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'STRAP:multiple sequence alignments ' | ||||||||
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object charite.christo.protein.Protein
public class Protein
PACKAGE:charite.christo.strap. The class Protein provides a protein model with amino acid sequences and coordinates for c-alpha atoms.
Field Summary | |
---|---|
int |
_mapRefSeqMC
|
UniqueList<ProteinViewer> |
_vProteinViewers
|
static boolean |
AMINO_ACIDS
|
static int |
B_INTO_SAME_LINE
|
static int |
B_PROCESSED
|
static int |
B_REGISTERD
|
static int |
CDS_GENE
|
static int |
CDS_NOTE
|
static int |
CDS_PRODUCT
|
static int |
CDS_PROTEIN
|
static int |
CDS_TRANSCRIPT_ID
|
static int |
CDS_TRANSLATION
|
static int |
CDS_XREFS
|
static int |
COMPLEMENT
|
static int |
FILE_TYPE_MAX
|
static int |
FORWARD
|
static long |
HETERO_ADD_APPLY_INVERSE_MX
|
static long |
HETERO_ADD_UNIQUE
|
static java.lang.Object |
KEY_BA_PARSE
|
static int |
m1stIdx
|
static int |
mANNO
|
static int |
mANNOsf
|
java.util.Map<java.lang.String,ReferenceSequence> |
mapReferenceSequence
|
static int |
mASSOCPDB
|
static int |
MAX_CACHE
|
static int |
mDNA
|
static int |
mGAPS
|
static int |
mICON
|
static int[] |
MODI_COUNTS_ALL
|
static int |
mTIPS
|
static int |
mTRANS
|
static int |
NO_TRANSLATE
|
static Protein[] |
NONE
|
static boolean |
NUCLEOTIDES
|
static int |
O_WEB_TOK
|
static int |
O_WEB_TOK1
|
static int |
O_WEB_TOKENS
|
java.lang.Object[] |
OBJECTS
|
static long |
PAINT_CHAIN_UNDERLINE
|
BA |
PARSING_INFO
|
static int |
POS_CLICKED_3D
|
static int |
POS_PRINT_COLUMN
|
static int |
REVERSE
|
static int |
REVERSE_COMPLEMENT
|
static java.lang.String[] |
TRANSLATIONS_AS_STRING
|
java.lang.Object |
WEAK_REF
|
Fields inherited from interface charite.christo.ChRunnable |
---|
APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT |
Fields inherited from interface charite.christo.HasRenderer |
---|
JLIST, STRIKE_THROUGH |
Constructor Summary | |
---|---|
Protein()
|
|
Protein(ProteinAlignment a)
|
Method Summary | ||
---|---|---|
boolean |
_isTransient()
|
|
void |
actionPerformed(java.awt.event.ActionEvent ev)
|
|
void |
addCDS(java.lang.String cds,
java.lang.String[] geneProductProteinidNote)
|
|
void |
addDatabaseRef(java.lang.String s)
|
|
boolean |
addHeteroCompounds(long options,
HeteroCompound... hh)
|
|
void |
addInvalidFeatureLine(java.lang.CharSequence s)
|
|
void |
addProteinViewer(ProteinViewer v)
|
|
int |
addResidueGap(int iA,
int gap)
|
|
boolean |
addResidueSelection(ResidueSelection s)
Add a selection of residues |
|
void |
addSequenceRef(java.lang.String s0)
|
|
static void |
addThreeLetterCode(java.lang.String s,
char ch)
|
|
int |
atomNumber2residueIdx(int pdbAtomNum)
Given a pdb Number (2nd column in pdb files) What is the residue index ? |
|
boolean |
cdsExpressionApplied()
|
|
|
cloneProtein(P pNew)
|
|
int[] |
coding2allPositions()
An array mapping nucleotide indices. |
|
int |
column2indexZ(int col)
Get index of residue at the horizontal alignment position col. |
|
int |
column2nextIndexZ(int h)
Get index of residue at the horizontal alignment position h or the next index if h points to a gap. |
|
int |
column2thisOrPreviousIndex(int col)
Get index of residue at the horizontal alignment position col. |
|
int[] |
columns2indices()
Get indeces of residues at horizontal alignment positions col. |
|
int[] |
columns2nextIndices()
An array to map horizontal residue positions to residue indices. |
|
static java.lang.String |
commonPdbId(Protein[] pp)
|
|
java.awt.Rectangle |
computeLabelSize(java.awt.Font f,
java.awt.Rectangle charBounds,
java.lang.String name,
java.awt.Rectangle rect)
|
|
boolean |
containsHeteroCompound(HeteroCompound h)
|
|
boolean |
containsInvalidFeatureLine(java.lang.CharSequence s)
|
|
boolean |
containsOnlyACTGNX()
|
|
int |
countAtoms()
number of atoms in the model. |
|
int |
countCalpha()
Are calpha-coordinates known ? |
|
int |
countNucleotides()
|
|
int |
countResidues()
number of residues, returns getResidueType().length |
|
short |
countResiduesInChain(byte chain)
|
|
static void |
debugMC(Protein[] pp)
|
|
void |
detach3DStructure()
|
|
static boolean |
equalsResidueType(Protein p1,
Protein p2)
|
|
void |
expandTreeNode(java.lang.Class c)
|
|
static java.io.File |
fileAllChains(java.io.File f0)
|
|
void |
findIconImage()
|
|
static int |
firstResIdx(Protein p)
|
|
boolean[] |
fromFullLengthB(boolean[] sel)
|
|
java.lang.String[] |
geneProductProteinNoteForCDS(java.lang.String cds)
|
|
java.lang.String |
getAccessionID()
|
|
ProteinAlignment |
getAlignment()
Get The alignment object. |
|
ResidueSelection[] |
getAllResidueSelections()
|
|
float[] |
getAtomBFactor()
|
|
float[] |
getAtomCoordinates()
Transformed Coordinates of all atoms order [x1,y1,z1,x2,y2,z2,x3,...]. |
|
float[] |
getAtomCoordinates(Matrix3D m3d)
|
|
int[] |
getAtomName32()
