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FRAMES NO FRAMES

A B C D E F G H I L M N O P Q R S T U V W _

A

about - Variable in class edu.upenn.crimson.gui.Root.RootFrame
accept(File) - Method in class edu.upenn.crimson.gui.GUIUtils.PyFilter
accept(File) - Method in class edu.upenn.crimson.gui.ViewHTML.HTMLFilter
accept(File) - Method in class edu.upenn.crimson.io.HTMLFile.HTMLFilter
actionPerformed(ActionEvent) - Method in class edu.upenn.crimson.gui.Root.RootFrame: Handle menu items.
addChild(Species) - Method in class edu.upenn.crimson.Species: This will add the child to the set of children and then set the parent of the child to be this Species object.
addChildrenToQueue(Queue, Species[]) - Method in class edu.upenn.crimson.Tree: This will add the children to the queue.
addLeaf(String) - Method in class edu.upenn.crimson.Query: Adds a leaf to the leaf list.
addMenuItem(JMenuItem, JMenu, String, int, ImageIcon) - Method in class edu.upenn.crimson.gui.Root.RootFrame: Add specified item to specified menu.
addModel(Model) - Static method in class edu.upenn.crimson.ObjectHandles: This will add the model to the relevant lists.
addPartition(Partition) - Static method in class edu.upenn.crimson.ObjectHandles: This will add the partition to the relevant lists.
addPartition(String) - Method in class edu.upenn.crimson.Query: Adds a partitions to the partitions list.
addPartition(Partition) - Method in class edu.upenn.crimson.Tree
addPosition(String) - Method in class edu.upenn.crimson.Query: Adds a positions to the positions list.
addPositions(String) - Method in class edu.upenn.crimson.Query: Adds a ':' separated list of positions to the positions list.
addQuery(Query) - Static method in class edu.upenn.crimson.ObjectHandles: This will add the query to the relevant lists.
addRow(Model) - Method in class edu.upenn.crimson.ModelTableModel: Append a new row to the end of the table.
addRow(Query) - Method in class edu.upenn.crimson.QueryTableModel: Append a new row to the end of the table.
addRow(Tree) - Method in class edu.upenn.crimson.TreeTableModel: Append a new row to the end of the table.
addRowAt(Model, int) - Method in class edu.upenn.crimson.ModelTableModel: Add new row to table.
addRowAt(Query, int) - Method in class edu.upenn.crimson.QueryTableModel: Add new row to table.
addRowAt(Tree, int) - Method in class edu.upenn.crimson.TreeTableModel: Add new row to table.
addSpecies(Species) - Method in class edu.upenn.crimson.Tree
addTree(Tree) - Static method in class edu.upenn.crimson.ObjectHandles: This will add the tree to the relevant lists.
append(String, String, String) - Static method in class edu.upenn.crimson.io.NexusFile: Appends a Nexus file into the current database.
appendB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
appendTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
appendTree(String) - Static method in class edu.upenn.crimson.gui.TreeUtils: This will process the NEXUS file selected and then append the file into the specified database table.

B

binary - Variable in class edu.upenn.crimson.Tree: True when all inner nodes have exactly 2 children.
buildLists() - Static method in class edu.upenn.crimson.ObjectHandles: This will (re)build the table lists based on the current connection.
buildTree() - Method in class edu.upenn.crimson.Tree: This will build the tree from the nexick string.

C

cancelB - Variable in class edu.upenn.crimson.gui.FieldEditDialog
cancelB - Variable in class edu.upenn.crimson.gui.ObjectSelectorDialog
cancelB - Variable in class edu.upenn.crimson.gui.QueryDialog
childIndex - Variable in class edu.upenn.crimson.Species: This is used by nextChild() to allow for traversing the tree in a recursive like fashion but without using recursion.
children - Variable in class edu.upenn.crimson.Species: This contains the set of children.
clearHistory - Variable in class edu.upenn.crimson.gui.Root.RootFrame
clearLists() - Static method in class edu.upenn.crimson.ObjectHandles: This will clear the lists.
clearMessages - Variable in class edu.upenn.crimson.gui.Root.RootFrame
clearModelLists() - Static method in class edu.upenn.crimson.ObjectHandles: This will clear the Model lists.
clearPartitionLists() - Static method in class edu.upenn.crimson.ObjectHandles: This will clear the Partition lists.
clearQueryLists() - Static method in class edu.upenn.crimson.ObjectHandles: This will clear the Query lists.
clearStructure() - Method in class edu.upenn.crimson.Tree: This will release the tree structure from memory.
clearTreeLists() - Static method in class edu.upenn.crimson.ObjectHandles: This will clear the Tree lists.
clone() - Method in class edu.upenn.crimson.Model: Create a shallow clone (just clone the structure, not the Objects) of the existing object.
clone(String) - Method in class edu.upenn.crimson.Model: Create a shallow clone (just clone the structure, not the Objects) of the existing object.
clone() - Method in class edu.upenn.crimson.Query: Create a shallow clone (just clone the structure, not the Objects) of the existing object.
clone(String) - Method in class edu.upenn.crimson.Query: Create a shallow clone (just clone the structure, not the Objects) of the existing object.
clone() - Method in class edu.upenn.crimson.Tree: This will duplicate the tree and all species.
close() - Static method in class edu.upenn.crimson.io.Database: Closes the connection to the database and sets dbConnection to null.
closeB - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
closeB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
closeB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
closeDB - Variable in class edu.upenn.crimson.gui.Root.RootFrame
collapse() - Method in class edu.upenn.crimson.Species: This will remove this internal species, linking all children to our parent and adjusting their stem lengths accordingly.
collapse() - Method in class edu.upenn.crimson.Tree: This will remove all internal species that have only one child, linking the child to species' parent and adjusting the child's stem lengths accordingly.
columnNames - Variable in class edu.upenn.crimson.ModelTableModel
columnNames - Variable in class edu.upenn.crimson.QueryTableModel
columnNames - Variable in class edu.upenn.crimson.TreeTableModel
commit() - Static method in class edu.upenn.crimson.io.Database: This will for a commit.
compareTo(Object) - Method in class edu.upenn.crimson.Species: When comparing Species objects, we actually just compare the index values.
computeBinary() - Method in class edu.upenn.crimson.Tree: Returns true if the tree is binary.
computeLevel() - Method in class edu.upenn.crimson.Species: This will compute the level of the species, assuming the parent's level has already been computed.
computeStats() - Method in class edu.upenn.crimson.Tree: This will compute the various tree statistics.
computeTempDepth() - Method in class edu.upenn.crimson.Species: This will compute the length to the root, assuming the parent's root length has already been computed.
console - Static variable in class edu.upenn.crimson.CrimsonMain
containsModel(String) - Static method in class edu.upenn.crimson.ObjectHandles: Returns true if the Model object exists in the modelPool.
containsPartition(String) - Static method in class edu.upenn.crimson.ObjectHandles: Returns true if the Partition object exists in the partitionPool.
containsQuery(String) - Static method in class edu.upenn.crimson.ObjectHandles: Returns true if the Query object exists in the queryPool.
containsTree(String) - Static method in class edu.upenn.crimson.ObjectHandles: Returns true if the Tree object exists in the treePool.
copy(Tree) - Method in class edu.upenn.crimson.Species: This will return a copy of the current species WITHOUT the parent, children, or level.
copyB - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
copyB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
copyHistory - Variable in class edu.upenn.crimson.gui.Root.RootFrame
createString(int) - Static method in class edu.upenn.crimson.CrimsonMain
createTable(String) - Static method in class edu.upenn.crimson.io.Database: This will create a table in the current database.
createTable(String) - Static method in class edu.upenn.crimson.io.SQL: This method will create all of the necessary tables.
createTmpDir() - Static method in class edu.upenn.crimson.CrimsonUtils: This will create the temporary directory, if necessary, returning 'true' if successful.
CrimsonException - Exception in edu.upenn.crimson: A wrapper for all Crimson exceptions.
CrimsonException() - Constructor for exception edu.upenn.crimson.CrimsonException: Create a new CrimsonException without a message.
CrimsonException(String) - Constructor for exception edu.upenn.crimson.CrimsonException: Create a new CrimsonException with a message.
CrimsonMain - Class in edu.upenn.crimson: CrimsonMain program.
CrimsonMain() - Constructor for class edu.upenn.crimson.CrimsonMain
CrimsonUtils - Class in edu.upenn.crimson: CrimsonUtils.
CrimsonUtils() - Constructor for class edu.upenn.crimson.CrimsonUtils

D

DATABASE - Static variable in class edu.upenn.crimson.CrimsonUtils: String containing database name (SID).
Database - Class in edu.upenn.crimson.io: Functions related to opening, closing, and quering a Database.
Database() - Constructor for class edu.upenn.crimson.io.Database
DB_TYPE - Static variable in class edu.upenn.crimson.CrimsonUtils: String containing type of database ("oracle" or "mysql").
dbConnection - Static variable in class edu.upenn.crimson.CrimsonMain: This is a reference to the actual database connection.
dbConnection - Static variable in class edu.upenn.crimson.io.Database: This is a reference to the actual database connection.
dbContains(String) - Static method in class edu.upenn.crimson.io.Models: This will return true if a model exists in MODELS with an id equal to 'id'.
dbContains(String) - Static method in class edu.upenn.crimson.io.Partitions: This will return true if a partition exists in PARTITIONS with an id equal to 'id'.
dbContains(String) - Static method in class edu.upenn.crimson.io.Queries: This will return true if a query exists in QUERIES with an id equal to 'id'.
dbContains(String) - Static method in class edu.upenn.crimson.io.Trees: This will return true if a tree exists in TREES with an id equal to 'id'.
dbDriver() - Static method in class edu.upenn.crimson.io.SQL
dbList() - Static method in class edu.upenn.crimson.io.Queries: This will return an ArrayList with id's for all queries in the QUERIES table.
dbLoad(ArrayList) - Static method in class edu.upenn.crimson.Query: This routine is only meant to be used by Queries when loading Queries from a database without using a proxy (ie CLOBs are not strings).
dbLoadProxy(StringBuilder) - Static method in class edu.upenn.crimson.Query: This routine is only meant to be used by Queries when loading Queries from a database via a proxy.
dbToArray(String) - Static method in class edu.upenn.crimson.io.Database
dbType - Static variable in class edu.upenn.crimson.io.SQL: This is a name of the database: -1 = none.
dbTypes - Static variable in class edu.upenn.crimson.io.SQL: This is the list of databases we can use.
dbURL() - Static method in class edu.upenn.crimson.io.SQL
DEBUG_OUTPUT - Static variable in class edu.upenn.crimson.io.Queries: If true, then whenever a (bp or codon) position selection query is run, the list of positions selected will be output to the file 'positions.list'.
DEBUG_OUTPUT - Static variable in class edu.upenn.crimson.Tree: If true, then whenever a tree is sampled, the list of species selected will be output to the file 'species.list'.
delete(String, String) - Static method in class edu.upenn.crimson.io.Database: Removes a record from the table.
delete(String) - Static method in class edu.upenn.crimson.io.Models: Removes a model from the database.
delete(String) - Static method in class edu.upenn.crimson.io.Partitions: Removes a partition from the database.
delete(String) - Static method in class edu.upenn.crimson.io.Queries: Removes a query from the database.
delete(String, boolean) - Static method in class edu.upenn.crimson.io.Trees: Removes a tree from the database.
deleteB - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
deleteB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
deleteB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
deleteModel(String) - Static method in class edu.upenn.crimson.gui.ModelUtils: This will delete the model specified by ModelSelector().
deleteModel - Variable in class edu.upenn.crimson.gui.Root.RootFrame
deleteModel(String) - Static method in class edu.upenn.crimson.ObjectHandles: This will delete the model from the relevant lists.
deleteQuery(String) - Static method in class edu.upenn.crimson.gui.QueryUtils: This will delete the specified query.
deleteQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame
deleteQuery(String) - Static method in class edu.upenn.crimson.ObjectHandles: This will delete the query from the relevant lists.
deleteTmpFile(String) - Static method in class edu.upenn.crimson.CrimsonUtils: This will delete the specified file, if it exists in TMP_DIR.
deleteTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
deleteTree(String) - Static method in class edu.upenn.crimson.gui.TreeUtils: This will delete the tree specified by TreeSelector().
details - Variable in class edu.upenn.crimson.Model: Brief description of this Model.
detailsTA - Variable in class edu.upenn.crimson.gui.ModelEditor
directoryChooser() - Static method in class edu.upenn.crimson.gui.GUIUtils: Create a file chooser for selecting a directory.
doQuote(String) - Static method in class edu.upenn.crimson.io.NexusFile: From Mark Holder

