charite.christo.protein
Class ProteinNT

java.lang.Object
  charite.christo.protein.Protein
      charite.christo.protein.ProteinNT

All Implemented Interfaces:

DialogStringMatch.Interface, ChRunnable, HasClientProperty, HasName, HasProtein, ActionListener, Comparator, EventListener

Direct Known Subclasses:

StrapProtein

public class ProteinNT
extends Protein
implements ChRunnable

This protein model extends JAVADOC:Protein. It has the additional feature that it can be defined from a nucleotide sequence which is translated into amino acid sequence. The class ProteinNT does not depend on classes of STRAP which reside in the folder charite/christo/strap/. STRAP extends ProteinNT by the class JAVADOC:charite.christo.strap.StrapProtein.

Field Summary

static boolean	AMINO_ACIDS
static String	FORWARD
static String	FORWARD_COMPLEMENT
static boolean	NUCLEOTIDES
static String[]	ORIENTATIONS
static String	REVERSE
static String	REVERSE_COMPLEMENT

Fields inherited from class charite.christo.protein.Protein

CDS_GENE, CDS_NOTE, CDS_PRODUCT, CDS_PROTEIN, CDS_XREFS, clientObjects_, FILE_MASKS, mANNO, mDNA, mGAPS, mICON, MODI_COUNTS, MODI_COUNTS_ALIGNMENT, mTIPS, mTRANS, PARSING_INFO, vProteinViewers, vResidueSelection, WEAK_REF

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, SET_ICON_IMAGE

Constructor Summary

ProteinNT()

Method Summary

int	aminoAcidIndex2nucleotideIndex(int i) Maps amino acid indices upon nucleotide indices See JAVADOC:ProteinNT#nucleotideIndex2aminoAcidIndex(int)
void	applyCDS_expression(String s) join(7940..7996,8095..8174,8287..8368,8506..8686, complement(join(1787209..1787388,1787427....
boolean[]	areNucleotidesCurrentStrandTranslated() True means a nucleotide is part of an triplet (exons).
boolean	cdsExpressionApplied()
int	countCodingNucleotides()
int	countNucleotides() Number of nucleotides or 0;
byte	getNucleotide(int i) Get the nucleotide of index i or -1;
byte	getNucleotideCurrentStrand(int i)
byte[]	getNucleotides() All nucleotides (with introns) including the non-translated (introns) ones
String	getNucleotidesAsString() This method is slow the first time after a change.
String	getNucleotidesAsStringUC() This method is slow the first time after a change.
byte[]	getNucleotidesCurrentStrand() The nucleotides after applying the necessary reverse and complement operations.
String	getNucleotidesCurrentStrandAsString()
byte[]	getNucleotidesCurrentStrandExactLength()
String	getNucleotidesReverseComplementAsStringUC()
byte[]	getResidueTriplet(int iAa, byte[] buffer) The triplet at amino acid position iAs
byte[]	getResidueTypeFullLength()
boolean	isComplement() Complement for the translation of nucleotides.
boolean	isNucleotideCurrentStrandTranslated(int i) True means a nucleotide is part of an triplet (exons).
boolean	isReverse() Direction translation of nucleotides.
int	nucleotideIdx2translatedNucleotideIdx(int idx) Given is the index of a nucleotide.
int	nucleotideIndex2aminoAcidIndex(int i) Maps nucleotide indices upon amino acid indices See JAVADOC:ProteinNT#aminoAcidIndex2nucleotideIndex(int)
int[]	nucleotideIndices2translatedNucleotideIndices() An array mapping nucleotide indices.
boolean[]	nucleotideSelection2aminoAcidSelection(boolean[] selNts, int offset)
boolean	parseFrameShift(byte[] z, int l)
Object	run(String id, Object arg)
void	setNucleotideCurrentStrandTranslated(int iNt, boolean isTranslated) the transformed nucleotide of index i is translated or not depending on b
void	setNucleotides(byte[] rawNtSequence, String orientation) Sets the sequence of nucleotides.
void	setNucleotides(String nts, String orientation) See JAVADOC:ProteinNT#setNucleotides(byte[],ProteinNT$Orientation)
void	setNucleotidesCurrentStrandTranslated(boolean[] bb) Determines which nucleotide needs to be translated (coding sequence).
void	setTranslatedStrand(String orientation) Set the way nucleotides are translated
int	translatedNucleotideIndex2nucleotideIndex(int idx) computes the nucleotide index from the translated idx.
int[]	translatedNucleotideIndices2nucleotideIndices() An array mapping nucleotide indices.

