IMPACT_S

Class GUIDialogs

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Frame

javax.swing.JFrame

IMPACT_S.GUIDialogs

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class GUIDialogs
extends javax.swing.JFrame

Implementation of several dialog messages.

Author:

Emanuel Maldonado

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JFrame

javax.swing.JFrame.AccessibleJFrame

Nested classes/interfaces inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
static int	QUESTION_ASK_CHOICE QUESTION_ASK_CHOICE: "Please select the file format:" "Choosing cancel, will not allow file selection."
static int	QUESTION_ASK_SAVE QUESTION_ASK_SAVE: "Choose file format to save in:"
static int	QUESTION_CHOICE QUESTION_CHOICE: "If the extension doesn't match the file format, please choose. Otherwise, choosing Cancel will try to get it through its extension."

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
GUIDialogs() General case.
GUIDialogs(java.awt.Component parent) Specific case. Parent component only in dialogs UTIL_BFF, UTIL_FEF and UTIL_FMF, used in initialization process. In other dialogs works like in general case constructor.

Method Summary

Modifier and Type	Method and Description
void	showFFC_DSLF(java.lang.String formattxt, java.lang.String seqdiff) FileFormatConverter class. DSLF : Error_Message Different Sequence Lengths Found.
void	showFFC_FBF(java.lang.String formattxt) FileFormatConverter class. FBF : Error_Message File Bad Format.
void	showFFC_FNC() FileFormatConverter class. FNC : Error_Message Format Not Chosen...
void	showFFC_RSAOB(java.lang.String formattxt, int seqcount, java.lang.String aiobex) FileFormatConverter class. RSAOB : Error_Message Reading Sequence Array Out Of Bounds
void	showFFC_VMPF() FileFormatConverter class. VMPF : Error_Message Values Missing in Phylip File first line.
void	showGUI_CNSF(java.lang.String fileNotsaved, java.lang.String title, java.lang.String addtext) GUI class. CNSF : Error_Message Could Not Save File.
void	showGUI_CO() GUI class. CO : Warning_Message Codeml about Options.
void	showGUI_CONC() GUI class. CONC : Error_Message Codeml Options Not Chosen.
int	showGUI_CV(java.lang.String question, java.lang.String title) GUI class. CV : Question_Message for Choice Value.
void	showGUI_EF(java.lang.String title, java.lang.String addText) GUI class. EF : Warning_Message Empty Fields.
int	showGUI_FAEM(java.lang.String title) GUI class. FAEM : Question_Message File Already Exists Make new?
void	showGUI_FBF(java.lang.String filename) GUI class. FBF : Error_Message File Bad Format.
void	showGUI_FNAN(java.lang.String title) GUI class. FNAN : Error_Message for Found Not A Number.
void	showGUI_FNE(java.lang.String title) GUI class. FNE : Error_Message for File does Not Exist.
void	showGUI_FNE(java.lang.String filename, java.lang.String title) GUI class. FNE : Error_Message for File does Not Exist.
void	showGUI_FNO(java.lang.String title) GUI class. FNO : Error_Message File Not Opened.
void	showGUI_FVR(java.lang.String title, java.lang.String infringement) GUI class. FVR : Error_Message Fields Violating Rules.
void	showGUI_GEM(java.lang.String title, java.lang.String addText) GUI class. GEM : Information_Message Generic Error Message.
void	showGUI_GIM(java.lang.String title, java.lang.String addText) GUI class. GIM : Information_Message Generic Information Message.
int	showGUI_GWM(java.lang.String title, java.lang.String reason) GUI class. GWM : Warning_Message Generic Warning Message.
void	showGUI_IFPSV(java.lang.String filename, java.lang.String program) GUI class. IFPSV : Error_Message Incorrect File for Program Stat Values.
java.lang.String	showGUI_IV(java.lang.String question, java.lang.String title) GUI class. IV : Question_Message for Insert Value.
void	showGUI_NAN(java.lang.String title) GUI class. NAN : Error_Message for Not A Number.
void	showGUI_NPPF(java.lang.String flname) GUI class. NPPF : Error_Message Not Proper PDB File.
int	showGUI_OCCF(java.lang.String existingFilename) GUI class. OCCF : Warning_Message Overwrite Codeml Control File.
void	showGUI_PVCF() GUI class. PVCF : Information_Message Please Verify Correct Format field.
int	showGUI_RCSC() GUI class. RCSC : Warning_Message Run Codeml without Save Changes