Names (4 characters) of atoms, as recorded in the 3rd column of PDB files. |
|
int |
getAtomName32(int iAtom)
|
|
int[] |
getAtomNumber()
The atom number is recorded in the 2nd column of pdb files |
|
float[] |
getAtomOccupancy()
|
|
byte[] |
getAtomType()
|
|
Matrix3D[] |
getBioMatrices()
|
|
java.lang.String[] |
getCDS()
|
|
int |
getChainFirstResidueIdx(char chain)
Indices of the residues each chain starts with. |
|
int |
getChainLastResidueIdx(char chain)
see JAVADOC:Protein#getChainFirstResidueIdx(char) |
|
java.lang.String |
getChainsAsString()
|
|
byte[] |
getCharacters()
The original character sequence which can be aminos or nucleotides. |
|
java.lang.Object |
getClientProperty(java.lang.Object o)
See equivalent method in JComponent. |
|
int |
getCodingStrand()
|
|
java.awt.Color |
getColor()
|
|
java.lang.String |
getCompound()
|
|
java.lang.String[] |
getDatabaseRefs()
|
|
HeteroCompound[] |
getDnaAndRnaAndHeteros()
|
|
HeteroCompound[] |
getDnaAndRnaStructures()
|
|
java.lang.String[] |
getEC()
|
|
java.io.File |
getFile()
|
|
boolean |
getFileHasSidechainAtoms()
|
|
java.io.File |
getFileMayBeWithSideChains()
|
|
java.lang.String |
getFileName()
|
|
int |
getFileNameHC()
|
|
java.lang.String |
getFilePath()
|
|
java.io.File |
getFileWithAllChains()
|
|
int[] |
getFirstAndLastResidueIndex()
|
|
byte[] |
getGappedSecStru()
|
|
byte[] |
getGappedSequence()
The amino acid sequence with gaps (0x20). |
|
java.lang.String |
getGappedSequenceAsString()
The amino acid sequence. |
|
java.lang.String |
getGappedSequenceAsStringUC()
The amino acid sequence. |
|
byte[] |
getGappedSequenceExactLength()
The amino acid sequence. |
|
float[] |
getGappedSolventAccessibility()
|
|
java.lang.String |
getHeader()
|
|
HeteroCompound[] |
getHeteroCompounds()
|
|
javax.swing.ImageIcon |
getIcon()
|
|
java.awt.Image |
getIconImage()
|
|
java.lang.String |
getIconUrl()
|
|
java.awt.Image |
getImage(java.awt.Component observer)
Get the icon of the protein or null |
|
java.lang.String |
getImageId()
|
|
int[] |
getInferred3dCountMatches()
|
|
java.lang.String |
getInferredPdbID()
|
|
java.lang.String |
getInfo(int iType)
|
|
ChJTree |
getJTree()
|
|
java.awt.Rectangle |
getLabelSize(java.awt.Font f,
java.awt.Rectangle charBounds)
|
|
int |
getMaxColumnZ()
Get the horizontal position of the last residue.. |
|
static BasicResidueSelection |
getMouseOverSelection()
|
|
java.lang.String |
getName()
A protein should have a name, usually the file-name |
|
java.lang.String |
getName0()
|
|
int |
getNameHC()
|
|
java.lang.String |
getNameURLE()
|
|
byte[] |
getNucleotides()
|
|
java.lang.String |
getNucleotidesAsStringUC()
This method is slow the first time after a change. |
|
byte[] |
getNucleotidesCodingStrand()
The nucleotides after applying the necessary reverse and complement operations. |
|
java.lang.String |
getNucleotidesReverseComplementAsStringUC()
|
|
java.lang.String |
getOnlyChains()
|
|
java.lang.String |
getOrganism()
|
|
java.lang.String |
getOrganismScientific()
|
|
java.lang.String |
getOriginalName()
|
|
long |
getParsingTime()
|
|
java.lang.String |
getPdbID()
|
|
java.lang.String |
getPdbRef()
|
|
BA |
getPdbTextSecStru()
|
|
int |
getPreferedOrder()
|
|
java.util.Map |
getPropertyMap(boolean create)
|
|
Protein |
getProtein()
returns itself. |
|
java.lang.Class |
getProteinParserClass()
|
|
Protein[] |
getProteinsSameComplex()
|
|
ProteinViewer[] |
getProteinViewers()
|
|
ReferenceSequence |
getReferenceSequence(java.lang.String otherId,
BA log,
boolean background,
java.lang.Runnable runWhenFinished)
|
|
java.lang.Object |
getRenderer(long options,
long[] rendOptions)
|
|
long |
getRendererModiCount()
|
|
java.lang.String |
getRendTxt()
|
|
float[] |
getResidueAnglePsi()
|
|
ResidueAnnotation[] |
getResidueAnnotations()
|
|
ResidueAnnotation[] |
getResidueAnnotationsNF()
|
|
ResidueAnnotation |
getResidueAnnotationWithName(java.lang.CharSequence name)
|
|
int[] |
getResidueAtomNumber()
Atom number of the first atom of the amino acid. |
|
int |
getResidueAtomNumber(int i)
Atom number of i-th residue, as recorded in the PDB files or -1. |
|
int[] |
getResidueAtomNumberFullLength()
|
|
float[] |
getResidueCalpha()
Get transformed calpha-coordinates [Anstrom] |
|
float[] |
getResidueCalpha(Matrix3D m3d)
|
|
float[] |
getResidueCalphaOriginalFullLength()
|
|
byte[] |
getResidueChain()
the chain denominators of each residue |
|
byte |
getResidueChain(int i)
chain denominators of the i-th residue, usually capital letter |
|
byte[] |
getResidueChainFullLength()
|
|
int[] |
getResidueColumn()
Maps residue indices upon horizontal text positions of the alignment. |
|
int |
getResidueColumn(int i)
Maps residue indices to horizontal text positions of the alignment. |
|
int |
getResidueColumnZ(int i)
|
|
int[] |
getResidueFirstAtomIdx()
|
|
int |
getResidueFirstAtomIdx(int resIdx)
Indices of the atoms each residue starts with. |
|