Methods inherited from class charite.christo.protein.Protein

actionPerformed, addCDS, addDatabaseRef, addHeteroCompounds, addHeteroCompoundsUniq, addProteinViewer, addResidueSelection, addSequenceRef, addThreeLetterCode, atomNumber2residueIdx, column2index, commonPdbId, comparator_aminoacidSequenceAlphabetically, compare, containsHeteroCompound, containsOnlyACTGNX, countAtoms, countResidues, countResiduesInChain, cursorPosAsString, equalsResidueType, fileAllChains, geneProductProteinNoteForCDS, getAccessionID, getAlignment, getAllResidueSelections, getAssertEDT, getAtomBFactor, getAtomCoordinates_modificationCount, getAtomCoordinates, getAtomCoordinates, getAtomName32, getAtomName32, getAtomNumber, getAtomOccupancy, getAtomType, getBioMatrices, getCalphaIndexToResidueIndex, getCDS, getChainFirstResidueIdx, getChainLastResidueIdx, getChainsAsString, getCharacters, getClientProperty, getClientPropertyMapAsString, getCompound, getDatabaseRefs, getDnaAndRnaAndHeteros, getDnaAndRnaStructures, getEC, getFile, getFileAsString, getFileHasSidechainAtoms, getFileLastModified, getFileMayBeWithSideChains, getFileName, getFileNameHC, getFilePath, getFileWithAllChains, getFirstResidueIndex, getGappedSequence_modificationCount, getHaystacksForStringSearch, getHeader, getHeteroCompounds, getIconImage, getInferred3dCountMatches, getInferredPdbID, getInfo, getLastResidueIndex, getMouseOverSelection, getName, getName0, getNameHC, getNucleotides_modificationCount, getOnlyChains, getOrganism, getOrganismScientific, getParsingTime, getPdbID, getPdbRef, getPdbTextSecStru, getProtein, getProteinParserClass, getProteinViewer, getProteinViewers, getResidueAnglePsi, getResidueAtomNumber, getResidueAtomNumber, getResidueCalpha, getResidueCalpha, getResidueCalpha, getResidueChain, getResidueChain, getResidueFirstAtomIdx, getResidueFirstAtomIdx, getResidueInsertionCode, getResidueInsertionCode, getResidueLastAtomIdx, getResidueLastAtomIdx, getResidueName32, getResidueName32, getResidueNumber, getResidueNumber, getResidueSecStrType, getResidueSecStrType, getResidueSelections_modificationCount, getResidueSelections, getResidueSelectionsAt, getResidueSolventAccessibility, getResidueSubsetAsBooleanArray, getResidueType_modificationCount, getResidueType, getResidueType, getResidueType, getResidueTypeAsString, getResidueTypeAsStringUC, getResidueTypeExactLength, getResidueTypeHashCode, getResolutionAnstroms, getRotationAndTranslation, getSequenceRefs, getTitle, getUniprotID, getURL, hasCalpha, hashTMalign, inferCoordinates, isInMsfFile, isLoadedFromStructureFile, isWaterInFile, loadSideChainAtoms, mouseOver, paintChain, pdbNumberToIdx, putClientProperty, removeAllSequenceRefs, removeHeteroCompound, removeProteinViewer, removeResidueSelection, removeSequenceRef, residueNumberAndChain2residueIdx, residueSubsetAsBooleanArray, residueSubsetAsBooleanArray, selectedPositionsToText, setAccessionID, setAssertEDT, setAtomBFactor, setAtomCoordOriginal, setAtomNumber, setAtomOccupancy, setAtomType, setAtomType32bit, setBioMatrices, setCharSequence, setCompound, setEC, setFile, setFileHasSidechainAtoms, setFileLastModified, setFileWithAllChains, setFileWithSideChains, setFileWithSideChainsObtainableFromPDB, setFirstResidueIndex, setHeader, setIsInMsfFile, setIsLoadedFromStructureFile, setName, setOnlyChains, setOrganism, setOrganismScientific, setParsingTime, setPdbID, setPdbTextSecStru, setProteinParserClass, setResidueAnglePhi, setResidueAnglePsi, setResidueAtomNumber, setResidueCalphaOriginal, setResidueChain, setResidueFirstAndLastAtomIdx, setResidueInsertionCode, setResidueNumber, setResidueSecStrType, setResidueSolventAccessibility, setResidueSubset, setResidueType, setResidueType, setResidueType32bit, setResidueTypeToUpperOrLower, setResolutionAnstroms, setRotationAndTranslation, setTitle, setUniprotID, setURL, strapFile, toOneLetterCode, toOneLetterCode, toString, toThreeLetterCode

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Comparator

equals

Field Detail

AMINO_ACIDS

public static final boolean AMINO_ACIDS

See Also:

Constant Field Values

NUCLEOTIDES

public static final boolean NUCLEOTIDES

See Also:

Constant Field Values

FORWARD

public static final String FORWARD

See Also:

Constant Field Values

REVERSE

public static final String REVERSE

See Also:

Constant Field Values

FORWARD_COMPLEMENT

public static final String FORWARD_COMPLEMENT

See Also:

Constant Field Values

REVERSE_COMPLEMENT

public static final String REVERSE_COMPLEMENT

See Also:

Constant Field Values

ORIENTATIONS

public static final String[] ORIENTATIONS

Constructor Detail

ProteinNT

public ProteinNT()

Method Detail

parseFrameShift

public boolean parseFrameShift(byte[] z,
                               int l)

isReverse

public final boolean isReverse()

Direction translation of nucleotides.

isComplement

public final boolean isComplement()

Complement for the translation of nucleotides.

