charite.christo.strap
Class StrapAlign

java.lang.Object
  charite.christo.strap.StrapAlign

All Implemented Interfaces:

ChRunnable, ProcessEv, ProteinAlignment, java.awt.dnd.DropTargetListener, java.util.EventListener

public class StrapAlign
extends java.lang.Object
implements ProteinAlignment, ProcessEv, ChRunnable, java.awt.dnd.DropTargetListener

The root class of the alignment from which all information is accessible. For each STRAP session exactly one instance of this class exists.

• JAVADOC:StrapAlign#getProteins(): The proteins loaded in STRAP can be obtained with this method. JAVADOC:Protein is the object for proteins.
• JAVADOC:StrapAlign#getSelectedProteins(): This method returns only the selected proteins.

Field Summary

static java.lang.String	ACTION_ignoreSEQRES
static java.lang.String	ACTION_newPan
static java.lang.String	ACTION_openPlugin
static long	ANIM_SET_CURS_SCROLL_TO_VISIBLE
static int	BUT_hiddenP
static int	BUT_NEW_PANEL
static int	BUT_NEW_STRAP
static int	BUT_SAVE
static int	BUT_SELECT_BY_NAME
static int	BUT_STOP_ALL
static int	BUT_UPDATEUI
static int	BUT_ZIP
static java.lang.String	CMD_ALL_MENUS
static java.lang.String	CMD_ALL_POPUP
static java.lang.String	CMD_DEL_ICONS
static java.lang.String	CMD_PDB_ICONS
static java.lang.String	CMD_SPECIES_ICONS
static java.lang.String	CMD_TABLE_ICONS
static java.lang.String	KOPT_DELETE_DISABLED
static java.lang.String	LABEL_ALL_OR_SELECTED_P
static int	OPTION_EVENT_PROTEINS_ADDED
static int	OPTION_PROCESS_LOADED_PROTS
static int	OPTION_SHOW_ORPHAN_HETEROS_IN_3D
static long	SORT_ALL
static long	SORT_PREFORDER
static long	SORT_WEB
static int	TOG_HIDE_GAPS
static int	TOG_HIGHLIGHT_IDENTICAL_SEQUENCES
static int	TOG_IN_NEW_FRAME
static int	TOG_MAXIMIZE_DIALOGS
static int	TOG_MULTI_MBARS
static int	TOG_OUTLINE_HSB
static int	TOG_SKIP_IDENTICAL_SEQUENCE
static int	TOG_TUTORIAL_SIMUL_MENUS
static java.lang.String	VIEW_SB
UniqueList<Protein>	vProteins
UniqueList<Protein>	vProteinsInAlignment
UniqueList<Protein>	vProteinsNotInAlignment
static int	WEB_OPTION_DOWNLOAD_ORIGINAL_PROTEINS
static int	WEB_OPTION_RENAME_SWISS
static int	WEB_OPTION_SCROLL
static int	WEB_OPTION_SEPARATE_PDB_CHAINS
static int	WEB_OPTION_SKIP_PDB_IF_ALREADY_LOADED
static int	WEB_OPTION_splitChains
static int	WEB_OPTION_USE_UNIPROT_SOAP

Fields inherited from interface charite.christo.protein.ProteinAlignment

DRAG_ALL_CHAINS, DRAG_MSA, DRAG_ORIG, RUN_ADD_LISTENERS, RUN_GET_DRAG_OPTIONS, RUN_NEW_DROP_TARGET

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

StrapAlign(boolean isWebViewer)

Method Summary

static void	addDialog(javax.swing.JComponent comp)
static javax.swing.JComponent	addDialog(java.lang.Object classOrNameOfClass, boolean multiInstances) Make an instance of a dialog and add it to the dialog pane.
static javax.swing.JComponent	addDialogSetClass(java.lang.Object dialog, java.lang.Object selectedClass)
void	addListener(StrapListener sl)
static void	addListeners(java.lang.Object o)
void	addProteins(int row, Protein[] pp) Load proteins
static StrapView	alignmentPanel()
static ChButton	butSetDefault(java.lang.Class interf, java.lang.String clazz)
static ChButton	button(int i)
static ChButton	button(java.lang.String s)
static ChCombo	classChoice(java.lang.Class anInterface)
int	countRows() How many alignment rows ?
static void	dialogSetProteins(long filter, Protein[] pp0, java.awt.Component d)
static void	dialogSetProteins(Protein[] pp, java.awt.Component d)
void	dispatch(StrapEvent ev)
<T> T	dndTarget(java.lang.Class<T> c)
static Protein[]	downloadProteinID(java.lang.String entry, java.lang.Object[] targets, java.util.List<Protein> vAll, long options)
static void	downloadProteins(java.lang.String[] tokens, java.lang.Object[] targets, java.util.List<Protein> vAll, java.util.Collection<java.lang.String> notLoaded, long options)
static ChButton	drag_buttonOptions()
void	dragEnter(java.awt.dnd.DropTargetDragEvent ev)
void	dragExit(java.awt.dnd.DropTargetEvent ev)
void	dragOver(java.awt.dnd.DropTargetDragEvent ev)
static void	drawMessage(java.lang.String s)
static void	drawProgress(int percent)
void	drop(java.awt.dnd.DropTargetDropEvent event)
void	dropActionChanged(java.awt.dnd.DropTargetDragEvent ev)
static void	editAnnotation(ResidueAnnotation s) Displays a named selection of residues so that the user can edit it
static void	errorMsg(java.lang.String s)
boolean	existsTablePanel(java.lang.String className)
static Protein3d	findBackbone3D(boolean exactly, Protein... pp)
int	findRow(Protein p) Get index of the row of a Protein returns -1 in case the protein object is not found
Gaps2Columns	gap2col()
static StrapView[]	getAlignmentPanels()
static int	getCursorColumn()
static Protein	getCursorProtein() get the protein where the cursor is located in.
static int	getCursorRow()
static java.lang.String	getDefaultC(java.lang.Class c)
static ChTabPane	getDialogPanel()
static ChFrame	getFrame()
static int	getIndexOfAminoAcidAtCursorZ(Protein p)
static StrapAlign	getInstance()
Protein	getProtein(int i)
static ProteinParser[]	getProteinParsers() Get all available protein parsers.
Protein[]	getProteins() get all loaded Proteins
static java.lang.Object[]	getProteinsAndAnnotationsWithRegex(java.lang.CharSequence list, Protein[] pp, char alsoSelections) 'A' means create ResidueAnnotation if slash in expression
Protein[]	getProteinsInAlignment() Get all proteins that are displayed in the alignment panel
Protein[]	getProteinsNotInAlignment()
static Protein[]	getProteinsWithRegex(java.lang.CharSequence list, Protein[] pp)
static java.lang.Object[]	getSelectedObjects() An array of all objects that are selected in the object tree
static long	getSelectedObjectsMC(char type)
static UniqueList<java.lang.Object>	getSelectedObjectsV()
Protein[]	getSelectedProteins()
static Protein[]	getSelectedProteinsInVisibleOrder()
static java.awt.Color[]	getShadingColors()
ChTableLayout	getTablePanel(java.lang.String className)
StrapTree	getTree()
static Protein[]	getVisibleProteins() Get the proteins that are displayed and not hidden in the focused view.
static void	highlightProteins(java.lang.String options, javax.swing.JComponent jc)
void	inferOrder(Protein[] ppSorted)
void	inferOrderOfProteins(java.lang.Object ppSorted, long options)
static boolean	isBusy()
static boolean	isOtherMenuBar()
static boolean	isShadingSecStru()
static boolean	isViewer()
static EvAdapter	li()
Protein[][]	loadTheProteinsInList(java.lang.CharSequence listOfProteins, long options) Loads proteins from the project directory into STRAP.
static BA	manPage(char mode)
static java.lang.Object[]	menu(java.lang.Class interf)
static java.lang.String	name2file(java.lang.String name)
static Protein3d	new3dBackbone(long options, Protein[] pp)
static Protein3d	new3dBackbone(Protein[] pp)
void	newAlignmentPanel(boolean evenIfOneIsOpened)
static void	newDropTarget(java.awt.Component c, boolean recursive)
javax.swing.JComponent	newProteinLabel(Protein p)
void	processEv(java.awt.AWTEvent ev)
void	processLoadedProteins(Protein[] pp, java.lang.Object[] targets, long options)
static void	progressBarTurn(int i)
static void	readAttributes(java.lang.String what, Protein p, java.io.File dir)
static Protein	readProtein(StrapAlign align, java.lang.String s, BA ba)
void	removeDialog(javax.swing.JComponent comp)
void	removeListener(StrapListener sl) Removes the object from the list of listeners.
void	removeProteins(boolean delete, Protein... pp) Closes proteins.
static void	repaintCursor(boolean add, ChRunnable r)
static void	replaceClassByButton(java.lang.Object[] oo, ChRunnable hook)
static void	rmListener(java.lang.Object sl)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
void	setChanged()
static void	setCursor(Protein p, int iAa) moves the cursor in the alignment panel that has the focus
static boolean	setDefaultC(java.lang.Class c, java.lang.String cn0)
static boolean	setDefaultClassByPara(java.lang.String a)
boolean	setIsInAlignment(boolean b, int eventDelay, Protein... pp)
static void	setMenuBar(javax.swing.JComponent[] mm0, int fg, int bg)
static void	setNotSaved()
static void	setNumOfProteins(javax.swing.AbstractButton b)
static void	setToolpane(javax.swing.JComponent c0)
static void	showContextMenu(char menuType, java.lang.Object[] ooMouse)
static ChJList	showInJList(long options, java.lang.Object id, java.lang.Object[] oo, java.lang.Object north, java.lang.Object south)
static void	showPreferencesDialog()
static void	showProgress(java.lang.String s)
static void	startAnimatePositionZ(long options, Protein p, int iA)
static java.lang.Thread	thread_addDialog(javax.swing.JComponent c) Adds a dialog to the dialog panel or brings it to front.
static java.lang.Thread	thread_downloadProteins(java.lang.String[] entry, java.lang.Object[] targets, java.util.List<Protein> vAll, java.util.Collection<java.lang.String> notLoaded, long options)
static java.lang.Thread	thread_loadTheProteinsInList(java.lang.CharSequence listOfProteins, long options)
static java.lang.Thread	thread_new3dBackbone(long options, Protein[] pp, Protein3d[] ret)
java.lang.Thread	thread_processLoadedProteins(Protein[] pp, java.lang.Object[] targets, long options)
java.lang.Thread	thread_setIsInAlignment(boolean b, int eventDelay, Protein[] pp, java.lang.Object[] ret)
static java.lang.Thread	threadWebAlignment(java.lang.CharSequence webAlignment, java.util.Collection<Protein> vLoaded, java.lang.Object[] targets, long option)
static void	webAlignment(java.lang.String webAlignment, java.util.Collection<Protein> vLoadedProteins, java.lang.Object[] targets0, long option)
static long	whenMovedCursor()

Methods inherited from class java.lang.Object

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

Field Detail

VIEW_SB

public static final java.lang.String VIEW_SB

See Also:

Constant Field Values

ACTION_newPan

public static final java.lang.String ACTION_newPan

See Also:

Constant Field Values

ACTION_ignoreSEQRES

public static final java.lang.String ACTION_ignoreSEQRES

See Also:

Constant Field Values

ACTION_openPlugin

public static final java.lang.String ACTION_openPlugin

See Also:

Constant Field Values

CMD_DEL_ICONS

public static final java.lang.String CMD_DEL_ICONS

See Also:

Constant Field Values

CMD_PDB_ICONS

public static final java.lang.String CMD_PDB_ICONS

See Also:

Constant Field Values

CMD_SPECIES_ICONS

public static final java.lang.String CMD_SPECIES_ICONS

See Also:

Constant Field Values

CMD_TABLE_ICONS

public static final java.lang.String CMD_TABLE_ICONS

See Also:

Constant Field Values

CMD_ALL_MENUS

public static final java.lang.String CMD_ALL_MENUS

See Also:

Constant Field Values

CMD_ALL_POPUP

public static final java.lang.String CMD_ALL_POPUP

See Also:

Constant Field Values

KOPT_DELETE_DISABLED

public static final java.lang.String KOPT_DELETE_DISABLED

See Also:

Constant Field Values

vProteinsInAlignment

public final UniqueList<Protein> vProteinsInAlignment

vProteinsNotInAlignment

public final UniqueList<Protein> vProteinsNotInAlignment

vProteins

public final UniqueList<Protein> vProteins

TOG_MAXIMIZE_DIALOGS

public static final int TOG_MAXIMIZE_DIALOGS

See Also:

Constant Field Values

TOG_HIGHLIGHT_IDENTICAL_SEQUENCES

public static final int TOG_HIGHLIGHT_IDENTICAL_SEQUENCES

See Also:

Constant Field Values

TOG_SKIP_IDENTICAL_SEQUENCE

public static final int TOG_SKIP_IDENTICAL_SEQUENCE

See Also:

Constant Field Values

TOG_HIDE_GAPS

public static final int TOG_HIDE_GAPS

See Also:

Constant Field Values

TOG_IN_NEW_FRAME

public static final int TOG_IN_NEW_FRAME

See Also:

Constant Field Values

TOG_OUTLINE_HSB

public static final int TOG_OUTLINE_HSB

See Also:

Constant Field Values

TOG_MULTI_MBARS

public static final int TOG_MULTI_MBARS

See Also:

Constant Field Values

TOG_TUTORIAL_SIMUL_MENUS

public static final int TOG_TUTORIAL_SIMUL_MENUS

See Also:

Constant Field Values

BUT_STOP_ALL

public static final int BUT_STOP_ALL

See Also:

Constant Field Values

BUT_SAVE

public static final int BUT_SAVE

See Also:

Constant Field Values

BUT_SELECT_BY_NAME

public static final int BUT_SELECT_BY_NAME

See Also:

Constant Field Values

BUT_UPDATEUI

public static final int BUT_UPDATEUI

See Also:

Constant Field Values

BUT_NEW_PANEL

public static final int BUT_NEW_PANEL

See Also:

Constant Field Values

BUT_NEW_STRAP

public static final int BUT_NEW_STRAP

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Constant Field Values

BUT_hiddenP

public static final int BUT_hiddenP

See Also:

Constant Field Values

BUT_ZIP

public static final int BUT_ZIP

See Also:

Constant Field Values

SORT_WEB

public static final long SORT_WEB

See Also:

Constant Field Values

SORT_ALL

public static final long SORT_ALL

See Also:

Constant Field Values

SORT_PREFORDER

public static final long SORT_PREFORDER

See Also:

Constant Field Values

ANIM_SET_CURS_SCROLL_TO_VISIBLE

public static final long ANIM_SET_CURS_SCROLL_TO_VISIBLE

See Also:

Constant Field Values

WEB_OPTION_SEPARATE_PDB_CHAINS

public static final int WEB_OPTION_SEPARATE_PDB_CHAINS

See Also:

Constant Field Values

WEB_OPTION_SKIP_PDB_IF_ALREADY_LOADED

public static final int WEB_OPTION_SKIP_PDB_IF_ALREADY_LOADED

See Also:

Constant Field Values

WEB_OPTION_RENAME_SWISS

public static final int WEB_OPTION_RENAME_SWISS

See Also:

Constant Field Values

WEB_OPTION_USE_UNIPROT_SOAP

public static final int WEB_OPTION_USE_UNIPROT_SOAP

See Also:

Constant Field Values

WEB_OPTION_DOWNLOAD_ORIGINAL_PROTEINS

public static final int WEB_OPTION_DOWNLOAD_ORIGINAL_PROTEINS

See Also:

Constant Field Values

WEB_OPTION_SCROLL

public static final int WEB_OPTION_SCROLL

See Also:

Constant Field Values

WEB_OPTION_splitChains

public static final int WEB_OPTION_splitChains

See Also:

Constant Field Values

OPTION_PROCESS_LOADED_PROTS

public static final int OPTION_PROCESS_LOADED_PROTS

See Also:

Constant Field Values

OPTION_EVENT_PROTEINS_ADDED

public static final int OPTION_EVENT_PROTEINS_ADDED

See Also:

Constant Field Values

OPTION_SHOW_ORPHAN_HETEROS_IN_3D

public static final int OPTION_SHOW_ORPHAN_HETEROS_IN_3D

See Also:

Constant Field Values

LABEL_ALL_OR_SELECTED_P

public static final java.lang.String LABEL_ALL_OR_SELECTED_P

See Also:

Constant Field Values

Constructor Detail

StrapAlign

public StrapAlign(boolean isWebViewer)

Method Detail

li

public static EvAdapter li()

getSelectedObjectsV

public static final UniqueList<java.lang.Object> getSelectedObjectsV()

getSelectedObjectsMC

public static final long getSelectedObjectsMC(char type)

button

public static ChButton button(java.lang.String s)

button

public static ChButton button(int i)

butSetDefault

public static ChButton butSetDefault(java.lang.Class interf,
                                     java.lang.String clazz)

menu

public static java.lang.Object[] menu(java.lang.Class interf)

isViewer

public static boolean isViewer()

getInstance

public static StrapAlign getInstance()

gap2col

public Gaps2Columns gap2col()

setChanged

public void setChanged()

addProteins

public void addProteins(int row,
                        Protein[] pp)

Load proteins

removeProteins

public void removeProteins(boolean delete,
                           Protein... pp)

Closes proteins. @param delete: Also delete on HD

thread_setIsInAlignment

public java.lang.Thread thread_setIsInAlignment(boolean b,
                                                int eventDelay,
                                                Protein[] pp,
                                                java.lang.Object[] ret)

setIsInAlignment

public boolean setIsInAlignment(boolean b,
                                int eventDelay,
                                Protein... pp)

getProteinsInAlignment

public Protein[] getProteinsInAlignment()

Get all proteins that are displayed in the alignment panel

getProteinsNotInAlignment

public Protein[] getProteinsNotInAlignment()

getProtein

public Protein getProtein(int i)

Specified by:

getProtein in interface ProteinAlignment

getProteins

public Protein[] getProteins()

get all loaded Proteins

getVisibleProteins

public static Protein[] getVisibleProteins()

Get the proteins that are displayed and not hidden in the focused view. Note that proteins can be hidden in a view.

inferOrder

public void inferOrder(Protein[] ppSorted)

inferOrderOfProteins

public void inferOrderOfProteins(java.lang.Object ppSorted,
                                 long options)

repaintCursor

public static void repaintCursor(boolean add,
                                 ChRunnable r)

startAnimatePositionZ

public static void startAnimatePositionZ(long options,
                                         Protein p,
                                         int iA)

countRows

public int countRows()

How many alignment rows ?

Specified by:

countRows in interface ProteinAlignment

findRow

public final int findRow(Protein p)

Get index of the row of a Protein returns -1 in case the protein object is not found

Specified by:

findRow in interface ProteinAlignment

isBusy

public static boolean isBusy()

whenMovedCursor

public static long whenMovedCursor()

getIndexOfAminoAcidAtCursorZ

public static int getIndexOfAminoAcidAtCursorZ(Protein p)

getCursorProtein

public static Protein getCursorProtein()

get the protein where the cursor is located in.

Returns:

the Protein where the cursor is currently on or null See JAVADOC:StrapAlign#getCursorAminoAcid()

newProteinLabel

public javax.swing.JComponent newProteinLabel(Protein p)

Specified by:

newProteinLabel in interface ProteinAlignment

getCursorColumn

public static int getCursorColumn()

getCursorRow

public static int getCursorRow()

setCursor

public static void setCursor(Protein p,
                             int iAa)

moves the cursor in the alignment panel that has the focus

alignmentPanel

public static StrapView alignmentPanel()

getShadingColors

public static java.awt.Color[] getShadingColors()

isShadingSecStru

public static boolean isShadingSecStru()

getAlignmentPanels

public static StrapView[] getAlignmentPanels()

newAlignmentPanel

public void newAlignmentPanel(boolean evenIfOneIsOpened)

showContextMenu

public static void showContextMenu(char menuType,
                                   java.lang.Object[] ooMouse)

replaceClassByButton

public static void replaceClassByButton(java.lang.Object[] oo,
                                        ChRunnable hook)

