import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.Hashtable;
import java.util.List;
import java.util.Scanner;
{
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;
+ boolean returnNoOfNewSeqs = false;
+
int seqsToReturn = Integer.MAX_VALUE;
+ boolean searchAlignment = true;
+
SequenceI[] seqs;
private String databaseName;
+ Hashtable sequencesHash;
+
/**
* Constructor for the HMMSearchThread
*
SequenceI hmmSeq = hmm.getConsensusSequence();
long msgId = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+ af.setProgressBar(MessageManager.getString("status.running_search"),
msgId);
try
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))
{
else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
.equals(name))
{
- if (CUTOFF_EVALUE.equals(arg.getValue()))
+ if (MessageManager.getString(CUTOFF_EVALUE)
+ .equals(arg.getValue()))
{
useEvalueCutoff = true;
}
- else if (CUTOFF_SCORE.equals(arg.getValue()))
+ else if (MessageManager.getString(CUTOFF_SCORE)
+ .equals(arg.getValue()))
{
useScoreCutoff = true;
}
}
else if (MessageManager.getString(DATABASE_KEY).equals(name))
{
- dbFound = true;
- dbPath = arg.getValue();
- if (!MessageManager.getString(THIS_ALIGNMENT_KEY)
- .equals(dbPath))
+ databaseFile = new File(arg.getValue());
+ if (!arg.getValue().isEmpty())
{
- int pos = dbPath.lastIndexOf(File.separator);
- databaseName = dbPath.substring(pos + 1);
- databaseFile = new File(dbPath);
+ searchAlignment = false;
}
}
+ else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
+ {
+ returnNoOfNewSeqs = true;
+ }
}
}
databaseFile = FileUtils.createTempFile("database", ".sto");
AlignmentI al = af.getViewport().getAlignment();
AlignmentI copy = new Alignment(al);
- List<SequenceI> hmms = copy.getHmmSequences();
- for (SequenceI hmmSeq : hmms)
+ deleteHmmSequences(copy);
+
+ if (searchAlignment)
{
- copy.deleteSequence(hmmSeq);
+ sequencesHash = stashSequences(copy.getSequencesArray());
}
+
exportStockholm(copy.getSequencesArray(), databaseFile, null);
+
}
args.add(getFilePath(hmmFile, true));
StockholmFile file = new StockholmFile(new FileParse(
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
+
+ if (searchAlignment)
+ {
+ recoverSequences(sequencesHash, seqs);
+ }
+
// look for PP cons and ref seq in alignment only annotation
AlignmentAnnotation modelpos = null, ppcons = null;
for (AlignmentAnnotation aa : file.getAnnotations())
}
}
}
+
if (realign)
{
realignResults(hmmAndSeqs);
+ hmmSeq.getName();
Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+
+ if (returnNoOfNewSeqs)
+ {
+ int nNew = checkForNewSequences();
+ JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
+ + MessageManager.getString("label.new_returned"));
+ }
+
}
+
hmmTemp.delete();
inputAlignmentTemp.delete();
searchOutputFile.delete();
}
}
+ private int checkForNewSequences()
+ {
+ int nNew = seqs.length;
+
+ for (SequenceI resultSeq : seqs)
+ {
+ for (SequenceI aliSeq : alignment.getSequencesArray())
+ {
+ if (resultSeq.getName().equals(aliSeq.getName()))
+ {
+ nNew--;
+ break;
+ }
+ }
+ }
+
+ return nNew;
+
+ }
+
/**
* Realigns the given sequences using hmmalign, to the HMM profile sequence
* which is the first in the array, and opens the results in a new frame
}
HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
hmmalign.run();
+
+ if (returnNoOfNewSeqs)
+ {
+ int nNew = checkForNewSequences();
+ JvOptionPane.showMessageDialog(frame.alignPanel,
+ nNew + " " + MessageManager.getString("label.new_returned"));
+ }
}
/**
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();
- 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);
+ String evalue = scanner.next();
+ String score = scanner.next();
+ checkSequenceOrder(index, scanner);
+ SequenceI seq = seqs[index];
+ 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)
- {
- 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)
+ 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 = null;
- if (pp == null)
- {
- new AlignmentAnnotation(label,
+ AlignmentAnnotation annot = new AlignmentAnnotation(label,
description, null);
- }
- else
- {
- annot = new AlignmentAnnotation(pp);
- annot.label = label;
- annot.description = description;
- }
+
+ 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);
}
}
+ private void checkSequenceOrder(int index, Scanner scanner)
+ {
+ String seqName = null;
+
+ for (int i = 0; i < 8; i++)
+ {
+ seqName = scanner.next();
+ }
+
+ if (!seqs[index].getName().equals(seqName))
+ {
+ SequenceI temp = seqs[index];
+
+ for (int j = 0; j < seqs.length; j++)
+ {
+ if (seqs[j].getName().equals(seqName))
+ {
+ seqs[index] = seqs[j];
+ seqs[j] = temp;
+ break;
+ }
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff