util
Class Constants

java.lang.Object
  extended by util.Constants

public class Constants
extends java.lang.Object

This class defines some constants for the whole software.


Field Summary
static java.util.HashMap<java.lang.String,java.lang.Integer> AA_CODES
           
static int AA_PER_LINE
           
static int ALIGNPANEL_HEIGHT
           
static int ALIGNPANEL_WIDTH
           
static java.lang.String ALIGNVIEW_FONT
           
static int ALIGNVIEW_FONTSIZE
           
static int ALIGNVIEW_FONTSTYLE
           
static java.lang.String APPNAME
           
static java.lang.String APPTITLE
           
static int AXESFRAME_HEIGHT
           
static int AXESFRAME_WIDTH
           
static float AXISFRAME_MAX
           
static float CLUSTER_POINT_SIZE
           
static java.lang.String CLUSTER_SHAPE_NAME
           
static int CLUSTERSETTINGSFRM_HEIGHT
           
static int CLUSTERSETTINGSFRM_WIDTH
           
static java.lang.String CONFIG_DIR
           
static java.lang.String CONVERSION_PLUGINS_DIR
           
static java.lang.String CONVERSION_PLUGINS_PACKAGE
           
static java.awt.Color DEFAULT_AXIS_COLOR
           
static java.awt.Color DEFAULT_CLUSTER_COLOR
           
static java.lang.String DEFAULT_CLUSTER_COLOR_NAME
           
static int DEFAULT_HEIGHT
           
static java.awt.Color DEFAULT_RESIDUE_COLOR
           
static java.lang.String DEFAULT_RESIDUE_COLOR_NAME
           
static int DEFAULT_WIDTH
           
static java.awt.Color DESCBOXPNL_BGCOLOR
           
static java.lang.String dS
           
static double ENTROPYCUTOFF_DEFAULT
           
static java.lang.String ENTROPYSLIDER_TOOLTIP
           
static java.lang.String FILE_PREFIX
           
static java.lang.String FILTER_PRESETS_FILE
           
static java.lang.String FTPSERVER
           
static java.awt.Color GREEN
           
static java.awt.Color[] GROUPCOLORS
           
static java.awt.Color INDEXPANEL_BGCOLOR
           
static int INDEXPANEL_HEIGHT
           
static int INDEXPANEL_WIDTH
           
static int INFOPANEL_HEIGHT
           
static int INFOPANEL_WIDTH
           
static int JAVA3DFRAME_HEIGHT
           
static int JAVA3DFRAME_WIDTH
           
static java.lang.String JDET_URL
           
static int JMOLPANEL_HEIGHT
           
static int JMOLPANEL_WIDTH
           
static int LABEL_FONT_SIZE
           
static int LETTER_WIDTH
           
static int LOADFRAME_HEIGHT
           
static int LOADFRAME_WIDTH
           
static int LOGO_HEIGHT
           
static java.lang.String LOGOHEADER_FONT
           
static int LOGOHEADER_FONT_SIZE
           
static int LOGOHEADER_FONTSIZE
           
static int LOGOHEADER_FONTSTYLE
           
static int LOGOHEADER_HEIGHT
           
static int LOGOHEADER_MARGIN
           
static java.lang.String MANUAL_PATH
           
static java.lang.String MANUAL_URL
           
static int MAX_LABEL_LENGTH
           
static int MAX_UDM_METHODS
           
static java.lang.String METHOD_METRICS_FILE
           
static int METHOD_OFFSET
           
static java.lang.String METHOD_PLUGINS_DIR
           
static java.lang.String METHOD_PLUGINS_PACKAGE
           
static java.awt.Color METHODDESCPNL_BGCOLOR
           
static int METHODDESCPNL_HEIGHT
           
static int METHODDESCPNL_WIDTH
           
static java.awt.Color METHODPANEL_BGCOLOR
           
static int METHODPANEL_HEIGHT
           
static int METHODPANEL_WIDTH
           
static java.lang.String METHODS_DIR
           
static double MIN_PDB_SEQ_ALIGNMENT
           
static int NAMEPANEL_HEIGHT
           
static java.awt.Color NAMEPANEL_SELECTED_BGSEQUENCE
           
static java.awt.Color NAMEPANEL_SELECTED_FGSEQUENCE
           
static int NAMEPANEL_WIDTH
           
static java.awt.Color ORANGE
           
static double OTHERCUTOFF_DEFAULT
           
static int[] OTHERSLIDER_DEFAULT
           
static java.lang.String OTHERSLIDER_TOOLTIP
           
static int PANEL_LOGO_MARGIN
           
static int PANEL_LOGO_WIDTH
           
static double PDB_EVALUE_THRESHOLD
           
static double PDB_IDENTITIES_THRESHOLD
           
static java.lang.String PDB_WSDLSERVER
           
static java.awt.Color PICK_AREA_COLOR
           
static int PLUGIN_TYPE_CONVERSION
           
static int PLUGIN_TYPE_METHOD
           
static java.awt.Color RED
           
static float RESIDUE_POINT_SIZE
           
static java.lang.String RESIDUE_SHAPE_NAME
           
static double S3DETCUTOFF_DEFAULT
           
static java.lang.String S3DETSLIDER_TOOLTIP
           
static java.awt.Color SELECTED_PROTEIN_COLOR
           
static java.awt.Color SELECTED_RESIDUE_COLOR
           
static float SELECTED_RESIDUE_POINT_SIZE
           