int[] |
getResidueGap()
|
|
int |
getResidueGap(int i)
|
|
int |
getResidueIndexOffset()
|
|
byte[] |
getResidueInsertionCode()
ATOM 200 CA LEU A 27B 8.378 37.835 28.244 1.00 37.40 C ATOM 208 CA LEU A 27C 6.042 34.960 27.222 1.00 42.03 C ATOM 216 CA ASN A 27D 2.874 36.266 25.650 1.00 42.04 C ^ used in only a few PDB entries as e.g. |
|
byte |
getResidueInsertionCode(int i)
|
|
byte[] |
getResidueInsertionCodeFullLength()
|
|
int[] |
getResidueLastAtomIdx()
|
|
int |
getResidueLastAtomIdx(int resIdx)
|
|
int[] |
getResidueName32()
Names (4 characters) of residues, as recorded in the 4th column of PDB files. |
|
int |
getResidueName32(int i)
|
|
int[] |
getResidueNumber()
Numbers of each residue, as recorded in the PDB files. |
|
int |
getResidueNumber(int i)
Number of i-th residue, as recorded in the PDB files or -1. |
|
int[] |
getResidueNumberFullLength()
|
|
byte[] |
getResidueSecStrType()
|
|
byte |
getResidueSecStrType(int i)
secondary structure (H,E,C) of i-th residue , H=helix, C=coil, E=Extended,Sheet |
|
byte[] |
getResidueSecStrTypeFullLenght()
H=helix, C=coil, E=Extended,Sheet |
|
ResidueSelection[] |
getResidueSelections()
The selections of residues excluding ResidueAnnotation-objects |
|
ResidueSelection[] |
getResidueSelectionsAt(long options,
int iA_from,
int iA_to,
int where)
|
|
ResidueSelection[] |
getResidueSelectionsWithName(java.lang.String[] names)
|
|
float[] |
getResidueSolventAccessibility()
Residue accessibility in square Anstroms, as taken from DSSP. |
|
boolean[] |
getResidueSubsetB()
|
|
int |
getResidueSubsetB1()
Index of the first true in getResidueSubsetB(); |
|
byte[] |
getResidueTripletZ(int ia,
byte[] buffer)
The triplet at amino acid position |
|
byte[] |
getResidueType()
The sequence in one letter format. |
|
byte |
getResidueType(int i)
|
|
static byte[][] |
getResidueType(Protein[] pp)
|
|
java.lang.String |
getResidueTypeAsString()
AA sequence as string |
|
java.lang.String |
getResidueTypeAsStringUC()
AA sequence as upper case string |
|
byte[] |
getResidueTypeExactLength()
|
|
byte[] |
getResidueTypeFullLength()
|
|
int |
getResidueTypeHashCode()
|
|
byte[] |
getResidueTypeLowerCaseMeansNo3dCoordinates()
|
|
float |
getResolutionAnstroms()
|
|
Matrix3D |
getRotationAndTranslation()
Get the rotation - translation matrix. |
|
int |
getRow()
|
|
byte[] |
getSelectedAminoacids()
Returns an array telling what residues are selected by at least one residue selection. |
|
byte[] |
getSelectedNucleotides()
|
|
ResidueAnnotation[] |
getSequenceFeatures()
|
|
java.lang.String[] |
getSequenceRefs()
|
|
java.lang.String |
getTitle()
|
|
java.lang.String |
getUniprotID()
|
|
java.net.URL |
getURL()
|
|
ValueOfProtein |
getValueOfProtein()
|
|
javax.swing.JComponent |
getVerticalRendererComponent()
|
|
java.lang.Object |
getWeakRef()
|
|
int |
getWebTokenIdx()
|
|
long |
hashCodeCalpha()
|
|
java.util.WeakHashMap<Protein,Superimpose3D.Result> |
hashTMalign()
|
|
boolean |
hasPdbId(java.lang.String s)
|
|
java.io.File |
iconLink()
|
|
static void |
incrementMC(int type,
java.lang.Object proteins)
|
|
float |
inferCoordinates(Protein[] pp3d,
java.lang.Class classAligner,
BA log)
|
|
void |
inferGapsFromGappedSequence(byte[] seq)
The original residue types are kept but the gaps are inferred from the gapped sequence seq. |
|
void |
inferredPDB_markMatches(boolean toLC,
boolean selection)
|
|
boolean[] |
isCoding()
True means a nucleotide is part of an triplet (exons). |
|
boolean |
isInAlignment()
|
|
boolean |
isInMsfFile()
|
|
boolean |
isLoadedFromStructureFile()
|
|
boolean |
isWaterInFile()
|
|
void |
loadSideChainAtoms(BA ba)
|
|
int |
mc(int type)
|
|
int |
mcSum(int t1,
int t2)
|
|
int |
mcSum(int t1,
int t2,
int t3)
|
|
static void |
mouseOver(Protein p,
int iAa0)
|
|
static Protein |
newInstance(java.io.File f)
creates Protein from a protein file The file type may be PDB, SWISSPROT, EMBL, FASTA The method is not thread safe because it uses a static byte buffer for file data. |
|
static Protein |
newInstance(long options,
java.io.File proteinFile)
|
|
boolean[] |
ntPositions2aa(boolean[] selNts,
int offset,
int[] returnMinIdx)
|
|
void |
paintChain(long options,
java.awt.Graphics g,
java.lang.String T,
int x0,
int y,
int w,
int h)
|
|
boolean |
parse(BA txt,
ProteinParser[] parsers,
long mode)
Interpretes the text and extracts the protein data and sets the fields such as residueType in the protein. |
|
void |
parseCDS(java.lang.String s)
join(7940..7996,8095..8174,8287..8368,8506..8686, complement(join(1787209..1787388,1787427.... |
|
void |
parseFrameShift(byte[] z,
int l)
|
|
boolean |
parseGaps(byte[] z,
int l)
Reads a line such as X2XXX3X1XXXX2XXXXX The numbers are gaps and the letters residue positions |
|
java.lang.String |
pdbFileName(boolean[] res,
long writerOptions)
|
|
java.lang.CharSequence |
pdbNumberToIdx1(java.lang.CharSequence expression)
|
|
BA |
