Serialized Form

Package org.proteinshader.graphics.exceptions

Class org.proteinshader.graphics.exceptions.GlyphConfigException extends GlyphException implements Serializable

Serialized Fields

m_configFilename

String m_configFilename

Class org.proteinshader.graphics.exceptions.GlyphException extends Exception implements Serializable

Class org.proteinshader.graphics.exceptions.GlyphImageException extends GlyphException implements Serializable

Serialized Fields

m_name

String m_name

m_x1

int m_x1

m_y1

int m_y1

m_x2

int m_x2

m_y2

int m_y2

m_bytesPerPixel

int m_bytesPerPixel

m_glyphWidth

int m_glyphWidth

m_glyphHeight

int m_glyphHeight

m_glyphSetImageWidth

int m_glyphSetImageWidth

m_glyphSetImageHeight

int m_glyphSetImageHeight

Class org.proteinshader.graphics.exceptions.ShaderException extends Exception implements Serializable

Class org.proteinshader.graphics.exceptions.TextureException extends Exception implements Serializable

Package org.proteinshader.gui

Class org.proteinshader.gui.ProteinShaderGUI extends JFrame implements Serializable

Serialized Fields

m_canvas

GLCanvas m_canvas

m_mediator

Mediator m_mediator

m_renderer

Renderer m_renderer

m_factory

WindowListenerFactory m_factory

Package org.proteinshader.gui.components

Class org.proteinshader.gui.components.SpringLoadedJFrame extends JFrame implements Serializable

Serialized Fields

m_parent

JFrame m_parent

m_position

OrientationEnum m_position

m_widthFactor

double m_widthFactor

m_heightFactor

double m_heightFactor

m_hideWhileParentInvisible

boolean m_hideWhileParentInvisible

m_hideWhileParentIconfied

boolean m_hideWhileParentIconfied

m_frameOpening

boolean m_frameOpening

m_timer

Timer m_timer

m_fractionVisible

double m_fractionVisible

Package org.proteinshader.gui.components.controlpanel

Class org.proteinshader.gui.components.controlpanel.AntialiasingPanel extends JPanel implements Serializable

Serialized Fields

m_factory

AntialiasingPanelListenerFactory m_factory

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_sceneAntialiasBox

JCheckBox m_sceneAntialiasBox

m_halftoningAntialiasBox

JCheckBox m_halftoningAntialiasBox

m_jitterMenu

JComboBox m_jitterMenu

m_debug

boolean m_debug

Class org.proteinshader.gui.components.controlpanel.AtomColorPanel extends ColorPanel implements Serializable

Serialized Fields

m_atomModifier

AtomModifier m_atomModifier

Class org.proteinshader.gui.components.controlpanel.AtomScalePanel extends JPanel implements Serializable

Serialized Fields

m_factory

ScalePanelListenerFactory m_factory

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_atomModifier

AtomModifier m_atomModifier

m_radioPanel

RadioPanel m_radioPanel

m_style

StyleEnum m_style

m_scaleSpinner

JSpinner m_scaleSpinner

m_applyButton

JButton m_applyButton

m_defaultButton

JButton m_defaultButton

Class org.proteinshader.gui.components.controlpanel.AtomVisibilityPanel extends VisibilityPanel implements Serializable

Serialized Fields

m_atomModifier

AtomModifier m_atomModifier

m_bondModifier

BondModifier m_bondModifier

Class org.proteinshader.gui.components.controlpanel.CartoonColorPanel extends ColorPanel implements Serializable

Serialized Fields

m_segmentModifier

SegmentModifier m_segmentModifier

Class org.proteinshader.gui.components.controlpanel.CartoonSideChainsPanel extends JPanel implements Serializable

Serialized Fields

m_factory

CartoonSideChainsPanelListenerFactory m_factory

m_segmentModifier

SegmentModifier m_segmentModifier

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_radioPanel

RadioPanel m_radioPanel

m_alphaCarbonCheckBox

JCheckBox m_alphaCarbonCheckBox

m_spaceFillingButton

JButton m_spaceFillingButton

m_ballsAndSticksButton

JButton m_ballsAndSticksButton

m_sticksButton

JButton m_sticksButton

m_noneButton

JButton m_noneButton

Class org.proteinshader.gui.components.controlpanel.CartoonVisibilityPanel extends VisibilityPanel implements Serializable

Serialized Fields

m_segmentModifier

SegmentModifier m_segmentModifier

Class org.proteinshader.gui.components.controlpanel.ColorPanel extends JPanel implements Serializable

Serialized Fields

m_factory

ColorPanelListenerFactory m_factory

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_radioPanel

RadioPanel m_radioPanel

m_chooserButton

JButton m_chooserButton

m_default1Button

JButton m_default1Button

m_default2Button

JButton m_default2Button

m_chooser

JColorChooser m_chooser

m_chooserDialog

JDialog m_chooserDialog

Class org.proteinshader.gui.components.controlpanel.ControlPanel extends JPanel implements Serializable

Serialized Fields

m_selectorPanel

SelectorPanel m_selectorPanel

m_modifierPanel

ModifierPanel m_modifierPanel

Class org.proteinshader.gui.components.controlpanel.DecorationsPanel extends JPanel implements Serializable

Serialized Fields

m_factory

DecorationsPanelListenerFactory m_factory

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_segmentModifier

SegmentModifier m_segmentModifier

m_radioPanel

RadioPanel m_radioPanel

m_currentDecoration

DecorationEnum m_currentDecoration

m_plainButton

JButton m_plainButton

m_wireframeButton

JButton m_wireframeButton

m_textLabelsButton

JButton m_textLabelsButton

m_patternsButton

JButton m_patternsButton

m_halftoningButton

JButton m_halftoningButton

m_patternsMenu

JComboBox m_patternsMenu

m_halftoningMenu

JComboBox m_halftoningMenu

m_bendMenu

JComboBox m_bendMenu

m_extraLinesCheckBox

JCheckBox m_extraLinesCheckBox

Class org.proteinshader.gui.components.controlpanel.ModifierPanel extends JPanel implements Serializable

Serialized Fields

m_factory

ModifierPanelListenerFactory m_factory

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_subpanelMenu

JComboBox m_subpanelMenu

m_defaultSubpanel

JPanel m_defaultSubpanel

m_centerPanel

JPanel m_centerPanel

m_atomRadioPanel

RadioPanel m_atomRadioPanel

m_cartoonRadioPanel

RadioPanel m_cartoonRadioPanel

m_cartoonColorPanel

CartoonColorPanel m_cartoonColorPanel

m_cartoonVisibilityPanel

CartoonVisibilityPanel m_cartoonVisibilityPanel

m_cartoonSideChainsPanel

CartoonSideChainsPanel m_cartoonSideChainsPanel

m_decorationsPanel

DecorationsPanel m_decorationsPanel

m_atomColorPanel

AtomColorPanel m_atomColorPanel

m_atomVisibilityPanel

AtomVisibilityPanel m_atomVisibilityPanel

m_atomScalePanel

AtomScalePanel m_atomScalePanel

m_motionPanel

MotionPanel m_motionPanel

m_antialiasingPanel

AntialiasingPanel m_antialiasingPanel

m_optimizePanel

OptimizePanel m_optimizePanel

Class org.proteinshader.gui.components.controlpanel.MotionPanel extends JPanel implements Serializable

Serialized Fields

m_factory

MotionPanelListenerFactory m_factory

m_numberFormatter

NumberFormat m_numberFormatter

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_xAxisSlider

JSlider m_xAxisSlider

m_yAxisSlider

JSlider m_yAxisSlider

m_startButton

JButton m_startButton

m_stopButton

JButton m_stopButton

m_fpsTextField

JTextField m_fpsTextField

m_xAxisTextField

JFormattedTextField m_xAxisTextField

m_yAxisTextField

JFormattedTextField m_yAxisTextField

m_animationIsRunning

boolean m_animationIsRunning

m_debug

boolean m_debug

Class org.proteinshader.gui.components.controlpanel.OptimizePanel extends JPanel implements Serializable

Serialized Fields

m_factory

OptimizePanelListenerFactory m_factory

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_autoTilingButton

JCheckBox m_autoTilingButton

m_centerPanel

JPanel m_centerPanel

m_spheresButton

JRadioButton m_spheresButton

m_cylindersButton

JRadioButton m_cylindersButton

m_cylinderCapsButton

JRadioButton m_cylinderCapsButton

m_spheresMenu

JComboBox m_spheresMenu

m_cylindersMenu

JComboBox m_cylindersMenu

m_cylinderCapsMenu

JComboBox m_cylinderCapsMenu

m_sphereTilingLabel

JLabel m_sphereTilingLabel

m_cylinderTilingLabel

JLabel m_cylinderTilingLabel

m_cylinderCapsTilingLabel

JLabel m_cylinderCapsTilingLabel

m_tilingSpinner

JSpinner m_tilingSpinner

m_applyButton

JButton m_applyButton

m_defaultButton

JButton m_defaultButton

m_debug

boolean m_debug

Class org.proteinshader.gui.components.controlpanel.RadioPanel extends JPanel implements Serializable

