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(HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_EVALUE,
150 HMMSearch.CUTOFF_SCORE),
151 HMMSearch.CUTOFF_EVALUE));
152 args.add(new LogarithmicParameter(
153 MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
154 MessageManager.getString("label.seq_e_value_desc"), false, 1D,
156 args.add(new LogarithmicParameter(
157 MessageManager.getString(HMMSearch.DOM_EVALUE_KEY),
158 MessageManager.getString("label.dom_e_value_desc"), false, 1D,
162 MessageManager.getString(HMMSearch.SEQ_SCORE_KEY),
163 MessageManager.getString("label.seq_score_desc"), false,
167 MessageManager.getString(HMMSearch.DOM_SCORE_KEY),
168 MessageManager.getString("label.dom_score_desc"), false,
173 * Answers default parameters for jackhmmer, taking into account any configured
174 * as user preferences
178 private void getJackhmmerParams(List<ArgumentI> args)
184 addChoiceOfSequence(args);
186 // addChoiceOfDatabase(args);
188 String database = MessageManager.getString("label.database");
189 args.add(new FileParameter(database, "", false, "", ""));
190 args.add(new RadioChoiceParameter(
191 MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
192 Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
193 MessageManager.getString(JackHMMER.CUTOFF_EVALUE),
194 MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
195 MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
196 args.add(new LogarithmicParameter(
197 MessageManager.getString(JackHMMER.SEQ_EVALUE_KEY),
198 MessageManager.getString("label.seq_e_value_desc"), false, 1D,
200 args.add(new LogarithmicParameter(
201 MessageManager.getString(JackHMMER.DOM_EVALUE_KEY),
202 MessageManager.getString("label.dom_e_value_desc"), false, 1D,
204 args.add(new DoubleParameter(
205 MessageManager.getString(JackHMMER.SEQ_SCORE_KEY),
206 MessageManager.getString("label.seq_score_desc"), false, 0d, 0d,
208 args.add(new DoubleParameter(
209 MessageManager.getString(JackHMMER.DOM_SCORE_KEY),
210 MessageManager.getString("label.dom_score_desc"), false, 0d, 0d,
215 * Constructs a choice parameter for database to search; always includes 'this
216 * alignment', and also includes any databases held under user preferences key
217 * "HMMSEARCH_DBS" as a comma-delimited list
221 protected void addChoiceOfDatabase(List<ArgumentI> args)
223 String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
224 if (names == null || names.isEmpty())
229 List<String> filePaths = new ArrayList<>();
230 List<String> fileNames = new ArrayList<>();
232 String thisAlignment = MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY);
233 filePaths.add(thisAlignment);
234 fileNames.add(thisAlignment);
236 Scanner nameScanner = new Scanner(names);
237 nameScanner.useDelimiter(Preferences.COMMA);
239 while (nameScanner.hasNext())
241 String next = nameScanner.next();
242 if ("null".equals(next))
244 Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
249 int pos = next.lastIndexOf(File.separator);
250 String fileName = next.substring(pos + 1);
251 fileNames.add(fileName);
255 ArgumentI databasesOption = new StringParameter(
256 MessageManager.getString(HMMSearch.DATABASE_KEY),
257 MessageManager.getString("label.database_for_hmmsearch"), true,
260 filePaths, fileNames);
261 args.add(databasesOption);
265 * Answers default parameters for hmmalign, taking into account any configured
266 * as user preferences
270 private void getHMMAlignParams(List<ArgumentI> args)
272 addChoiceOfHmm(args);
274 boolean def = Cache.getDefault(Preferences.HMMALIGN_TRIM_TERMINI,
276 args.add(new BooleanOption(
277 MessageManager.getString("label.trim_termini"),
278 MessageManager.getString("label.trim_termini_desc"),
279 false, false, def, null));
283 * Adds an argument representing the choice of HMM sequences (profiles)
284 * against which to perform align or search, provided at least one is found
288 protected void addChoiceOfHmm(List<ArgumentI> args)
290 List<SequenceI> hmms = viewport.getAlignment().getHmmSequences();
293 List<String> options = new ArrayList<>();
294 for (SequenceI hmmSeq : hmms)
296 options.add(hmmSeq.getName());
298 String defseq = options.get(0);
299 ArgumentI arg = new StringParameter(
300 MessageManager.getString("label.use_hmm"), null, true, defseq,
301 defseq, options, null);
307 * Adds an argument representing the choice of sequence against which to perform
312 protected void addChoiceOfSequence(List<ArgumentI> args)
314 List<SequenceI> sequences = viewport.getAlignment().getSequences();
316 List<String> options = new ArrayList<>();
318 for (SequenceI seq : sequences)
320 options.add(seq.getName());
323 String defseq = options.get(0);
324 ArgumentI arg = new StringParameter(
325 MessageManager.getString("label.use_sequence"), null, true,
327 defseq, options, null);
332 * Answers default parameters for hmmbuild, taking into account any configured
333 * as user preferences
337 private void getHMMBuildParams(List<ArgumentI> args)
340 * name to give the computed alignment HMM consensus sequence
341 * (Jalview constructs group HMM consensus sequence names)
343 String defValue = "Alignment_HMM";
344 StringParameter nameParam = new StringParameter(MessageManager.getString("label.hmm_name"),
345 MessageManager.getString("label.hmm_name_desc"), true, defValue,
350 * only enable Use Reference Annotation if RF is present
352 if (viewport.hasReferenceAnnotation())
354 args.add(new BooleanOption(
355 MessageManager.getString("label.use_reference"),
356 MessageManager.getString("label.use_reference_desc"), true,
361 * choice of whether to compute HMM for alignment and/or group(s)
362 * - only if there are any groups
364 if (!viewport.getAlignment().getGroups().isEmpty())
366 List<String> options = new ArrayList<>();
367 options.add(MessageManager.getString("label.alignment"));
368 options.add(MessageManager.getString("label.groups_and_alignment"));
369 options.add(MessageManager.getString("label.groups"));
370 options.add(MessageManager.getString("label.selected_group"));
371 args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
372 MessageManager.getString("label.hmmbuild_for_desc"), true,
373 MessageManager.getString("label.alignment"),
374 MessageManager.getString("label.alignment"), options, null));
379 public boolean presetExists(String forName)
385 public void deletePreset(String forName)
390 public void storePreset(String presetName, String text,
391 List<ArgumentI> jobParams)
396 public void updatePreset(String oldName, String presetName, String text,
397 List<ArgumentI> jobParams)
402 public WsParamSetI parseServiceParameterFile(String forName,
403 String description, String[] serviceURL, String parameters)
410 public String generateServiceParameterFile(WsParamSetI pset)