E

editB - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
editB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
editModel(String) - Static method in class edu.upenn.crimson.gui.ModelUtils: This will edit the model.
editQuery(String) - Static method in class edu.upenn.crimson.gui.QueryUtils: This will edit the query.
edu.upenn.crimson - package edu.upenn.crimson
edu.upenn.crimson.gui - package edu.upenn.crimson.gui
edu.upenn.crimson.io - package edu.upenn.crimson.io
equals(Object) - Method in class edu.upenn.crimson.Species: When comparing Species to be equal, we compare their IDs.
ERROR - Static variable in class edu.upenn.crimson.CrimsonUtils
exec(String) - Static method in class edu.upenn.crimson.CrimsonMain: On Windows machines, exec() requires "cmd /c" to envoke the command prompt.
exec(String, boolean) - Static method in class edu.upenn.crimson.CrimsonMain
execFull(String, boolean) - Static method in class edu.upenn.crimson.CrimsonMain: On Windows machines, exec() requires "cmd /c" to envoke the command prompt.
execUpdate(String) - Static method in class edu.upenn.crimson.io.Database: This will execute SQL commands that update the database (ie CREATE, DROP, INSERT, DELETE, etc).
exit(int) - Static method in class edu.upenn.crimson.CrimsonMain
expandPositions(HashSet, boolean) - Static method in class edu.upenn.crimson.io.Queries: This will convert a set of bp ranges to bp positions.
exportB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
exportB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
exportQuery(String) - Static method in class edu.upenn.crimson.gui.QueryUtils: This will export a query as a python file.
exportQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame
exportQuery(String) - Static method in class edu.upenn.crimson.io.FileIO: Export the Query to a file based on it's ID.
exportQuery(String, String, boolean) - Static method in class edu.upenn.crimson.io.FileIO: Export the Query to a python file.
exportTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
exportTree(String) - Static method in class edu.upenn.crimson.gui.TreeUtils: This will export the tree specified by TreeSelector().

F

FEEDBACK - Static variable in class edu.upenn.crimson.CrimsonUtils
FieldEditDialog - Class in edu.upenn.crimson.gui: This class is used to present a modal dialog for editing text in the 'text' HashMap.
FieldEditDialog(String, String[], ArrayList) - Constructor for class edu.upenn.crimson.gui.FieldEditDialog
file - Variable in class edu.upenn.crimson.gui.QueryEditor
fileBrowseB - Variable in class edu.upenn.crimson.gui.QueryDialog
fileBrowseB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
fileChooser - Static variable in class edu.upenn.crimson.gui.GUIUtils: The file chooser begins with the current working directory.
fileIntSeqCB - Variable in class edu.upenn.crimson.gui.QueryDialog
fileIntSeqCB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
FileIO - Class in edu.upenn.crimson.io: Import and export utilities.
FileIO() - Constructor for class edu.upenn.crimson.io.FileIO
fileNameTF - Variable in class edu.upenn.crimson.gui.QueryDialog
fileNameTF - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
fileRepeatS - Variable in class edu.upenn.crimson.gui.QueryDialog
fileRepeatS - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
findLabelEnd(String, int) - Static method in class edu.upenn.crimson.io.NexusFile: Keep incrementing until we find the end of the number or label.
firstChild() - Method in class edu.upenn.crimson.Species: This will return the true if this is the first child to be returned.