posAsTextZ(int type,
int ias)
|
|
void |
putClientProperty(java.lang.Object key,
java.lang.Object value)
See equivalent method in JComponent. |
|
void |
removeAllSequenceRefs()
|
|
boolean |
removeHeteroCompound(HeteroCompound h)
|
|
void |
removeProteinViewer(ProteinViewer v)
|
|
void |
removeResidueSelection(java.lang.Class c)
Remove all selection of residues that are instances of c |
|
boolean |
removeResidueSelection(ResidueSelection s)
Remove selection of residues |
|
void |
removeSequenceRef(java.lang.String s)
|
|
void |
reportIconWidth(int w)
|
|
boolean[] |
residueSubsetAsBool(java.lang.CharSequence expr,
int[] returnMinIdx)
Converts String denominating a subset of residues into a boolean array E.g. |
|
boolean[] |
residueSubsetAsBooleanZ(java.lang.CharSequence expr)
|
|
int |
resNumAndChain2resIdxZ(boolean fullLength,
int resNum,
char chain,
char insCode)
Given a residue number and a chain denominator What is the residue index ? |
|
java.lang.Object |
run(java.lang.String id,
java.lang.Object arg)
|
|
void |
save(boolean isViewer,
java.io.File dir,
BA error)
|
|
void |
selectCodingStrand(int orientation)
|
|
static java.lang.String |
selectedPositionsToText(boolean[] bb,
int offset,
Protein protein)
|
|
static java.lang.String |
selectedPositionsToText(boolean pdbNumbers,
boolean[] bb,
int offset,
Protein protein)
|
|
static java.lang.String |
selectedPositionsToText(ResidueSelection s)
|
|
void |
setAccessionID(java.lang.String s0)
|
|
void |
setAlignment(ProteinAlignment a)
|
|
void |
setAtomBFactor(float[] atomBFactor)
|
|
void |
setAtomCoordOriginal(float[] ii)
|
|
void |
setAtomNumber(int[] atomNumber)
The atom number is recorded in the 2nd column of pdb files |
|
void |
setAtomOccupancy(float[] atomOccupancy)
|
|
void |
setAtomType(byte[] at)
|
|
void |
setAtomType32bit(int[] at)
|
|
void |
setBalloonText(java.lang.String t)
|
|
void |
setBioMatrices(Matrix3D[] mm)
|
|
void |
setCharSequence(byte[] tt)
The original character sequence which can be aminos or nucleotides. |
|
void |
setCoding(boolean[] bb)
Determines which nucleotide needs to be translated (coding sequence). |
|
void |
setColor(java.awt.Color c)
|
|
void |
setCompound(java.lang.String s)
|
|
void |
setEC(java.lang.String... s)
|
|
Protein |
setFile(java.io.File f)
|
|
void |
setFileHasSidechainAtoms(boolean b)
|
|
void |
setFileWithAllChains(java.io.File f)
|
|
void |
setFileWithSideChains(java.io.File f)
|
|
void |
setFileWithSideChainsObtainableFromPDB(boolean b)
|
|
void |
setGappedSequence(byte[] seq,
int len)
set the gapped sequence |
|
void |
setGappedSequence(java.lang.CharSequence seq)
See JAVADOC:Protein#setGappedSequence(byte[]) |
|
void |
setHeader(java.lang.String s)
|
|
void |
setIconImage(java.lang.String url)
|
|
void |
setInfoAssociatedPdb(java.lang.String info)
|
|
void |
setIsInAlignment(boolean b)
|
|
void |
setIsInMsfFile(boolean b)
|
|
void |
setIsLoadedFromStructureFile(boolean b)
|
|
boolean |
setModiCount(int type,
int value)
|
|
Protein |
setName(java.lang.String n)
|
|
void |
setNucleotides(java.lang.Object rawNtSequence,
int orientation)
Sets the sequence of nucleotides. |
|
void |
setOnlyChains(java.lang.String s)
|
|
void |
setOrganism(java.lang.String s)
|
|
void |
setOrganismScientific(java.lang.String s)
|
|
void |
setOriginalName(java.lang.String s)
|
|
void |
setParsingTime(long t)
|
|
void |
setPdbID(java.lang.String s0)
|
|
void |
setPdbTextSecStru(BA txt)
|
|
void |
setPreferedOrder(int t)
|
|
void |
setProteinParserClass(java.lang.Class p)
|
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void |
setProteinsSameComplex(Protein[] pp)
|
|
void |
setResidueAnglePhi(float[] angle)
|
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void |
setResidueAnglePsi(float[] angle)
|
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void |
setResidueAtomNumber(int[] rai)
set atom numbers of each residue, as recorded in the PDB files. |
|
void |
setResidueCalphaOriginal(float[] xyz)
set the array of untransformed calpha-coordinates {x0,y0,z0, x1,y1,z1, x2,y2,z2 ...} |
|
void |
setResidueChain(byte[] bb)
|
|
void |
setResidueFirstAndLastAtomIdx(int[] first,
int[] last)
|
|
void |
setResidueGap(int[] rg)
|
|
void |
setResidueGap(int iA,
int gap)
|
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void |
setResidueIndexOffset(int first)
|
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void |
setResidueInsertionCode(byte[] ic)
|
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void |
setResidueNumber(int[] rn)
set Numbers of each residue, as recorded in the PDB files. |
|
void |
setResidueSecStrType(byte[] a)
Secondary structure (H,E,C) |
|
void |
setResidueSolventAccessibility(float[] a)
Set accessibilities of residues |
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void |
setResidueSubset(boolean[] b)
|
|
void |
setResidueSubset(java.lang.String expression)
