3 import jalview.bin.Cache;
4 import jalview.datamodel.SequenceI;
5 import jalview.gui.Preferences;
6 import jalview.util.MessageManager;
7 import jalview.viewmodel.AlignmentViewport;
8 import jalview.ws.params.ArgumentI;
9 import jalview.ws.params.ParamDatastoreI;
10 import jalview.ws.params.WsParamSetI;
11 import jalview.ws.params.simple.BooleanOption;
12 import jalview.ws.params.simple.DoubleParameter;
13 import jalview.ws.params.simple.FileParameter;
14 import jalview.ws.params.simple.IntegerParameter;
15 import jalview.ws.params.simple.LogarithmicParameter;
16 import jalview.ws.params.simple.Option;
17 import jalview.ws.params.simple.RadioChoiceParameter;
18 import jalview.ws.params.simple.StringParameter;
21 import java.io.IOException;
22 import java.util.ArrayList;
23 import java.util.Arrays;
24 import java.util.List;
25 import java.util.Scanner;
27 public final class HMMERParamStore implements ParamDatastoreI
29 private static final String HMMBUILD = "hmmbuild";
31 private static final String HMMALIGN = "hmmalign";
33 private static final String HMMSEARCH = "hmmsearch";
35 private static final String JACKHMMER = "jackhmmer";
39 private List<WsParamSetI> presets = new ArrayList<>();
41 private AlignmentViewport viewport;
43 private HMMERParamStore(String nam, AlignmentViewport av)
49 public static HMMERParamStore forBuild(AlignmentViewport viewport)
51 return new HMMERParamStore(HMMBUILD, viewport);
54 public static HMMERParamStore forAlign(AlignmentViewport viewport)
56 return new HMMERParamStore(HMMALIGN, viewport);
59 public static HMMERParamStore forSearch(AlignmentViewport viewport)
61 return new HMMERParamStore(HMMSEARCH, viewport);
64 public static HMMERParamStore forJackhmmer(AlignmentViewport viewport)
66 return new HMMERParamStore(JACKHMMER, viewport);
70 public List<WsParamSetI> getPresets()
76 public WsParamSetI getPreset(String nam)
82 public List<ArgumentI> getServiceParameters()
84 List<ArgumentI> args = new ArrayList<>();
88 getHMMSearchParams(args);
91 getHMMAlignParams(args);
94 getHMMBuildParams(args);
97 getJackhmmerParams(args);
105 * Answers default parameters for hmmsearch, taking into account any
106 * configured as user preferences
110 private void getHMMSearchParams(List<ArgumentI> args)
115 args.add(new BooleanOption(
116 MessageManager.getString(HMMSearch.AUTO_ALIGN_SEQS_KEY),
117 MessageManager.getString("label.auto_align_seqs_desc"), false,
118 false, false, null));
119 args.add(new BooleanOption(
120 MessageManager.getString(HMMSearch.USE_ACCESSIONS_KEY),
121 MessageManager.getString("label.use_accessions_desc"), false,
123 args.add(new BooleanOption(
124 MessageManager.getString(HMMSearch.TRIM_TERMINI_KEY),
125 MessageManager.getString("label.trim_termini_desc"), false,
127 args.add(new BooleanOption(
128 MessageManager.getString(HMMSearch.RETURN_N_NEW_SEQ),
129 MessageManager.getString("label.check_for_new_sequences_desc"),
130 false, false, false, null));
135 addChoiceOfHmm(args);
137 // addChoiceOfDatabase(args);
139 String thisAlignment = MessageManager
140 .getString(HMMSearch.THIS_ALIGNMENT_KEY);
141 String database = MessageManager.getString("label.database");
142 args.add(new FileParameter(database, "", false, "", ""));
143 args.add(new IntegerParameter(
144 MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
145 MessageManager.getString("label.number_of_results_desc"), true,
147 args.add(new RadioChoiceParameter(
148 MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
149 Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_NONE),
150 MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
151 MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
152 MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
153 args.add(new LogarithmicParameter(
154 MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
155 MessageManager.getString("label.seq_e_value_desc"), false, 1D,
157 args.add(new LogarithmicParameter(
158 MessageManager.getString(HMMSearch.DOM_EVALUE_KEY),
159 MessageManager.getString("label.dom_e_value_desc"), false, 1D,
163 MessageManager.getString(HMMSearch.SEQ_SCORE_KEY),
164 MessageManager.getString("label.seq_score_desc"), false,
168 MessageManager.getString(HMMSearch.DOM_SCORE_KEY),
169 MessageManager.getString("label.dom_score_desc"), false,
174 * Answers default parameters for jackhmmer, taking into account any configured
175 * as user preferences
179 private void getJackhmmerParams(List<ArgumentI> args)
185 addChoiceOfSequence(args);
187 // addChoiceOfDatabase(args);
189 String database = MessageManager.getString("label.database");
190 args.add(new FileParameter(database, "", false, "", ""));
191 args.add(new RadioChoiceParameter(
192 MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
193 Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
194 MessageManager.getString(JackHMMER.CUTOFF_EVALUE),
195 MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
196 MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
197 args.add(new LogarithmicParameter(
198 MessageManager.getString(JackHMMER.SEQ_EVALUE_KEY),
199 MessageManager.getString("label.seq_e_value_desc"), false, 1D,