int	showGUI_RE() GUI class. RE : Question_Message Really Exit.
int	showGUI_RETR() GUI class. RETR : Question_Message Really Exit Tasks Running.
int	showGUI_RETRW() GUIProtToSwissModel class. RETRW : Question_Message Really Exit Task Running on Window.
int	showGUI_REWO() GUI class. REWO : Question_Message Really Exit Windows Open.
int	showGUI_SFC() GUI class. SFC : Question_Message Set File as Current ?
int	showGUI_UNMA() GUI class. UNMA : Question_Message Use New MSA File also?
java.lang.String	showGUI_VC(java.lang.String question, java.lang.String title, java.lang.Object[] selValues, java.lang.Object initialValue) GUI class. VC : Question_Message for Value Choice.
java.lang.String	showGUI_VE(java.lang.String question, java.lang.String title, java.lang.Object initialValue) GUI class. VE : Question_Message for Value Edition.
void	showGUI_VP(java.lang.String addtext) GUI class. VP : Information_Message Viewing Property name.
void	showGUI_WD(java.lang.String dirname) GUI class. WD : Information_Message Wrong Directory name.
void	showGUI_WF(java.lang.String filename) GUI class. WF : Information_Message Wrong File name.
java.lang.String	showGUIAE_CFF(java.lang.String[] formats, int quest) GUIAlignmentEditor class. CFF : Question_Message Choose File Format.
int	showGUIAE_FAEO(java.lang.String title) GUIAlignmentEditor class. FAEO : Question_Message File Already Exists Overwrite?
void	showGUIAE_FENF(java.lang.String title) GUIAlignmentEditor class. FENF : Error_Message File Extension Not Found.
void	showGUIAE_FS(java.lang.String filesaved) GUIAlignmentEditor class. FS : Information_Message File Saved.
void	showGUIAE_PONC() GUIAlignmentEditor class. PONC : Error_Message PhyML Options Not Chosen.
int	showGUIAE_RPSC() GUIAlignmentEditor class. RPSC : Warning_Message Run PhyML without Save Changes
void	showGUICP_DC(java.lang.String text) GUIConfPreferences class. DC : Information_Message Directory Created.
void	showGUICP_IURL(java.lang.String err) GUIConfPreferences class. IURL : Error_Message Invalid URL.
void	showGUICP_NPAF() GUIConfPreferences class. NPAF : Error_Message Not Proper AAIndex1 file.
void	showGUICP_OS() GUIPreferences class. OS : Information_Message Options Saved.
void	showGUICP_PW() GUIConfPreferences class. PW : Plain_Message Please Wait.
void	showGUICP_UOK(java.lang.String text) GUIConfPreferences class. UOK : Information_Message URL OK.
void	showGUICP_URNA() GUIConfPreferences class. URNA : ERROR_Message URL Resource does Not seem to be Available.
void	showGUICP_URNE() GUIConfPreferences class. URNE : ERROR_Message URL Resource does Not Exist.
java.lang.String	showGUIFFC_CPFT(java.lang.String[] pformats) GUIFileFormatConverter class. CPFT : Question_Message Choose Phylip Format Type
int	showGUIRS_NSS(java.lang.String title) ResultsSummary class. NSS : Warning_Message No Selected Sequences.
void	showRS_FBF() ResultsSummary class. FBF : Error_Message File Bad Format.
void	showRS_SCNF() ResultsSummary class. SCNF : Error_Message Selected Column Not Found.
void	showRV_RCAOB(java.lang.String flname, int csvrow, java.lang.String aiobex) ResultsView class. RCAOB : Error_Message Reading CSV file Array Out Of Bounds
void	showTSTP_ATS(int maxcodon, int foundcodon) AlignmentOperations class. ATS : Error_Message Alignment Too Short.
void	showUTIL_BFF(java.lang.String file, java.lang.String errorline) Utilities class. BFF : Error_Message Bad File Format.
void	showUTIL_FEF(java.lang.String program_file, int nummsg) Utilities class. FEF: Warning_Message File with Empty Fields.
void	showUTIL_FMF(java.lang.String program_file) Utilities class. FMF : Warning_Message File with Missing Fields.
void	showUTIL_FNF(java.lang.String program_file) Utilities class. FNF: Warning_Message File Not Found.
void	showUTIL_GWL(java.lang.String rightLoc) Utilities class. GWL : Error_Message GUI in Wrong Location
void	showUTIL_IOF() Utilities class. IOF : Error_Message Incorrect Options File syntax.
void	showUTIL_MD(java.lang.String rightDir, java.lang.String otherinfo) Utilities class. MD : Error_Message Missing Directory
void	showUTIL_NAF(java.lang.String aai1Name) Utilities class. NAF : Error_Message Not an AAIndex1 File.