residueSubset("10-20,40-50") will return a new protein instance with residues from 10-20 and 40-50 In PDB-files the pdb-residue-number can be referred to: 10:-20:, 40:-50: One can add a chain identifier like 10:A-20:A, 40:A-50:A Note: counting of residues starts here at 1 and not 0 !! |
|
void |
setResidueType(java.lang.Object seq)
set the array of amino acids |
|
void |
setResidueType32bit(int[] rn)
set Names of each residue, as recorded in the PDB files. |
|
void |
setResolutionAnstroms(float r)
|
|
void |
setRotationAndTranslation(Matrix3D m3d)
see JAVADOC:Protein#getRotationAndTranslation() |
|
void |
setRow(int i)
|
|
void |
setTitle(java.lang.String s)
|
|
void |
setTransient(boolean b)
Non-transient proteins are not saved |
|
void |
setUniprotID(java.lang.String s0)
|
|
void |
setURL(java.net.URL u)
|
|
void |
setValueOfProtein(ValueOfProtein v)
|
|
static java.io.File |
strapFile(int t,
java.lang.Object protein)
|
|
static java.io.File |
strapFile(int t,
java.lang.Object protein,
java.io.File dir)
|
|
int |
sumUpGaps(int ias)
|
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java.lang.Thread |
thread_parseCDS(java.lang.String s)
|
|
int[] |
toCodingPositions()
An array mapping nucleotide indices. |
|
boolean[] |
toFullLengthB(boolean[] sel)
|
|
static byte |
toOneLetterCode(int name32)
Equivalent to toOneLetterCode(n&255,(n>>>8)&255, (n>>>16)&255); |
|
static byte |
toOneLetterCode(int c0,
int c1,
int c2)
Conversion from three-letter- to one-letter-code. |
|
java.lang.String |
toString()
|
|
static java.lang.String |
toThreeLetterCode(int i)
F ==> PHE |
|
static java.lang.String |
urlCd(boolean encode,
java.lang.CharSequence text,
int from)
|
|
int |
wideColumn2nextIndex(int column)
|
|
java.io.File |
writePdbFile(boolean[] res,
long writerOptions)
|
|
java.io.File |
writePdbFile(long writerOptions)
|
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final int CDS_GENE
public static final int CDS_PRODUCT
public static final int CDS_PROTEIN
public static final int CDS_NOTE
public static final int CDS_XREFS
public static final int CDS_TRANSCRIPT_ID
public static final int CDS_TRANSLATION
public static final long HETERO_ADD_UNIQUE
public static final long HETERO_ADD_APPLY_INVERSE_MX
public static final int m1stIdx
public static final int mANNO
public static final int mANNOsf
public static final int mASSOCPDB
public static final int mDNA
public static final int mGAPS
public static final int mICON
public static final int mTIPS
public static final int mTRANS
public static final int FILE_TYPE_MAX
public final UniqueList<ProteinViewer> _vProteinViewers
public final java.lang.Object WEAK_REF
public static final int POS_CLICKED_3D
public static final int POS_PRINT_COLUMN
public final BA PARSING_INFO
public static final long PAINT_CHAIN_UNDERLINE
public static final Protein[] NONE
public static final int[] MODI_COUNTS_ALL
public static final int MAX_CACHE
public static final boolean AMINO_ACIDS
public static final boolean NUCLEOTIDES
public static final java.lang.String[] TRANSLATIONS_AS_STRING
public static final int NO_TRANSLATE
public static final int FORWARD
public static final int REVERSE
public static final int COMPLEMENT
public static final int REVERSE_COMPLEMENT
public static final java.lang.Object KEY_BA_PARSE
public static final int O_WEB_TOK
public static final int O_WEB_TOKENS
public static final int O_WEB_TOK1
public static final int B_PROCESSED
public static final int B_INTO_SAME_LINE
public static final int B_REGISTERD
public final java.lang.Object[] OBJECTS
public java.util.Map<java.lang.String,ReferenceSequence> mapReferenceSequence
public int _mapRefSeqMC
Constructor Detail |
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public Protein(ProteinAlignment a)
public Protein()
Method Detail |
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public static Protein newInstance(java.io.File f)
public static Protein newInstance(long options, java.io.File proteinFile)
public Protein getProtein()
getProtein
in interface HasProtein
public int getChainFirstResidueIdx(char chain)
public int getChainLastResidueIdx(char chain)
public int getResidueFirstAtomIdx(int resIdx)
public int getResidueLastAtomIdx(int resIdx)
public void setResidueFirstAndLastAtomIdx(int[] first, int[] last)
public int[] getResidueFirstAtomIdx()
public int[] getResidueLastAtomIdx()
public void setResidueAnglePsi(float[] angle)
public float[] getResidueAnglePsi()
public void setResidueAnglePhi(float[] angle)
public HeteroCompound[] getDnaAndRnaAndHeteros()
public HeteroCompound[] getDnaAndRnaStructures()
public HeteroCompound[] getHeteroCompounds()
public boolean containsHeteroCompound(HeteroCompound h)
public boolean addHeteroCompounds(long options, HeteroCompound... hh)
public boolean removeHeteroCompound(HeteroCompound h)
public void setCharSequence(byte[] tt)
public final byte[] getCharacters()
public final byte[] getResidueType()
