Index of all Fields and Methods

All Packages  Class Hierarchy

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Index of all Fields and Methods

A

about(). Method in class pmr.simplegraph.JUMBO
absSumAllElements(). Method in class pmr.euclid.IntArray: absolute sum of all elements
absSumAllElements(). Method in class pmr.euclid.RealArray: absolute sum of all elements
accept(File, String). Method in class pmr.util.EndsWithFilter
action(Event, Object). Method in class pmr.simplegraph.AppletFrame
action(Event, Object). Method in class pmr.simplegraph.ButtonBar: the button bar has the responsibility of sending messages to the target directly
action(Event, Object). Method in interface pmr.simplegraph.Drawable: pass any action events to theDrawable
action(Event, Object). Method in class pmr.simplegraph.DrawableHelp: trap any button press
action(Event, Object). Method in class pmr.simplegraph.DrawableObject: pass action to the object
action(Event, Object). Method in class pmr.sgml.DrawableSGMLNode: pass any button actions to the object
action(Event, Object). Method in class pmr.stat.DrawableStat: pass any button actions to the object
action(Event, Object). Method in class pmr.cml.DrawableX_Node: pass any button actions to the object
action(Event, Object). Method in class pmr.simplegraph.InfoDialog
action(Event, Object). Method in class pmr.cml.MOLNode: Reset button has to reset transformation matrix (rotMat) as well as scaling the scaler2d
action(Event, Object). Method in class pmr.simplegraph.MultiDialog
action(Event, Object). Method in class pmr.simplegraph.MultiScrollableTopLevel: Actions from the buttonBar are routed to here; the String from the widgets is used to decide what to do
action(Event, Object). Method in class pmr.simplegraph.Paragraph: pass any action events to theDrawable
action(Event, Object). Method in class pmr.simplegraph.ScrollableTopLevel: this handles button events in the buttonBar provided by simpleFrame; if there is a Drawable, passes the event to it
action(Event, Object). Method in class pmr.sgml.SGMLTOC: this handles button events in the buttonBar provided by simpleFrame; if there is a Drawable, passes the event to it
action(Event, Object). Method in class pmr.simplegraph.SimpleFrame: This is messy because Java doesn't have a callback mechanism - still under development...
action(Event, Object). Method in class pmr.simplegraph.SimpleText: pass any action events to theDrawable
action(Event, Object). Method in class pmr.cml.TERMENTRYNode: pass any button actions to the object
action(int, int). Method in class pmr.simplegraph.ObjectTable: takes action when a cell is clicked.
add(Choice3, double). Method in class pmr.euclid.Real3Range: add a single value
add(double). Method in class pmr.euclid.RealRange: add a value to a range
add(int). Method in class pmr.euclid.IntRange: add a value to a range
add(int, double). Method in class pmr.euclid.Real3Range: add a single value - not for general use
add(Int2). Method in class pmr.euclid.Int2Range: add a Int2 to a range
add(Point3). Method in class pmr.euclid.Real3Range: add a Point3 to a range
add(Real2). Method in class pmr.euclid.Real2Range: add a Real2 to a range
add(SGMLNode). Method in class pmr.sgml.Clipboard: adds a parentless node with all of its subtree to DOCROOT
add(SGMLNode). Method in class pmr.sgml.TreeContainer: adds a parentless node with all of its subtree to DOCROOT
add(SGMLTree). Method in class pmr.sgml.TreeContainer
add(String). Method in class pmr.util.StringList
addAdmin(GlossaryAdmin). Method in class pmr.cml.Glossary
addAfterMenuItem(MenuBar, String, Menu). Static method in class pmr.simplegraph.SimpleGraph: adds the Menu 'menu' after the Menu with label 'after' on MenuBar menuBar.
addArray(IntArray). Method in class pmr.euclid.IntArray: append elements
addArray(ObjectArray). Method in class pmr.euclid.ObjectArray: append elements
addArray(RealArray). Method in class pmr.euclid.RealArray: append elements
addAuthor(PERSONNode). Method in class pmr.cml.BIBNode
addBeforeMenuItem(Menu, String, MenuItem). Static method in class pmr.simplegraph.SimpleGraph: adds the MenuItem 'mi' before the MenuItem with label 'before'.
addBeforeMenuItem(Menu, String, String). Static method in class pmr.simplegraph.SimpleGraph: adds the String 'label' before the MenuItem with label 'before'.
addBookmark(SGMLNode). Method in class pmr.sgml.SGMLTOC: add a node to 'bookmark' list
addBuiltin(Hashtable, String, String). Static method in class pmr.cml.DataPrimitive: for use by other DTDs which use BUILTINs
addBuiltin(String, String). Static method in class pmr.cml.ARRAYNode: for use by other DTDs which use BUILTINs
addButton(String). Method in class pmr.simplegraph.ButtonBar
addButton(String). Method in class pmr.simplegraph.DrawableObject: may wish to add other buttons to the Drawable Object (if it has a stl)
addButton(String). Method in class pmr.simplegraph.ScrollableTopLevel: add a button to the bar, creating if required
addButton(String, Helpable). Method in class pmr.simplegraph.DrawableHelp: add a button pointing to an object which has its own help
addButtonBar(ButtonBar). Method in class pmr.simplegraph.ScrollableTopLevel: the STL can have a ButtonBar at the top which can be manipluated separately
addButtons(String[]). Method in class pmr.simplegraph.ButtonBar
addCellAngles(Angle, Angle, Angle). Method in class pmr.cml.CRYSTNode: add cell angles as a Angle[3] If angles already present, returns false without action.
addCellLengths(double, double, double). Method in class pmr.cml.CRYSTNode: add cell lengths as a double[3] If cell already present, returns false without action.
addChild(int). Method in class pmr.cml.BIBNode: checks that parent knows about children
addChild(int). Method in class pmr.cml.PERSONNode: checks that parent knows about children
addChild(int). Method in class pmr.sgml.SGMLNode: the parent may react to adding a child; usually subclassed
addChild(int, SGMLNode). Method in class pmr.sgml.SGMLNode: add a child newNode at childIndex (runs from 0 to nchild); values outside this throw exception
addChoice(String[]). Method in class pmr.simplegraph.ButtonBar: a Choice has several alternative options
addClipboard(). Method in class pmr.sgml.SGMLTOC
addColumn(ObjectArray, String). Method in class pmr.simplegraph.ObjectTable: add a column; checks that it is homogeneous, non-zero length and the same size as any exisiting columns
addContent(String). Method in class pmr.sgml.SGMLNode
addContentModel(String). Method in class pmr.sgml.GI
addDrawableSGMLNode(DrawableSGMLNode). Method in class pmr.sgml.SGMLNode
addDTDName(String). Method in class pmr.sgml.DTD: adds a DTD - ignores it if already present and gives no message (but returns false)
addElement(double). Method in class pmr.euclid.RealArray: append element
addElement(double). Method in class pmr.stat.Univariate
addElement(double, double). Method in class pmr.stat.Bivariate: add a point; this is possible whether 'this' is initilised or not
addElement(int). Method in class pmr.euclid.IntArray: append element
addElement(int). Method in class pmr.euclid.IntSet: add integer.
addElement(Int2). Method in class pmr.euclid.Int2Vector
addElement(IntRange). Method in class pmr.euclid.IntRangeVector
addElement(Object). Method in class pmr.euclid.ObjectArray: append element
addElement(Paragraph). Method in class pmr.simplegraph.SimpleText: add a Paragraph child to a SimpleText.
addElement(Point3). Method in class pmr.euclid.Point3Vector
addElement(Real2). Method in class pmr.euclid.Real2Vector
addElement(RealRange). Method in class pmr.euclid.RealRangeVector
addElement(SGMLNode). Method in class pmr.sgml.SGMLNodeIndexSet: add a Node to this set
addElement(String). Method in class pmr.util.StringList: synonymous with above
addElement(String). Method in class pmr.euclid.StringSet: adds an element.
addElement(String, Drawable). Method in class pmr.simplegraph.MultiScrollableTopLevel
addElement(String, Object). Method in class pmr.euclid.HashedVector: add Object using key (default case-sensitive).
addEntry(TERMENTRYNode). Method in class pmr.cml.Glossary: add an entry; any existing entry is replaced, in which case false is returned
addFileTransporter(). Method in class pmr.sgml.SGMLTOC
addFileTransporter(FileTransporter). Method in class pmr.sgml.SGMLTOC: specialist File Transporter (subclassed)
addFirstname(String). Method in class pmr.cml.PERSONNode
addGIName(String). Method in class pmr.sgml.SGMLNode
addGIs(StringSet). Method in class pmr.sgml.DTD
addHelp(String[]). Method in class pmr.simplegraph.DrawableObject
addHelp(String[]). Method in class pmr.sgml.DrawableSGMLNode
addHelp(String[]). Method in interface pmr.simplegraph.Helpable: add help text.
addHelp(String[]). Method in class pmr.simplegraph.JUMBO
addHelp(String[]). Method in class pmr.simplegraph.ScrollableTopLevel
addHelp(String[]). Method in class pmr.sgml.SGMLApplet
addHelp(String[]). Method in class pmr.simplegraph.SimpleApplet
addIndexTable(String, IndexTable). Method in class pmr.cml.Glossary: add an indextable - there may be several - and hash them.
addInitials(String). Method in class pmr.cml.PERSONNode
addIsotope(int[], double[]). Method in class pmr.molecule.ChemicalElement
addJournal(String). Method in class pmr.cml.BIBNode: the following add x a content subelement; they fail without message if already present
addLastname(String). Method in class pmr.cml.PERSONNode
addLine(String). Method in class pmr.simplegraph.Paragraph: add a line of text - EOR assumed (i.e.
addMenuBar(). Method in class pmr.simplegraph.SimpleFrame: add a menu bar and display it.
addMessageArea(). Method in class pmr.simplegraph.ScrollableTopLevel
addMolecularObject(MolecularObject, String). Method in class pmr.cml.MOLNode: add a MolecularObject (usually called from constructor of MolecularObject)
addNode(int, SGMLNode). Method in class pmr.sgml.SGMLTree
addNode(SGMLNode). Method in class pmr.sgml.SGMLNode: add a pre-formed node to this; returns index
addObject(DrawableObject). Method in class pmr.simplegraph.DrawableObject: adds a DrawableObject as a subObject
addObjectArray(Panel, ObjectArray, String). Method in class pmr.simplegraph.ObjectTable
addPages(String). Method in class pmr.cml.BIBNode: Pages is a String at present until I get fuzzy working
addPELNode(int, String). Method in class pmr.sgml.SGMLTree: add a PEL node (see CoST documentation if you really care).
addRadii(double, double). Method in class pmr.molecule.ChemicalElement
addRange(IntRange). Method in class pmr.euclid.IntSet: add all values from an IntRange
addSet(IntSet). Method in class pmr.euclid.IntSet: concatenate sets
addSet(SGMLNodeIndexSet). Method in class pmr.sgml.SGMLNodeIndexSet: catenate one list onto another
addSet(StringSet). Method in class pmr.euclid.StringSet: catenates one set onto another.
addSGMLAttlist(SGMLAttlist). Method in class pmr.sgml.SGMLNode
addSGMLAttribute(SGMLAttribute). Method in class pmr.sgml.SGMLAttlist: adds a new attribute with value, OR replaces old value (no message)
addSGMLAttribute(SGMLAttribute). Method in class pmr.sgml.SGMLNode: adds SGMLAttribute, or replaces old value
addSGMLAttribute(String, String). Method in class pmr.sgml.SGMLNode: adds SGMLAttribute, or replaces old value
addSGMLAttributes(SGMLAttlist). Method in class pmr.sgml.GI
addSpacegroup(String). Method in class pmr.cml.CRYSTNode: adds spacegroup as String; No checks at present, and no defined convention
addSpacegroupNumber(int). Method in class pmr.cml.CRYSTNode: adds spacegroup as number; No checks at present.
addString(String). Method in class pmr.simplegraph.Paragraph: add a String - NO EOR assumed
addString(String). Method in class pmr.util.StringCounter: add a String.
addSubAddress(IntRange). Method in class pmr.cml.BONDSNode
addSubAddress(IntRange). Method in class pmr.cml.MOLNode
addSubAddress(IntRange). Method in class pmr.cml.SEQUENCENode
addSubAddress(IntRange). Method in interface pmr.cml.SubAddressable
addSubAddress(IntRange). Method in class pmr.cml.XLISTNode
addSubAddresses(IntRangeVector). Method in class pmr.cml.BONDSNode
addSubAddresses(IntRangeVector). Method in class pmr.cml.MOLNode
addSubAddresses(IntRangeVector). Method in class pmr.cml.SEQUENCENode
addSubAddresses(IntRangeVector). Method in interface pmr.cml.SubAddressable
addSubAddresses(IntRangeVector). Method in class pmr.cml.XLISTNode
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.DrawableHTMLNode: add a DrawableHTMLNode subObject ; could be overridden to validate types
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_ADDRESSNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_ANode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_BASENode: cannot add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_BlockNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_BodyNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_BRNode: cannot add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_DDNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_DLNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_DTNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_FlowNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_FontPhraseNode: add a subObject (only HTML_TextNode allowed) (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_HEADNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_HNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_HRNode: cannot add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_IMGNode: cannot add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_LINKNode: cannot add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_LINode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_ListNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_METANode: cannot add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_PNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_TextNode: add a subObject (if not allowed, squeak)
addSubObject(DrawableHTMLNode). Method in class pmr.sgml.HTML_TITLENode: add a subObject (if not allowed, squeak)
addSubObject(HTML_FlowNode). Method in class pmr.sgml.HTML_FlowContainerNode: add a subObject (if not allowed, squeak)
addSubObject(HTML_TextNode). Method in class pmr.sgml.HTML_TextContainerNode: add a subObject (if not allowed, squeak)
addSubordinateTerm(TERMENTRYNode). Method in class pmr.cml.TERMENTRYNode: add subordinate class.
addSuperordinateTerm(TERMENTRYNode). Method in class pmr.cml.TERMENTRYNode: add superordinate class.
addSymmetryOperator(RealMatrix). Method in class pmr.cml.CRYSTNode: adds symmetry operator as 4*3 matrix; No checks at present (apart from shape).
addSynonym(String). Method in class pmr.molecule.Unit: add a synonym (might be an abbreviation) for a Unit.
addTitle(String). Method in class pmr.cml.DrawableX_Node: replaces current title with title and adds TITLE Attribute
addToList(String, String, String, String). Method in class pmr.chemime.CMLEditor
addToList(String, String, String, String). Method in class pmr.chemime.Spectator
addTrashCan(). Method in class pmr.sgml.SGMLTOC
addTree(SGMLNode). Method in class pmr.sgml.SGMLNode: add a tree to a Node (as the last child.
addTree(Vector, SGMLNode). Method in class pmr.sgml.SGMLTree: add an SGMLTree at a given node
addTreeToClipboard(SGMLTree). Method in class pmr.sgml.FileTransporter
addTreeTransporter(). Method in class pmr.sgml.SGMLTOC
addTreeTransporter(TreeTransporter). Method in class pmr.sgml.SGMLTOC: add a specialist TreeTransporter (subclassed)
addURL(String, String, String). Method in class pmr.cml.TERMENTRYNode: add a URL (e.g.
addVolume(String). Method in class pmr.cml.BIBNode
addWithConstraints(Container, Component, int, int, int, int, int, int, double, double, int, int, int, int). Static method in class pmr.simplegraph.SimpleGraph: grid bag contraints (lifted from Java in a Nutshell, p111) with thanx
addYear(String). Method in class pmr.cml.BIBNode
adjustScrollTranslation(Graphics). Method in class pmr.simplegraph.ScrollableTopLevel: adjust for the scrolling
ADMINNode(String, SGMLTree). Constructor for class pmr.cml.ADMINNode
align(double). Method in class pmr.molecule.DynamicAligner: this does the alignment; the gap penalty should be given
AminoAcid(String, String, String, String, String[]). Constructor for class pmr.molecule.AminoAcid: create from 1-letter, 3-letter, name, smiles, pdb atom names.
AminoAcidMatrix(String, double[][]). Constructor for class pmr.molecule.AminoAcidMatrix: construct a matrix, given the values and the aminoacids as a string
AminoAcidMatrix(String, int[][]). Constructor for class pmr.molecule.AminoAcidMatrix
Angle(). Constructor for class pmr.euclid.Angle: create deafult Angle (0.0)
Angle(Angle). Constructor for class pmr.euclid.Angle: copy constructor
Angle(double). Constructor for class pmr.euclid.Angle: create an angle IN RADIANS
Angle(double, AngleType). Constructor for class pmr.euclid.Angle: construct using degrees or radians
Angle(double, double). Constructor for class pmr.euclid.Angle: from X and Y components (uses atan2)
angle(int, int, int). Method in class pmr.euclid.Point3Vector: get angle between 3 points
angle(int, int, int). Method in class pmr.euclid.Real2Vector: get angle between 3 points
angle(IntSet). Method in class pmr.euclid.Point3Vector: get angle between 3 points
angle(IntSet). Method in class pmr.euclid.Real2Vector: get angle between 3 points
AngleType(int). Constructor for class pmr.euclid.AngleType
announce(DrawableX_Node). Method in class pmr.cml.FEATURENode: called (at least) by SEQUENCENode.
ANYDTD(). Constructor for class pmr.sgml.ANYDTD
ANYDTD(DTD). Constructor for class pmr.sgml.ANYDTD: create the DTD if required; I haven't used this so far
append(String[]). Method in class pmr.util.StringList: append an array of Strings
append(StringList). Method in class pmr.util.StringList: add another StringList; by REFERENCE
appendColumnData(IntArray). Method in class pmr.euclid.IntMatrix: append data to matrix columnwise
appendColumnData(IntMatrix). Method in class pmr.euclid.IntMatrix: append data to matrix columnwise
appendColumnData(RealArray). Method in class pmr.euclid.RealMatrix: append data to matrix columnwise
appendColumnData(RealMatrix). Method in class pmr.euclid.RealMatrix: append data to matrix columnwise
appendRowData(IntArray). Method in class pmr.euclid.IntMatrix: append data to matrix rowwise
appendRowData(IntMatrix). Method in class pmr.euclid.IntMatrix: append data to matrix rowwise
appendRowData(RealArray). Method in class pmr.euclid.RealMatrix: append data to matrix rowwise
appendRowData(RealMatrix). Method in class pmr.euclid.RealMatrix: append data to matrix rowwise
AppletFrame(String, Applet, int, int). Constructor for class pmr.simplegraph.AppletFrame
applyFilter(IntArray). Method in class pmr.euclid.IntArray: apply filter (i.e.
applyFilter(RealArray). Method in class pmr.euclid.RealArray: apply filter (i.e.
areChildrenHidden(). Method in class pmr.sgml.GI
areChildrenHidden(). Method in class pmr.sgml.SGMLNode: are node's children hidden either by GI or by user?
areChildrenHiddenByGI(). Method in class pmr.sgml.SGMLNode: are the children of this node hidden by virtue of this node's GI or GI context? To be overridden if required
AROMATIC. Static variable in class pmr.cml.BONDSNode: bond orders normalised (to some extent) - values are irrelevant
ARRAYNode(String, SGMLTree). Constructor for class pmr.cml.ARRAYNode: construct from a SGMLNode in a tree
ArrayTooSmallException(). Constructor for class pmr.euclid.ArrayTooSmallException
ArrayTooSmallException(String). Constructor for class pmr.euclid.ArrayTooSmallException
ATOMSNode(String, SGMLTree). Constructor for class pmr.cml.ATOMSNode
attribs. Variable in class pmr.sgml.SGMLNode
ATTRIBUTENode(String, SGMLTree). Constructor for class pmr.sgml.ATTRIBUTENode
ATTVALNode(String, SGMLTree). Constructor for class pmr.sgml.ATTVALNode
AVLINK. Static variable in class pmr.stat.Multivariate
Axis(int). Constructor for class pmr.simplegraph.Axis

B

BadAttributeException(). Constructor for class pmr.sgml.BadAttributeException
BadAttributeException(String). Constructor for class pmr.sgml.BadAttributeException
BadCCDCFileException(). Constructor for class pmr.chemime.BadCCDCFileException
BadCCDCFileException(String). Constructor for class pmr.chemime.BadCCDCFileException
BadCMLFileException(). Constructor for class pmr.cml.BadCMLFileException
BadCMLFileException(String). Constructor for class pmr.cml.BadCMLFileException
BadESISFileException(). Constructor for class pmr.sgml.BadESISFileException
BadESISFileException(String). Constructor for class pmr.sgml.BadESISFileException
BadFileException(). Constructor for class pmr.util.BadFileException
BadFileException(String). Constructor for class pmr.util.BadFileException
BadJCAMPFileException(). Constructor for class pmr.chemime.BadJCAMPFileException
BadJCAMPFileException(String). Constructor for class pmr.chemime.BadJCAMPFileException
BadMolFileException(). Constructor for class pmr.chemime.BadMolFileException
BadMolFileException(String). Constructor for class pmr.chemime.BadMolFileException
BadPDBFileException(). Constructor for class pmr.chemime.BadPDBFileException
BadPDBFileException(String). Constructor for class pmr.chemime.BadPDBFileException
BadRELATIONNodeException(). Constructor for class pmr.cml.BadRELATIONNodeException
BadRELATIONNodeException(String). Constructor for class pmr.cml.BadRELATIONNodeException
BadSGMLFileException(). Constructor for class pmr.sgml.BadSGMLFileException
BadSGMLFileException(String). Constructor for class pmr.sgml.BadSGMLFileException
BadSMILESException(). Constructor for class pmr.chemime.BadSMILESException
BadSMILESException(String). Constructor for class pmr.chemime.BadSMILESException
BadSubscriptException(). Constructor for class pmr.euclid.BadSubscriptException
BadSubscriptException(String). Constructor for class pmr.euclid.BadSubscriptException
BadSwissProtFileException(). Constructor for class pmr.chemime.BadSwissProtFileException
BadSwissProtFileException(String). Constructor for class pmr.chemime.BadSwissProtFileException
BadTecMLAddressException(). Constructor for class pmr.cml.BadTecMLAddressException
BadTecMLAddressException(String). Constructor for class pmr.cml.BadTecMLAddressException
BadX_NodeException(). Constructor for class pmr.cml.BadX_NodeException
BadX_NodeException(String). Constructor for class pmr.cml.BadX_NodeException
BAR. Static variable in class pmr.stat.Bivariate
base64Decode(byte[]). Static method in class pmr.util.Codecs: This method decodes the given byte[] using the base64-encoding specified in RFC-1521.
base64Decode(String). Static method in class pmr.util.Codecs: This method decodes the given string using the base64-encoding specified in RFC-1521.
base64Encode(byte[]). Static method in class pmr.util.Codecs: This method encodes the given byte[] using the base64-encoding specified in RFC-1521.
base64Encode(String). Static method in class pmr.util.Codecs: This method encodes the given string using the base64-encoding specified in RFC-1521.
BasicSequence(). Constructor for class pmr.molecule.BasicSequence
BasicSequence(String). Constructor for class pmr.molecule.BasicSequence: create in one-letter form
bestPlane(). Method in class pmr.euclid.Point3Vector: get best plane
BIBNode(String, SGMLTree). Constructor for class pmr.cml.BIBNode
Bivariate(). Constructor for class pmr.stat.Bivariate: creates it with default data arrays
Bivariate(RealArray). Constructor for class pmr.stat.Bivariate: form a Bivariate from a RealArray.
Bivariate(Univariate). Constructor for class pmr.stat.Bivariate: form a Bivariate from a Univariate.
Bivariate(Univariate, Univariate). Constructor for class pmr.stat.Bivariate: form a Bivariate from two Univariates.
BOLD. Static variable in class pmr.cml.XHTMLNode
BONDSNode(String, SGMLTree). Constructor for class pmr.cml.BONDSNode: normal constructor
BookmarkWindow(SGMLTree). Constructor for class pmr.sgml.BookmarkWindow
BOTTOM. Static variable in class pmr.simplegraph.Axis
BOTTOM. Static variable in class pmr.simplegraph.SimpleText
bug(Exception). Static method in class pmr.util.Util
bug(String). Static method in class pmr.util.Util: record that we have hit a program bug!!!
ButtonBar(Component). Constructor for class pmr.simplegraph.ButtonBar
ButtonBar(String[], Component). Constructor for class pmr.simplegraph.ButtonBar: this generates just Buttons although others can be added
buttonNumber(). Method in class pmr.simplegraph.MultiDialog: which button was pressed? -1 for none yet
buttonPress(String). Method in class pmr.sgml.SGMLTOC

C

calculateTOC(int, int). Method in class pmr.sgml.SGMLTOC
capitalise(String). Static method in class pmr.util.Util: capitalise a String (whatever the starting case)
CCDC(String). Constructor for class pmr.chemime.CCDC: read as many files of the form root.bib, root.con, root.dat as exist.
CENTROID. Static variable in class pmr.stat.Multivariate
checkMatrix(). Method in class pmr.euclid.Transform2: get new matrix type
checkMatrix(). Method in class pmr.euclid.Transform3: get new matrix type
ChemicalElement(String, int, double). Constructor for class pmr.molecule.ChemicalElement
ChemTree(). Constructor for class pmr.chemime.ChemTree: create from an SGMLStream (either text/sgml or chemical/x-cml)
ChemTree(SGMLStream). Constructor for class pmr.chemime.ChemTree: create from an SGMLStream (either text/sgml or chemical/x-cml)
child. Variable in class pmr.sgml.SGMLNode
CHILD. Static variable in class pmr.sgml.SGMLTOC
childCount(). Method in class pmr.sgml.SGMLNode
childrenHiddenManually. Variable in class pmr.sgml.SGMLNode
childrenToHTML(). Method in class pmr.sgml.SGMLNode: returns (maybe recursively) the HTML representation of the children
childrenToString(). Method in class pmr.cml.ARRAYNode: this is required as we have to deal with _PEL subnodes; note that this returns the UNALTERED input (i.e.
childrenToString(). Method in class pmr.sgml.SGMLNode: returns (maybe recursively) the SGML representation of the children
childrenToString(). Method in class pmr.cml.XVARNode: this is required as we have to deal with _PEL subnodes
chooseMIME(String). Method in class pmr.cml.CMLApplet
chunkedDecode(InputStream). Static method in class pmr.util.Codecs: Decodes chunked data.
chunkedEncode(byte[], NVPair[], boolean). Static method in class pmr.util.Codecs: Encodes data used the chunked encoding.
CIF(String, StringList). Constructor for class pmr.chemime.CIF: create a CMLTree from a CIF file
Circle(int, int, int). Constructor for class pmr.simplegraph.Circle: normal constructor ; x, y are coordinates of centre; radius of zero > 1
clear(). Method in class pmr.euclid.Int2: set to 0, 0
clear(). Method in class pmr.euclid.Real2: set to 0, 0
clearArray(). Method in class pmr.euclid.IntArray: clear all elements of array
clearArray(). Method in class pmr.euclid.ObjectArray: clear all elements of array to null (or 0 or 0.0)
clearArray(). Method in class pmr.euclid.RealArray: clear all elements of array
clearButtons(). Method in class pmr.simplegraph.ButtonBar
clearGraphics(Graphics). Method in class pmr.simplegraph.ScrollableTopLevel: clear to background colour
clearMatrix(). Method in class pmr.euclid.IntMatrix: clear matrix
clearMatrix(). Method in class pmr.euclid.RealMatrix: clear matrix
clearSubAddresses(). Method in class pmr.cml.BONDSNode
clearSubAddresses(). Method in class pmr.cml.MOLNode
clearSubAddresses(). Method in class pmr.cml.SEQUENCENode
clearSubAddresses(). Method in interface pmr.cml.SubAddressable
clearSubAddresses(). Method in class pmr.cml.XLISTNode
clearWorkStationViewPort(Graphics). Method in class pmr.simplegraph.Scaler2D: clears everything within WorkStationViewPort
CLINK. Static variable in class pmr.stat.Multivariate
Clipboard(SGMLTOC). Constructor for class pmr.sgml.Clipboard
Clipboard(SGMLTOC, String). Constructor for class pmr.sgml.Clipboard
clipToBoundingBox(Graphics). Method in class pmr.simplegraph.Scaler2D: clip to boundingBox.
clipToScreenBoundingBox(Graphics). Method in class pmr.simplegraph.Scaler2D: clip to screen limits (usually larger than object bounding box
clone(). Method in class pmr.euclid.IntArray: clones another IntArray
clone(). Method in class pmr.euclid.RealArray: clones another RealArray
clone(Angle). Method in class pmr.euclid.Angle
clone(double[]). Method in class pmr.euclid.Point3: overloaded assignment from a double[] (or a RealArray)
clone(IntMatrix). Method in class pmr.euclid.IntMatrix
clone(Plane3). Method in class pmr.euclid.Plane3
clone(Point3). Method in class pmr.euclid.Point3
clone(Point3). Method in class pmr.euclid.Vector3: from Point3
clone(RealMatrix). Method in class pmr.euclid.RealMatrix
clone(Transform2). Method in class pmr.euclid.Transform2: clone
clone(Transform3). Method in class pmr.euclid.Transform3: clone
clone(Vector3). Method in class pmr.euclid.Point3: from Vector3
clone(Vector3). Method in class pmr.euclid.Vector3
cml2html(String). Static method in class pmr.cml.IndexTable: reads an Index Table in CML format and outputs the corresponding HTML
CMLApplet(). Constructor for class pmr.cml.CMLApplet
CMLApplet(String). Constructor for class pmr.cml.CMLApplet
CMLDTD(). Constructor for class pmr.cml.CMLDTD
CMLDTD(DTD). Constructor for class pmr.cml.CMLDTD: create the DTD if required; I haven't used this so far
CMLEditor(). Constructor for class pmr.chemime.CMLEditor
CMLEditor(String). Constructor for class pmr.chemime.CMLEditor
cmlIndex. Variable in class pmr.chemime.ChemTree
CMLNode(String, SGMLTree). Constructor for class pmr.cml.CMLNode
CMLTransporter(SGMLTOC). Constructor for class pmr.cml.CMLTransporter
CMLTransporter(SGMLTOC, String). Constructor for class pmr.cml.CMLTransporter
CMLTree(). Constructor for class pmr.cml.CMLTree
CMLTree(ESISStream). Constructor for class pmr.cml.CMLTree
CMLTree(SGMLStream). Constructor for class pmr.cml.CMLTree
CoincidentDataException(). Constructor for class pmr.stat.CoincidentDataException
CoincidentDataException(String). Constructor for class pmr.stat.CoincidentDataException
color. Variable in class pmr.sgml.SGMLNode
cols. Variable in class pmr.euclid.IntMatrix: number of columns
cols. Variable in class pmr.euclid.RealMatrix: number of columns
columnwiseDivide(RealArray). Method in class pmr.euclid.RealMatrix: divide each column of a matrix by a vector of scalars (i.e.
Complex(). Constructor for class pmr.euclid.Complex
Complex(Complex). Constructor for class pmr.euclid.Complex
Complex(double). Constructor for class pmr.euclid.Complex: real component only
Complex(double, Angle). Constructor for class pmr.euclid.Complex: in polar coords
Complex(double, double). Constructor for class pmr.euclid.Complex: from components
Complex(Polar). Constructor for class pmr.euclid.Complex
Complex(Real2). Constructor for class pmr.euclid.Complex: from base class
component. Variable in class pmr.simplegraph.DrawableObject
component. Variable in class pmr.sgml.DrawableSGMLNode
concatenate(EuclidVector). Method in class pmr.euclid.EuclidVector: concatenate two vectors (must be of same type - hence protected)
concatenate(Transform2). Method in class pmr.euclid.Transform2: concatenate
concatenate(Transform3). Method in class pmr.euclid.Transform3: concatenate
containedDOs. Variable in class pmr.simplegraph.DrawableObject
contains(double). Method in class pmr.euclid.RealRange: synonym for includes()
contains(int). Method in class pmr.cml.FEATURENode: does a feature contain a given residue number?
contains(int). Method in class pmr.euclid.IntRange: synonym for includes()
contains(int). Method in class pmr.euclid.IntSet
contains(String). Method in class pmr.euclid.StringSet: does Set contain String? (according to case-sensitivity
containsObjectWithKey(String). Method in class pmr.euclid.HashedVector: has key been used to store an object?
containsPoint(Point3). Method in class pmr.euclid.Line3: is a point on a line?
containsPoint(Point3). Method in class pmr.euclid.Plane3: is a point on a plane?
containsTag(String). Static method in class pmr.sgml.HTML_BlockNode: is tag among those that this Node contains.
containsTag(String). Static method in class pmr.sgml.HTML_EmptyNode: is tag among those that this Node contains.
containsTag(String). Static method in class pmr.sgml.HTML_FlowContainerNode: is tag among those that this Node contains.
containsTag(String). Static method in class pmr.sgml.HTML_TextContainerNode: is tag among those that this Node contains.
containsTag(String). Static method in class pmr.sgml.HTML_TextNode: is tag among those that this Node contains.
content. Variable in class pmr.sgml.SGMLNode
contentNode. Variable in class pmr.sgml.SGMLNode: Some SGMLNodes are just containers for others - a contentNode is one such
CONTENTNode(String, SGMLTree). Constructor for class pmr.sgml.CONTENTNode
continueBox(Frame). Static method in class pmr.simplegraph.SimpleGraph: asks user to continue (and blocks till then)
contract(). Method in class pmr.util.StringList: return unused buffer space
convertFromOtherUnit(double, Unit). Method in class pmr.molecule.Unit
convertFromSI(double). Method in class pmr.molecule.Unit
convertFromTo(double, String, String). Static method in class pmr.molecule.Unit
convertToSI(double). Method in class pmr.molecule.Unit
copy(double[]). Static method in class pmr.euclid.RealArray: copy a double[] into a new one
copy(int[]). Static method in class pmr.euclid.IntArray: copy a int[] into a new one
copy(Object[]). Static method in class pmr.euclid.ObjectArray: copy a Object[] into a new one
copyLowerToUpper(). Method in class pmr.euclid.IntSquareMatrix: copy lower triangle into upper triangle (i.e.
copyLowerToUpper(). Method in class pmr.euclid.RealSquareMatrix: copy lower triangle into upper triangle (i.e.
copyUpperToLower(). Method in class pmr.euclid.IntSquareMatrix: copy upper triangle into lower triangle (i.e.
copyUpperToLower(). Method in class pmr.euclid.RealSquareMatrix: copy upper triangle into lower triangle (i.e.
cos(). Method in class pmr.euclid.Angle: trigonometric functions
createAdd0(SGMLTree, int, String, FEATURENode, String, String, String). Static method in class pmr.cml.FEATURENode
createADMINNode(). Method in class pmr.cml.TERMENTRYNode
createAndAdd(SGMLTree, int). Static method in class pmr.cml.CRYSTNode
createAndAdd(SGMLTree, int). Static method in class pmr.cml.FORMULANode: create from a data entry; this has to add it to the tree as well
createAndAdd(SGMLTree, int). Static method in class pmr.cml.XLISTNode: create from a data entry and add to tree
createAndAdd(SGMLTree, int, Date). Static method in class pmr.cml.XVARNode: create from a data entry as date and add to tree
createAndAdd(SGMLTree, int, double). Static method in class pmr.cml.XVARNode: create from a data entry as float and add to tree
createAndAdd(SGMLTree, int, double[]). Static method in class pmr.cml.ARRAYNode: create from a double[] - still being tested
createAndAdd(SGMLTree, int, int). Static method in class pmr.cml.XVARNode: create from a data entry as integer and add to tree
createAndAdd(SGMLTree, int, int, int, int, int, int, int). Static method in class pmr.cml.XVARNode: create from a data entry as date and add to tree ; if hrs, sec are negative, they are ignored
createAndAdd(SGMLTree, int, int[]). Static method in class pmr.cml.ARRAYNode: create from a int[] - still being tested
createAndAdd(SGMLTree, int, RealMatrix). Static method in class pmr.cml.ARRAYNode: create from a RealMatrix - still being tested
createAndAdd(SGMLTree, int, String). Static method in class pmr.cml.ADMINNode
createAndAdd(SGMLTree, int, String). Static method in class pmr.cml.BIBNode
createAndAdd(SGMLTree, int, String). Static method in class pmr.cml.TERMENTRYNode
createAndAdd(SGMLTree, int, String). Static method in class pmr.cml.XVARNode: create from a data entry as string and add to tree
createAndAdd(SGMLTree, int, String, String, DrawableX_Node, int, int, String, String). Static method in class pmr.cml.FEATURENode: create from a data entry; this has to add it to the tree as well
The target is a node such as a SEQUENCENode or ATOMSNode
createAndAdd(SGMLTree, int, String, String, int, String). Static method in class pmr.cml.SEQUENCENode
createAndAdd(SGMLTree, int, String, String, String). Static method in class pmr.cml.PERSONNode
createAndAdd(SGMLTree, int, String, String, Vector, String, String). Static method in class pmr.cml.FEATURENode: this adds a range of addresses to the Feature
createAndAdd(SGMLTree, int, String[]). Static method in class pmr.cml.ARRAYNode: create from a String[] - still being tested
createAndAdd(SGMLTree, int, Vector, Vector, boolean). Static method in class pmr.cml.RELATIONNode
createAndAdd(SGMLTree, String, int, String). Static method in class pmr.cml.XVARNode: create from a data entry as TYPE=type and add to tree
createGeneralTOC(int). Method in class pmr.cml.CMLTree: create a chemical TOC
createGeneralTOC(int). Method in class pmr.sgml.SGMLTree: generalTOC has icons for editing
createPELandAdd(int, String). Method in class pmr.sgml.SGMLNode: add PEL node (often from subclasses); addes the current node (this) and also creates a PEL node from content which it then also adds
createSheet(). Method in class pmr.simplegraph.ObjectTable
createSubclassedNode(String, SGMLTree). Static method in class pmr.sgml.ANYDTD: A means of creating sub-objects in a ANY document;
createSubclassedNode(String, SGMLTree). Static method in class pmr.cml.CMLDTD: A means of creating sub-objects in a CML document; in practice this is delegated to TecML and MOL
createSubclassedNode(String, SGMLTree). Static method in class pmr.sgml.DTD: creates a new SGMLNode of the appropriate Subclass (if it exists).
createSubclassedNode(String, SGMLTree). Static method in class pmr.sgml.DTDDTD: creates a new SGMLNode of the appropriate Subclass (if it exists).
createSubclassedNode(String, SGMLTree). Static method in class pmr.sgml.HTMLDTD: creates a new SGMLNode of the appropriate Subclass (if it exists).
createSubclassedNode(String, SGMLTree). Static method in class pmr.cml.MOLDTD: creates a new SGMLNode of the appropriate Subclass (if it exists).
createSubclassedNode(String, SGMLTree). Static method in class pmr.cml.TecMLDTD: creates a new SGMLNode of the appropriate Subclass (if it exists).
createTERMENTRYNode(CMLTree, String). Static method in class pmr.cml.TERMENTRYNode: standalone TERMENTRYNode (i.e.
createTitle(). Method in class pmr.chemime.ChemTree: and an optional title; I'm not sure this is a good idea for all cases.
createTOC(int). Method in class pmr.sgml.SGMLTree: to be used after the tree has been created
createTree(). Method in class pmr.chemime.ChemTree: all ChemTrees have a default root structure
createTree(). Method in class pmr.sgml.SGMLApplet: create a Tree from the file that has just been read in
createTree(String). Method in class pmr.cml.CMLApplet
cross(Vector3). Method in class pmr.euclid.Vector3: Vector product
CRYSTNode(String, SGMLTree). Constructor for class pmr.cml.CRYSTNode
CUMULATIVE. Static variable in class pmr.stat.Univariate
cumulativeSum(). Method in class pmr.euclid.IntArray: cumulative sum of array (new RA contains
elem[i] = sum(k = 0 to i) f[k]
does not modify 'this'
cumulativeSum(). Method in class pmr.euclid.RealArray: cumulative sum of array (new RA contains
elem[i] = sum(k = 0 to i) f[k]
does not modify 'this'
currentURL. Static variable in class pmr.simplegraph.SimpleApplet

D

DataPrimitive(String, SGMLTree). Constructor for class pmr.cml.DataPrimitive: construct from a SGMLNode in a tree
debug(). Method in class pmr.cml.ADMINNode: for debug
debug(). Method in class pmr.molecule.AminoAcid
debug(). Method in class pmr.cml.ARRAYNode: for debug
debug(). Method in class pmr.cml.ATOMSNode: for debug
debug(). Method in class pmr.cml.BIBNode: for debug
debug(). Method in class pmr.stat.Bivariate
debug(). Method in class pmr.cml.BONDSNode: for debug
debug(). Method in class pmr.simplegraph.Circle
debug(). Method in interface pmr.simplegraph.Drawable: for debug
debug(). Method in class pmr.sgml.DrawableHTMLNode: for debug
debug(). Method in class pmr.simplegraph.DrawableObject
debug(). Method in class pmr.sgml.DrawableSGMLNode: for debug
debug(). Method in class pmr.stat.DrawableStat
debug(). Method in class pmr.cml.DrawableX_Node: for debug
debug(). Method in class pmr.sgml.DTD
debug(). Method in class pmr.cml.FEATURENode: for debug
debug(). Method in class pmr.cml.FORMULANode: for debug
debug(). Method in class pmr.sgml.GI
debug(). Method in class pmr.euclid.IntSet
debug(). Method in class pmr.cml.MOLNode: for debug
debug(). Method in class pmr.simplegraph.Paragraph: for debug
debug(). Method in class pmr.cml.PERSONNode: for debug
debug(). Method in class pmr.cml.RELATIONNode: for debug
debug(). Method in class pmr.cml.SEQUENCENode: for debug
debug(). Method in class pmr.sgml.SGMLAttlist
debug(). Method in class pmr.sgml.SGMLAttribute
debug(). Method in class pmr.sgml.SGMLNode
debug(). Method in class pmr.sgml.SGMLNodeIndexSet
debug(). Method in class pmr.sgml.SGMLTree
debug(). Method in class pmr.sgml.SGMLUserClass
debug(). Method in class pmr.molecule.SimpleSMILES
debug(). Method in class pmr.simplegraph.SimpleText: for debug
debug(). Method in class pmr.simplegraph.Square
debug(). Method in class pmr.util.StringList
debug(). Method in class pmr.euclid.StringSet
debug(). Method in class pmr.cml.TERMENTRYNode: for debug
debug(). Method in class pmr.stat.Univariate
debug(). Method in class pmr.cml.XMatrix
DEGREES. Static variable in class pmr.euclid.Angle
DEGREES_IN_RADIAN. Static variable in class pmr.euclid.Angle
deleteButton(String). Method in class pmr.simplegraph.ButtonBar: remove a button (synonymous with the above
deleteColumn(int). Method in class pmr.euclid.IntMatrix: delete column from matrix and close up
deleteColumn(int). Method in class pmr.euclid.RealMatrix: delete column from matrix and close up
deleteColumns(int, int). Method in class pmr.euclid.IntMatrix: delete 2 or more adjacent columns (inclusive) from matrix and close up
deleteColumns(int, int). Method in class pmr.euclid.RealMatrix: delete 2 or more adjacent columns (inclusive) from matrix and close up
deleteElement(int). Method in class pmr.euclid.IntArray: delete element and close up; if outside range, take no action
deleteElement(int). Method in class pmr.euclid.ObjectArray: delete element and close up; if outside range, take no action
deleteElement(int). Method in class pmr.euclid.RealArray: delete element and close up; if outside range, take no action
deleteElements(double[], int, int). Static method in class pmr.euclid.RealArray: delete elements (lo - > hi inclusive) in a float[] and close up; if hi >= float.length hi is reset to float.length-1.
deleteElements(int, int). Method in class pmr.euclid.IntArray: delete elements and close up; if outside range take no action
deleteElements(int, int). Method in class pmr.euclid.ObjectArray: delete elements and close up; if outside range take no action
deleteElements(int, int). Method in class pmr.euclid.RealArray: delete elements and close up; if outside range take no action
deleteElements(int[], int, int). Static method in class pmr.euclid.IntArray: delete elements (lo - > hi inclusive) in a float[] and close up; if hi >= float.length hi is reset to float.length-1.
deleteNode(SGMLNode). Method in class pmr.sgml.SGMLTOC
deleteNodeAndSubtree(). Method in class pmr.sgml.SGMLNode: delete a node and all its descendants
deleteRow(int). Method in class pmr.euclid.IntMatrix: delete row from matrix and close up
deleteRow(int). Method in class pmr.euclid.RealMatrix: delete row from matrix and close up
deleteRows(int, int). Method in class pmr.euclid.IntMatrix: delete 2 or more adjacent rows (inclusive) from matrix and close up; if (high > rows-1 high -> rows-1; or low < 0, low -> 0
deleteRows(int, int). Method in class pmr.euclid.RealMatrix: delete 2 or more adjacent rows (inclusive) from matrix and close up; if (high > rows-1 high -> rows-1; or low < 0, low -> 0
deleteSelected(String). Method in class pmr.chemime.CMLEditor
deleteSelected(String). Method in class pmr.chemime.Spectator
deleteSubtree(). Method in class pmr.sgml.SGMLNode: delete all descendants of a node
deQuote(String). Static method in class pmr.util.Util: remove balanced quotes from ends of (trimmed) string, else no action
deselect(String). Method in class pmr.chemime.CMLEditor
deselect(String). Method in class pmr.chemime.Spectator
deselectList(String). Method in class pmr.chemime.CMLEditor: deselect any selected item on this list
deselectList(String). Method in class pmr.chemime.Spectator: deselect any selected item on this list
destroy(). Method in class pmr.sgml.SGMLTOC: kill the Frame in which the SGMLTOC is housed
destroy(). Method in class pmr.sgml.SGMLTree: frees memory in this tree (hopefully)
detachFromTree(). Method in class pmr.sgml.SGMLNode: delete this but not its descendants
determinant(). Method in class pmr.euclid.IntSquareMatrix: determinant - only goes up to order 3 at present :-(
determinant(). Method in class pmr.euclid.RealSquareMatrix: determinant - only goes up to order 3 at present :-(
deviationsFromPlane(Plane3). Method in class pmr.euclid.Point3Vector: get deviations of coordinates from plane
diagonal(IntArray). Static method in class pmr.euclid.IntSquareMatrix: make diagonal matrix
diagonal(RealArray). Static method in class pmr.euclid.RealSquareMatrix: make diagonal matrix
diagonaliseAndReturnRank(RealArray, RealSquareMatrix, IllConditionedMatrixException). Method in class pmr.euclid.RealSquareMatrix: diagonalisation - returns eigenvalues and vectors as MODIFIED arguments; this is NOT affected
Note that IllConditionedMatrixException is RETURNED and not thrown
DifferentSGMLTreesException(). Constructor for class pmr.sgml.DifferentSGMLTreesException
DifferentSGMLTreesException(String). Constructor for class pmr.sgml.DifferentSGMLTreesException
display(). Method in class pmr.cml.ARRAYNode: dummy until we write one...
display(). Method in class pmr.cml.ATOMSNode: display() is unlikely to be possible without help from MOL or CRYST, so just ignore it
display(). Method in class pmr.cml.BONDSNode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.chemime.CCDC: displays the molecule automatically
display(). Method in class pmr.sgml.Clipboard: displays the TreeContainer; override thsi
display(). Method in class pmr.cml.CMLNode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.cml.CMLTransporter: displays the TreeContainer; override thsi
display(). Method in class pmr.cml.CMLTree: the 'default' display for this object, rather than the tree.
display(). Method in class pmr.cml.CRYSTNode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.simplegraph.DrawableObject: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.sgml.DrawableSGMLNode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.stat.DrawableStat: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.cml.FEATURENode: displays the nodes.
display(). Method in class pmr.sgml.FileTransporter: displays the TreeContainer; override thsi
display(). Method in class pmr.cml.FORMULANode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.cml.FullAddress: display itself; works out the Node and then tells the node to display itself with any subaddress
display(). Method in class pmr.sgml.HTML_PNode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.chemime.JCAMP: displays the spectrum automatically
display(). Method in class pmr.cml.MOLNode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.molecule.MySequence: this creates a ScrollableTopLevel and gets the Graphics context from it
display(). Method in class pmr.simplegraph.NumericTable
display(). Method in class pmr.cml.RELATIONNode: displays the nodes.
display(). Method in class pmr.sgml.SGMLNode: display.
display(). Method in class pmr.chemime.SMILES: the 'default' display for this object, rather than the tree.
display(). Method in class pmr.chemime.SpectatorContainer: displays the TreeContainer; override thsi
display(). Method in class pmr.chemime.SwissProt: displays the sequence automatically
display(). Method in class pmr.cml.SYMMETRYNode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.cml.TERMENTRYNode: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.sgml.TrashCan: displays the TreeContainer; override thsi
display(). Method in class pmr.sgml.TreeContainer: displays the TreeContainer; override thsi
display(). Method in class pmr.sgml.TreeTransporter: displays the TreeContainer; override thsi
display(). Method in class pmr.stat.Univariate: Kicks off a ScrollableTopLevel which contains the object.
display(). Method in class pmr.cml.XLISTNode: this is so that undeveloped options don't throw empty windows
display(). Method in class pmr.cml.XVARNode: Kicks off a ScrollableTopLevel which contains the object.
display(File). Method in class pmr.simplegraph.ObjectTable
display(Graphics). Method in class pmr.cml.ADMINNode: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.cml.ARRAYNode: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.sgml.ATTRIBUTENode: a very simplistic display which displays the untagged event stream including children content
display(Graphics). Method in class pmr.sgml.ATTVALNode: a very simplistic display which displays the untagged event stream including children content
display(Graphics). Method in class pmr.simplegraph.Axis: displays the object in the correct position for the box (defined by Scaler2D
display(Graphics). Method in class pmr.molecule.BasicSequence: simple output of sequence - normally overwritten
display(Graphics). Method in class pmr.cml.BIBNode: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.stat.Bivariate: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.simplegraph.Circle: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.cml.CMLTree: as above, but output to preselected Graphics; not sure yet what to do about Scaler2D for multiple nodes
display(Graphics). Method in class pmr.sgml.CONTENTNode: a very simplistic display which displays the untagged event stream including children content
display(Graphics). Method in interface pmr.simplegraph.Drawable: displays the object to a pre-selected graphics context
display(Graphics). Method in class pmr.sgml.DrawableHTMLNode: displays the object to a pre-selected graphics context
display(Graphics). Method in class pmr.simplegraph.DrawableObject: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.sgml.DrawableSGMLNode: displays the object to a pre-selected graphics context
display(Graphics). Method in class pmr.stat.DrawableStat: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.simplegraph.DrawableText: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.cml.DrawableX_Node: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.sgml.DTDNode: a very simplistic display which displays the untagged event stream including children content
display(Graphics). Method in class pmr.sgml.ELEMENTNode: a very simplistic display which displays the untagged event stream including children content
display(Graphics). Method in class pmr.cml.FEATURENode: no routine yet to display the relationships...
display(Graphics). Method in class pmr.sgml.HTML_FontPhraseNode: display saves the current Font, sets the opne corresponding to type and recursively displays the HTML_TextNode subObjects
display(Graphics). Method in class pmr.sgml.HTML_TextNode
display(Graphics). Method in class pmr.sgml.HTMLNode: a very simplistic display which displays the untagged event stream including children content
display(Graphics). Method in class pmr.sgml.LISTNode: a very simplistic display which displays the untagged event stream including children content
display(Graphics). Method in class pmr.cml.MolecularObject: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.cml.MOLNode: called from the display() routine of DrawableX_Node
display(Graphics). Method in class pmr.stat.Multivariate: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.molecule.MySequence: a fun routine which plots the sequence (using the superclass) and then draws a plot underneath
display(Graphics). Method in class pmr.simplegraph.Paragraph: displays the object to a pre-selected graphics context
display(Graphics). Method in class pmr.cml.PERSONNode: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.molecule.ProteinSequence: simple output of sequence - normally overwritten
display(Graphics). Method in class pmr.cml.RELATIONNode: no routine yet to display the relationships...
display(Graphics). Method in class pmr.cml.SEQUENCENode: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.sgml.SGMLNode: display a SGMLNode to Graphics provided from some other SGMLNode (e.g.
display(Graphics). Method in class pmr.sgml.SGMLTOC
display(Graphics). Method in class pmr.simplegraph.SimpleText: displays the object to a pre-selected graphics context
display(Graphics). Method in class pmr.simplegraph.Square: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.cml.TERMENTRYNode: called from the display() routine of DrawableX_Node
display(Graphics). Method in class pmr.stat.Univariate: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.cml.XHTMLNode: called from the display() routine of DrawableX_Node
display(Graphics). Method in class pmr.cml.XLISTNode: used by the ScrollableTopLevel to paint the object, or can be used to draw the object to somewhere else.
display(Graphics). Method in class pmr.cml.XVARNode: only for large chunks of text at present
display(Graphics, Component). Method in class pmr.stat.Bivariate: this may encapsulate the above routine, as we often need the component, e.g.
display(Graphics, Component). Method in interface pmr.simplegraph.Drawable: this may encapsulate the above routine, as we often need the component, e.g.