static java.lang.String SELECTED_RESIDUE_SHAPE_NAME
           
static int SELECTION_AND
           
static int SELECTION_ONLY
           
static int SELECTION_OR
           
static float SELECTION_PRECISION
           
static int SEQPANEL_HEIGHT
           
static int SEQPANEL_WIDTH
           
static float SEQUENCE_POINT_SIZE
           
static java.lang.String SEQUENCE_SHAPE_NAME
           
static java.lang.String TEXTFIELD_TOOLTIP
           
static java.lang.String TMP_DIR
           
static java.lang.String TUTORIAL_PATH
           
static java.lang.String TUTORIAL_URL
           
static java.lang.String VERSION
           
static java.lang.String VERSIONDATE
           
static double XDETCUTOFF_DEFAULT
           
static java.lang.String XDETSLIDER_TOOLTIP
           
static java.awt.Color YELLOW
           
 
Constructor Summary
Constants()
           
 
Method Summary
static boolean isGap(char c)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

APPNAME

public static final java.lang.String APPNAME
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Constant Field Values

VERSIONDATE

public static final java.lang.String VERSIONDATE
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Constant Field Values

VERSION

public static final java.lang.String VERSION
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Constant Field Values

APPTITLE

public static final java.lang.String APPTITLE
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Constant Field Values

DEFAULT_WIDTH

public static final int DEFAULT_WIDTH
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Constant Field Values

DEFAULT_HEIGHT

public static final int DEFAULT_HEIGHT
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MAX_UDM_METHODS

public static final int MAX_UDM_METHODS
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Constant Field Values

dS

public static final java.lang.String dS

FILE_PREFIX

public static final java.lang.String FILE_PREFIX
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Constant Field Values

MANUAL_PATH

public static final java.lang.String MANUAL_PATH

TUTORIAL_PATH

public static final java.lang.String TUTORIAL_PATH

JDET_URL

public static final java.lang.String JDET_URL
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Constant Field Values

MANUAL_URL

public static final java.lang.String MANUAL_URL
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Constant Field Values

TUTORIAL_URL

public static final java.lang.String TUTORIAL_URL
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Constant Field Values

AA_PER_LINE

public static final int AA_PER_LINE
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Constant Field Values

FTPSERVER

public static final java.lang.String FTPSERVER
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Constant Field Values

PDB_WSDLSERVER

public static final java.lang.String PDB_WSDLSERVER
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Constant Field Values

PDB_IDENTITIES_THRESHOLD

public static final double PDB_IDENTITIES_THRESHOLD
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Constant Field Values

PDB_EVALUE_THRESHOLD

public static final double PDB_EVALUE_THRESHOLD
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Constant Field Values

CONFIG_DIR

public static final java.lang.String CONFIG_DIR

METHODS_DIR

public static final java.lang.String METHODS_DIR

TMP_DIR

public static final java.lang.String TMP_DIR

FILTER_PRESETS_FILE

public static final java.lang.String FILTER_PRESETS_FILE

METHOD_METRICS_FILE

public static final java.lang.String METHOD_METRICS_FILE

LOADFRAME_WIDTH

public static final int LOADFRAME_WIDTH
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Constant Field Values

LOADFRAME_HEIGHT

public static final int LOADFRAME_HEIGHT
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Constant Field Values

JMOLPANEL_WIDTH

public static final int JMOLPANEL_WIDTH
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Constant Field Values

JMOLPANEL_HEIGHT

public static final int JMOLPANEL_HEIGHT
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Constant Field Values

JAVA3DFRAME_WIDTH

public static final int JAVA3DFRAME_WIDTH
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Constant Field Values

JAVA3DFRAME_HEIGHT

public static final int JAVA3DFRAME_HEIGHT
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Constant Field Values

ALIGNPANEL_WIDTH

public static final int ALIGNPANEL_WIDTH
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Constant Field Values

ALIGNPANEL_HEIGHT

public static final int ALIGNPANEL_HEIGHT
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Constant Field Values

