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
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 = "";
databaseFile = FileUtils.createTempFile("database", ".sto");
AlignmentI al = af.getViewport().getAlignment();
AlignmentI copy = new Alignment(al);
- List<SequenceI> hmms = copy.getHmmSequences();
- for (SequenceI hmmSeq : hmms)
- {
- copy.deleteSequence(hmmSeq);
- }
+ deleteHmmSequences(copy);
exportStockholm(copy.getSequencesArray(), databaseFile, null);
}
- args.add(getFilePath(hmmFile));
- args.add(getFilePath(databaseFile));
+ 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)
{
SequenceI seq = seqs[index];
Scanner scanner = new Scanner(line);
- String str = scanner.next();
- addScoreAnnotation(str, seq, "hmmsearch E-value",
- "Full sequence E-value");
- str = scanner.next();
- addScoreAnnotation(str, seq, "hmmsearch Score",
- "Full sequence bit score");
+ String evalue = scanner.next();
+ String score = scanner.next();
+ addScoreAnnotations(evalue, score, seq);
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)
+
+ protected void addScoreAnnotations(String eValue, String bitScore,
+ SequenceI seq)
{
+ String label = "Search Scores";
+ String description = "Full sequence bit score and E-Value";
+
try
{
AlignmentAnnotation annot = new AlignmentAnnotation(label,
description, null);
+
+ annot.label = label;
+ annot.description = description;
+
annot.setCalcId(HMMSEARCH);
- double eValue = Double.parseDouble(value);
- annot.setScore(eValue);
+
+ double dEValue = Double.parseDouble(eValue);
+ annot.setEValue(dEValue);
+
+ double dBitScore = Double.parseDouble(bitScore);
+ annot.setBitScore(dBitScore);
+
annot.setSequenceRef(seq);
seq.addAlignmentAnnotation(annot);
} catch (NumberFormatException e)
{
- System.err.println("Error parsing " + label + " from " + value);
+ System.err.println("Error parsing " + label + " from " + eValue
+ + " & " + bitScore);
}
}
git://source.jalview.org / jalview.git / blobdiff