201 args.add(new LogarithmicParameter(
202 MessageManager.getString(JackHMMER.DOM_EVALUE_KEY),
203 MessageManager.getString("label.dom_e_value_desc"), false, 1D,
205 args.add(new DoubleParameter(
206 MessageManager.getString(JackHMMER.SEQ_SCORE_KEY),
207 MessageManager.getString("label.seq_score_desc"), false, 0d, 0d,
209 args.add(new DoubleParameter(
210 MessageManager.getString(JackHMMER.DOM_SCORE_KEY),
211 MessageManager.getString("label.dom_score_desc"), false, 0d, 0d,
216 * Constructs a choice parameter for database to search; always includes 'this
217 * alignment', and also includes any databases held under user preferences key
218 * "HMMSEARCH_DBS" as a comma-delimited list
222 protected void addChoiceOfDatabase(List<ArgumentI> args)
224 String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
225 if (names == null || names.isEmpty())
230 List<String> filePaths = new ArrayList<>();
231 List<String> fileNames = new ArrayList<>();
233 String thisAlignment = MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY);
234 filePaths.add(thisAlignment);
235 fileNames.add(thisAlignment);
237 Scanner nameScanner = new Scanner(names);
238 nameScanner.useDelimiter(Preferences.COMMA);
240 while (nameScanner.hasNext())
242 String next = nameScanner.next();
243 if ("null".equals(next))
245 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
250 int pos = next.lastIndexOf(File.separator);
251 String fileName = next.substring(pos + 1);
252 fileNames.add(fileName);
256 ArgumentI databasesOption = new StringParameter(
257 MessageManager.getString(HMMSearch.DATABASE_KEY),
258 MessageManager.getString("label.database_for_hmmsearch"), true,
261 filePaths, fileNames);
262 args.add(databasesOption);
266 * Answers default parameters for hmmalign, taking into account any configured
267 * as user preferences
271 private void getHMMAlignParams(List<ArgumentI> args)
273 addChoiceOfHmm(args);
275 boolean def = Cache.getDefault(Preferences.HMMALIGN_TRIM_TERMINI,
277 args.add(new BooleanOption(
278 MessageManager.getString("label.trim_termini"),
279 MessageManager.getString("label.trim_termini_desc"),
280 false, false, def, null));
284 * Adds an argument representing the choice of HMM sequences (profiles)
285 * against which to perform align or search, provided at least one is found
289 protected void addChoiceOfHmm(List<ArgumentI> args)
291 List<SequenceI> hmms = viewport.getAlignment().getHmmSequences();
294 List<String> options = new ArrayList<>();
295 for (SequenceI hmmSeq : hmms)
297 options.add(hmmSeq.getName());
299 String defseq = options.get(0);
300 ArgumentI arg = new StringParameter(
301 MessageManager.getString("label.use_hmm"), null, true, defseq,
302 defseq, options, null);
308 * Adds an argument representing the choice of sequence against which to perform
313 protected void addChoiceOfSequence(List<ArgumentI> args)
315 List<SequenceI> sequences = viewport.getAlignment().getSequences();
317 List<String> options = new ArrayList<>();
319 for (SequenceI seq : sequences)
321 options.add(seq.getName());
324 String defseq = options.get(0);
325 ArgumentI arg = new StringParameter(
326 MessageManager.getString("label.use_sequence"), null, true,
328 defseq, options, null);
333 * Answers default parameters for hmmbuild, taking into account any configured
334 * as user preferences
338 private void getHMMBuildParams(List<ArgumentI> args)
341 * name to give the computed alignment HMM consensus sequence
342 * (Jalview constructs group HMM consensus sequence names)
344 String defValue = "Alignment_HMM";
345 StringParameter nameParam = new StringParameter(MessageManager.getString("label.hmm_name"),
346 MessageManager.getString("label.hmm_name_desc"), true, defValue,
351 * only enable Use Reference Annotation if RF is present
353 if (viewport.hasReferenceAnnotation())
355 args.add(new BooleanOption(
356 MessageManager.getString("label.use_reference"),
357 MessageManager.getString("label.use_reference_desc"), true,
362 * choice of whether to compute HMM for alignment and/or group(s)
363 * - only if there are any groups
365 if (!viewport.getAlignment().getGroups().isEmpty())
367 List<String> options = new ArrayList<>();
368 options.add(MessageManager.getString("label.alignment"));
369 options.add(MessageManager.getString("label.groups_and_alignment"));
370 options.add(MessageManager.getString("label.groups"));
371 options.add(MessageManager.getString("label.selected_group"));
372 args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
373 MessageManager.getString("label.hmmbuild_for_desc"), true,
374 MessageManager.getString("label.alignment"),
375 MessageManager.getString("label.alignment"), options, null));
380 public boolean presetExists(String forName)
386 public void deletePreset(String forName)
391 public void storePreset(String presetName, String text,
392 List<ArgumentI> jobParams)
397 public void updatePreset(String oldName, String presetName, String text,
398 List<ArgumentI> jobParams)
403 public WsParamSetI parseServiceParameterFile(String forName,
404 String description, String[] serviceURL, String parameters)
411 public String generateServiceParameterFile(WsParamSetI pset)