G

getChildren() - Method in class edu.upenn.crimson.Species
getClassName(Object) - Static method in class edu.upenn.crimson.CrimsonUtils: Get the class name without any package info.
getColumnCount() - Method in class edu.upenn.crimson.ModelTableModel
getColumnCount() - Method in class edu.upenn.crimson.QueryTableModel
getColumnCount() - Method in class edu.upenn.crimson.TreeTableModel
getColumnName(int) - Method in class edu.upenn.crimson.ModelTableModel
getColumnName(int) - Method in class edu.upenn.crimson.QueryTableModel
getColumnName(int) - Method in class edu.upenn.crimson.TreeTableModel
getConnection() - Static method in class edu.upenn.crimson.io.Database: Get the DBConnection.
getDatabase() - Static method in class edu.upenn.crimson.CrimsonUtils: Get the DATABASE flag.
getDate() - Static method in class edu.upenn.crimson.io.SQL: This will return the database date, as is used to test database connectivity.
getDBType() - Static method in class edu.upenn.crimson.CrimsonUtils: Get the DB_TYPE flag.
getDBType() - Static method in class edu.upenn.crimson.io.SQL: Get the type of database (oracle or mysql).
getDBTypes() - Static method in class edu.upenn.crimson.io.SQL
getDBTypeValue() - Static method in class edu.upenn.crimson.io.SQL: Get the index value of the type of database.
getDescription() - Method in class edu.upenn.crimson.gui.GUIUtils.PyFilter
getDescription() - Method in class edu.upenn.crimson.gui.ViewHTML.HTMLFilter
getDescription() - Method in class edu.upenn.crimson.io.HTMLFile.HTMLFilter
getDetails() - Method in class edu.upenn.crimson.Model
getDocLengthFilter() - Static method in class edu.upenn.crimson.gui.GUIUtils
getExec(String) - Static method in class edu.upenn.crimson.CrimsonMain
getExec(String, boolean) - Static method in class edu.upenn.crimson.CrimsonMain
getFilename(File) - Static method in class edu.upenn.crimson.gui.GUIUtils: On Windows machines the path contains "\\", however, when converted to a String, this becomes "\".
getHTML() - Method in class edu.upenn.crimson.gui.ViewHTML.HTMLEditorPane
getID() - Method in class edu.upenn.crimson.Model: Get the ID.
getID() - Method in class edu.upenn.crimson.Partition
getID() - Method in class edu.upenn.crimson.Query: Set the ID.
getID() - Method in class edu.upenn.crimson.Species
getID() - Method in class edu.upenn.crimson.Tree: Get the ID.
getLCA(Species, Species) - Static method in class edu.upenn.crimson.Tree: Returns the LCA for the tree, assuming this species is the root of the tree.
getLeafCounts(ArrayList) - Method in class edu.upenn.crimson.Tree: This will return a list of leaf counts for each subtree specified by the subroots.
getLeafSelection() - Method in class edu.upenn.crimson.Query
getLeafSelectionString() - Method in class edu.upenn.crimson.Query
getLeaves() - Method in class edu.upenn.crimson.Query
getLeaves() - Method in class edu.upenn.crimson.Tree: Returns the set of all leaves in the tree.
getLength() - Method in class edu.upenn.crimson.Partition
getLength() - Method in class edu.upenn.crimson.Tree: This is the sum of the length of all partitions.
getLevel() - Method in class edu.upenn.crimson.Species
getLevelThresh() - Method in class edu.upenn.crimson.Query
getMaxLevel() - Method in class edu.upenn.crimson.Tree
getMaxStemLength() - Method in class edu.upenn.crimson.Tree
getMaxTempDepth() - Method in class edu.upenn.crimson.Tree
getMinLevel() - Method in class edu.upenn.crimson.Tree
getMinStemLength() - Method in class edu.upenn.crimson.Tree
getMinTempDepth() - Method in class edu.upenn.crimson.Tree
getModel(String) - Static method in class edu.upenn.crimson.ObjectHandles: Returns the Model object for the given ID.
getModelID(String) - Static method in class edu.upenn.crimson.gui.ModelUtils: This will use a FieldEditDialog to ask the user for a model ID.
getModelID() - Method in class edu.upenn.crimson.Partition: Returns the ID for the model underlying this partition.
getModelID() - Method in class edu.upenn.crimson.Tree: Returns the ID for the model underlying this tree.
getModelList() - Static method in class edu.upenn.crimson.ObjectHandles
getModelPool() - Static method in class edu.upenn.crimson.ObjectHandles
getModels() - Static method in class edu.upenn.crimson.ObjectHandles: Returns the set of all Model IDs.
getModelTableModel() - Static method in class edu.upenn.crimson.ObjectHandles
getNewick() - Method in class edu.upenn.crimson.Tree: Returns the newick string for this tree, as stored in the database.
getNotes() - Method in class edu.upenn.crimson.Model
getNotes() - Method in class edu.upenn.crimson.Partition
getNotes() - Method in class edu.upenn.crimson.Query
getNotes() - Method in class edu.upenn.crimson.Tree
getNumLeaves() - Method in class edu.upenn.crimson.Query
getNumLeaves() - Method in class edu.upenn.crimson.Tree: This will return the number of leaves in the tree.
getNumPartitions() - Method in class edu.upenn.crimson.Tree: The number of partitions loaded for this tree.
getNumPositions() - Method in class edu.upenn.crimson.Query
getNumSpecies() - Method in class edu.upenn.crimson.Tree: This will return the number of species in the tree.
getParent() - Method in class edu.upenn.crimson.Species
getPartition(String) - Static method in class edu.upenn.crimson.ObjectHandles: Returns the Partition object for the given ID.
getPartitionPool() - Static method in class edu.upenn.crimson.ObjectHandles
getPartitions() - Static method in class edu.upenn.crimson.ObjectHandles: Returns the set of all Partition IDs.
getPartitions() - Method in class edu.upenn.crimson.Query
getPartitions() - Method in class edu.upenn.crimson.Tree: This will return the set of partitions.
getPartitionsByModel(String) - Method in class edu.upenn.crimson.Tree: This will return an ArrayList containing all of the partitions in the current tree that are based on the specified model.
getPort() - Static method in class edu.upenn.crimson.CrimsonUtils: Get the PORT flag.
getPositions() - Method in class edu.upenn.crimson.Query
getPyFilter() - Static method in class edu.upenn.crimson.gui.GUIUtils
getQueries() - Static method in class edu.upenn.crimson.ObjectHandles: Returns the set of all Query IDs.
getQuery(String) - Static method in class edu.upenn.crimson.ObjectHandles: Returns the Query object for the given ID.
getQueryID(String) - Static method in class edu.upenn.crimson.gui.QueryUtils: This will use a FieldEditDialog to ask the user for a query id.
getQueryPool() - Static method in class edu.upenn.crimson.ObjectHandles
getQueryTableModel() - Static method in class edu.upenn.crimson.ObjectHandles
getRandomPositions(int, int, boolean) - Static method in class edu.upenn.crimson.io.Queries
getRoot() - Method in class edu.upenn.crimson.Tree
getRootLCA(int) - Method in class edu.upenn.crimson.Tree: This will return the LCA for a random sampling of leaves from the tree.
getRow(int) - Method in class edu.upenn.crimson.ModelTableModel: Returns the Model that represents the specified row in the table.
getRow(int) - Method in class edu.upenn.crimson.QueryTableModel: Returns the Query that represents the specified row in the table.
getRow(int) - Method in class edu.upenn.crimson.TreeTableModel: Returns the Tree that represents the specified row in the table.
getRowCount() - Method in class edu.upenn.crimson.ModelTableModel
getRowCount() - Method in class edu.upenn.crimson.QueryTableModel
getRowCount() - Method in class edu.upenn.crimson.TreeTableModel
getSeed() - Method in class edu.upenn.crimson.Query
getSequenceSelection() - Method in class edu.upenn.crimson.Query
getSequenceSelectionString() - Method in class edu.upenn.crimson.Query
getServer() - Static method in class edu.upenn.crimson.CrimsonUtils: Get the SERVER flag.
getSiblings() - Method in class edu.upenn.crimson.Species: It is assumed that all trees have a single root.
getSpeciesByID(ArrayList) - Method in class edu.upenn.crimson.Tree: This will take a list of species IDs and return a list of species objects.
getSpeciesByID(String) - Method in class edu.upenn.crimson.Tree: This steps through every species in the tree and compares the species IDs until it finds the species requested.
getSpeciesList() - Method in class edu.upenn.crimson.Tree: Returns the list of all species in the tree.
getStatement() - Static method in class edu.upenn.crimson.io.Database: Get a the database Statement object necessary to perform a database query.
getStemLength() - Method in class edu.upenn.crimson.Species
getSubtree(Species) - Method in class edu.upenn.crimson.Tree: Returns the subtree given the specified root.
getSystemProperty(String) - Static method in class edu.upenn.crimson.CrimsonMain
getTempDepth() - Method in class edu.upenn.crimson.Species
getTempDepthThresh() - Method in class edu.upenn.crimson.Query
getTmpDir() - Static method in class edu.upenn.crimson.CrimsonUtils: Get the TMP_DIR.
getTree(String) - Static method in class edu.upenn.crimson.ObjectHandles: Returns the Tree object for the given ID.
getTreeID() - Method in class edu.upenn.crimson.Partition: Get the ID for the tree containing this partition.
getTreeID() - Method in class edu.upenn.crimson.Query
getTreeList() - Static method in class edu.upenn.crimson.ObjectHandles
getTreePool() - Static method in class edu.upenn.crimson.ObjectHandles
getTrees() - Static method in class edu.upenn.crimson.ObjectHandles: Returns the set of all Tree IDs.
getTreesByLevel(int) - Method in class edu.upenn.crimson.Tree: Returns the set of root species for any subtrees that are below a specified level.
getTreesByTempDepth(double) - Method in class edu.upenn.crimson.Tree: Returns the set of root species for any subtrees that are below a specified level.
getTreeTableModel() - Static method in class edu.upenn.crimson.ObjectHandles
getUsername() - Static method in class edu.upenn.crimson.CrimsonUtils: Get the USERNAME flag.
getValueAt(int, int) - Method in class edu.upenn.crimson.ModelTableModel: "ID", "Notes"
getValueAt(int, int) - Method in class edu.upenn.crimson.QueryTableModel: "ID", "Tree", "Leaf Selection", "Seq Selection"
getValueAt(int, int) - Method in class edu.upenn.crimson.TreeTableModel: "ID", "Partitions", "Species", "maxTempDepth", "Tot Seq Length"
getVerbose() - Static method in class edu.upenn.crimson.CrimsonUtils: Get the VERBOSE flag.
guiMessages - Static variable in class edu.upenn.crimson.CrimsonUtils: If not null, all error and warning messages will be sent here.
GUIUtils - Class in edu.upenn.crimson.gui: Static methods used throughout the GUI.
GUIUtils() - Constructor for class edu.upenn.crimson.gui.GUIUtils
GUIUtils.DocumentLengthFilter - Class in edu.upenn.crimson.gui: Filter used to limit JTextAreas to 4000 characters.
GUIUtils.DocumentLengthFilter() - Constructor for class edu.upenn.crimson.gui.GUIUtils.DocumentLengthFilter
GUIUtils.PyFilter - Class in edu.upenn.crimson.gui: Python specific FileFilter.
GUIUtils.PyFilter() - Constructor for class edu.upenn.crimson.gui.GUIUtils.PyFilter