public final int getResidueTypeHashCode()
public final byte[] getResidueTypeExactLength()
public byte getResidueType(int i)
public void setResidueType(java.lang.Object seq)
public final int countResidues()
public final java.lang.String getResidueTypeAsStringUC()
public final java.lang.String getResidueTypeAsString()
public byte[] getResidueChain()
public byte[] getResidueChainFullLength()
public byte getResidueChain(int i)
public void setResidueChain(byte[] bb)
public java.lang.String getChainsAsString()
public short countResiduesInChain(byte chain)
public int[] getResidueNumber()
public int[] getResidueNumberFullLength()
public final int getResidueNumber(int i)
public void setResidueNumber(int[] rn)
public byte[] getResidueInsertionCode()
public byte[] getResidueInsertionCodeFullLength()
public byte getResidueInsertionCode(int i)
public void setResidueInsertionCode(byte[] ic)
public int[] getResidueName32()
public int getResidueName32(int i)
public void setResidueType32bit(int[] rn)
public int[] getResidueAtomNumber()
ATOM 39607 CG GLN V 195 18.039-150.197 79.532 1.00 76.24 CThe atom number is 39607.
public int[] getResidueAtomNumberFullLength()
public int getResidueAtomNumber(int i)
public void setResidueAtomNumber(int[] rai)
public float[] getResidueSolventAccessibility()
public void setResidueSolventAccessibility(float[] a)
public byte getResidueSecStrType(int i)
public void setResidueSecStrType(byte[] a)
public byte[] getResidueSecStrType()
public byte[] getResidueSecStrTypeFullLenght()
public int[] getAtomName32()
public int getAtomName32(int iAtom)
public void setAtomType32bit(int[] at)
public byte[] getAtomType()
public void setAtomType(byte[] at)
public void setAtomNumber(int[] atomNumber)
public int[] getAtomNumber()
public void setAtomCoordOriginal(float[] ii)
public float[] getAtomCoordinates()
public int countAtoms()
public void setAtomBFactor(float[] atomBFactor)
public float[] getAtomBFactor()
public void setAtomOccupancy(float[] atomOccupancy)
public float[] getAtomOccupancy()
public void setHeader(java.lang.String s)
public void setOrganism(java.lang.String s)
public void setOrganismScientific(java.lang.String s)
public void setCompound(java.lang.String s)
public void setTitle(java.lang.String s)
public java.lang.String getCompound()
public java.lang.String getTitle()
public java.lang.String getHeader()
public java.lang.String getOrganism()
public java.lang.String getOrganismScientific()
public java.lang.String getInfo(int iType)
public java.lang.String[] getEC()
public void setEC(java.lang.String... s)
public java.lang.String getUniprotID()
public void setUniprotID(java.lang.String s0)
public java.lang.String getPdbID()
public boolean hasPdbId(java.lang.String s)
public void setPdbID(java.lang.String s0)
public java.lang.String getPdbRef()
public java.lang.String getAccessionID()
public void setAccessionID(java.lang.String s0)
public java.lang.String[] getSequenceRefs()
public java.lang.String[] getDatabaseRefs()
public void removeAllSequenceRefs()
public void removeSequenceRef(java.lang.String s)
public void addSequenceRef(java.lang.String s0)
public void addDatabaseRef(java.lang.String s)
public java.lang.String[] getCDS()
public java.lang.String[] geneProductProteinNoteForCDS(java.lang.String cds)
public void addCDS(java.lang.String cds, java.lang.String[] geneProductProteinidNote)
public Protein setName(java.lang.String n)
public final java.lang.String getName0()
public final int getNameHC()
public final java.lang.String getName()
getName
in interface HasName
public final java.lang.String getNameURLE()
public static java.lang.String urlCd(boolean encode, java.lang.CharSequence text, int from)
public final java.lang.String toString()
toString
in class java.lang.Object
public void setURL(java.net.URL u)
public java.net.URL getURL()
public java.lang.String getOriginalName()
public void setOriginalName(java.lang.String s)
public final java.io.File getFile()
public java.lang.String getFilePath()
public java.lang.String getFileName()
public final int getFileNameHC()
public Protein setFile(java.io.File f)
public final void setFileWithAllChains(java.io.File f)
public final void setFileWithSideChainsObtainableFromPDB(boolean b)
public void setFileWithSideChains(java.io.File f)
public java.io.File getFileMayBeWithSideChains()
public final java.io.File getFileWithAllChains()
public boolean getFileHasSidechainAtoms()
public void setFileHasSidechainAtoms(boolean b)
public static java.io.File strapFile(int t, java.lang.Object protein)
public static java.io.File strapFile(int t, java.lang.Object protein, java.io.File dir)
public void setIsInMsfFile(boolean b)
public boolean isInMsfFile()
public final java.lang.String pdbFileName(boolean[] res, long writerOptions)
public final java.io.File writePdbFile(long writerOptions)
public final java.io.File writePdbFile(boolean[] res, long writerOptions)
