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;
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;
22 public class HMMERParamStore implements ParamDatastoreI
27 List<WsParamSetI> presets = new ArrayList<>();
29 public HMMERParamStore(String name)
35 public List<WsParamSetI> getPresets()
37 // TODO Auto-generated method stub
42 public WsParamSetI getPreset(String name)
44 // TODO Auto-generated method stub
49 public List<ArgumentI> getServiceParameters()
51 List<ArgumentI> args = new ArrayList<>();
52 if ("hmmsearch".equals(name))
54 args.add(new IntegerParameter(
55 MessageManager.getString("label.number_of_results"),
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())
62 Collection<String> databases = new ArrayList<>();
63 databases.add("This Alignment");
64 Scanner nameScanner = new Scanner(names);
66 if (nameScanner.hasNext())
68 while (nameScanner.hasNext())
70 String next = nameScanner.next();
73 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
74 Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
83 args.add(new Option(MessageManager.getString("label.database"),
84 MessageManager.getString("label.database_for_hmmsearch"),
85 true, "This Alignment", "This Alignment", databases, null));
87 args.add(new BooleanOption(
88 MessageManager.getString("label.auto_align_seqs"),
89 MessageManager.getString("label.auto_align_seqs_desc"),
90 false, false, true, null));
91 args.add(new BooleanOption(
92 MessageManager.getString("label.use_accessions"),
93 MessageManager.getString("label.use_accessions_desc"),
94 false, false, true, null));
95 args.add(new BooleanOption(
96 MessageManager.getString("label.trim_termini"),
97 MessageManager.getString("label.trim_termini_desc"), false,
99 args.add(new LogarithmicParameter(
100 MessageManager.getString("label.seq_e_value"),
101 MessageManager.getString("label.seq_e_value_desc"), false,
102 0.001d, -63d, 9d, 4d));
104 args.add(new DoubleParameter(
105 MessageManager.getString("label.seq_score"),
106 MessageManager.getString("label.seq_score_desc"), false,
109 args.add(new LogarithmicParameter(
110 MessageManager.getString("label.dom_e_value_desc"),
111 MessageManager.getString("label.dom_e_value_desc"), false,
112 0.001d, -63d, 9d, 4d));
114 args.add(new DoubleParameter(
115 MessageManager.getString("label.dom_score"),
116 MessageManager.getString("label.dom_score_desc"), false, 0d,
121 if ("hmmalign".equals(name))
123 args.add(new BooleanOption(
124 MessageManager.getString("label.trim_termini"),
125 MessageManager.getString(
126 "label.trim_termini = Trim Non-Matching Termini_desc"),
127 false, false, true, null));
130 if ("hmmbuild".equals(name))
132 args.add(new BooleanOption(
133 MessageManager.getString("label.trim_termini"),
134 MessageManager.getString(
135 "label.trim_termini = Trim Non-Matching Termini_desc"),
136 false, false, true, null));
143 public boolean presetExists(String name)
145 // TODO Auto-generated method stub
150 public void deletePreset(String name)
152 // TODO Auto-generated method stub
157 public void storePreset(String presetName, String text,
158 List<ArgumentI> jobParams)
160 // TODO Auto-generated method stub
165 public void updatePreset(String oldName, String presetName, String text,
166 List<ArgumentI> jobParams)
168 // TODO Auto-generated method stub
173 public WsParamSetI parseServiceParameterFile(String name,
174 String description, String[] serviceURL, String parameters)
177 // TODO Auto-generated method stub
182 public String generateServiceParameterFile(WsParamSetI pset)
185 // TODO Auto-generated method stub