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Frame

addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

QUESTION_CHOICE

public static final int QUESTION_CHOICE

QUESTION_CHOICE:
"If the extension doesn't match the file format, please choose.

Otherwise, choosing Cancel will try to get it through its extension."

See Also:

showGUIAE_CFF(java.lang.String[], int), Constant Field Values

QUESTION_ASK_SAVE

public static final int QUESTION_ASK_SAVE

QUESTION_ASK_SAVE:
"Choose file format to save in:"

See Also:

showGUIAE_CFF(java.lang.String[], int), Constant Field Values

QUESTION_ASK_CHOICE

public static final int QUESTION_ASK_CHOICE

QUESTION_ASK_CHOICE:
"Please select the file format:"
"Choosing cancel, will not allow file selection."

See Also:

showGUIAE_CFF(java.lang.String[], int), Constant Field Values

Constructor Detail

GUIDialogs

public GUIDialogs()

General case. Creates new form GUIDialogs.

GUIDialogs

public GUIDialogs(java.awt.Component parent)

Specific case.
Parent component only in dialogs UTIL_BFF, UTIL_FEF and UTIL_FMF, used in initialization process.
In other dialogs works like in general case constructor.

Parameters:

parent - in this specific case normally its value is GUIInitializeBox object.

Method Detail

showGUI_IV

public java.lang.String showGUI_IV(java.lang.String question,
                                   java.lang.String title)

GUI class.
IV : Question_Message for Insert Value.

Parameters:

question - dialog text.

title - dialog title.

Returns:

value entered; or null if canceled.

See Also:

showGUI_VE(java.lang.String, java.lang.String, java.lang.Object)

showGUI_VE

public java.lang.String showGUI_VE(java.lang.String question,
                                   java.lang.String title,
                                   java.lang.Object initialValue)

GUI class.
VE : Question_Message for Value Edition.

Parameters:

question - dialog text.

title - dialog title.

initialValue - value to be changed/edited.

Returns:

value entered; or null if canceled.

See Also:

showGUI_IV(java.lang.String, java.lang.String)

showGUI_VC

public java.lang.String showGUI_VC(java.lang.String question,
                                   java.lang.String title,
                                   java.lang.Object[] selValues,
                                   java.lang.Object initialValue)

GUI class.
VC : Question_Message for Value Choice.

Parameters:

question - dialog text.

title - dialog title.

selValues - possible selections of values.

initialValue - value to be changed/edited.

Returns:

value entered; or null if canceled.

See Also:

showGUI_IV(java.lang.String, java.lang.String)

showGUI_CV

public int showGUI_CV(java.lang.String question,
                      java.lang.String title)

GUI class.
CV : Question_Message for Choice Value.

Parameters:

question - question message.

title - dialog window title.

Returns:

value entered.

showGUI_NAN

public void showGUI_NAN(java.lang.String title)

GUI class.
NAN : Error_Message for Not A Number.

Parameters:

title - dialog window title.

showGUI_FNAN

public void showGUI_FNAN(java.lang.String title)

GUI class.
FNAN : Error_Message for Found Not A Number.