Serialized Fields

m_factory

RadioPanelListenerFactory m_factory

m_visitor

ModifierVisitor m_visitor

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_type

RadioPanel.Type m_type

m_upperPanel

JPanel m_upperPanel

m_lowerPanel

JPanel m_lowerPanel

m_selectedButton

JRadioButton m_selectedButton

m_helicesButton

JRadioButton m_helicesButton

m_strandsButton

JRadioButton m_strandsButton

m_loopsButton

JRadioButton m_loopsButton

m_globalButton

JRadioButton m_globalButton

m_selectedMenu

JComboBox m_selectedMenu

m_helicesMenu

JComboBox m_helicesMenu

m_strandsMenu

JComboBox m_strandsMenu

m_loopsMenu

JComboBox m_loopsMenu

m_globalMenu

JComboBox m_globalMenu

m_applyToMenu

JComboBox m_applyToMenu

m_activeRadioButton

RadioButtonEnum m_activeRadioButton

Class org.proteinshader.gui.components.controlpanel.SelectorPanel extends JPanel implements Serializable

Serialized Fields

m_factory

SelectorPanelListenerFactory m_factory

m_mediator

Mediator m_mediator

m_residuesLabel

JLabel m_residuesLabel

m_atomsLabel

JLabel m_atomsLabel

m_residueIDLabel

JLabel m_residueIDLabel

m_modelMenu

JComboBox m_modelMenu

m_chainMenu

JComboBox m_chainMenu

m_residueMenu

JComboBox m_residueMenu

m_residueListModel

DefaultListModel m_residueListModel

m_atomListModel

DefaultListModel m_atomListModel

m_residueList

JList m_residueList

m_atomList

JList m_atomList

m_atomListDialog

JDialog m_atomListDialog

m_dialogOwner

Frame m_dialogOwner

m_atomsButton

JButton m_atomsButton

m_atomCloseButton

JButton m_atomCloseButton

m_debug

boolean m_debug

Class org.proteinshader.gui.components.controlpanel.VisibilityPanel extends JPanel implements Serializable

Serialized Fields

m_factory

VisibilityPanelListenerFactory m_factory

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_radioPanel

RadioPanel m_radioPanel

m_percentField

JFormattedTextField m_percentField

m_alphaSlider

JSlider m_alphaSlider

m_opaqueButton

JButton m_opaqueButton

m_invisibleButton

JButton m_invisibleButton

m_translucentButton

JButton m_translucentButton

Package org.proteinshader.gui.components.menubar

Class org.proteinshader.gui.components.menubar.AboutBox extends JDialog implements Serializable

Serialized Fields

m_listenerFactory

AboutBoxListenerFactory m_listenerFactory

m_closeButton

JButton m_closeButton

m_webSiteButton

JButton m_webSiteButton

Class org.proteinshader.gui.components.menubar.BackgroundMenu extends JMenu implements Serializable

Serialized Fields

m_factory

BackgroundMenuListenerFactory m_factory

m_chooser

JColorChooser m_chooser

m_chooserDialog

JDialog m_chooserDialog

m_dialogOwner

Frame m_dialogOwner

m_blackMenuItem

JMenuItem m_blackMenuItem

m_grayMenuItem

JMenuItem m_grayMenuItem

m_lightGrayMenuItem

JMenuItem m_lightGrayMenuItem

m_whiteMenuItem

JMenuItem m_whiteMenuItem

m_customMenuItem

JMenuItem m_customMenuItem

Class org.proteinshader.gui.components.menubar.FileMenu extends JMenu implements Serializable

Serialized Fields

m_factory

FileMenuListenerFactory m_factory

m_openMenuItem

JMenuItem m_openMenuItem

m_jpgFileItem

JMenuItem m_jpgFileItem

m_pngFileItem

JMenuItem m_pngFileItem

m_gifFileItem

JMenuItem m_gifFileItem

m_invisibleCanvasPngFileItem

JMenuItem m_invisibleCanvasPngFileItem

m_quitMenuItem

JMenuItem m_quitMenuItem

Class org.proteinshader.gui.components.menubar.HelpMenu extends JMenu implements Serializable

