import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
{
static final String HMMSEARCH = "hmmsearch";
- /*
- * constants for i18n lookup of passed parameter names
- */
- static final String DATABASE_KEY = "label.database";
-
- static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
-
- static final String USE_ACCESSIONS_KEY = "label.use_accessions";
-
- static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
-
- static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
-
- static final String TRIM_TERMINI_KEY = "label.trim_termini";
-
- static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
-
- static final String CUTOFF_NONE = "None";
-
- static final String CUTOFF_SCORE = "Score";
-
- static final String CUTOFF_EVALUE = "E-Value";
-
- static final String SEQ_EVALUE_KEY = "label.seq_evalue";
-
- static final String DOM_EVALUE_KEY = "label.dom_evalue";
-
- static final String SEQ_SCORE_KEY = "label.seq_score";
-
- static final String DOM_SCORE_KEY = "label.dom_score";
-
boolean realign = false;
boolean trim = false;
SequenceI hmmSeq = hmm.getConsensusSequence();
long msgId = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+ af.setProgressBar(MessageManager.getString("status.running_search"),
msgId);
try
List<String> args = new ArrayList<>();
args.add(command);
+ buildArguments(args, searchOutputFile, hitsAlignmentFile, hmmFile);
+
+ return runCommand(args);
+ }
+
+ /**
+ * Appends command line arguments to the given list, to specify input and
+ * output files for the search, and any additional options that may have been
+ * passed from the parameters dialog
+ *
+ * @param args
+ * @param searchOutputFile
+ * @param hitsAlignmentFile
+ * @param hmmFile
+ * @throws IOException
+ */
+ protected void buildArguments(List<String> args, File searchOutputFile,
+ File hitsAlignmentFile, File hmmFile) throws IOException
+ {
args.add("-o");
- args.add(getFilePath(searchOutputFile));
+ args.add(getFilePath(searchOutputFile, true));
args.add("-A");
- args.add(getFilePath(hitsAlignmentFile));
+ args.add(getFilePath(hitsAlignmentFile, true));
boolean dbFound = false;
String dbPath = "";
String seqScoreCutoff = null;
String domScoreCutoff = null;
databaseName = "Alignment";
+ boolean searchAlignment = false;
if (params != null)
{
{
seqsToReturn = Integer.parseInt(arg.getValue());
}
+ else if (MessageManager.getString("action.search").equals(name))
+ {
+ searchAlignment = arg.getValue().equals(
+ MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
+ }
+ else if (MessageManager.getString(DATABASE_KEY).equals(name))
+ {
+ dbPath = arg.getValue();
+ int pos = dbPath.lastIndexOf(File.separator);
+ databaseName = dbPath.substring(pos + 1);
+ databaseFile = new File(dbPath);
+ }
else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
.equals(name))
{
args.add(domScoreCutoff);
}
- if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
- .equals(dbPath))
+// if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
+// .equals(dbPath))
+ if (searchAlignment)
{
/*
* no external database specified for search, so
exportStockholm(copy.getSequencesArray(), databaseFile, null);
}
- args.add(getFilePath(hmmFile));
- args.add(getFilePath(databaseFile));
-
- return runCommand(args);
+ args.add(getFilePath(hmmFile, true));
+ args.add(getFilePath(databaseFile, true));
}
/**
StockholmFile file = new StockholmFile(new FileParse(
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
-
+ // look for PP cons and ref seq in alignment only annotation
+ AlignmentAnnotation modelpos = null, ppcons = null;
+ for (AlignmentAnnotation aa : file.getAnnotations())
+ {
+ if (aa.sequenceRef == null)
+ {
+ if (aa.label.equals("Reference Positions")) // RF feature type in
+ // stockholm parser
+ {
+ modelpos = aa;
+ }