public long hashCodeCalpha()
public void setOnlyChains(java.lang.String s)
public java.lang.String getOnlyChains()
public static java.lang.String toThreeLetterCode(int i)
public static void addThreeLetterCode(java.lang.String s, char ch)
public static final byte toOneLetterCode(int c0, int c1, int c2)
public static final byte toOneLetterCode(int name32)
public ResidueSelection[] getResidueSelections()
public boolean addResidueSelection(ResidueSelection s)
public ResidueSelection[] getResidueSelectionsWithName(java.lang.String[] names)
public boolean removeResidueSelection(ResidueSelection s)
public void setResidueCalphaOriginal(float[] xyz)
public float[] getResidueCalphaOriginalFullLength()
public final int countCalpha()
public byte[] getResidueTypeLowerCaseMeansNo3dCoordinates()
public float[] getResidueCalpha()
public float[] getResidueCalpha(Matrix3D m3d)
m3d
- The coordinate system
If m3d==null then the coriginal coordinates as recorded in the PDB file are returned.
p.getResidueCalpha(p.getRotationAndTranslation()) is identical to p.getResidueCalpha()
public float[] getAtomCoordinates(Matrix3D m3d)
public final Matrix3D getRotationAndTranslation()
public final void setRotationAndTranslation(Matrix3D m3d)
public ProteinViewer[] getProteinViewers()
public void addProteinViewer(ProteinViewer v)
public void removeProteinViewer(ProteinViewer v)
public java.lang.CharSequence pdbNumberToIdx1(java.lang.CharSequence expression)
public boolean[] residueSubsetAsBool(java.lang.CharSequence expr, int[] returnMinIdx)
public boolean[] residueSubsetAsBooleanZ(java.lang.CharSequence expr)
public int atomNumber2residueIdx(int pdbAtomNum)
public int resNumAndChain2resIdxZ(boolean fullLength, int resNum, char chain, char insCode)
public java.lang.Object getWeakRef()
getWeakRef
in interface HasWeakRef
public java.util.Map getPropertyMap(boolean create)
getPropertyMap
in interface HasPropertyMap
public final void putClientProperty(java.lang.Object key, java.lang.Object value)
public final java.lang.Object getClientProperty(java.lang.Object o)
public int getResidueIndexOffset()
public void setResidueIndexOffset(int first)
public int[] getFirstAndLastResidueIndex()
public static int firstResIdx(Protein p)
public void setResidueSubset(java.lang.String expression)
public void setResidueSubset(boolean[] b)
public int getResidueSubsetB1()
public boolean[] getResidueSubsetB()
public boolean[] fromFullLengthB(boolean[] sel)
public boolean[] toFullLengthB(boolean[] sel)
public float getResolutionAnstroms()
public void setResolutionAnstroms(float r)
public java.util.WeakHashMap<Protein,Superimpose3D.Result> hashTMalign()
public static byte[][] getResidueType(Protein[] pp)
public void setProteinParserClass(java.lang.Class p)
public void setParsingTime(long t)
public java.lang.Class getProteinParserClass()
public long getParsingTime()
public final boolean containsOnlyACTGNX()
public int[] getInferred3dCountMatches()
public float inferCoordinates(Protein[] pp3d, java.lang.Class classAligner, BA log)
public void inferredPDB_markMatches(boolean toLC, boolean selection)
public void detach3DStructure()
public java.lang.String getInferredPdbID()
public void paintChain(long options, java.awt.Graphics g, java.lang.String T, int x0, int y, int w, int h)
public static final java.io.File fileAllChains(java.io.File f0)
public void setBioMatrices(Matrix3D[] mm)
public Matrix3D[] getBioMatrices()
public void setPdbTextSecStru(BA txt)
public BA getPdbTextSecStru()
public static BasicResidueSelection getMouseOverSelection()
public static void mouseOver(Protein p, int iAa0)
public void actionPerformed(java.awt.event.ActionEvent ev)
actionPerformed
in interface java.awt.event.ActionListener
public static java.lang.String selectedPositionsToText(ResidueSelection s)
public static java.lang.String selectedPositionsToText(boolean[] bb, int offset, Protein protein)
public static java.lang.String selectedPositionsToText(boolean pdbNumbers, boolean[] bb, int offset, Protein protein)
public boolean isWaterInFile()
public void loadSideChainAtoms(BA ba)
public static boolean equalsResidueType(Protein p1, Protein p2)
public boolean isLoadedFromStructureFile()
public void setIsLoadedFromStructureFile(boolean b)
public static java.lang.String commonPdbId(Protein[] pp)
public <P extends Protein> P cloneProtein(P pNew)
public Protein[] getProteinsSameComplex()
public void setProteinsSameComplex(Protein[] pp)
public void setColor(java.awt.Color c)
setColor
in interface Colored
public java.awt.Color getColor()
getColor
in interface Colored
public final int mc(int type)
public final int mcSum(int t1, int t2)
public final int mcSum(int t1, int t2, int t3)
public static void incrementMC(int type, java.lang.Object proteins)
public boolean setModiCount(int type, int value)
public static void debugMC(Protein[] pp)
public void selectCodingStrand(int orientation)