manPage

public static BA manPage(char mode)

getFrame

public static ChFrame getFrame()

isOtherMenuBar

public static boolean isOtherMenuBar()

setMenuBar

public static void setMenuBar(javax.swing.JComponent[] mm0,
                              int fg,
                              int bg)

getTree

public StrapTree getTree()

addListeners

public static void addListeners(java.lang.Object o)

setToolpane

public static void setToolpane(javax.swing.JComponent c0)

showPreferencesDialog

public static void showPreferencesDialog()

threadWebAlignment

public static java.lang.Thread threadWebAlignment(java.lang.CharSequence webAlignment,
                                                  java.util.Collection<Protein> vLoaded,
                                                  java.lang.Object[] targets,
                                                  long option)

webAlignment

public static void webAlignment(java.lang.String webAlignment,
                                java.util.Collection<Protein> vLoadedProteins,
                                java.lang.Object[] targets0,
                                long option)

thread_downloadProteins

public static java.lang.Thread thread_downloadProteins(java.lang.String[] entry,
                                                       java.lang.Object[] targets,
                                                       java.util.List<Protein> vAll,
                                                       java.util.Collection<java.lang.String> notLoaded,
                                                       long options)

downloadProteins

public static void downloadProteins(java.lang.String[] tokens,
                                    java.lang.Object[] targets,
                                    java.util.List<Protein> vAll,
                                    java.util.Collection<java.lang.String> notLoaded,
                                    long options)

downloadProteinID

public static Protein[] downloadProteinID(java.lang.String entry,
                                          java.lang.Object[] targets,
                                          java.util.List<Protein> vAll,
                                          long options)

loadTheProteinsInList

public Protein[][] loadTheProteinsInList(java.lang.CharSequence listOfProteins,
                                         long options)

Loads proteins from the project directory into STRAP.

Parameters:

listOfProteins - A string containing the names of proteins to be loaded separated by space, \t or \n. Proteins can be groupped useing curly brackets.

Returns:

An array of all loaded proteins

thread_loadTheProteinsInList

public static java.lang.Thread thread_loadTheProteinsInList(java.lang.CharSequence listOfProteins,
                                                            long options)

thread_processLoadedProteins

public final java.lang.Thread thread_processLoadedProteins(Protein[] pp,
                                                           java.lang.Object[] targets,
                                                           long options)

processLoadedProteins

public void processLoadedProteins(Protein[] pp,
                                  java.lang.Object[] targets,
                                  long options)

setNotSaved

public static void setNotSaved()

run

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

Specified by:

run in interface ChRunnable

thread_new3dBackbone

public static java.lang.Thread thread_new3dBackbone(long options,
                                                    Protein[] pp,
                                                    Protein3d[] ret)

new3dBackbone

public static Protein3d new3dBackbone(Protein[] pp)

new3dBackbone

public static Protein3d new3dBackbone(long options,
                                      Protein[] pp)

findBackbone3D

public static Protein3d findBackbone3D(boolean exactly,
                                       Protein... pp)

existsTablePanel

public boolean existsTablePanel(java.lang.String className)

getTablePanel

public ChTableLayout getTablePanel(java.lang.String className)

addListener

public void addListener(StrapListener sl)

Specified by:

addListener in interface ProteinAlignment

removeListener

public final void removeListener(StrapListener sl)

Removes the object from the list of listeners. If the object is not in the list nothing happens.

Specified by:

removeListener in interface ProteinAlignment

Parameters:

sl - Object which might implement StrapListener

rmListener

public static void rmListener(java.lang.Object sl)

highlightProteins

public static void highlightProteins(java.lang.String options,
                                     javax.swing.JComponent jc)

dispatch

public void dispatch(StrapEvent ev)

Specified by:

dispatch in interface ProteinAlignment

thread_addDialog

public static java.lang.Thread thread_addDialog(javax.swing.JComponent c)

Adds a dialog to the dialog panel or brings it to front.

