charite.christo.strap
Class ResSelUtils

java.lang.Object
  charite.christo.strap.ResSelUtils

All Implemented Interfaces:

ChRunnable, java.util.Comparator

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

Field Summary

static long	CHOOSE_CONTEXT
static long	CHOOSE_EDIT
static long	CHOOSE_SINGLE
static int	COPY_ADD_TO_PROTEIN
static int	COPY_ASK_NAME
static int	COPY_REPORT
static int	COPY_SINGLE
static int	NARROW_IS_ALIGNMENT_MATCH

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

Method Summary

static void	chooseResSels(long options, ResidueSelection[] ss, java.awt.AWTEvent ev, java.lang.String msg, java.lang.Runnable run)
int	compare(java.lang.Object o1, java.lang.Object o2)
static ResidueAnnotation[]	convertToResidueAnnotation(boolean edit, ResidueSelection... ss)
static int	countType(char type, ResidueSelection[] ss)
static void	cropSequences(int opt, ResidueSelection[] aa)
static boolean	equalAminoPositions(ResidueSelection s1, ResidueSelection s2)
static ResidueSelection[]	filter(int type, ResidueSelection[] ss0, Protein[] pp)
static int	firstAmino(ResidueSelection s)
static int	getResidueindexOfAnnotation(Protein p, java.lang.String annoName)
static boolean[]	getSelectedAminoacidsDisplayed(ResidueSelection s)
static boolean	isSelectedAAZ(int iA, ResidueSelection s)
static VisibleIn123	isShownIn(ResidueSelection s, int where)
static int	lastAmino(ResidueSelection s)
static BA	listFromTo(ResidueSelection[] ss, int minLen, BA sb)
static boolean[]	mapPositionsZ(boolean[] bbSrc, int offsetSrc, Protein src, Protein dest, boolean[] buffer)
static boolean[]	mapPositionsZ(ResidueSelection[] ss, Protein pDest)
static void	noHide(java.lang.Object noHide)
static void	openDialogRealign(ResidueSelection[] ss)
static java.lang.CharSequence	replaceVariable(java.lang.CharSequence s0, java.lang.Object o0)
static java.lang.CharSequence	replaceVariableBB(java.lang.CharSequence s0, boolean[] bb, int offset, java.lang.String name, Protein p, Protein[] allPP)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
static int	selAminoOffsetZ(ResidueSelection s)
static BA	selectedAsString(ResidueSelection sel, BA sb)
static SelectorOfNucleotides[]	selOfNuclAt(Protein p, int iN)
static void	setHide(java.lang.Object[] hide)
static void	sortResidueSelectionsByVisibility(ResidueSelection[] ss)
static int	style(java.lang.Object o)
static java.lang.String[]	styles()
static boolean	styleUL(java.lang.Object o)
static void	texshade(java.lang.CharSequence txt, Protein p)
static java.lang.String	texshadeRange(boolean[] bb, int offset, Protein p)
static boolean[]	toAlignmentColumns(ResidueSelection s)
static java.lang.String	ttSelect()
static char	type(java.lang.Object o)
static void	useResNum(boolean b)
static java.lang.String	value(java.lang.String key, ResidueSelection s)
static java.lang.String[]	variables(int n)
static boolean	visible(int where, java.lang.Object o)

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

COPY_ADD_TO_PROTEIN

public static final int COPY_ADD_TO_PROTEIN

See Also:

Constant Field Values

COPY_SINGLE

public static final int COPY_SINGLE

See Also:

Constant Field Values

COPY_ASK_NAME

public static final int COPY_ASK_NAME

See Also:

Constant Field Values

COPY_REPORT

public static final int COPY_REPORT

See Also:

Constant Field Values

CHOOSE_SINGLE

public static final long CHOOSE_SINGLE

See Also:

Constant Field Values

CHOOSE_CONTEXT

public static final long CHOOSE_CONTEXT

See Also:

Constant Field Values

CHOOSE_EDIT

public static final long CHOOSE_EDIT

See Also:

Constant Field Values

NARROW_IS_ALIGNMENT_MATCH

public static int NARROW_IS_ALIGNMENT_MATCH

Method Detail

sortResidueSelectionsByVisibility

public static void sortResidueSelectionsByVisibility(ResidueSelection[] ss)

compare

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

Specified by:

compare in interface java.util.Comparator

equalAminoPositions

public static boolean equalAminoPositions(ResidueSelection s1,
                                          ResidueSelection s2)

convertToResidueAnnotation

public static ResidueAnnotation[] convertToResidueAnnotation(boolean edit,
                                                             ResidueSelection... ss)

selOfNuclAt

public static SelectorOfNucleotides[] selOfNuclAt(Protein p,
                                                  int iN)

selectedAsString

public static BA selectedAsString(ResidueSelection sel,
                                  BA sb)

getSelectedAminoacidsDisplayed

public static boolean[] getSelectedAminoacidsDisplayed(ResidueSelection s)

getResidueindexOfAnnotation

public static int getResidueindexOfAnnotation(Protein p,
                                              java.lang.String annoName)

isShownIn

public static VisibleIn123 isShownIn(ResidueSelection s,
                                     int where)

style

public static int style(java.lang.Object o)

styleUL

public static boolean styleUL(java.lang.Object o)

mapPositionsZ

public static boolean[] mapPositionsZ(ResidueSelection[] ss,
                                      Protein pDest)

mapPositionsZ

public static boolean[] mapPositionsZ(boolean[] bbSrc,
                                      int offsetSrc,
                                      Protein src,
                                      Protein dest,
                                      boolean[] buffer)

toAlignmentColumns

public static boolean[] toAlignmentColumns(ResidueSelection s)

texshade

public static void texshade(java.lang.CharSequence txt,
                            Protein p)

filter

public static ResidueSelection[] filter(int type,
                                        ResidueSelection[] ss0,
                                        Protein[] pp)

type

public static char type(java.lang.Object o)

countType

public static int countType(char type,
                            ResidueSelection[] ss)

setHide

public static void setHide(java.lang.Object[] hide)

noHide

public static void noHide(java.lang.Object noHide)

visible

public static boolean visible(int where,
                              java.lang.Object o)

openDialogRealign

public static void openDialogRealign(ResidueSelection[] ss)

listFromTo

public static BA listFromTo(ResidueSelection[] ss,
                            int minLen,
                            BA sb)

firstAmino

public static int firstAmino(ResidueSelection s)

lastAmino

public static int lastAmino(ResidueSelection s)

chooseResSels

public static void chooseResSels(long options,
                                 ResidueSelection[] ss,
                                 java.awt.AWTEvent ev,
                                 java.lang.String msg,
                                 java.lang.Runnable run)

isSelectedAAZ

public static boolean isSelectedAAZ(int iA,
                                    ResidueSelection s)

selAminoOffsetZ

public static int selAminoOffsetZ(ResidueSelection s)

run

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

Specified by:

run in interface ChRunnable

variables

public static java.lang.String[] variables(int n)

replaceVariable

public static java.lang.CharSequence replaceVariable(java.lang.CharSequence s0,
                                                     java.lang.Object o0)

replaceVariableBB

public static java.lang.CharSequence replaceVariableBB(java.lang.CharSequence s0,
                                                       boolean[] bb,
                                                       int offset,
                                                       java.lang.String name,
                                                       Protein p,
                                                       Protein[] allPP)

texshadeRange

public static java.lang.String texshadeRange(boolean[] bb,
                                             int offset,
                                             Protein p)

useResNum

public static void useResNum(boolean b)

cropSequences

public static void cropSequences(int opt,
                                 ResidueSelection[] aa)

ttSelect

public static java.lang.String ttSelect()

styles

public static java.lang.String[] styles()

value

public static java.lang.String value(java.lang.String key,
                                     ResidueSelection s)