ALIGNVIEW_FONT

public static final java.lang.String ALIGNVIEW_FONT
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Constant Field Values

ALIGNVIEW_FONTSTYLE

public static final int ALIGNVIEW_FONTSTYLE
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Constant Field Values

ALIGNVIEW_FONTSIZE

public static final int ALIGNVIEW_FONTSIZE
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Constant Field Values

SEQPANEL_WIDTH

public static final int SEQPANEL_WIDTH
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Constant Field Values

SEQPANEL_HEIGHT

public static final int SEQPANEL_HEIGHT
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Constant Field Values

INFOPANEL_WIDTH

public static final int INFOPANEL_WIDTH
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INFOPANEL_HEIGHT

public static final int INFOPANEL_HEIGHT
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Constant Field Values

INDEXPANEL_WIDTH

public static final int INDEXPANEL_WIDTH
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Constant Field Values

INDEXPANEL_HEIGHT

public static final int INDEXPANEL_HEIGHT
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Constant Field Values

INDEXPANEL_BGCOLOR

public static final java.awt.Color INDEXPANEL_BGCOLOR

DESCBOXPNL_BGCOLOR

public static final java.awt.Color DESCBOXPNL_BGCOLOR

METHODDESCPNL_WIDTH

public static final int METHODDESCPNL_WIDTH
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Constant Field Values

METHODDESCPNL_HEIGHT

public static int METHODDESCPNL_HEIGHT

METHODDESCPNL_BGCOLOR

public static final java.awt.Color METHODDESCPNL_BGCOLOR

METHODPANEL_WIDTH

public static final int METHODPANEL_WIDTH
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Constant Field Values

METHODPANEL_HEIGHT

public static int METHODPANEL_HEIGHT

METHODPANEL_BGCOLOR

public static final java.awt.Color METHODPANEL_BGCOLOR

METHOD_OFFSET

public static int METHOD_OFFSET

NAMEPANEL_WIDTH

public static final int NAMEPANEL_WIDTH
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Constant Field Values

NAMEPANEL_HEIGHT

public static final int NAMEPANEL_HEIGHT
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Constant Field Values

NAMEPANEL_SELECTED_BGSEQUENCE

public static final java.awt.Color NAMEPANEL_SELECTED_BGSEQUENCE

NAMEPANEL_SELECTED_FGSEQUENCE

public static final java.awt.Color NAMEPANEL_SELECTED_FGSEQUENCE

MIN_PDB_SEQ_ALIGNMENT

public static final double MIN_PDB_SEQ_ALIGNMENT
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Constant Field Values

CLUSTERSETTINGSFRM_WIDTH

public static final int CLUSTERSETTINGSFRM_WIDTH
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Constant Field Values

CLUSTERSETTINGSFRM_HEIGHT

public static final int CLUSTERSETTINGSFRM_HEIGHT
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Constant Field Values

AXESFRAME_WIDTH

public static final int AXESFRAME_WIDTH
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Constant Field Values

AXESFRAME_HEIGHT

public static final int AXESFRAME_HEIGHT
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Constant Field Values

AXISFRAME_MAX

public static final float AXISFRAME_MAX
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Constant Field Values

SEQUENCE_SHAPE_NAME

public static final java.lang.String SEQUENCE_SHAPE_NAME
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Constant Field Values

RESIDUE_SHAPE_NAME

public static final java.lang.String RESIDUE_SHAPE_NAME
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Constant Field Values

SELECTED_RESIDUE_SHAPE_NAME

public static final java.lang.String SELECTED_RESIDUE_SHAPE_NAME
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Constant Field Values

CLUSTER_SHAPE_NAME

public static final java.lang.String CLUSTER_SHAPE_NAME
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Constant Field Values

SEQUENCE_POINT_SIZE

public static final float SEQUENCE_POINT_SIZE
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Constant Field Values

RESIDUE_POINT_SIZE

public static final float RESIDUE_POINT_SIZE
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Constant Field Values

SELECTED_RESIDUE_POINT_SIZE

public static final float SELECTED_RESIDUE_POINT_SIZE
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Constant Field Values

CLUSTER_POINT_SIZE

public static final float CLUSTER_POINT_SIZE
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Constant Field Values

SELECTION_PRECISION

public static final float SELECTION_PRECISION
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Constant Field Values

XDETSLIDER_TOOLTIP

public static final java.lang.String XDETSLIDER_TOOLTIP
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Constant Field Values

ENTROPYSLIDER_TOOLTIP

public static final java.lang.String ENTROPYSLIDER_TOOLTIP
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Constant Field Values

S3DETSLIDER_TOOLTIP

public static final java.lang.String S3DETSLIDER_TOOLTIP
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Constant Field Values