• 1st case: o is an instance of JComponent
• 2nd case: o instanceof HasPanel

See JAVADOC:TabItemTipIcon

addDialog

public static void addDialog(javax.swing.JComponent comp)

removeDialog

public void removeDialog(javax.swing.JComponent comp)

addDialogSetClass

public static javax.swing.JComponent addDialogSetClass(java.lang.Object dialog,
                                                       java.lang.Object selectedClass)

addDialog

public static javax.swing.JComponent addDialog(java.lang.Object classOrNameOfClass,
                                               boolean multiInstances)

Make an instance of a dialog and add it to the dialog pane. The constructor either has no parameter or StrapAlign.this as parameter.

dialogSetProteins

public static void dialogSetProteins(Protein[] pp,
                                     java.awt.Component d)

dialogSetProteins

public static void dialogSetProteins(long filter,
                                     Protein[] pp0,
                                     java.awt.Component d)

getDialogPanel

public static ChTabPane getDialogPanel()

classChoice

public static ChCombo classChoice(java.lang.Class anInterface)

processEv

public void processEv(java.awt.AWTEvent ev)

Specified by:

processEv in interface ProcessEv

See Also:

EvAdapter

getSelectedObjects

public static java.lang.Object[] getSelectedObjects()

An array of all objects that are selected in the object tree

getSelectedProteinsInVisibleOrder

public static Protein[] getSelectedProteinsInVisibleOrder()

getSelectedProteins

public Protein[] getSelectedProteins()

setNumOfProteins

public static void setNumOfProteins(javax.swing.AbstractButton b)

newDropTarget

public static void newDropTarget(java.awt.Component c,
                                 boolean recursive)

dndTarget

public <T> T dndTarget(java.lang.Class<T> c)

dropActionChanged

public void dropActionChanged(java.awt.dnd.DropTargetDragEvent ev)

Specified by:

dropActionChanged in interface java.awt.dnd.DropTargetListener

dragEnter

public void dragEnter(java.awt.dnd.DropTargetDragEvent ev)

Specified by:

dragEnter in interface java.awt.dnd.DropTargetListener

dragOver

public void dragOver(java.awt.dnd.DropTargetDragEvent ev)

Specified by:

dragOver in interface java.awt.dnd.DropTargetListener

drag_buttonOptions

public static ChButton drag_buttonOptions()

dragExit

public void dragExit(java.awt.dnd.DropTargetEvent ev)

Specified by:

dragExit in interface java.awt.dnd.DropTargetListener

drop

public void drop(java.awt.dnd.DropTargetDropEvent event)

Specified by:

drop in interface java.awt.dnd.DropTargetListener

name2file

public static java.lang.String name2file(java.lang.String name)

readProtein

public static Protein readProtein(StrapAlign align,
                                  java.lang.String s,
                                  BA ba)

readAttributes

public static void readAttributes(java.lang.String what,
                                  Protein p,
                                  java.io.File dir)

getProteinParsers

public static ProteinParser[] getProteinParsers()

Get all available protein parsers.

editAnnotation

public static void editAnnotation(ResidueAnnotation s)

Displays a named selection of residues so that the user can edit it

showInJList

public static ChJList showInJList(long options,
                                  java.lang.Object id,
                                  java.lang.Object[] oo,
                                  java.lang.Object north,
                                  java.lang.Object south)

getDefaultC

public static java.lang.String getDefaultC(java.lang.Class c)

setDefaultC

public static boolean setDefaultC(java.lang.Class c,
                                  java.lang.String cn0)

setDefaultClassByPara

public static boolean setDefaultClassByPara(java.lang.String a)

getProteinsWithRegex

public static final Protein[] getProteinsWithRegex(java.lang.CharSequence list,
                                                   Protein[] pp)

getProteinsAndAnnotationsWithRegex

public static final java.lang.Object[] getProteinsAndAnnotationsWithRegex(java.lang.CharSequence list,
                                                                          Protein[] pp,
                                                                          char alsoSelections)

'A' means create ResidueAnnotation if slash in expression

showProgress

public static void showProgress(java.lang.String s)

drawMessage

public static void drawMessage(java.lang.String s)

errorMsg

public static void errorMsg(java.lang.String s)

drawProgress

public static void drawProgress(int percent)

progressBarTurn

public static void progressBarTurn(int i)