Parameters:

title - dialog window title.

showGUI_NPPF

public void showGUI_NPPF(java.lang.String flname)

GUI class.
NPPF : Error_Message Not Proper PDB File.

Parameters:

flname - (incorrect) PDB file name.

showGUI_FNE

public void showGUI_FNE(java.lang.String title)

GUI class.
FNE : Error_Message for File does Not Exist.

Parameters:

title - dialog window title.

showGUI_FNE

public void showGUI_FNE(java.lang.String filename,
                        java.lang.String title)

GUI class.
FNE : Error_Message for File does Not Exist.

Parameters:

filename - specify name of nonexistent file.

title - dialog window title.

showGUI_FNO

public void showGUI_FNO(java.lang.String title)

GUI class.
FNO : Error_Message File Not Opened.

Parameters:

title - dialog title.

showGUI_SFC

public int showGUI_SFC()

GUI class.
SFC : Question_Message Set File as Current ?

Returns:

user choice.

showGUI_PVCF

public void showGUI_PVCF()

GUI class.
PVCF : Information_Message Please Verify Correct Format field.

showGUI_RCSC

public int showGUI_RCSC()

GUI class.
RCSC : Warning_Message Run Codeml without Save Changes

Returns:

user choice.

showGUI_EF

public void showGUI_EF(java.lang.String title,
                       java.lang.String addText)

GUI class.
EF : Warning_Message Empty Fields.

Parameters:

title - dialog title.

addText - specify which fields are empty; or set to empty string.

showGUI_FVR

public void showGUI_FVR(java.lang.String title,
                        java.lang.String infringement)

GUI class.
FVR : Error_Message Fields Violating Rules.

Parameters:

title - dialog title.

infringement - specify which fields are empty; or set to empty string.

showTSTP_ATS

public void showTSTP_ATS(int maxcodon,
                         int foundcodon)

AlignmentOperations class.
ATS : Error_Message Alignment Too Short.

Parameters:

maxcodon - maximum number of codons.

foundcodon - number of codons found.

showGUI_GWM

public int showGUI_GWM(java.lang.String title,
                       java.lang.String reason)

GUI class.
GWM : Warning_Message Generic Warning Message.

Parameters:

title - dialog title.

reason - specify which fields are empty; or set to empty string.

Returns:

the option selected by the user.

showGUI_GIM

public void showGUI_GIM(java.lang.String title,
                        java.lang.String addText)

GUI class.
GIM : Information_Message Generic Information Message.

Parameters:

title - dialog title.

addText - specify which fields are empty; or set to empty string.

showGUI_GEM

public void showGUI_GEM(java.lang.String title,
                        java.lang.String addText)

GUI class.
GEM : Information_Message Generic Error Message.

Parameters:

title - dialog title.

addText - specify which fields are empty; or set to empty string.

showGUI_WD

public void showGUI_WD(java.lang.String dirname)

GUI class.
WD : Information_Message Wrong Directory name.

Parameters:

dirname - correct directory name.

showGUI_WF

public void showGUI_WF(java.lang.String filename)

GUI class.
WF : Information_Message Wrong File name.

Parameters:

filename - correct directory name.

showGUI_VP

public void showGUI_VP(java.lang.String addtext)

GUI class.
VP : Information_Message Viewing Property name.

Parameters:

addtext - information text.

showGUI_CO

public void showGUI_CO()

GUI class.
CO : Warning_Message Codeml about Options.

showGUI_CONC

public void showGUI_CONC()

GUI class.
CONC : Error_Message Codeml Options Not Chosen.

showGUI_OCCF

public int showGUI_OCCF(java.lang.String existingFilename)

GUI class.
OCCF : Warning_Message Overwrite Codeml Control File.

Parameters:

existingFilename - name of the questioned file.

Returns:

the option selected by the user.

showGUI_IFPSV

public void showGUI_IFPSV(java.lang.String filename,
                          java.lang.String program)

GUI class.
IFPSV : Error_Message Incorrect File for Program Stat Values.

Parameters:

filename - incorrect file.

program - program of corresponding file.

showGUI_RE

public int showGUI_RE()

GUI class.
RE : Question_Message Really Exit.