H

hashCode() - Method in class edu.upenn.crimson.Species: We use the hash of the ID as the object's hash code.
hasNextChild() - Method in class edu.upenn.crimson.Species: This will return true if there are more children.
helpTopics - Variable in class edu.upenn.crimson.gui.Root.RootFrame
history - Static variable in class edu.upenn.crimson.gui.Root: This will contain all commands that the GUI generates and sends to the console to be run.
history - Variable in class edu.upenn.crimson.gui.Root.RootFrame
HTMLFile - Class in edu.upenn.crimson.io: Save URL, HTML text, or InputStream as HTML file.
HTMLFile() - Constructor for class edu.upenn.crimson.io.HTMLFile
HTMLFile.HTMLFilter - Class in edu.upenn.crimson.io: HTML FileFilter.
HTMLFile.HTMLFilter() - Constructor for class edu.upenn.crimson.io.HTMLFile.HTMLFilter
htmlText - Variable in class edu.upenn.crimson.gui.ViewHTML
hyperlinkUpdate(HyperlinkEvent) - Method in class edu.upenn.crimson.gui.ViewHTML.Hyperactive

I

id - Variable in class edu.upenn.crimson.Model: This is a unique name for the Model object.
id - Variable in class edu.upenn.crimson.Partition: This is a unique name for the partition object.
id - Variable in class edu.upenn.crimson.Query: This is a unique name for the Query object.
id - Variable in class edu.upenn.crimson.Species: The ID of the species.
id - Variable in class edu.upenn.crimson.Tree: This is a unique name for the Tree object.
importB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
importQuery() - Static method in class edu.upenn.crimson.gui.QueryUtils: This will import a query from a python file.
importQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame
ImportQuery(String) - Static method in class edu.upenn.crimson.io.Database: This is a specialized version of proxyToArray() to import queries.
incSequence - Variable in class edu.upenn.crimson.gui.QueryEditor
INPUTSTREAM - Static variable in class edu.upenn.crimson.gui.ViewHTML
insertString(DocumentFilter.FilterBypass, int, String, AttributeSet) - Method in class edu.upenn.crimson.gui.GUIUtils.DocumentLengthFilter
InvalidIDException - Exception in edu.upenn.crimson
InvalidIDException() - Constructor for exception edu.upenn.crimson.InvalidIDException: Create a new InvalidIDException without a message.
InvalidIDException(String) - Constructor for exception edu.upenn.crimson.InvalidIDException: Create a new InvalidIDException with a message.
ISBATCH - Static variable in class edu.upenn.crimson.CrimsonMain: Batch mode.
isBinary() - Method in class edu.upenn.crimson.Species: Returns true if this node is binary.
isBinary() - Method in class edu.upenn.crimson.Tree
isBuilt() - Method in class edu.upenn.crimson.Tree: Returns true if the tree has been built from the newick string.
ISDOS - Static variable in class edu.upenn.crimson.CrimsonMain: Dos interpreter.
isEmpty(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Returns true if 'str' is empty (ignores spaces) or null.
isEmpty(Collection) - Static method in class edu.upenn.crimson.CrimsonUtils: Returns true if 'collection' is empty or null.
isLeaf() - Method in class edu.upenn.crimson.Species: Returns true if this species is a leaf (ie has no children).
isMySQL() - Static method in class edu.upenn.crimson.io.SQL
isOnlyStruct() - Method in class edu.upenn.crimson.Query
isOpen() - Static method in class edu.upenn.crimson.io.Database: Returns true if a database connection exists or using proxy server and false otherwise.
isOracle() - Static method in class edu.upenn.crimson.io.SQL
isProxy() - Static method in class edu.upenn.crimson.io.Database: This will return true if using a web proxy.
isRoot() - Method in class edu.upenn.crimson.Species: Returns true if this species doesn't have a parent.
isSaved() - Method in class edu.upenn.crimson.Query
isTreeBuilt(Tree) - Static method in class edu.upenn.crimson.gui.TreeUtils
isUltrametric() - Method in class edu.upenn.crimson.Tree
isVisible() - Static method in class edu.upenn.crimson.gui.Root

