public class SearchIO extends java.lang.Object implements java.lang.Iterable<Result>
Constructor and Description |
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SearchIO(java.io.File f)
Build a SearchIO reader and tries to select the appropriate parser inspecting
file extension.
|
SearchIO(java.io.File f,
ResultFactory factory)
Build a SearchIO reader and specify a ResultFactory object to be used
for parsing
|
SearchIO(java.io.File f,
ResultFactory factory,
double maxEvalue)
Build a SearchIO reader, specify a ResultFactory object to be used for parsing
and filter hsp retrieved by a e-value threshold.
|
Modifier and Type | Method and Description |
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double |
getEvalueThreshold() |
java.util.Iterator<Result> |
iterator() |
void |
writeResults()
used to write a search report using the guessed or specified factory
|
public SearchIO(java.io.File f) throws java.io.IOException, java.text.ParseException
f
- java.lang.Exception
java.io.IOException
java.text.ParseException
public SearchIO(java.io.File f, ResultFactory factory) throws java.io.IOException, java.text.ParseException
f
- factory
- java.io.IOException
- for file access related issuesjava.text.ParseException
- for file format related issuespublic SearchIO(java.io.File f, ResultFactory factory, double maxEvalue) throws java.io.IOException, java.text.ParseException
f
- factory
- maxEvalue
- java.io.IOException
- for file access related issuesjava.text.ParseException
- for file format related issuespublic void writeResults() throws java.io.IOException, java.text.ParseException
java.io.IOException
- for file access related issuesjava.text.ParseException
- for file format related issuespublic double getEvalueThreshold()