display(Graphics, Component). Method in class pmr.simplegraph.DrawableObject: in case we know the Component
display(Graphics, Component). Method in class pmr.sgml.DrawableSGMLNode: dummy at present until worked out
display(Graphics, Component). Method in class pmr.cml.DrawableX_Node: this is the primary mechanism for calling the display and the component can be captured here.
display(Graphics, Component). Method in class pmr.stat.Multivariate: this may encapsulate the above routine, as we often need the component, e.g.
display(Graphics, Component). Method in class pmr.simplegraph.Paragraph: dummy at present until worked out
display(Graphics, Component). Method in class pmr.simplegraph.SimpleText: dummy at present until worked out
display(Graphics, Component). Method in class pmr.stat.Univariate: this may encapsulate the above routine, as we often need the component, e.g.
display(Graphics, Scaler2D). Method in class pmr.stat.Bivariate: normally called from an object which otherwise uses Scaler2D, but wants to reroute graphics through Bivariate
display(Int2Range). Method in class pmr.stat.DrawableStat: alternative display routine when we know the target screen area for the object
display(Int2Range). Method in class pmr.cml.DrawableX_Node: alternative display routine when we know the target screen area for the object
display(IntSet). Method in class pmr.stat.DrawableStat: display the subaddresses in the node; we might need to alter the hierarchy to cater for this...
display(IntSet). Method in class pmr.cml.DrawableX_Node: display the subaddresses in the node; we might need to alter the hierarchy to cater for this...
display(String, String, CMLTree). Method in class pmr.chemime.CMLEditor: displays object - looks to headerChoice to see where
display(String, String, CMLTree). Method in class pmr.chemime.Spectator: displays object - looks to headerChoice to see where
displayAddress(). Method in class pmr.cml.XVARNode: for an XVAR of ADDRESS, display it if possible
displayBoundingBox(boolean). Method in class pmr.stat.Bivariate
displayChildren(Graphics). Method in class pmr.sgml.SGMLNode: display all children.
displayChildrenRecursively(Graphics). Method in class pmr.sgml.SGMLNode: the same, but recurse
displayHydrophobicity(). Method in class pmr.molecule.ProteinSequence
displayIDs(). Method in class pmr.cml.ARRAYNode: for an ARRAY of IDs, display them if possible
displayNodeAsChild(int). Method in class pmr.sgml.SGMLTree
displayRELATIONTargets(FullAddress). Static method in class pmr.cml.RELATIONNode: display all RELATION
displayXAxis(boolean). Method in class pmr.stat.Bivariate
displayYAxis(boolean). Method in class pmr.stat.Bivariate
dispose(). Method in class pmr.simplegraph.ScrollableTopLevel: destroy the ScrollableTopLevel
dispose(). Method in class pmr.simplegraph.SimpleApplet: dispose of Applet
dist. Variable in class pmr.euclid.Plane3: distance of plane from origin
distance(int, int). Method in class pmr.euclid.Point3Vector: get distance between 2 points
distance(int, int). Method in class pmr.euclid.Real2Vector: get distance between 2 points
distance(IntSet). Method in class pmr.euclid.Point3Vector: get distance between 2 points
distance(IntSet). Method in class pmr.euclid.Real2Vector: get distance between 2 points
distanceFromLine(Line3). Method in class pmr.euclid.Point3
distanceFromPlane(Plane3). Method in class pmr.euclid.Point3
divideBy(Complex). Method in class pmr.euclid.Complex: divide a complex by a complex
divideBy(double). Method in class pmr.euclid.Point3
divideBy(Polar). Method in class pmr.euclid.Polar: divide a polar by a polar
docBase. Static variable in class pmr.simplegraph.SimpleApplet
docroot. Variable in class pmr.chemime.ChemTree
doctypeString. Variable in class pmr.sgml.DTD
dot(double[]). Method in class pmr.euclid.Vector3: dot product - protected
dot(Vector3). Method in class pmr.euclid.Vector3: dot product
dotPlot(Bivariate, double). Method in class pmr.stat.Bivariate: do a dot-plot of two Bivariates.
dotProduct(Int2). Method in class pmr.euclid.Int2: get dot product
dotProduct(IntArray). Method in class pmr.euclid.IntArray: dot product of two IntArrays - if of same length - else zero
dotProduct(Real2). Method in class pmr.euclid.Real2: get dot product
dotProduct(RealArray). Method in class pmr.euclid.RealArray: dot product of two RealArrays - if of same length - else zero
doubleBuffer1(). Method in class pmr.simplegraph.ScrollableTopLevel
doubleBuffer2(Graphics). Method in class pmr.simplegraph.ScrollableTopLevel
draw(Graphics, RealArray). Method in class pmr.simplegraph.Scaler2D: draw a simple graph of a RealArray with connecting lines
drawableHelp. Variable in class pmr.sgml.DrawableSGMLNode
drawableHelp. Variable in class pmr.sgml.SGMLTree
DrawableHelp(StringList, String). Constructor for class pmr.simplegraph.DrawableHelp: create a DrawableHelp with text
DrawableHTMLNode(). Constructor for class pmr.sgml.DrawableHTMLNode: create the DrawableHTMLNode
DrawableHTMLNode(String, SGMLTree). Constructor for class pmr.sgml.DrawableHTMLNode
DrawableObject(). Constructor for class pmr.simplegraph.DrawableObject: normal constructor
DrawableSGMLNode(). Constructor for class pmr.sgml.DrawableSGMLNode: create the DrawableSGMLNode
DrawableSGMLNode(String, SGMLTree). Constructor for class pmr.sgml.DrawableSGMLNode
drawableSGMLNodes. Variable in class pmr.sgml.SGMLNode: DrawableSGMLNodes which refer to this node
DrawableStat(). Constructor for class pmr.stat.DrawableStat: normal constructor
DrawableText(StringList). Constructor for class pmr.simplegraph.DrawableText: create a DrawableText with text
DrawableX_Node(SGMLTree). Constructor for class pmr.cml.DrawableX_Node: some nodes will not have GIs - they are given a GI of "UNKNOWN"
DrawableX_Node(String, SGMLTree). Constructor for class pmr.cml.DrawableX_Node
drawArrow(Graphics, int, int, int, int). Static method in class pmr.simplegraph.SimpleGraph: needs work - only draws a line at present
drawBib(Graphics). Method in class pmr.cml.BIBNode
drawBond(Graphics, int, int, int, int, int, double, double). Method in class pmr.cml.MOLNode
drawBoundingBox(Graphics). Method in class pmr.simplegraph.Scaler2D: only useful if continually redrawn...
drawCircle(Graphics, double, double, int). Method in class pmr.simplegraph.Scaler2D
drawDefaultIcon(Graphics, int, int). Method in class pmr.sgml.GI: early steps at providing graphic hints!
drawFeature(Graphics, FEATURENode, int, int, int). Method in class pmr.cml.SEQUENCENode
drawFeature0(Graphics, FEATURENode, int, int, int, int, int, int). Method in class pmr.cml.SEQUENCENode
drawFeatures(Graphics). Method in class pmr.cml.SEQUENCENode
drawHide(Graphics, SGMLNode, int, int, int). Method in class pmr.sgml.SGMLTOC: draw a box with - or + to hide node or its children.
drawIcon(Component, Graphics, int, int). Method in class pmr.sgml.Clipboard: this must be subclassed or the wrong static is accessed
drawIcon(Component, Graphics, int, int). Method in class pmr.cml.CMLTransporter: this must be subclassed or the wrong static is accessed
drawIcon(Component, Graphics, int, int). Static method in class pmr.simplegraph.DrawableHelp
drawIcon(Component, Graphics, int, int). Method in class pmr.sgml.FileTransporter: this must be subclassed or the wrong static is accessed
drawIcon(Component, Graphics, int, int). Method in class pmr.chemime.SpectatorContainer: this must be subclassed or the wrong static is accessed
drawIcon(Component, Graphics, int, int). Method in class pmr.sgml.TrashCan: this must be subclassed or the wrong static is accessed
drawIcon(Component, Graphics, int, int). Method in class pmr.sgml.TreeContainer: this must be subclassed or the wrong static is accessed
drawIcon(Component, Graphics, int, int). Method in class pmr.sgml.TreeTransporter: this must be subclassed or the wrong static is accessed
drawIcon(Graphics, int, int). Method in class pmr.cml.ADMINNode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.cml.ARRAYNode: at some stage make this useful to subclasses
drawIcon(Graphics, int, int). Method in class pmr.cml.ATOMSNode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.sgml.ATTRIBUTENode: draws an icon based on the GI - crude at present!! Overridden by subclasses.
drawIcon(Graphics, int, int). Method in class pmr.sgml.ATTVALNode: draws an icon based on the GI - crude at present!! Overridden by subclasses.
drawIcon(Graphics, int, int). Method in class pmr.cml.BIBNode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.cml.CMLNode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.sgml.CONTENTNode: draws an icon based on the GI - crude at present!! Overridden by subclasses.
drawIcon(Graphics, int, int). Method in class pmr.cml.CRYSTNode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.cml.DataPrimitive: at some stage make this useful to subclasses
drawIcon(Graphics, int, int). Method in class pmr.cml.DrawableX_Node: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.sgml.DTDNode: draws an icon based on the GI - crude at present!! Overridden by subclasses.
drawIcon(Graphics, int, int). Method in class pmr.sgml.ELEMENTNode: draws an icon based on the GI - crude at present!! Overridden by subclasses.
drawIcon(Graphics, int, int). Method in class pmr.cml.FORMULANode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.sgml.GI: this is just proof of concept - requires proper class loading via interfaces, as does the GI/DTD stuff anayway
drawIcon(Graphics, int, int). Method in class pmr.sgml.HTMLNode: draws an icon based on the GI - crude at present!! Overridden by subclasses.
drawIcon(Graphics, int, int). Method in class pmr.sgml.LISTNode: draws an icon based on the GI - crude at present!! Overridden by subclasses.
drawIcon(Graphics, int, int). Method in class pmr.cml.MOLNode: draw Icon
drawIcon(Graphics, int, int). Method in class pmr.cml.PERSONNode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.cml.SEQUENCENode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.sgml.SGMLNode: draws an icon based on the GI - crude at present!! Overridden by subclasses.
drawIcon(Graphics, int, int). Method in class pmr.sgml.SGMLTOC
drawIcon(Graphics, int, int). Method in class pmr.cml.SYMMETRYNode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.cml.TERMENTRYNode: draw a CML icon
drawIcon(Graphics, int, int). Method in class pmr.cml.XLISTNode: draw Icon
drawIcon(Graphics, int, int). Method in class pmr.cml.XVARNode: at some stage make this useful to subclasses
drawIcon1(Component, Graphics, int, int, Image, Image). Method in class pmr.sgml.TreeContainer
drawImageFromPM(Component, Graphics, int, int, String[], String[]). Static method in class pmr.simplegraph.SimpleImageOne: draw an Image at a specified position
drawLine(Graphics, double, double, double, double). Method in class pmr.simplegraph.Scaler2D: analogues of awt.Graphics, but in double WC coords;
drawLine(Graphics, int, int, int, int, int). Static method in class pmr.simplegraph.SimpleGraph: crude routine for drawing thick lines till Java do it better
drawManipulatorBox(Graphics). Method in class pmr.simplegraph.Scaler2D: default manipulator is whole screen port (WorkStationViewPort)
drawManipulatorBox(Graphics, Int2Range). Method in class pmr.simplegraph.Scaler2D: screen coordinates drawing of manipulator box
drawManipulatorBox(Graphics, Real2Range). Method in class pmr.simplegraph.Scaler2D: WorldCoords drawing of manipulator box
drawNode(Graphics, SGMLNode, Int2, int). Method in class pmr.sgml.SGMLTOC
drawNodes(Graphics). Method in class pmr.sgml.SGMLTOC: draw the nodes, but don't start till after the calculateTOC has been done
drawNullIcon(Graphics, int, int). Static method in class pmr.sgml.GI: early steps at providing graphic hints!
drawRect(Graphics, double, double, double, double). Method in class pmr.simplegraph.Scaler2D
drawRect(Graphics, Int2Range). Method in class pmr.simplegraph.Scaler2D: draw a box in screen coords - should be in Util...
drawRect(Graphics, Real2Range). Method in class pmr.simplegraph.Scaler2D
drawSequenceString(Graphics). Method in class pmr.cml.SEQUENCENode
drawString(Graphics, String, double, double). Method in class pmr.simplegraph.Scaler2D
drawString(Graphics, String, int, int). Static method in class pmr.simplegraph.SimpleGraph: draws a string at a given position and returns the new coordinates of the 'cursor.
drawTransparentDrawable(Graphics, Drawable). Method in class pmr.simplegraph.ScrollableTopLevel: draw moving/scaling Drawable (avoids flicker).
drawTrash(Graphics, int, int). Method in class pmr.sgml.SGMLTOC
drawTruncated(Graphics, int, int, int, int, double, double). Method in class pmr.cml.MOLNode
drawVLine(Graphics, int, int, int). Method in class pmr.cml.SEQUENCENode
drawWorkStationViewPort(Graphics). Method in class pmr.simplegraph.Scaler2D: draws box round limits of screen VP.
DTD(). Constructor for class pmr.sgml.DTD: this constructor should only be used by subclasses
DTD(String). Constructor for class pmr.sgml.DTD: construct a DTD; including all its contained DTDs (recursively).
DTDDoc(String). Constructor for class pmr.sgml.DTDDoc
DTDDTD(). Constructor for class pmr.sgml.DTDDTD
DTDDTD(DTD). Constructor for class pmr.sgml.DTDDTD
DTDNode(String, SGMLTree). Constructor for class pmr.sgml.DTDNode
DTDViolationException(). Constructor for class pmr.sgml.DTDViolationException
DTDViolationException(String). Constructor for class pmr.sgml.DTDViolationException
DuplicateATOMSException(). Constructor for class pmr.cml.DuplicateATOMSException
DuplicateATOMSException(String). Constructor for class pmr.cml.DuplicateATOMSException
DuplicateBONDSException(). Constructor for class pmr.cml.DuplicateBONDSException
DuplicateBONDSException(String). Constructor for class pmr.cml.DuplicateBONDSException
DuplicateGIException(). Constructor for class pmr.sgml.DuplicateGIException
DuplicateGIException(String). Constructor for class pmr.sgml.DuplicateGIException
DuplicateUnitException(). Constructor for class pmr.molecule.DuplicateUnitException
DuplicateUnitException(String). Constructor for class pmr.molecule.DuplicateUnitException
DynamicAligner(int[][], double[][]). Constructor for class pmr.molecule.DynamicAligner: create a DynamicAligner from a substitution matrix
dynamicAlignment(double). Method in class pmr.molecule.SequenceAligner: this does the alignment; the gap penalty should be given

