ("hmmbuild".equals(name))
+ {
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString(
+ "label.trim_termini = Trim Non-Matching Termini_desc"),
+ false, false, true, null));
+
+ }
+ return args;
+ }
+
+ @Override
+ public boolean presetExists(String name)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public void deletePreset(String name)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void storePreset(String presetName, String text,
+ List<ArgumentI> jobParams)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void updatePreset(String oldName, String presetName, String text,
+ List<ArgumentI> jobParams)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public WsParamSetI parseServiceParameterFile(String name,
+ String description, String[] serviceURL, String parameters)
+ throws IOException
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String generateServiceParameterFile(WsParamSetI pset)
+ throws IOException
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}