Returns:

user choice

showGUI_RETR

public int showGUI_RETR()

GUI class.
RETR : Question_Message Really Exit Tasks Running.

Returns:

user choice

showGUI_RETRW

public int showGUI_RETRW()

GUIProtToSwissModel class.
RETRW : Question_Message Really Exit Task Running on Window.

Returns:

user choice

showGUI_REWO

public int showGUI_REWO()

GUI class.
REWO : Question_Message Really Exit Windows Open.

Returns:

user choice

showGUI_UNMA

public int showGUI_UNMA()

GUI class.
UNMA : Question_Message Use New MSA File also?

Returns:

user choice

showGUI_FAEM

public int showGUI_FAEM(java.lang.String title)

GUI class.
FAEM : Question_Message File Already Exists Make new?

Parameters:

title - dialog title.

Returns:

user choice.

showGUIAE_CFF

public java.lang.String showGUIAE_CFF(java.lang.String[] formats,
                                      int quest)

GUIAlignmentEditor class.
CFF : Question_Message Choose File Format.

Parameters:

formats - file formats.

quest - decide which question to use. Values: QUESTION_CHOICE, QUESTION_ASK.

Returns:

format or null if user did not make a choice.

showGUIAE_FAEO

public int showGUIAE_FAEO(java.lang.String title)

GUIAlignmentEditor class.
FAEO : Question_Message File Already Exists Overwrite?

Parameters:

title - dialog title.

Returns:

user choice.

showGUIAE_FENF

public void showGUIAE_FENF(java.lang.String title)

GUIAlignmentEditor class.
FENF : Error_Message File Extension Not Found.

Parameters:

title - dialog title.

showGUIAE_FS

public void showGUIAE_FS(java.lang.String filesaved)

GUIAlignmentEditor class.
FS : Information_Message File Saved.

Parameters:

filesaved - name of saved file.

showGUICP_OS

public void showGUICP_OS()

GUIPreferences class.
OS : Information_Message Options Saved.

showGUI_CNSF

public void showGUI_CNSF(java.lang.String fileNotsaved,
                         java.lang.String title,
                         java.lang.String addtext)

GUI class.
CNSF : Error_Message Could Not Save File.

Parameters:

fileNotsaved - name of not saved file.

title - dialog title.

addtext - additional text to be added, if any.

showGUIAE_PONC

public void showGUIAE_PONC()

GUIAlignmentEditor class.
PONC : Error_Message PhyML Options Not Chosen.

showGUIAE_RPSC

public int showGUIAE_RPSC()

GUIAlignmentEditor class.
RPSC : Warning_Message Run PhyML without Save Changes

Returns:

user choice

showGUICP_DC

public void showGUICP_DC(java.lang.String text)

GUIConfPreferences class.
DC : Information_Message Directory Created.

Parameters:

text - Information message.

showGUICP_URNE

public void showGUICP_URNE()

GUIConfPreferences class.
URNE : ERROR_Message URL Resource does Not Exist.

showGUICP_URNA

public void showGUICP_URNA()

GUIConfPreferences class.
URNA : ERROR_Message URL Resource does Not seem to be Available.

showGUICP_UOK

public void showGUICP_UOK(java.lang.String text)

GUIConfPreferences class.
UOK : Information_Message URL OK.

Parameters:

text - Information message.

showGUICP_IURL

public void showGUICP_IURL(java.lang.String err)

GUIConfPreferences class.
IURL : Error_Message Invalid URL.

Parameters:

err - java exception.

showGUICP_PW

public void showGUICP_PW()

GUIConfPreferences class.
PW : Plain_Message Please Wait.

showGUICP_NPAF

public void showGUICP_NPAF()

GUIConfPreferences class.
NPAF : Error_Message Not Proper AAIndex1 file.

showGUIFFC_CPFT

public java.lang.String showGUIFFC_CPFT(java.lang.String[] pformats)

GUIFileFormatConverter class.
CPFT : Question_Message Choose Phylip Format Type

Parameters:

pformats - array with values Classic/Extended.