E

elementAt(int). Method in class pmr.stat.Bivariate
elementAt(int). Method in class pmr.euclid.Int2: get either value; counts from ZERO
elementAt(int). Method in class pmr.euclid.IntArray: extracts a given element from the array
elementAt(int). Method in class pmr.euclid.IntSet
elementAt(int). Method in class pmr.euclid.ObjectArray: extracts a given element from the array
elementAt(int). Method in class pmr.euclid.Point3: subscript operator counts from ZERO
elementAt(int). Method in class pmr.euclid.Real2: get either value; counts from ZERO
elementAt(int). Method in class pmr.euclid.RealArray: extracts a given element from the array
elementAt(int). Method in class pmr.sgml.SGMLAttlist
elementAt(int). Method in class pmr.util.StringList: synonymous with above
elementAt(int). Method in class pmr.euclid.StringSet: return (case-sensitive) element
elementAt(int). Method in class pmr.stat.Univariate
elementAt(int). Method in class pmr.euclid.Vector3: subscript operator: counts from ZERO
elementAt(int, int). Method in class pmr.euclid.IntMatrix: extracts a given element from the matrix
elementAt(int, int). Method in class pmr.euclid.RealMatrix: extracts a given element from the matrix
elementAt(Int2). Method in class pmr.euclid.IntMatrix: extracts a given element from the matrix
elementAt(Int2). Method in class pmr.euclid.RealMatrix: extracts a given element from the matrix
ELEMENTNode(String, SGMLTree). Constructor for class pmr.sgml.ELEMENTNode
elementsInRange(IntRange). Method in class pmr.euclid.IntMatrix: produce a mask of those elements which fall in a range (1) else (0)
elementsInRange(RealRange). Method in class pmr.euclid.RealMatrix: produce a mask of those elements which fall in a range (1) else (0)
EndsWithFilter(String). Constructor for class pmr.util.EndsWithFilter
EntitySet(). Constructor for class pmr.sgml.EntitySet
equals(Angle). Method in class pmr.euclid.Angle: are two angles equal?
equals(double). Method in class pmr.euclid.Angle: are two angles equal? RADIANS
equals(FullAddress). Method in class pmr.cml.FullAddress
equals(Int2). Method in class pmr.euclid.Int2
equals(Int2Range). Method in class pmr.euclid.Int2Range
equals(IntArray). Method in class pmr.euclid.IntArray: are two arrays equal in all elements? (use epsilon as tolerance)
equals(IntMatrix). Method in class pmr.euclid.IntMatrix: are two matrices equal in all elements?
equals(IntRange). Method in class pmr.euclid.IntRange: invalid ranges return false
equals(IntSet). Method in class pmr.euclid.IntSet: element-by-element comparison of sets
equals(IntSquareMatrix). Method in class pmr.euclid.IntSquareMatrix: are two matrices identical?
equals(Line3). Method in class pmr.euclid.Line3: are two lines identical (coincident and parallel)?
equals(ObjectArray). Method in class pmr.euclid.ObjectArray: are two arrays equal in all elements?
equals(Plane3). Method in class pmr.euclid.Plane3: are two planes coincident and parllel
equals(Point3). Method in class pmr.euclid.Point3: are two points identical?
equals(Polar). Method in class pmr.euclid.Polar: are two polar equal?
equals(Real2). Method in class pmr.euclid.Real2
equals(Real2Range). Method in class pmr.euclid.Real2Range
equals(Real3Range). Method in class pmr.euclid.Real3Range
equals(RealArray). Method in class pmr.euclid.RealArray: are two arrays equal in all elements?
equals(RealArray, double). Method in class pmr.euclid.RealArray: are two arrays equal in all elements? (use epsilon as tolerance)
equals(RealMatrix). Method in class pmr.euclid.RealMatrix: are two matrices equal in all elements?
equals(RealRange). Method in class pmr.euclid.RealRange: invalid ranges return false
equals(RealSquareMatrix). Method in class pmr.euclid.RealSquareMatrix: are two matrices identical?
equals(Transform2). Method in class pmr.euclid.Transform2
equals(Transform3). Method in class pmr.euclid.Transform3
equals(Vector3). Method in class pmr.euclid.Vector3: are two vectors equal lengths?
ERROR. Static variable in class pmr.simplegraph.InfoDialog
ERROR. Static variable in class pmr.simplegraph.ScrollableTopLevel
error(Frame, String). Static method in class pmr.simplegraph.SimpleGraph: public static void setErrorOutput(Dialog d) { errorDialog = d; if (d == null) { System.err.println("MESSAGES BEING RE-ROUTED TO STDERR"); } }
error(String). Method in class pmr.sgml.SGMLNode: I must replace this by exceptions...
error(String). Static method in class pmr.simplegraph.SimpleGraph
ESISStream(). Constructor for class pmr.sgml.ESISStream
ESISStream(String). Constructor for class pmr.sgml.ESISStream
ESISStream(StringList). Constructor for class pmr.sgml.ESISStream
euclideanColumnLength(int). Method in class pmr.euclid.RealMatrix: get Euclidean length of column
euclideanColumnLengths(). Method in class pmr.euclid.RealMatrix: get array of Euclidean column lengths
euclideanLength(). Method in class pmr.euclid.RealArray: Euclidean length of vector
euclideanRowLength(int). Method in class pmr.euclid.RealMatrix: get Euclidean length of row
euclideanRowLengths(). Method in class pmr.euclid.RealMatrix: get array of Euclidean row lengths
EuclidVector(). Constructor for class pmr.euclid.EuclidVector
EuclidVector(int). Constructor for class pmr.euclid.EuclidVector
exists(String). Static method in class pmr.sgml.DTD: does a DTD exist in the DTDNameSet?
extractAlignment(). Method in class pmr.molecule.DynamicAligner: get the two sequences as gapped arrays of integers (e.g.
extractColumnData(int). Method in class pmr.euclid.IntMatrix: get column data from matrix
extractColumnData(int). Method in class pmr.euclid.RealMatrix: get column data from matrix
extractRowData(int). Method in class pmr.euclid.IntMatrix: get row data from matrix
extractRowData(int). Method in class pmr.euclid.RealMatrix: get row data from matrix
extractSubMatrixData(int, int, int, int). Method in class pmr.euclid.IntMatrix: extract a IntMatrix submatrix from a IntMatrix
extractSubMatrixData(int, int, int, int). Method in class pmr.euclid.RealMatrix: extract a RealMatrix submatrix from a RealMatrix