public final int getCodingStrand()
public final byte[] getNucleotides()
public final byte[] getNucleotidesCodingStrand()
public final int countNucleotides()
public final void setNucleotides(java.lang.Object rawNtSequence, int orientation)
public final byte[] getResidueTypeFullLength()
public final byte[] getResidueTripletZ(int ia, byte[] buffer)
ia
- the index of the amino acidbuffer
- a buffer of 3 bytespublic void setCoding(boolean[] bb)
public final boolean[] isCoding()
public final int[] toCodingPositions()
public final int[] coding2allPositions()
public final boolean[] ntPositions2aa(boolean[] selNts, int offset, int[] returnMinIdx)
public java.lang.Thread thread_parseCDS(java.lang.String s)
public void parseCDS(java.lang.String s)
public boolean cdsExpressionApplied()
public void parseFrameShift(byte[] z, int l)
public java.lang.String getNucleotidesAsStringUC()
public java.lang.String getNucleotidesReverseComplementAsStringUC()
public final ProteinAlignment getAlignment()
public void setAlignment(ProteinAlignment a)
public void setIsInAlignment(boolean b)
public boolean isInAlignment()
public void setValueOfProtein(ValueOfProtein v)
public ValueOfProtein getValueOfProtein()
public void setResidueGap(int[] rg)
public void setResidueGap(int iA, int gap)
public int addResidueGap(int iA, int gap)
public int[] getResidueGap()
public final int getResidueGap(int i)
public int sumUpGaps(int ias)
public int wideColumn2nextIndex(int column)
public int[] getResidueColumn()
public final int getResidueColumn(int i)
public final int getResidueColumnZ(int i)
public int getMaxColumnZ()
public int[] columns2nextIndices()
public int[] columns2indices()
public int column2indexZ(int col)
col
- the alignment position (column)
public int column2thisOrPreviousIndex(int col)
col
- the alignment position (column)
public int column2nextIndexZ(int h)
h
- the alignment position (column)
public byte[] getGappedSequence()
public byte[] getGappedSequenceExactLength()
public java.lang.String getGappedSequenceAsString()
public java.lang.String getGappedSequenceAsStringUC()
public byte[] getGappedSecStru()
public float[] getGappedSolventAccessibility()
public void inferGapsFromGappedSequence(byte[] seq)
public void setGappedSequence(byte[] seq, int len)
public void setGappedSequence(java.lang.CharSequence seq)
public boolean parseGaps(byte[] z, int l)
public int getWebTokenIdx()
public int getPreferedOrder()
public void setPreferedOrder(int t)
public void setRow(int i)
public int getRow()
public void save(boolean isViewer, java.io.File dir, BA error)
public boolean _isTransient()
public void setTransient(boolean b)
public boolean parse(BA txt, ProteinParser[] parsers, long mode)
parsers
- An array of parsers to do the job. Try all until one succeeds.txt
- the protein text in fasta or pdb or swissprot format.
public java.awt.Image getImage(java.awt.Component observer)
getImage
in interface HasImage
public javax.swing.ImageIcon getIcon()
public java.awt.Image getIconImage()
public void setIconImage(java.lang.String url)
public java.lang.String getIconUrl()
public java.lang.String getImageId()
public void findIconImage()
public java.io.File iconLink()
public void setInfoAssociatedPdb(java.lang.String info)
public void setBalloonText(java.lang.String t)
public void reportIconWidth(int w)
public long getRendererModiCount()
getRendererModiCount
in interface HasRendererModiCount
public java.lang.Object getRenderer(long options, long[] rendOptions)
getRenderer
in interface HasRenderer
public javax.swing.JComponent getVerticalRendererComponent()
public java.lang.String getRendTxt()
public final java.awt.Rectangle getLabelSize(java.awt.Font f, java.awt.Rectangle charBounds)
public java.awt.Rectangle computeLabelSize(java.awt.Font f, java.awt.Rectangle charBounds, java.lang.String name, java.awt.Rectangle rect)
public byte[] getSelectedAminoacids()
public byte[] getSelectedNucleotides()
public ResidueSelection[] getAllResidueSelections()
public void removeResidueSelection(java.lang.Class c)
public BA posAsTextZ(int type, int ias)
public ResidueSelection[] getResidueSelectionsAt(long options, int iA_from, int iA_to, int where)
public ResidueAnnotation getResidueAnnotationWithName(java.lang.CharSequence name)
public ResidueAnnotation[] getResidueAnnotations()
public ResidueAnnotation[] getSequenceFeatures()
public ResidueAnnotation[] getResidueAnnotationsNF()
public ReferenceSequence getReferenceSequence(java.lang.String otherId, BA log, boolean background, java.lang.Runnable runWhenFinished)
public void addInvalidFeatureLine(java.lang.CharSequence s)
public boolean containsInvalidFeatureLine(java.lang.CharSequence s)
public java.lang.Object run(java.lang.String id, java.lang.Object arg)
run
in interface ChRunnable
public ChJTree getJTree()
public void expandTreeNode(java.lang.Class c)
|
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