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de.unibi.techfak.InSilicoDicer.OperatingPackage
Class PrecursorContainer

java.lang.Object
  extended by java.util.AbstractCollection<E>
      extended by java.util.AbstractList<E>
          extended by java.util.Vector<Precursor>
              extended by de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<Precursor>, java.util.Collection<Precursor>, java.util.List<Precursor>, java.util.RandomAccess
public class PrecursorContainer
extends java.util.Vector<Precursor>
implements java.io.Serializable

Author:
Sylvia Tippmann Jan Krueger An Object containing multiple precursor objects. This class extends Vector.
See Also:
Serialized Form

Field Summary
static int MINIMUM_SEQUENCE_LENGTH
          Minimum sequence length, which is accepted.
static java.lang.String NUCLEICACID_CHARS
          small nucleo acid alphabet following IUPAC norm :
code: description: A Adenosine C Cytidine G Guanine T Thymidine U Uracil N A G C T U (aNy)
static long serialVersionUID
           
 
Fields inherited from class java.util.Vector
capacityIncrement, elementCount, elementData
 
Fields inherited from class java.util.AbstractList
modCount
 
Constructor Summary
PrecursorContainer()
          Contructs an empty PrecursorContainer,
PrecursorContainer(java.lang.Object[] pcarr)
          Constructor : constructs an PreCursorContainer from a Precursor Array
 
Method Summary
 void addWarning(java.lang.String warn)
          Add a warning to internal warning list
 void appendFasta(java.io.InputStream in)
          reads sequences in FASTA from Inputstream and append it to current PrecursorContainer
 void appendVienna(java.io.InputStream in)
           
 void cleanWarnings()
          Clean internal warning list.
 java.lang.String getFormatWarnString()
          Return internal warning list as formated string and clean internal warning list afterwards.
 ILocalAlign getLocalalign()
           
 IPatternMatching getPatternmatching()
           
 Precursor getPrecursorByID(java.lang.String theID)
          Searches the miRNA Registry for the given ID
 PrecursorContainer getPrecursorByName(java.lang.String theName)
          Searches all Precursor Descriptions of the miRNA Registry for the given String with the BM Algorithm
 PrecursorContainer getPrecursorBySequence(java.lang.String theSeq, int cutOFF)
          Searches all Precursor Sequences of miRNA Registry for Precursors with a Similarity to the given Sequence higher then the cutOff value
 java.util.List getWarnings()
          Return a reference of internal warning list.
 void setLocalalign(ILocalAlign localalign)
           
 void setPatternmatching(IPatternMatching patternmatching)
           
 java.lang.String toFasta(boolean withSecStruc)
          Returns a String containing all Precursor information in Fasta format with or without secundary structure information
 java.lang.String toString()
           
 boolean warn()
           
 
Methods inherited from class java.util.Vector
add, add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, removeRange, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, 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
 

Field Detail

serialVersionUID

public static final long serialVersionUID
See Also:
Constant Field Values

NUCLEICACID_CHARS

public static final java.lang.String NUCLEICACID_CHARS
small nucleo acid alphabet following IUPAC norm :
code: description:
A Adenosine
C Cytidine
G Guanine
T Thymidine
U Uracil
N A G C T U (aNy)

See Also:
Constant Field Values

MINIMUM_SEQUENCE_LENGTH

public static final int MINIMUM_SEQUENCE_LENGTH
Minimum sequence length, which is accepted.

See Also:
Constant Field Values
Constructor Detail

PrecursorContainer

public PrecursorContainer(java.lang.Object[] pcarr)
Constructor : constructs an PreCursorContainer from a Precursor Array

Parameters:
pcarr - - Array of PreCursor

PrecursorContainer

public PrecursorContainer()
Contructs an empty PrecursorContainer,

Method Detail

getPrecursorByName

public PrecursorContainer getPrecursorByName(java.lang.String theName)
Searches all Precursor Descriptions of the miRNA Registry for the given String with the BM Algorithm

Parameters:
theName -
Returns:
PrecursorContainer of all Precursors matchng the String

getPrecursorByID

public Precursor getPrecursorByID(java.lang.String theID)
Searches the miRNA Registry for the given ID

Parameters:
theID -
Returns:
Precursor with given ID

getPrecursorBySequence

public PrecursorContainer getPrecursorBySequence(java.lang.String theSeq,
                                                 int cutOFF)
Searches all Precursor Sequences of miRNA Registry for Precursors with a Similarity to the given Sequence higher then the cutOff value

Parameters:
theSeq -
cutOFF -
Returns:
PrecursorContainer of all similar Precursors

toString

public java.lang.String toString()
Overrides:
toString in class java.util.Vector<Precursor>
Returns:
Returns the amount of precursors contained in this PrecursorContainer.

getLocalalign

public ILocalAlign getLocalalign()
Returns:
Returns the localalign.

setLocalalign

public void setLocalalign(ILocalAlign localalign)
Parameters:
localalign - The localalign to set.

getPatternmatching

public IPatternMatching getPatternmatching()
Returns:
Returns the patternmatching.

setPatternmatching

public void setPatternmatching(IPatternMatching patternmatching)
Parameters:
patternmatching - The patternmatching to set.

appendFasta

public void appendFasta(java.io.InputStream in)
                 throws java.io.IOException,
                        java.text.ParseException
reads sequences in FASTA from Inputstream and append it to current PrecursorContainer

Parameters:
in - - InputStream containg sequence information in FASTA format
Throws:
java.io.IOException - - Thorws an IOException if an error occurred reading the inputstream
java.text.ParseException - - Throws a ParseException if Inputstream is NOT in FASTA format

appendVienna

public void appendVienna(java.io.InputStream in)
                  throws java.io.IOException,
                         java.text.ParseException
Parameters:
in -
Throws:
java.io.IOException
java.text.ParseException

toFasta

public java.lang.String toFasta(boolean withSecStruc)
Returns a String containing all Precursor information in Fasta format with or without secundary structure information

Parameters:
withSecStruct - - A boolean which determines, if secundary structure should be returned or not.
Returns:
Return a String in Fasta/Vienna format

addWarning

public void addWarning(java.lang.String warn)
Add a warning to internal warning list

Parameters:
warn - - Warning to be add

getWarnings

public java.util.List getWarnings()
Return a reference of internal warning list.

Returns:
A reference of internal warning list.

getFormatWarnString

public java.lang.String getFormatWarnString()
Return internal warning list as formated string and clean internal warning list afterwards.

Returns:
Warnings as formated string.

warn

public boolean warn()

cleanWarnings

public void cleanWarnings()
Clean internal warning list.

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