F

FASTA(String, StringList). Constructor for class pmr.chemime.FASTA: create a CMLTree from a FASTA file
FEATURENode(String, SGMLTree). Constructor for class pmr.cml.FEATURENode
FIGURENode(String, SGMLTree). Constructor for class pmr.cml.FIGURENode
fileMenu(String[]). Method in class pmr.cml.CMLApplet
fileMenu(String[]). Method in class pmr.sgml.SGMLApplet
fileMenu(String[]). Method in class pmr.simplegraph.SimpleApplet
filename. Variable in class pmr.simplegraph.SimpleApplet
FileTransporter(SGMLTOC). Constructor for class pmr.sgml.FileTransporter
FileTransporter(SGMLTOC, String). Constructor for class pmr.sgml.FileTransporter
fitTo(Point3Vector). Method in class pmr.euclid.Point3Vector: fit two coordinates of same length and alignment CURRENTLY NOT VALIDATED
flarray. Variable in class pmr.euclid.Point3: the coordinates of the point
flipAboutVector(Real2). Static method in class pmr.euclid.Transform2: get Transformation to mirror ('flip') across an axis NOT YET CHECKED
flmat. Variable in class pmr.euclid.IntMatrix: the matrix
flmat. Variable in class pmr.euclid.RealMatrix: the matrix
FLOAT. Static variable in class pmr.simplegraph.NumericTable
FORMULANode(String, SGMLTree). Constructor for class pmr.cml.FORMULANode
freeMemory(long). Static method in class pmr.util.Util: runs the grabage collector if memory drops below mem.
full. Variable in class pmr.sgml.TreeContainer
FullAddress(DrawableX_Node, int). Constructor for class pmr.cml.FullAddress
FullAddress(DrawableX_Node, IntRange). Constructor for class pmr.cml.FullAddress: create from a known Node and a known subaddress (which could be a single point for an IntRange n-n
FullAddress(String, SGMLTree). Constructor for class pmr.cml.FullAddress: create from a String.
fullDebug(). Method in class pmr.sgml.SGMLNodeIndexSet: prints debug info FOR ALL NODES IN SET.

G

G94(String, StringList). Constructor for class pmr.chemime.G94

form a G94 object from a local file

G94(String, StringList, String). Constructor for class pmr.chemime.G94

for a G94 object as above, but OMIT all modules in String omit (e.g.

GAMESS(String, StringList). Constructor for class pmr.chemime.GAMESS

form a GAMESS object from a local file

generalDisplay(Graphics). Method in class pmr.stat.DrawableStat

generic display unrelated to object details.

generalDisplay(Graphics). Method in class pmr.cml.DrawableX_Node

generic display unrelated to object details.

generalTOC. Variable in class pmr.sgml.SGMLTree

GeneralTOC(SGMLTree, int). Constructor for class pmr.sgml.GeneralTOC

get1Letter(String). Static method in class pmr.molecule.AminoAcid

return 1-letter code if valid 3-letter arg, else "?"

get1LetterSequence(String[]). Static method in class pmr.molecule.AminoAcid

get a gapless string of 1-letter codes from an array of 3-letter Strings

get2DMolecule(). Method in class pmr.cml.MOLNode

probably obsolete - just calculates mol2d

get3Letter(String). Static method in class pmr.molecule.AminoAcid

if the arg is 1-letter, return the 3-letter, else return unchanged; unknown 1-letter returns "UNK"

get3LetterSequence(String). Static method in class pmr.molecule.AminoAcid

get an array of 3-letter Strings from a string of 1-letters; gaps are skipped

getAllowedAttributeValues(String). Method in class pmr.cml.ARRAYNode

give the list of possible values for BUILTIN, FUZZY, STRUCT or TYPE

getAllRELATIONNodes(SGMLTree). Static method in class pmr.cml.RELATIONNode

get all RELATION in the document

getAminoAcid(String). Static method in class pmr.molecule.AminoAcid

get AminoAcid, hashed by one-letter or three-letter codes

getAminoAcids(). Method in class pmr.molecule.AminoAcidMatrix

get the aminoacids as an array of AminoAcids

getAminoAcidString(). Method in class pmr.molecule.AminoAcidMatrix

get the aminoacids as 1-letter String

getAncestors(). Method in class pmr.sgml.SGMLNode

get all ancestors excluding current Node and DOCROOT

getAncestors(). Method in class pmr.sgml.SGMLNodeIndexSet

getAncestors(int). Method in class pmr.sgml.SGMLNodeIndexSet

getAngle(). Method in class pmr.euclid.Angle

get angle in radians

getAngle(Point3, Point3, Point3). Static method in class pmr.euclid.Point3

angle (p1-p2-p3; vertex is p2)

getAngle(Real2, Real2, Real2). Static method in class pmr.euclid.Real2

get angle between 3 Real2s (the second is in the centre).

getAngleMadeWith(Plane3). Method in class pmr.euclid.Plane3

the angle between 2 planes (as an Angle)

getAngleMadeWith(Vector2). Method in class pmr.euclid.Vector2

I *think* I have written this so that the angle is positive as this rotates anticlockwise to v.

getAngleMadeWith(Vector3). Method in class pmr.euclid.Vector3

angle between two vectors

getAngleOfRotation(). Method in class pmr.euclid.Transform2

interpret current matrix as rotation about axis NOT YET CHECKED; only worsk for orthornormal matrices

getAngles(). Method in class pmr.cml.CRYSTNode

get cell angles IN DEGREES or null if not present

getApplet(). Static method in class pmr.simplegraph.SimpleApplet

getArray(). Method in class pmr.euclid.IntArray

return the array as a int[]; this has to resize the array to the precise length used , or confusion will result! Note that this gives the user access to the actual array, so that they can alter its contents.

getArray(). Method in class pmr.euclid.ObjectArray

return the array as a Object[]; this has to resize the array to the precise length used , or confusion will result! Note that this gives the user access to the actual array, so that they can alter its contents.

getArray(). Method in class pmr.euclid.Point3

get components as double[]

getArray(). Method in class pmr.euclid.RealArray

return the array as a double[]; this has to resize the array to the precise length used , or confusion will result! Note that this gives the user access to the actual array, so that they can alter its contents.

getArray(). Method in class pmr.euclid.Vector3

get the vector components

getAtomCount(). Method in class pmr.cml.ATOMSNode

getAtomCount(). Method in class pmr.cml.MOLNode

common get routines

getAtomicNumber(). Method in class pmr.molecule.ChemicalElement

getAtomicWeight(). Method in class pmr.molecule.ChemicalElement

getAtomSerial(String). Method in class pmr.cml.ATOMSNode

get serial number of atom (0...natoms-1) from ATOMID; -1 if not found

getAttname(). Method in class pmr.sgml.SGMLAttribute

getAttval(). Method in class pmr.sgml.SGMLAttribute

getAttval(String). Method in class pmr.sgml.SGMLAttlist

getAttval(String). Method in class pmr.sgml.SGMLNode

CoST: get SGMLAttribute value (if non-existent attribute, return "") attname is case-insensitive

getAuthors(). Method in class pmr.cml.BIBNode

returns the authors as a Vector of PERSONNodes

getAxisAndAngle(Vector3, Angle). Method in class pmr.euclid.Transform3

returns chirality

getBivariate(). Method in class pmr.cml.XLISTNode

extract GRAPH as a Bivariate

requires that CONTENT=GRAPH; no check on semantic validity at present...

getBondAtom(Choice2). Method in class pmr.cml.MOLNode

get array of all first atoms in bond or all second atoms

getBondCount(). Method in class pmr.cml.BONDSNode

getBondCount(). Method in class pmr.cml.MOLNode

getBondOrderCount(int). Method in class pmr.cml.MOLNode

return the number of bonds with a given (integer) order.

getBonds(). Method in class pmr.cml.MOLNode

get serial numbers of bonded atoms, 2 per bond

getBookmarks(). Method in class pmr.sgml.SGMLTOC

get 'bookmark' list

getButton(String). Method in class pmr.simplegraph.ButtonBar

gets the Button associated with a name; if none, returns null

getButtonBar(). Method in class pmr.simplegraph.ScrollableTopLevel

getButtonHeight(). Method in class pmr.simplegraph.ScrollableTopLevel

getCause(Exception). Static method in class pmr.util.Util

Recursive exception build up long strings, or which only the end is often useful.

getCentreOfRotation(). Method in class pmr.euclid.Transform2

get centre of rotation

getCentreOfRotation(). Method in class pmr.euclid.Transform3

get centre of rotation

getCentroid(). Method in class pmr.euclid.Point3Vector

get centroid of all points

getCentroid(). Method in class pmr.euclid.Real2Vector

get centroid of all points

getChainID(). Method in class pmr.cml.SEQUENCENode

getChainLength(). Method in class pmr.cml.SEQUENCENode

getCharValue(String). Static method in class pmr.sgml.EntitySet

return the character value of the entity (CASE-SENSITIVE).

getChemTree(String, String, StringList). Static method in class pmr.chemime.ChemTree

returns a CMLTree from a file/URL.

getChildIndex(int). Method in class pmr.sgml.SGMLNode

getChildNode(int). Method in class pmr.sgml.SGMLNode

getChildrenHiddenManually(). Method in class pmr.sgml.SGMLNode

are the children manually hidden; "YES", "NO", ""

getChildrenIndexSet(). Method in class pmr.sgml.SGMLNode

children of node as SGMLNodeIndexSet

getChildrenIndexSet(). Method in class pmr.sgml.SGMLNodeIndexSet

getChoice(String). Method in class pmr.simplegraph.ButtonBar

gets the Choice associated with a name; if none, returns null

getClassnameFromDTD(String). Static method in class pmr.sgml.DTD

getClosestPoint(Int2). Method in class pmr.euclid.Int2Vector

get the closest point (both ranges are assumed to have the same scales

getClosestPoint(Real2). Method in class pmr.euclid.Real2Vector

get the closest point (both ranges are assumed to have the same scales

getClosestPointOnLine(Line3). Method in class pmr.euclid.Point3

getClosestPointTo(Point3). Method in class pmr.euclid.Line3

point on line closest to another point

getClosestPointTo(Point3). Method in class pmr.euclid.Plane3

point on plane closest to another point

getCMLTreeFromMIME(String, String). Static method in class pmr.cml.CMLTree

returns a CMLTree from a file/URL.

getColor(). Method in class pmr.molecule.AminoAcid

get the color of this AminoAcid

getColor(). Method in class pmr.sgml.ATTRIBUTENode