charite.christo.strap
Class SPUtils

java.lang.Object
  charite.christo.strap.SPUtils

All Implemented Interfaces:

ChRunnable, java.util.Comparator

public class SPUtils
extends java.lang.Object
implements java.util.Comparator, ChRunnable

Field Summary

static long	ALIGN_CHANGE_ORDER
static java.lang.String[]	INFER3D_AUTO
static long	INFER3D_HOMOLOGOUS
static long	INFER3D_IF_NOT_ALREADY
static long	INFER3D_SET_FILE
static long	INFER3D_SHOW_BACKBONE
static long	SUPERIMP_COMPLEX_BEST
static long	SUPERIMP_EVENT
static boolean[]	SUPERIMPOSING

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

Constructor Summary

SPUtils()

Method Summary

static SequenceAligner	alignerInstance()
static SequenceAligner	alignProteins(SequenceAligner aligner0, java.util.List<Protein> vP, boolean[] shouldStop, long options)
static java.util.Set	allFiles()
int	compare(java.lang.Object o1, java.lang.Object o2)
static void	downloadOriginalProteins(boolean newThread, Protein[] pp, long webOptions)
static void	downloadOriginalProteins(boolean newThread, Protein[] pp, java.lang.String database, java.io.File[] files, long webOptions)
static void	fetchIdsAndDownloadOriginalProteins(boolean newThread, Protein[] pp)
static java.util.Comparator	getComparator(char type)
static byte[][]	getGappedSequences(Protein[] pp, int colFrom, int colTo, char gap)
static int	getMaxColumn(Protein[] pp)
static long	getParserOptions()
static Protein[]	getProteinsOfObjects(java.lang.Object[] oo)
static Protein[]	getProteinsSameRow(Protein p)
static Protein[]	getProteinsWithNames(BA ba, Protein[] pp)
static Protein	getProteinWithName(java.lang.String name, Protein[] pp0) returns the 1st protein whose name equals to name.
static Protein	getProteinWithNameAndFile(java.lang.String n, java.io.File file, java.lang.Object[] pp)
static boolean	hasResidueSelection(Protein p, java.lang.String[] names)
static boolean	infc_Blocking(Protein[] pp, Protein[][] pp3d_array, BA log, long options)
static void	inferCoordinates_TS(Protein[] pp, java.lang.String[] pdbID, BA chLog0, long options)
static void	inferCoordinates1(Protein p, java.lang.String pdbID)
static int[]	leadingAndTrailingLowerCaseLettersInMSA(Protein[] pp)
static void	loopSuperimposeProteinsV(UniqueList<? extends Protein> vP, boolean[] stop, boolean[] superimposing, long options)
static Protein	newProteinColumnFromTo(Protein p, int west, int east)
static Protein	newProteinSubset(Protein p, java.lang.String expr)
static boolean	parseProtein(java.io.File proteinFile, BA text, long mode, Protein p)
static Protein[]	ppWithAminos(Protein[] pp0)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
static void	setParserOptions(long options)
static void	setProteinIcon(Protein[] pp, boolean overwrite, char type)
static void	setResidueSubsetFromColumnRange(Protein p, int from, int to)
static void	setSeqs(SequenceAligner aligner, Protein[] pp)
static void	sortVisibleOrder(Protein[] pp)
static java.lang.String	speciesName2Icon(Protein p)
static java.lang.String	speciesName2Icon(java.lang.String name)
static Protein	superimposeProteins(java.util.List<? extends Protein> vP, boolean[] shouldStop, long options)
static java.lang.Thread	thread_fetchIdsAndDownloadOriginalProteins(Protein[] pp)
static java.lang.Thread	threadAlignProteins(SequenceAligner aligner, java.util.List<Protein> vP, boolean[] shouldStop, long options)
static java.lang.Thread	threadDownloadOriginalProteins(Protein[] pp, long webOptions)
static java.lang.Thread	threadDownloadOriginalProteins(Protein[] pp, java.lang.String key, java.io.File[] files, long webOptions)
static java.lang.Thread	threadInferCoordinates(Protein[] pp, java.lang.String[] pdbID, BA chLog, long options)
static java.lang.Thread	threadLoopSuperimposeProteinsV(UniqueList<? extends Protein> vP, boolean[] stop, boolean[] superimposing, long options)
static java.lang.Thread	threadSuperimposeProteins(java.util.List<? extends Protein> vP, boolean[] isInterrupted, long options)
static java.lang.Thread	threadSuperimposeProteins(java.util.List<? extends Protein> vP, boolean[] isInterrupted, Protein[] pBest, long options)
static void	viewComparison(Protein p0, Protein p1, java.lang.Object clazzOrInstance)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Comparator