L

launchWalrus(String) - Static method in class edu.upenn.crimson.gui.GUIUtils: This will start a Walrus 3D session using the file given.
LEAF_SELECTION - Variable in class edu.upenn.crimson.gui.QueryEditor
leafCB - Variable in class edu.upenn.crimson.gui.QueryEditor
leafL - Variable in class edu.upenn.crimson.gui.QueryEditor
leafSelection - Variable in class edu.upenn.crimson.Query: LEAF SELECTION: 0 = Select All, 1 = Random Selection, 2 = Select By Temporal Depth (distributed), 3 = Select By Temporal Depth (weighted), 4 = Selection by Level (distributed), 5 = Selection by Level (weighted), 6 = Manual Selection
leaves - Variable in class edu.upenn.crimson.Query: Set of IDs for the leaves to include.
length - Variable in class edu.upenn.crimson.Partition: Total length of the partition's sequence.
level - Variable in class edu.upenn.crimson.Species: Level from root to this species.
levelS - Variable in class edu.upenn.crimson.gui.QueryEditor
levelSM - Variable in class edu.upenn.crimson.gui.QueryEditor
levelThresh - Variable in class edu.upenn.crimson.Query: Level of the leaves to be selected.
load(String, String, String) - Static method in class edu.upenn.crimson.io.NexusFile: Loads a Nexus file.
load(String) - Static method in class edu.upenn.crimson.io.Queries: This will load the specified query from the QUERIES table in the current database.
loadAll() - Static method in class edu.upenn.crimson.io.Models: This will load all models from the MODELS table.
loadAll() - Static method in class edu.upenn.crimson.io.Partitions: This will load all partitions from the PARTITIONS table.
loadAll() - Static method in class edu.upenn.crimson.io.Trees: This will load all trees from the TREES table.
loadAllQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame
loadB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
loadB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
loadNewick(String) - Static method in class edu.upenn.crimson.io.NexusFile: Loads a tree structure from a Nexus file into memory.
loadPython(String) - Static method in class edu.upenn.crimson.io.FileIO
loadQuery() - Static method in class edu.upenn.crimson.gui.QueryUtils: This will load a query object from the databasee.
loadQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame
loadTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
loadTree() - Static method in class edu.upenn.crimson.gui.TreeUtils: This will process the NEXUS file selected and then load the file into the specified database table.
loadTree(File, String, String) - Static method in class edu.upenn.crimson.gui.TreeUtils

M

main(String[]) - Static method in class edu.upenn.crimson.CrimsonMain
manageModel - Variable in class edu.upenn.crimson.gui.Root.RootFrame
manageQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame
manageTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
manualSampleByID(ArrayList) - Method in class edu.upenn.crimson.Tree: This will return a subtree that contains the specified leaves.
MAX_LEAVES - Variable in class edu.upenn.crimson.gui.QueryEditor: This is the total number of leaves that will be displayed in the leaf list for the user to manually select.
MAX_LENGTH - Variable in class edu.upenn.crimson.gui.GUIUtils.DocumentLengthFilter
MAX_SEED - Variable in class edu.upenn.crimson.gui.QueryEditor: This is a determined by the random number generator used in randomselect.
maxDoubleValue - Variable in class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel
maxIntValue - Variable in class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel
maxLevel - Variable in class edu.upenn.crimson.Tree: The maximum number of species between the leaves and root.
maxPositions - Variable in class edu.upenn.crimson.gui.QueryEditor
maxStemLength - Variable in class edu.upenn.crimson.Tree: The maximum distance between the species and their parents.
maxTempDepth - Variable in class edu.upenn.crimson.Tree: The maximum distance between the leaves and root.
messages - Static variable in class edu.upenn.crimson.gui.Root: This will contain all error and warning messages.
messages - Variable in class edu.upenn.crimson.gui.Root.RootFrame
minLevel - Variable in class edu.upenn.crimson.Tree: The minimum number of species between the leaves and root.
minStemLength - Variable in class edu.upenn.crimson.Tree: The minimum distance between the species and their parents.
minTempDepth - Variable in class edu.upenn.crimson.Tree: The minimum distance between the leaves and root.
model - Variable in class edu.upenn.crimson.gui.ModelEditor
model - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame: Reference to the selected model.
Model - Class in edu.upenn.crimson: Contains model info.
Model(String) - Constructor for class edu.upenn.crimson.Model: Create a new Model object.
Model(String, boolean) - Constructor for class edu.upenn.crimson.Model: Create a new Model object.
ModelEditor - Class in edu.upenn.crimson.gui: This is a graphical model editor.
ModelEditor(Model) - Constructor for class edu.upenn.crimson.gui.ModelEditor
modelID - Variable in class edu.upenn.crimson.Partition: Model specific to this partition object.
modelID - Variable in class edu.upenn.crimson.Tree: Model specific to this Tree object.
modelIterator() - Static method in class edu.upenn.crimson.ObjectHandles: Returns a iterator over all Models in modelPool.
modelList - Static variable in class edu.upenn.crimson.ObjectHandles: This is a duplicate list of Models in the modelPool.
ModelManager - Class in edu.upenn.crimson.gui: Browse existing Queries.
ModelManager() - Constructor for class edu.upenn.crimson.gui.ModelManager
ModelManager.PanelFrame - Class in edu.upenn.crimson.gui
ModelManager.PanelFrame() - Constructor for class edu.upenn.crimson.gui.ModelManager.PanelFrame
modelPool - Static variable in class edu.upenn.crimson.ObjectHandles: The HashMap of all existing Models.
Models - Class in edu.upenn.crimson.io: Functions related to the MODELS table.
Models() - Constructor for class edu.upenn.crimson.io.Models
models - Variable in class edu.upenn.crimson.ModelTableModel: Stores the Models that are in the table.
modelSelector() - Static method in class edu.upenn.crimson.gui.ModelUtils: Present a dialog box for selecting a particular Model.
ModelTableModel - Class in edu.upenn.crimson: ModelTableModel.
ModelTableModel() - Constructor for class edu.upenn.crimson.ModelTableModel
modelTableModel - Static variable in class edu.upenn.crimson.ObjectHandles: This is a duplicate list of Models in the modelPool.
ModelUtils - Class in edu.upenn.crimson.gui: Static methods used throughout the GUI for Model objects.
ModelUtils() - Constructor for class edu.upenn.crimson.gui.ModelUtils
multiCharStringNeedsQuotes(String) - Static method in class edu.upenn.crimson.io.NexusFile: From Mark Holder

