Constant Field Values

Contents

• org.biojava.*

org.biojava.*

org.biojava.nbio.structure.align.gui.ChooseDirAction

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	0L

org.biojava.nbio.structure.align.gui.MemoryMonitor

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	56289234782130L

org.biojava.nbio.structure.align.gui.MemoryMonitor.Surface

Modifier and Type	Constant Field	Value
public static final long	serialVersionUID	2387409854370432908L

org.biojava.nbio.structure.align.gui.MenuCreator

Modifier and Type	Constant Field	Value
public static final String	ALIGNMENT_PANEL	"Alignment Panel"
public static final String	DIST_MATRICES	"Show Distance Matrices"
public static final String	DOT_PLOT	"Show Dot Plot"
public static final String	EQR_COLOR	"Color By EQR"
public static final String	FASTA_FORMAT	"View FASTA Alignment"
public static final String	FATCAT_BLOCK	"Color By Alignment Block"
public static final String	FATCAT_TEXT	"View as FATCAT result"
public static final String	LOAD_ALIGNMENT_XML	"Load Alignment XML"
public static final String	LOAD_DB_RESULTS	"Load DB search results"
public static final String	MULTIPLE_ALIGN	"New Multiple Alignment"
public static final String	PAIRS_ONLY	"View Aligned Pairs"
public static final String	PAIRWISE_ALIGN	"New Pairwise Alignment"
public static final String	PHYLOGENETIC_TREE	"Phylogenetic Tree"
public static final String	PRINT	"Print"
public static final String	SAVE_ALIGNMENT_XML	"Save Alignment XML"
public static final String	SELECT_EQR	"Select Equivalent Positions"
public static final String	SIMILARITY_COLOR	"Color By Similarity"
public static final String	TEXT_ONLY	"View Text Only"

org.biojava.nbio.structure.align.gui.SystemInfo

Modifier and Type	Constant Field	Value
public static final String	defaultProperties	"browser file.separator java.class.version java.vendor java.vendor.url java.version line.separator os.arch os.name os.version path.separator "
public static final String	hexPropertyNames	" file.separator line.separator path.separator "
public static final String	urlPropertyNames	" browser.vendor.url java.class.path java.home user.dir user.home user.name "

org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_CHAR_SIZE	12
public static final int	DEFAULT_LINE_LENGTH	70
public static final int	DEFAULT_LINE_SEPARATION	20
public static final int	DEFAULT_RIGHT_SPACER	10
public static final int	DEFAULT_X_SPACE	20
public static final int	DEFAULT_Y_SPACE	40
public static final int	DEFAULT_Y_STEP	60
public static final int	SUMMARY_POS	20

org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_CHAR_SIZE	12
public static final int	DEFAULT_LINE_LENGTH	70
public static final int	DEFAULT_LINE_SEPARATION	20
public static final int	DEFAULT_RIGHT_SPACER	10
public static final int	DEFAULT_X_SPACE	20
public static final int	DEFAULT_Y_SPACE	40
public static final int	SUMMARY_POS	20

org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol

Modifier and Type	Constant Field	Value
protected static final String	COMMAND_LINE_HELP	"enter Jmol scripting command..."
protected static final int	DEFAULT_HEIGHT	500
protected static final int	DEFAULT_WIDTH	500

org.biojava.nbio.structure.gui.BiojavaJmol

Modifier and Type	Constant Field	Value
public static final String	adapter	"org.jmol.api.JmolAdapter"
public static final String	smartAdapter	"org.jmol.adapter.smarter.SmarterJmolAdapter"
public static final String	viewer	"org.jmol.api.JmolSimpleViewer"

org.biojava.nbio.structure.gui.JmolViewerImpl

Modifier and Type	Constant Field	Value
public static final String	adapter	"org.jmol.api.JmolAdapter"
public static final String	smartAdapter	"org.jmol.adapter.smarter.SmarterJmolAdapter"
public static final String	viewer	"org.jmol.api.JmolSimpleViewer"

org.biojava.nbio.structure.gui.ScaleableMatrixPanel

Modifier and Type	Constant Field	Value
protected static final int	SLIDER_STEPS	8

org.biojava.nbio.structure.gui.SequenceDisplay

Modifier and Type	Constant Field	Value
public static final int	MAX_SCALE	10

org.biojava.nbio.structure.gui.util.AlignedPosition

Modifier and Type	Constant Field	Value
public static final int	EQUIVALENT	1
public static final int	NOT_ALIGNED	0

org.biojava.nbio.structure.gui.util.SequenceScalePanel

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_X_RIGHT_BORDER	40
public static final int	DEFAULT_X_START	10
public static final int	DEFAULT_Y_BOTTOM	16
public static final int	DEFAULT_Y_HEIGHT	8
public static final int	DEFAULT_Y_START	0
public static final int	DEFAULT_Y_STEP	10
public static final int	LINE_HEIGHT	10
public static final int	MINIMUM_HEIGHT	20
public static final int	SIZE	20

org.biojava.nbio.structure.gui.util.color.GradientMapper

Modifier and Type	Constant Field	Value
public static final int	BLACK_WHITE_GRADIENT	1
public static final int	RAINBOW_GRADIENT	4
public static final int	RAINBOW_INTENSITY_GRADIENT	5
public static final int	RED_BLUE_GRADIENT	3
public static final int	WHITE_BLACK_GRADIENT	2

org.biojava.nbio.structure.gui.util.color.HSVColorSpace

Modifier and Type	Constant Field	Value
public static final int	CS_HSV	1007