org.strbio.mol
Class ProfileSet

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.Vector
              org.strbio.mol.PolymerSet
                  org.strbio.mol.ProteinSet
                      org.strbio.mol.ProfileSet

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

Direct Known Subclasses:

PCPSet, ProfilePSISet

public class ProfileSet
extends ProteinSet

Class to represent a set of proteins with profile information.

 Version 1.3, 7/18/01 - added SAF format
 Version 1.2, 2/11/00 - added writeClustal
 Version 1.11, 2/27/99 - moved most blast code to Profile
 Version 1.1, 1/19/99 - added blast option
 Version 1.01, 7/10/98 - added combine(), writeXXX(outfile)
 Version 1.0, 5/5/98 - original version
 

Version:

1.3, 7/18/01

Author:

JMC

See Also:

Profile, Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.strbio.mol.PolymerSet

PolymerSet.PolymerEnumeration

Field Summary

Fields inherited from class java.util.Vector

capacityIncrement, elementCount, elementData

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

ProfileSet()
Create an empty set of Profiles.

ProfileSet(ProfileSet q)
Copy another profile set, but not the profiles themselves.

Method Summary

void	blast(Printf outfile) Run BLAST on all proteins in the set, using NCBI's blast server.
void	blast(Printf outfile, Blast blastServer) Run BLAST on all proteins in the set, using a specified blast server.
void	combine() Combine all proteins in this set into one Profile.
Polymer	newPolymer() Everything in this set should be a Profile (or subclass of it).
Polymer	newPolymer(ProteinSet q)
boolean	write(java.lang.String filename) Write set to a file, with name determined by the suffix.
void	writeClustal(Printf outfile) Write set to Clustal file.
void	writeClustal(java.lang.String filename) Write set to Clustal file.
void	writeMSF(Printf outfile) Write set to MSF file.
void	writeMSF(java.lang.String filename) Write set to MSF file.
void	writeProf(Printf outfile) Write set to Prof file.
void	writeProf(java.lang.String filename) Write set to Prof file.
void	writeSAF(Printf outfile) Write set to SAF file.
void	writeSAF(java.lang.String filename) Write set to SAF file.
void	writeTDP(java.lang.String filename) A simple way of printing profiles, that var-tom uses as input.

Methods inherited from class org.strbio.mol.ProteinSet

findDSSP, findPDB, fixDistanceGaps, predictSS, predictSS, protein, residues, thread, thread, writeCASP, writeCASP, writeConv, writeConv, writeEA, writeEA, writePDB, writePDB, writePDB, writePDB, writeVar2, writeVar2

Methods inherited from class org.strbio.mol.PolymerSet

add, add, add, addReversedCopies, clear, clearPolymers, clearProperties, clearProperty, ensureNames, findClosest, getNames, getPropertyAll, getPropertyOne, isEqual, keepOnlyChainID, keepOnlyNames, keepOnlyNamesFuzzy, load, n, nMonomers, noSpaceNames, nPolymersInFile, p, polymer, polymers, polymersInFile, polymersInFile, polymersInFile, polymersInFile, printNames, read, read, read, readList, remove, remove, removeRedundantSequences, save, searchByName, searchByNameFuzzy, searchByNameFuzzy, searchByNameFuzzyIndex, searchByNameFuzzyIndex, searchByNameIndex, setPolymerAt, setProperty, stripNoAtoms, writeFasta, writeFasta, writeList, writeList, writePTS, writePTS, writeYAPF, writeYAPF

Methods inherited from class java.util.Vector

add, add, addAll, addAll, addElement, capacity, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeRange, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, toString, trimToSize

Methods inherited from class java.util.AbstractList

iterator, listIterator, listIterator

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

iterator, listIterator, listIterator

Constructor Detail

ProfileSet

public ProfileSet()

Create an empty set of Profiles.

ProfileSet

public ProfileSet(ProfileSet q)

Copy another profile set, but not the profiles themselves.

Method Detail

newPolymer

public Polymer newPolymer()

Everything in this set should be a Profile (or subclass of it).

Overrides:

newPolymer in class ProteinSet

newPolymer

public Polymer newPolymer(ProteinSet q)

combine

public void combine()

Combine all proteins in this set into one Profile.

blast

public void blast(Printf outfile,
                  Blast blastServer)

Run BLAST on all proteins in the set, using a specified blast server.

blast

public void blast(Printf outfile)

Run BLAST on all proteins in the set, using NCBI's blast server.

writeProf

public final void writeProf(java.lang.String filename)
                     throws java.io.IOException

Write set to Prof file.

Throws:

java.io.IOException

See Also:

Profile.writeProf(org.strbio.io.Printf)

writeProf

public final void writeProf(Printf outfile)
                     throws java.io.IOException

Write set to Prof file.

Throws:

java.io.IOException

See Also:

Profile.writeProf(org.strbio.io.Printf)

writeMSF

public final void writeMSF(java.lang.String filename)
                    throws java.io.IOException

Write set to MSF file.

Throws:

java.io.IOException

See Also:

Profile.writeMSF(org.strbio.io.Printf)

writeSAF

public final void writeSAF(java.lang.String filename)
                    throws java.io.IOException

Write set to SAF file.

Throws:

java.io.IOException

See Also:

Profile.writeSAF(org.strbio.io.Printf)

writeMSF

public final void writeMSF(Printf outfile)
                    throws java.io.IOException

Write set to MSF file.

Throws:

java.io.IOException

See Also:

Profile.writeMSF(org.strbio.io.Printf)

writeSAF

public final void writeSAF(Printf outfile)
                    throws java.io.IOException

Write set to SAF file.

Throws:

java.io.IOException

See Also:

Profile.writeSAF(org.strbio.io.Printf)

writeClustal

public final void writeClustal(java.lang.String filename)
                        throws java.io.IOException

Write set to Clustal file.

Throws:

java.io.IOException

See Also:

Profile.writeClustal(org.strbio.io.Printf)

writeClustal

public final void writeClustal(Printf outfile)
                        throws java.io.IOException

Write set to Clustal file.

Throws:

java.io.IOException

See Also:

Profile.writeClustal(org.strbio.io.Printf)

writeTDP

public final void writeTDP(java.lang.String filename)
                    throws java.io.IOException

A simple way of printing profiles, that var-tom uses as input. TDP = Tom Defay Profile

Throws:

java.io.IOException

See Also:

Profile.writeTDP(org.strbio.io.Printf)

write

public boolean write(java.lang.String filename)
              throws java.io.IOException

Write set to a file, with name determined by the suffix. Returns true if the name was understood, or false if a default (YAPF format) file was written.

Overrides:

write in class ProteinSet

Throws:

java.io.IOException