equals

Field Detail

INFER3D_HOMOLOGOUS

public static final long INFER3D_HOMOLOGOUS

See Also:

Constant Field Values

INFER3D_SHOW_BACKBONE

public static final long INFER3D_SHOW_BACKBONE

See Also:

Constant Field Values

INFER3D_IF_NOT_ALREADY

public static final long INFER3D_IF_NOT_ALREADY

See Also:

Constant Field Values

INFER3D_SET_FILE

public static final long INFER3D_SET_FILE

See Also:

Constant Field Values

ALIGN_CHANGE_ORDER

public static final long ALIGN_CHANGE_ORDER

See Also:

Constant Field Values

SUPERIMP_EVENT

public static final long SUPERIMP_EVENT

See Also:

Constant Field Values

SUPERIMP_COMPLEX_BEST

public static final long SUPERIMP_COMPLEX_BEST

See Also:

Constant Field Values

INFER3D_AUTO

public static final java.lang.String[] INFER3D_AUTO

SUPERIMPOSING

public static final boolean[] SUPERIMPOSING

Constructor Detail

SPUtils

public SPUtils()

Method Detail

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

Specified by:

run in interface ChRunnable

inferCoordinates1

public static void inferCoordinates1(Protein p,
                                     java.lang.String pdbID)

threadInferCoordinates

public static java.lang.Thread threadInferCoordinates(Protein[] pp,
                                                      java.lang.String[] pdbID,
                                                      BA chLog,
                                                      long options)

inferCoordinates_TS

public static void inferCoordinates_TS(Protein[] pp,
                                       java.lang.String[] pdbID,
                                       BA chLog0,
                                       long options)

infc_Blocking

public static boolean infc_Blocking(Protein[] pp,
                                    Protein[][] pp3d_array,
                                    BA log,
                                    long options)

alignerInstance

public static SequenceAligner alignerInstance()

threadAlignProteins

public static java.lang.Thread threadAlignProteins(SequenceAligner aligner,
                                                   java.util.List<Protein> vP,
                                                   boolean[] shouldStop,
                                                   long options)

alignProteins

public static SequenceAligner alignProteins(SequenceAligner aligner0,
                                            java.util.List<Protein> vP,
                                            boolean[] shouldStop,
                                            long options)

threadSuperimposeProteins

public static java.lang.Thread threadSuperimposeProteins(java.util.List<? extends Protein> vP,
                                                         boolean[] isInterrupted,
                                                         long options)

threadSuperimposeProteins

public static java.lang.Thread threadSuperimposeProteins(java.util.List<? extends Protein> vP,
                                                         boolean[] isInterrupted,
                                                         Protein[] pBest,
                                                         long options)

superimposeProteins

public static Protein superimposeProteins(java.util.List<? extends Protein> vP,
                                          boolean[] shouldStop,
                                          long options)

loopSuperimposeProteinsV

public static void loopSuperimposeProteinsV(UniqueList<? extends Protein> vP,
                                            boolean[] stop,
                                            boolean[] superimposing,
                                            long options)