Serialized Fields

m_factory

HelpMenuListenerFactory m_factory

m_mediator

Mediator m_mediator

m_dialogOwner

Frame m_dialogOwner

m_aboutMenuItem

JMenuItem m_aboutMenuItem

m_localHelpMenuItem

JMenuItem m_localHelpMenuItem

m_sourceForgeMenuItem

JMenuItem m_sourceForgeMenuItem

m_graphicsCardMenuItem

JMenuItem m_graphicsCardMenuItem

Class org.proteinshader.gui.components.menubar.MainMenuBar extends JMenuBar implements Serializable

Serialized Fields

m_visibilityMenu

VisibilityMenu m_visibilityMenu

m_toolsMenu

ToolsMenu m_toolsMenu

m_styleMenu

StyleMenu m_styleMenu

m_helpMenu

HelpMenu m_helpMenu

Class org.proteinshader.gui.components.menubar.OrientationMenu extends JMenu implements Serializable

Serialized Fields

m_factory

OrientationMenuListenerFactory m_factory

Class org.proteinshader.gui.components.menubar.StyleMenu extends JMenu implements Serializable

Serialized Fields

m_factory

StyleMenuListenerFactory m_factory

m_mediator

Mediator m_mediator

m_defaultRadioButton

JRadioButtonMenuItem m_defaultRadioButton

Class org.proteinshader.gui.components.menubar.ToolsMenu extends JMenu implements Serializable

Serialized Fields

m_factory

ToolsMenuListenerFactory m_factory

m_controlPanelCheckBox

JCheckBoxMenuItem m_controlPanelCheckBox

Class org.proteinshader.gui.components.menubar.VisibilityMenu extends JMenu implements Serializable

Serialized Fields

m_factory

VisibilityMenuListenerFactory m_factory

m_aminoAcidsCheckBox

JCheckBoxMenuItem m_aminoAcidsCheckBox

m_heterogensCheckBox

JCheckBoxMenuItem m_heterogensCheckBox

m_watersCheckBox

JCheckBoxMenuItem m_watersCheckBox

Package org.proteinshader.gui.exceptions

Class org.proteinshader.gui.exceptions.ScreenShotException extends Exception implements Serializable

Serialized Fields

m_format

ImageFormatEnum m_format

m_file

File m_file

m_lowerLevelMessage

String m_lowerLevelMessage

Package org.proteinshader.gui.utils

Class org.proteinshader.gui.utils.CenteredListCellRenderer extends DefaultListCellRenderer implements Serializable

Class org.proteinshader.gui.utils.ImageFileChooser extends JFileChooser implements Serializable

Serialized Fields

m_format

ImageFormatEnum m_format

Class org.proteinshader.gui.utils.PaddedListCellRenderer extends DefaultListCellRenderer implements Serializable

Class org.proteinshader.gui.utils.SeparatorListCellRenderer extends DefaultListCellRenderer implements Serializable

Serialized Fields

m_separators

String[] m_separators

m_lineColor

Color m_lineColor

Package org.proteinshader.structure.exceptions

Class org.proteinshader.structure.exceptions.BondLengthException extends Exception implements Serializable

Serialized Fields

m_calculatedLength

double m_calculatedLength

m_expectedLength

double m_expectedLength

m_toleranceFactor

double m_toleranceFactor

m_srcAtomType

AtomEnum m_srcAtomType

m_dstAtomType

AtomEnum m_dstAtomType

m_srcAtomSerialNo

int m_srcAtomSerialNo

m_dstAtomSerialNo

int m_dstAtomSerialNo

Class org.proteinshader.structure.exceptions.ColorOutOfRangeException extends Exception implements Serializable

Class org.proteinshader.structure.exceptions.InvalidIDException extends Exception implements Serializable

Class org.proteinshader.structure.exceptions.InvalidRegionException extends Exception implements Serializable

Class org.proteinshader.structure.exceptions.MissingAATypeException extends Exception implements Serializable

Class org.proteinshader.structure.exceptions.MissingAtomTypeException extends Exception implements Serializable

Class org.proteinshader.structure.exceptions.MissingHetNameException extends Exception implements Serializable

Class org.proteinshader.structure.exceptions.SegmentException extends Exception implements Serializable

Package org.proteinshader.structure.io.exceptions

Class org.proteinshader.structure.io.exceptions.PDBFieldExtractorException extends Exception implements Serializable

Class org.proteinshader.structure.io.exceptions.PDBLineParserException extends Exception implements Serializable

Class org.proteinshader.structure.io.exceptions.StructureReaderException extends Exception implements Serializable

Package org.proteinshader.structure.visitor.exceptions

Class org.proteinshader.structure.visitor.exceptions.VisitorException extends Exception implements Serializable

Class org.proteinshader.structure.visitor.exceptions.WriterVisitorException extends VisitorException implements Serializable