charite.christo.strap
Class BiojavaSequence2StrapProtein

java.lang.Object
  charite.christo.protein.Protein
      charite.christo.protein.ProteinNT
          charite.christo.strap.StrapProtein
              charite.christo.strap.BiojavaSequence2StrapProtein

All Implemented Interfaces:

DialogStringMatch.Interface, ChRunnable, HasClientProperty, HasDndFiles, HasImage, HasName, HasProtein, HasRendererComponent, ActionListener, Comparator, EventListener

public class BiojavaSequence2StrapProtein
extends StrapProtein

Converting a Biojava sequence objects into a StrapProtein object. This class extends StrapProtein and is instantiated with a biojava sequence object. The gapped sequence as well as the annotations and features are converted.

Field Summary

Fields inherited from class charite.christo.strap.StrapProtein

METHOD_PARSE, NONE

Fields inherited from class charite.christo.protein.ProteinNT

AMINO_ACIDS, FORWARD, FORWARD_COMPLEMENT, NUCLEOTIDES, ORIENTATIONS, REVERSE, 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, LOG, SET_ICON_IMAGE

Constructor Summary

BiojavaSequence2StrapProtein(org.biojava.bio.seq.Sequence seq)

Method Summary

Methods inherited from class charite.christo.strap.StrapProtein

addResidueSelection, column2index, column2nextIndex, column2thisOrPreviousIndex, columns2indices, columns2nextIndices, cursorPosAsString, dispose, getAlignment, getAllResidueSelections, getDndFiles, getGappedSequence, getGappedSequenceAsString, getGappedSequenceAsStringUC, getGappedSequenceExactLength, getGappedSequences, getGappedSequences, getGappedSequenceTS, getIcon, getIconImage, getIconUrl, getImage, getImageId, getMaxColumn, getMaxColumn, getParserOptions, getProteinsWithNames, getProteinWithName, getProteinWithNameAndFile, getReferenceSequence, getRendererComponent, getRendererText, getResidueAnnotations, getResidueAnnotationWithName, getResidueColumn, getResidueColumn, getResidueGap, getResidueGap, getResidueSelectionsAt, getResidueSelectionsAt, getResiduesInAlignmentcolumnrangeAsBoolean, getSelectedAminoacids, getSelectedNucleotides, getVerticalRendererComponent, inferCoordinates_BG, inferCoordinates_EDT, inferGapsFromGappedSequence, isTransient, loadProteinsInList, loadProteinsInList, newInstance, newInstance, parse, removeResidueSelection, removeResidueSelection, run, save, setAlignment, setGappedSequence, setGappedSequence, setIconImage, setInfoAssociatedPdb, setParserOptions, setResidueGap, setResidueGap, setTransient, texshade

Methods inherited from class charite.christo.protein.ProteinNT

aminoAcidIndex2nucleotideIndex, applyCDS_expression, areNucleotidesCurrentStrandTranslated, cdsExpressionApplied, countCodingNucleotides, countNucleotides, getNucleotide, getNucleotideCurrentStrand, getNucleotides, getNucleotidesAsString, getNucleotidesAsStringUC, getNucleotidesCurrentStrand, getNucleotidesCurrentStrandAsString, getNucleotidesCurrentStrandExactLength, getNucleotidesReverseComplementAsStringUC, getResidueTriplet, getResidueTypeFullLength, isComplement, isNucleotideCurrentStrandTranslated, isReverse, nucleotideIdx2translatedNucleotideIdx, nucleotideIndex2aminoAcidIndex, nucleotideIndices2translatedNucleotideIndices, nucleotideSelection2aminoAcidSelection, parseFrameShift, setNucleotideCurrentStrandTranslated, setNucleotides, setNucleotides, setNucleotidesCurrentStrandTranslated, setTranslatedStrand, translatedNucleotideIndex2nucleotideIndex, translatedNucleotideIndices2nucleotideIndices

Methods inherited from class charite.christo.protein.Protein

actionPerformed, addCDS, addDatabaseRef, addHeteroCompounds, addHeteroCompoundsUniq, addProteinViewer, addSequenceRef, addThreeLetterCode, atomNumber2residueIdx, commonPdbId, comparator_aminoacidSequenceAlphabetically, compare, containsHeteroCompound, containsOnlyACTGNX, countAtoms, countResidues, countResiduesInChain, equalsResidueType, fileAllChains, geneProductProteinNoteForCDS, getAccessionID, 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, 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, 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, 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

Constructor Detail

BiojavaSequence2StrapProtein

public BiojavaSequence2StrapProtein(org.biojava.bio.seq.Sequence seq)