+ if (aa.label.equals("Posterior Probability"))
+ {
+ ppcons = aa;
+ }
+ }
+ }
readTable(searchOutputFile);
int seqCount = Math.min(seqs.length, seqsToReturn);
SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
+ hmmSeq = hmmSeq.deriveSequence(); // otherwise all bad things happen
hmmAndSeqs[0] = hmmSeq;
System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
-
+ if (modelpos != null)
+ {
+ // TODO need - get ungapped sequence method
+ hmmSeq.setSequence(
+ hmmSeq.getDatasetSequence().getSequenceAsString());
+ Annotation[] refpos = modelpos.annotations;
+ // insert gaps to match with refseq positions
+ int gc = 0, lcol = 0;
+ for (int c = 0; c < refpos.length; c++)
+ {
+ if (refpos[c] != null && ("x".equals(refpos[c].displayCharacter)))
+ {
+ if (gc > 0)
+ {
+ hmmSeq.insertCharAt(lcol + 1, gc, '-');
+ }
+ gc = 0;
+ lcol = c;
+ }
+ else
+ {
+ gc++;
+ }
+ }
+ }
if (realign)
{
realignResults(hmmAndSeqs);
else
{
AlignmentI al = new Alignment(hmmAndSeqs);
+ if (ppcons != null)
+ {
+ al.addAnnotation(ppcons);
+ }
+ if (modelpos != null)
+ {
+ al.addAnnotation(modelpos);
+ }
AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
String ttl = "hmmSearch of " + databaseName + " using "
{
line = br.readLine();
}
- for (int i = 0; i < 5; i++)
+ while (!line.contains("-------"))
{
line = br.readLine();
}
+ line = br.readLine();
int index = 0;
while (!" ------ inclusion threshold ------".equals(line)
&& !"".equals(line))
{
+ SequenceI seq = seqs[index];
+ AlignmentAnnotation pp = seq
+ .getAlignmentAnnotations("", "Posterior Probability")
+ .get(0);
Scanner scanner = new Scanner(line);
-
- String str = scanner.next(); // full sequence eValue score
- // float eValue = Float.parseFloat(str);
- // int seqLength = seqs[index].getLength();
- // Annotation[] annots = new Annotation[seqLength];
- // for (int j = 0; j < seqLength; j++)
- // {
- // annots[j] = new Annotation(eValue);
- // }
- AlignmentAnnotation annot = new AlignmentAnnotation("E-value",
- "Score", null);
- annot.setCalcId(HMMSEARCH);
- double eValue = Double.parseDouble(str);
- annot.setScore(eValue);
- annot.setSequenceRef(seqs[index]);
- seqs[index].addAlignmentAnnotation(annot);
-
+ String str = scanner.next();
+ addScoreAnnotation(str, seq, "hmmsearch E-value",
+ "Full sequence E-value", pp);
+ str = scanner.next();
+ addScoreAnnotation(str, seq, "hmmsearch Score",
+ "Full sequence bit score", pp);
+ seq.removeAlignmentAnnotation(pp);
scanner.close();
line = br.readLine();
index++;
br.close();
}
+ /**
+ * A helper method that adds one score-only (non-positional) annotation to a
+ * sequence
+ *
+ * @param value
+ * @param seq
+ * @param label
+ * @param description
+ */
+ protected void addScoreAnnotation(String value, SequenceI seq,
+ String label, String description)
+ {
+ addScoreAnnotation(value, seq, label, description, null);
+ }
+
+ /**
+ * A helper method that adds one score-only (non-positional) annotation to a
+ * sequence
+ *
+ * @param value
+ * @param seq
+ * @param label
+ * @param description
+ * @param pp
+ * existing posterior probability annotation - values copied to new
+ * annotation row
+ */
+ protected void addScoreAnnotation(String value, SequenceI seq,
+ String label, String description, AlignmentAnnotation pp)
+ {
+ try
+ {
+ AlignmentAnnotation annot = null;
+ if (pp == null)
+ {
+ new AlignmentAnnotation(label,
+ description, null);
+ }
+ else
+ {
+ annot = new AlignmentAnnotation(pp);
+ annot.label = label;
+ annot.description = description;
+ }
+ annot.setCalcId(HMMSEARCH);
+ double eValue = Double.parseDouble(value);
+ annot.setScore(eValue);
+ annot.setSequenceRef(seq);
+ seq.addAlignmentAnnotation(annot);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Error parsing " + label + " from " + value);
+ }
+ }
+
}