Returns:

phylip format (sub)type

showFFC_VMPF

public void showFFC_VMPF()

FileFormatConverter class.
VMPF : Error_Message Values Missing in Phylip File first line.

showFFC_FNC

public void showFFC_FNC()

FileFormatConverter class.
FNC : Error_Message Format Not Chosen...

showFFC_RSAOB

public void showFFC_RSAOB(java.lang.String formattxt,
                          int seqcount,
                          java.lang.String aiobex)

FileFormatConverter class.
RSAOB : Error_Message Reading Sequence Array Out Of Bounds

Parameters:

formattxt - format where reading is taking place.

seqcount - sequence number identifying sequence where error ocurred.

aiobex - java error.

showFFC_FBF

public void showFFC_FBF(java.lang.String formattxt)

FileFormatConverter class.
FBF : Error_Message File Bad Format.

Parameters:

formattxt - format where reading is taking place.

showGUI_FBF

public void showGUI_FBF(java.lang.String filename)

GUI class.
FBF : Error_Message File Bad Format.

Parameters:

filename - file name or field where reading is taking place.

showFFC_DSLF

public void showFFC_DSLF(java.lang.String formattxt,
                         java.lang.String seqdiff)

FileFormatConverter class.
DSLF : Error_Message Different Sequence Lengths Found.

Parameters:

formattxt - format where reading is taking place.

seqdiff - number of differing sequences.

showRV_RCAOB

public void showRV_RCAOB(java.lang.String flname,
                         int csvrow,
                         java.lang.String aiobex)

ResultsView class.
RCAOB : Error_Message Reading CSV file Array Out Of Bounds

Parameters:

flname - file name where reading is taking place.

csvrow - csv row number identifying where error ocurred.

aiobex - java error.

showGUIRS_NSS

public int showGUIRS_NSS(java.lang.String title)

ResultsSummary class.
NSS : Warning_Message No Selected Sequences.

Parameters:

title - dialog title.

Returns:

user choice.

showRS_FBF

public void showRS_FBF()

ResultsSummary class.
FBF : Error_Message File Bad Format.

showRS_SCNF

public void showRS_SCNF()

ResultsSummary class.
SCNF : Error_Message Selected Column Not Found.

showUTIL_FNF

public void showUTIL_FNF(java.lang.String program_file)

Utilities class.
FNF: Warning_Message File Not Found.

Parameters:

program_file - name of file not found.

showUTIL_FEF

public void showUTIL_FEF(java.lang.String program_file,
                         int nummsg)

Utilities class.
FEF: Warning_Message File with Empty Fields.

Parameters:

program_file - file with empty fields.

nummsg - value 0 or other.
-&value 0 for message: "Configure Preferences:Executables window."
-&otherwise: "Edit file with appropriate names or Configure Preferences:Executables window."

showUTIL_IOF

public void showUTIL_IOF()

Utilities class.
IOF : Error_Message Incorrect Options File syntax.

showUTIL_BFF

public void showUTIL_BFF(java.lang.String file,
                         java.lang.String errorline)

Utilities class.
BFF : Error_Message Bad File Format.

Parameters:

file - File giving errors.

errorline - line that produced error.

showUTIL_FMF

public void showUTIL_FMF(java.lang.String program_file)

Utilities class.
FMF : Warning_Message File with Missing Fields.

Parameters:

program_file - file with error.

showUTIL_GWL

public void showUTIL_GWL(java.lang.String rightLoc)

Utilities class.
GWL : Error_Message GUI in Wrong Location

Parameters:

rightLoc - Correct location for jar archive.

showUTIL_MD

public void showUTIL_MD(java.lang.String rightDir,
                        java.lang.String otherinfo)

Utilities class.
MD : Error_Message Missing Directory

Parameters:

rightDir - Correct location for jar archive.

otherinfo - other info to add to message, use otherwise empty.

showUTIL_NAF

public void showUTIL_NAF(java.lang.String aai1Name)

Utilities class.
NAF : Error_Message Not an AAIndex1 File.

Parameters:

aai1Name - (incorrect) AAIndex1 file name.