RemoteHmmerScan

java.lang.Object
- org.biojava.nbio.ws.hmmer.RemoteHmmerScan

All Implemented Interfaces:

HmmerScan
```
public class RemoteHmmerScan
extends java.lang.Object
implements HmmerScan
```
Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.

Since:

3.0.3

Author:

Andreas Prlic

Field Summary

Fields
Modifier and Type Field Description

static java.lang.String HMMER_SERVICE

Fields
Modifier and Type	Field	Description
`static java.lang.String`	`HMMER_SERVICE`

Constructor Summary

Constructors
Constructor Description

RemoteHmmerScan()

Constructors
Constructor	Description
`RemoteHmmerScan()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.util.SortedSet<HmmerResult>`	`scan(ProteinSequence sequence)`
`java.util.SortedSet<HmmerResult>`	`scan(ProteinSequence sequence, java.net.URL serviceLocation)`	Scans a protein sequence for Pfam profile matches.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- HMMER_SERVICE
```
public static final java.lang.String HMMER_SERVICE
```
  See Also:
  
  Constant Field Values

Constructor Detail
- RemoteHmmerScan
```
public RemoteHmmerScan()
```

Method Detail

scan

public java.util.SortedSet<HmmerResult> scan(ProteinSequence sequence)
                                      throws java.io.IOException

Specified by:: scan in interface HmmerScan
Throws:: java.io.IOException

scan

public java.util.SortedSet<HmmerResult> scan(ProteinSequence sequence,
                                             java.net.URL serviceLocation)
                                      throws java.io.IOException

Scans a protein sequence for Pfam profile matches.

Parameters:: sequence -; serviceLocation -
Returns:
Throws:: java.io.IOException

Class RemoteHmmerScan

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

HMMER_SERVICE

Constructor Detail

RemoteHmmerScan

Method Detail

scan

scan