threadLoopSuperimposeProteinsV

public static java.lang.Thread threadLoopSuperimposeProteinsV(UniqueList<? extends Protein> vP,
                                                              boolean[] stop,
                                                              boolean[] superimposing,
                                                              long options)

viewComparison

public static void viewComparison(Protein p0,
                                  Protein p1,
                                  java.lang.Object clazzOrInstance)

speciesName2Icon

public static java.lang.String speciesName2Icon(Protein p)

speciesName2Icon

public static java.lang.String speciesName2Icon(java.lang.String name)

setProteinIcon

public static void setProteinIcon(Protein[] pp,
                                  boolean overwrite,
                                  char type)

threadDownloadOriginalProteins

public static java.lang.Thread threadDownloadOriginalProteins(Protein[] pp,
                                                              long webOptions)

threadDownloadOriginalProteins

public static java.lang.Thread threadDownloadOriginalProteins(Protein[] pp,
                                                              java.lang.String key,
                                                              java.io.File[] files,
                                                              long webOptions)

downloadOriginalProteins

public static void downloadOriginalProteins(boolean newThread,
                                            Protein[] pp,
                                            long webOptions)

downloadOriginalProteins

public static void downloadOriginalProteins(boolean newThread,
                                            Protein[] pp,
                                            java.lang.String database,
                                            java.io.File[] files,
                                            long webOptions)

thread_fetchIdsAndDownloadOriginalProteins

public static java.lang.Thread thread_fetchIdsAndDownloadOriginalProteins(Protein[] pp)

fetchIdsAndDownloadOriginalProteins

public static void fetchIdsAndDownloadOriginalProteins(boolean newThread,
                                                       Protein[] pp)

ppWithAminos

public static Protein[] ppWithAminos(Protein[] pp0)

sortVisibleOrder

public static void sortVisibleOrder(Protein[] pp)

getComparator

public static java.util.Comparator getComparator(char type)

compare

public int compare(java.lang.Object o1,
                   java.lang.Object o2)

Specified by:

compare in interface java.util.Comparator

hasResidueSelection

public static boolean hasResidueSelection(Protein p,
                                          java.lang.String[] names)

setSeqs

public static void setSeqs(SequenceAligner aligner,
                           Protein[] pp)

leadingAndTrailingLowerCaseLettersInMSA

public static int[] leadingAndTrailingLowerCaseLettersInMSA(Protein[] pp)

setResidueSubsetFromColumnRange

public static void setResidueSubsetFromColumnRange(Protein p,
                                                   int from,
                                                   int to)

allFiles

public static java.util.Set allFiles()

newProteinColumnFromTo

public static Protein newProteinColumnFromTo(Protein p,
                                             int west,
                                             int east)

newProteinSubset

public static Protein newProteinSubset(Protein p,
                                       java.lang.String expr)

getProteinsWithNames

public static final Protein[] getProteinsWithNames(BA ba,
                                                   Protein[] pp)

getProteinWithName

public static Protein getProteinWithName(java.lang.String name,
                                         Protein[] pp0)

returns the 1st protein whose name equals to name.

getProteinWithNameAndFile

public static Protein getProteinWithNameAndFile(java.lang.String n,
                                                java.io.File file,
                                                java.lang.Object[] pp)

getMaxColumn

public static int getMaxColumn(Protein[] pp)

getProteinsOfObjects

public static Protein[] getProteinsOfObjects(java.lang.Object[] oo)

getParserOptions

public static long getParserOptions()

setParserOptions

public static void setParserOptions(long options)

getGappedSequences

public static byte[][] getGappedSequences(Protein[] pp,
                                          int colFrom,
                                          int colTo,
                                          char gap)

getProteinsSameRow

public static Protein[] getProteinsSameRow(Protein p)

parseProtein

public static boolean parseProtein(java.io.File proteinFile,
                                   BA text,
                                   long mode,
                                   Protein p)