setTranslatedStrand

public final void setTranslatedStrand(String orientation)

Set the way nucleotides are translated

getNucleotides

public final byte[] getNucleotides()

All nucleotides (with introns) including the non-translated (introns) ones

Returns:

a byte array of nucleotides or null

getNucleotidesCurrentStrand

public final byte[] getNucleotidesCurrentStrand()

The nucleotides after applying the necessary reverse and complement operations. The string is 0-terminated.

getNucleotidesCurrentStrandExactLength

public final byte[] getNucleotidesCurrentStrandExactLength()

getNucleotidesAsString

public String getNucleotidesAsString()

This method is slow the first time after a change. Then the cached result is returned.

getNucleotidesAsStringUC

public String getNucleotidesAsStringUC()

This method is slow the first time after a change. Then the cached result is returned.

getNucleotidesReverseComplementAsStringUC

public String getNucleotidesReverseComplementAsStringUC()

getNucleotidesCurrentStrandAsString

public String getNucleotidesCurrentStrandAsString()

getNucleotideCurrentStrand

public final byte getNucleotideCurrentStrand(int i)

getNucleotide

public final byte getNucleotide(int i)

Get the nucleotide of index i or -1;

countNucleotides

public final int countNucleotides()

Number of nucleotides or 0;

setNucleotides

public final void setNucleotides(byte[] rawNtSequence,
                                 String orientation)

Sets the sequence of nucleotides. e.g. "CAGTTGTACTG".getBytes()

setNucleotides

public final void setNucleotides(String nts,
                                 String orientation)

See JAVADOC:ProteinNT#setNucleotides(byte[],ProteinNT$Orientation)

setNucleotidesCurrentStrandTranslated

public final void setNucleotidesCurrentStrandTranslated(boolean[] bb)

Determines which nucleotide needs to be translated (coding sequence). True for exon and false for intron or UTR.

setNucleotideCurrentStrandTranslated

public final void setNucleotideCurrentStrandTranslated(int iNt,
                                                       boolean isTranslated)

the transformed nucleotide of index i is translated or not depending on b

areNucleotidesCurrentStrandTranslated

public final boolean[] areNucleotidesCurrentStrandTranslated()

True means a nucleotide is part of an triplet (exons). False means the nucleotide is not translated (intron,UTR)

isNucleotideCurrentStrandTranslated

public final boolean isNucleotideCurrentStrandTranslated(int i)

True means a nucleotide is part of an triplet (exons). False means the nucleotide is not translated (intron,UTR)

countCodingNucleotides

public final int countCodingNucleotides()

getResidueTypeFullLength

public final byte[] getResidueTypeFullLength()

nucleotideIndices2translatedNucleotideIndices

public final int[] nucleotideIndices2translatedNucleotideIndices()

An array mapping nucleotide indices. E.g. the 100th translated nucleotide may be found at position 200 of the original nucleotide array if there is an untranslated region of 100 nucleotides. JAVADOC:ProteinNT#translatedNucleotideIndices2nucleotideIndices()

nucleotideIdx2translatedNucleotideIdx

public final int nucleotideIdx2translatedNucleotideIdx(int idx)

Given is the index of a nucleotide.

Returns:

the index of translated nucleotides, where introns and UTRs are not counted.

translatedNucleotideIndices2nucleotideIndices

public final int[] translatedNucleotideIndices2nucleotideIndices()

An array mapping nucleotide indices. E.g. the 100th translated nucleotide may be found at position 200 of the original nucleotide array if there is an untranslated region of 100 nucleotides. See JAVADOC:ProteinNT#nucleotideIndices2translatedNucleotideIndices()

translatedNucleotideIndex2nucleotideIndex

public final int translatedNucleotideIndex2nucleotideIndex(int idx)

computes the nucleotide index from the translated idx. Translated are exons but not introns and UTRs

aminoAcidIndex2nucleotideIndex

public final int aminoAcidIndex2nucleotideIndex(int i)

Maps amino acid indices upon nucleotide indices See JAVADOC:ProteinNT#nucleotideIndex2aminoAcidIndex(int)

nucleotideIndex2aminoAcidIndex

public final int nucleotideIndex2aminoAcidIndex(int i)

Maps nucleotide indices upon amino acid indices See JAVADOC:ProteinNT#aminoAcidIndex2nucleotideIndex(int)

getResidueTriplet

public final byte[] getResidueTriplet(int iAa,
                                      byte[] buffer)

The triplet at amino acid position iAs

Parameters:

iAa - the index of the amino acid

buffer - a buffer of 3 bytes

nucleotideSelection2aminoAcidSelection

public final boolean[] nucleotideSelection2aminoAcidSelection(boolean[] selNts,
                                                              int offset)

applyCDS_expression

public void applyCDS_expression(String s)

join(7940..7996,8095..8174,8287..8368,8506..8686, complement(join(1787209..1787388,1787427.... join(complement(2261..2639),complement(881..1620))

cdsExpressionApplied

public boolean cdsExpressionApplied()

run

public Object run(String id,
                  Object arg)

Specified by:

run in interface ChRunnable