OTHERSLIDER_TOOLTIP

public static final java.lang.String OTHERSLIDER_TOOLTIP
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Constant Field Values

SELECTION_ONLY

public static final int SELECTION_ONLY
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Constant Field Values

SELECTION_AND

public static final int SELECTION_AND
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Constant Field Values

SELECTION_OR

public static final int SELECTION_OR
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Constant Field Values

OTHERSLIDER_DEFAULT

public static final int[] OTHERSLIDER_DEFAULT

LABEL_FONT_SIZE

public static final int LABEL_FONT_SIZE
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Constant Field Values

MAX_LABEL_LENGTH

public static final int MAX_LABEL_LENGTH
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Constant Field Values

XDETCUTOFF_DEFAULT

public static final double XDETCUTOFF_DEFAULT
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Constant Field Values

ENTROPYCUTOFF_DEFAULT

public static final double ENTROPYCUTOFF_DEFAULT
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S3DETCUTOFF_DEFAULT

public static final double S3DETCUTOFF_DEFAULT
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Constant Field Values

OTHERCUTOFF_DEFAULT

public static final double OTHERCUTOFF_DEFAULT
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Constant Field Values

TEXTFIELD_TOOLTIP

public static final java.lang.String TEXTFIELD_TOOLTIP
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Constant Field Values

GREEN

public static final java.awt.Color GREEN

YELLOW

public static final java.awt.Color YELLOW

ORANGE

public static final java.awt.Color ORANGE

RED

public static final java.awt.Color RED

GROUPCOLORS

public static final java.awt.Color[] GROUPCOLORS

SELECTED_PROTEIN_COLOR

public static final java.awt.Color SELECTED_PROTEIN_COLOR

SELECTED_RESIDUE_COLOR

public static final java.awt.Color SELECTED_RESIDUE_COLOR

DEFAULT_RESIDUE_COLOR

public static final java.awt.Color DEFAULT_RESIDUE_COLOR

DEFAULT_RESIDUE_COLOR_NAME

public static final java.lang.String DEFAULT_RESIDUE_COLOR_NAME
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Constant Field Values

DEFAULT_CLUSTER_COLOR

public static final java.awt.Color DEFAULT_CLUSTER_COLOR

DEFAULT_CLUSTER_COLOR_NAME

public static final java.lang.String DEFAULT_CLUSTER_COLOR_NAME
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Constant Field Values

DEFAULT_AXIS_COLOR

public static final java.awt.Color DEFAULT_AXIS_COLOR

PICK_AREA_COLOR

public static final java.awt.Color PICK_AREA_COLOR

AA_CODES

public static final java.util.HashMap<java.lang.String,java.lang.Integer> AA_CODES

PANEL_LOGO_WIDTH

public static final int PANEL_LOGO_WIDTH
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Constant Field Values

LOGO_HEIGHT

public static final int LOGO_HEIGHT
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Constant Field Values

PANEL_LOGO_MARGIN

public static final int PANEL_LOGO_MARGIN
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Constant Field Values

LETTER_WIDTH

public static final int LETTER_WIDTH
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Constant Field Values

LOGOHEADER_HEIGHT

public static final int LOGOHEADER_HEIGHT
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Constant Field Values

LOGOHEADER_FONT_SIZE

public static final int LOGOHEADER_FONT_SIZE
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Constant Field Values

LOGOHEADER_FONT

public static final java.lang.String LOGOHEADER_FONT
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Constant Field Values

LOGOHEADER_FONTSTYLE

public static final int LOGOHEADER_FONTSTYLE

LOGOHEADER_FONTSIZE

public static final int LOGOHEADER_FONTSIZE
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Constant Field Values

LOGOHEADER_MARGIN

public static final int LOGOHEADER_MARGIN
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Constant Field Values

PLUGIN_TYPE_METHOD

public static final int PLUGIN_TYPE_METHOD
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Constant Field Values

PLUGIN_TYPE_CONVERSION

public static final int PLUGIN_TYPE_CONVERSION
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Constant Field Values

METHOD_PLUGINS_DIR

public static final java.lang.String METHOD_PLUGINS_DIR
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Constant Field Values

METHOD_PLUGINS_PACKAGE

public static final java.lang.String METHOD_PLUGINS_PACKAGE
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Constant Field Values

CONVERSION_PLUGINS_DIR

public static final java.lang.String CONVERSION_PLUGINS_DIR
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Constant Field Values

CONVERSION_PLUGINS_PACKAGE

public static final java.lang.String CONVERSION_PLUGINS_PACKAGE
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Constant Field Values
Constructor Detail

Constants

public Constants()
Method Detail

isGap

public static final boolean isGap(char c)