boolean trim = false;
+ boolean returnNoOfNewSeqs = false;
+
int seqsToReturn = Integer.MAX_VALUE;
+ boolean searchAlignment = true;
+
SequenceI[] seqs;
private String databaseName;
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))
{
databaseName = dbPath.substring(pos + 1);
databaseFile = new File(dbPath);
}
+ searchAlignment = false;
+ }
+ else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
+ {
+ returnNoOfNewSeqs = true;
}
}
}
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
- recoverSequences(sequencesHash, seqs);
+ if (searchAlignment)
+ {
+ recoverSequences(sequencesHash, seqs);
+ }
// look for PP cons and ref seq in alignment only annotation
AlignmentAnnotation modelpos = null, ppcons = null;
}
}
}
+
if (realign)
{
realignResults(hmmAndSeqs);
+ hmmSeq.getName();
Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+
+ 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--;
+ }
+ }
+ }
+
+ 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();
+
+ int nNew = checkForNewSequences();
+ JvOptionPane.showMessageDialog(frame.alignPanel,
+ nNew + " " + MessageManager.getString("label.new_returned"));
}
/**