N

needsQuotesPattern - Static variable in class edu.upenn.crimson.io.NexusFile: From Mark Holder
newB - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
newB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
newickB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
newickTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
newickTree(String) - Static method in class edu.upenn.crimson.gui.TreeUtils: This will display the tree's newick string.
newModel - Variable in class edu.upenn.crimson.gui.Root.RootFrame
newQuery() - Static method in class edu.upenn.crimson.gui.QueryUtils: This will create a new query object.
newQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame
nextChild() - Method in class edu.upenn.crimson.Species: This will return the next child keeping track of the children returned.
NexusFile - Class in edu.upenn.crimson.io: Functions related to loading NEXUS files.
NexusFile() - Constructor for class edu.upenn.crimson.io.NexusFile
notes - Variable in class edu.upenn.crimson.Model: Notes specific to this Model object.
notes - Variable in class edu.upenn.crimson.Partition: Notes specific to this partition object.
notes - Variable in class edu.upenn.crimson.Query: Notes specific to this Query object.
notes - Variable in class edu.upenn.crimson.Tree: Notes specific to this Tree object.
notesB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
notesL - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
notesL - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
notesTA - Variable in class edu.upenn.crimson.gui.ModelEditor
NOX - Static variable in class edu.upenn.crimson.CrimsonMain: No X11 or similar windowing environment.
npPartition - Variable in class edu.upenn.crimson.gui.TreeManager.NotesPanel
npPartitionID - Variable in class edu.upenn.crimson.gui.TreeManager.NotesPanel
npQuery - Variable in class edu.upenn.crimson.gui.QueryEditor.NotesPanel
npQueryID - Variable in class edu.upenn.crimson.gui.QueryEditor.NotesPanel
npTextArea - Variable in class edu.upenn.crimson.gui.QueryEditor.NotesPanel
npTextArea - Variable in class edu.upenn.crimson.gui.TreeManager.NotesPanel
npTree - Variable in class edu.upenn.crimson.gui.TreeManager.NotesPanel
npTreeID - Variable in class edu.upenn.crimson.gui.TreeManager.NotesPanel
numChildren() - Method in class edu.upenn.crimson.Species: Returns the number of children.
numLeaves - Variable in class edu.upenn.crimson.Query: Number of leaves to include when choosen randomly.
numLeaves - Variable in class edu.upenn.crimson.Tree: The number of leaves is stored, in case the tree has not been built from the newick string.
numLeavesS - Variable in class edu.upenn.crimson.gui.QueryEditor
numLeavesSM - Variable in class edu.upenn.crimson.gui.QueryEditor
numPositions - Variable in class edu.upenn.crimson.Query: Number of positions (base pairs or codons) to include when choosen randomly.
numPositionsS - Variable in class edu.upenn.crimson.gui.QueryEditor
numPositionsSM - Variable in class edu.upenn.crimson.gui.QueryEditor
numSpecies - Variable in class edu.upenn.crimson.Tree: The number of species is equivalent to speciesList.size().

O

ObjectHandles - Class in edu.upenn.crimson: ObjectHandles.
ObjectHandles() - Constructor for class edu.upenn.crimson.ObjectHandles
objectL - Variable in class edu.upenn.crimson.gui.ObjectSelectorDialog
ObjectSelectorDialog - Class in edu.upenn.crimson.gui: This class is used to present a modal dialog for selecting an item from the 'objects' array and includes the selected item in the 'out' arraylist.
ObjectSelectorDialog(String, Object[], ArrayList) - Constructor for class edu.upenn.crimson.gui.ObjectSelectorDialog
okB - Variable in class edu.upenn.crimson.gui.FieldEditDialog
onlyStruct - Variable in class edu.upenn.crimson.Query: When true, no data will be included in the output file (ie the partitions list will be ignored).
open(String) - Static method in class edu.upenn.crimson.io.Database: Opens a connection to the database, using the default username and password.
open(String, String, String, int, String) - Static method in class edu.upenn.crimson.io.Database: Opens a connection to the database.
openDatabase() - Static method in class edu.upenn.crimson.gui.GUIUtils: Use a FieldEditDialog to query the user for 'username', 'password', and 'database' info and then use this info to open a connection to the database.
openDB - Variable in class edu.upenn.crimson.gui.Root.RootFrame
openFileChooser(String, FileFilter) - Static method in class edu.upenn.crimson.gui.GUIUtils: Create a file chooser for opening files.
origHTML - Variable in class edu.upenn.crimson.gui.ViewHTML.HTMLEditorPane
output - Variable in class edu.upenn.crimson.gui.ObjectSelectorDialog

P

panelFrame - Static variable in class edu.upenn.crimson.gui.ModelManager
panelFrame - Static variable in class edu.upenn.crimson.gui.QueryManager
panelFrame - Static variable in class edu.upenn.crimson.gui.TreeManager
parent - Variable in class edu.upenn.crimson.Species: The parent will be null if this Species is the root.
parseNewick(Tree) - Static method in class edu.upenn.crimson.io.NexusFile: This might be faster if we use char[] instead of String for "newick".
parseNewick(Tree, String) - Static method in class edu.upenn.crimson.io.NexusFile: This might be faster if we use char[] instead of String for "newick".
partition - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame: Reference to the Partition selected.
Partition - Class in edu.upenn.crimson: Partition header info.
Partition(String, Tree) - Constructor for class edu.upenn.crimson.Partition
Partition(String, Tree, Model, int, String) - Constructor for class edu.upenn.crimson.Partition
partitionIterator() - Static method in class edu.upenn.crimson.ObjectHandles: Returns a iterator over all Partitions in partitionPool.
partitionPool - Static variable in class edu.upenn.crimson.ObjectHandles: The HashMap of all existing Partitions.
Partitions - Class in edu.upenn.crimson.io: Functions related to the PARTITIONS table.
Partitions() - Constructor for class edu.upenn.crimson.io.Partitions
partitions - Variable in class edu.upenn.crimson.Query: This set contains the IDs for the partitions to be queried.
partitions - Variable in class edu.upenn.crimson.Tree: This contains the partitions loaded for this tree.
partitionsL - Variable in class edu.upenn.crimson.gui.QueryEditor
partitionsL - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
password - Static variable in class edu.upenn.crimson.io.Database: Need to store this in the case of using a web proxy.
pDeleteB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
pExportB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
pLengthTF - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
pModelCB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
pNotesB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
PORT - Static variable in class edu.upenn.crimson.CrimsonUtils: String containing port connection information (default = 1521).
positions - Variable in class edu.upenn.crimson.Query: Base pair or codon positions to include.
positionTF - Variable in class edu.upenn.crimson.gui.QueryEditor
printError(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Display the message to either the gui or stderr.
printMsg(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Display the message to either the gui or stderr.
printMsg(String, int) - Static method in class edu.upenn.crimson.CrimsonUtils: Display the message to either the gui or stderr.
printMsg(String, boolean) - Static method in class edu.upenn.crimson.CrimsonUtils: Display the message to either the gui or stderr.
printMsg(String, int, boolean) - Static method in class edu.upenn.crimson.CrimsonUtils: Display the message to either the gui or stderr.
printNexus() - Method in class edu.upenn.crimson.Species: This will print out this species and all children as a NEXUS formatted tree.
printPositions(TreeSet) - Static method in class edu.upenn.crimson.io.FileIO: This will print the list of positions to the output file ('positions.list'), one position per line.
printSpecies(Collection, boolean) - Static method in class edu.upenn.crimson.io.FileIO: This will print the list of species to the output file ('species.list'), one species ID per line.
printTree(String) - Method in class edu.upenn.crimson.Species: This will print out the tree, one species per line, indenting each level.
printTree() - Method in class edu.upenn.crimson.Tree: This will print out the tree, one species per line, indenting each level.
printWarning(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Display the message to either the gui or stderr.
progressBar - Static variable in class edu.upenn.crimson.gui.Root: This will be used to display the progress during importing and exporting of trees.
progressBar - Variable in class edu.upenn.crimson.gui.Root.RootFrame
proxyToArray(String) - Static method in class edu.upenn.crimson.io.Database
publish(Query) - Static method in class edu.upenn.crimson.io.Queries: This will publish the specified query in the QUERIES table in the current database.
publish(Query, String, boolean) - Static method in class edu.upenn.crimson.io.Queries: This will publish the specified query in the QUERIES table in the current database.
publishB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
publishQuery(String) - Static method in class edu.upenn.crimson.gui.QueryUtils: This will save the query to the database.
publishQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame

Q

Queries - Class in edu.upenn.crimson.io: Functions related to QUERIES table.
Queries() - Constructor for class edu.upenn.crimson.io.Queries
queries - Variable in class edu.upenn.crimson.QueryTableModel: Stores the Queries that are in the table.
query - Variable in class edu.upenn.crimson.gui.QueryDialog
query - Variable in class edu.upenn.crimson.gui.QueryEditor
query - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame: Reference to the selected query.
Query - Class in edu.upenn.crimson: Contains query info.
Query(String) - Constructor for class edu.upenn.crimson.Query: Create a new Query object.
Query(String, String) - Constructor for class edu.upenn.crimson.Query: Create a new Query object.
queryB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
QueryDialog - Class in edu.upenn.crimson.gui: This will query the specified query, using a dialog box to get the filename, repeat, and incSequence info.
QueryDialog(String) - Constructor for class edu.upenn.crimson.gui.QueryDialog
QueryDialog(String, String, boolean, int) - Constructor for class edu.upenn.crimson.gui.QueryDialog
QueryEditor - Class in edu.upenn.crimson.gui: This is a graphical query editor.
QueryEditor(Query) - Constructor for class edu.upenn.crimson.gui.QueryEditor
QueryEditor(Query, String, boolean, int) - Constructor for class edu.upenn.crimson.gui.QueryEditor
QueryEditor.NotesPanel - Class in edu.upenn.crimson.gui: Edit notes field.
QueryEditor.NotesPanel(Query) - Constructor for class edu.upenn.crimson.gui.QueryEditor.NotesPanel
QueryEditor.ViewDistributePanel - Class in edu.upenn.crimson.gui: View tempDepth distribution.
QueryEditor.ViewDistributePanel(Tree, int) - Constructor for class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel
queryIterator() - Static method in class edu.upenn.crimson.ObjectHandles: Returns a iterator over all Querys in queryPool.
QueryManager - Class in edu.upenn.crimson.gui: Browse existing Queries.
QueryManager() - Constructor for class edu.upenn.crimson.gui.QueryManager
QueryManager.PanelFrame - Class in edu.upenn.crimson.gui
QueryManager.PanelFrame() - Constructor for class edu.upenn.crimson.gui.QueryManager.PanelFrame
queryPool - Static variable in class edu.upenn.crimson.ObjectHandles: The set of all existing Queries.
querySelector() - Static method in class edu.upenn.crimson.gui.QueryUtils: Present a dialog box for selecting a particular Query, from the set of queries in memory.
querySelectorDB() - Static method in class edu.upenn.crimson.gui.QueryUtils: Present a dialog box for selecting a particular Query, from the queries in the QUERIES table.
queryTableModel - Static variable in class edu.upenn.crimson.ObjectHandles: This is a duplicate list of Queries in the queryPool.
QueryTableModel - Class in edu.upenn.crimson: QueryTableModel.
QueryTableModel() - Constructor for class edu.upenn.crimson.QueryTableModel
QueryUtils - Class in edu.upenn.crimson.gui: Static methods used throughout the GUI for Query objects.
QueryUtils() - Constructor for class edu.upenn.crimson.gui.QueryUtils
quit - Variable in class edu.upenn.crimson.gui.Root.RootFrame
quote(String) - Static method in class edu.upenn.crimson.io.NexusFile: From Mark Holder This will properly quote a word that is to be included in a NEXUS file.
quote(String[]) - Static method in class edu.upenn.crimson.io.NexusFile: From Mark Holder This will properly quote a word that is to be included in a NEXUS file.

R

random - Static variable in class edu.upenn.crimson.CrimsonUtils: Global random object.
randomModelID(String) - Static method in class edu.upenn.crimson.ObjectHandles: Uses 'base' to create a random Model ID string that doesn't already exist in the modelPool.
randomQueryID(String) - Static method in class edu.upenn.crimson.ObjectHandles: Uses 'base' to create a random Query ID string that doesn't already exist in the queryPool.
randomSample(int) - Method in class edu.upenn.crimson.Tree: This will randomly sample the tree, returning a subtree that contains 'num' leaves.
randomTreeID(String) - Static method in class edu.upenn.crimson.ObjectHandles: Uses 'base' to create a random Tree ID string that doesn't already exist in the treePool.
readClob(Object) - Static method in class edu.upenn.crimson.io.Database: This will load the specified CLOB and return the CLOB data as a String.
readClobSet(Object) - Static method in class edu.upenn.crimson.io.Database: This will load the specified CLOB and return the CLOB data as a HashSet.
redraw() - Static method in class edu.upenn.crimson.gui.ModelManager: Redraw the window.
refreshB - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
refreshB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
refreshModel - Variable in class edu.upenn.crimson.gui.Root.RootFrame
refreshTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
regexPat - Static variable in class edu.upenn.crimson.io.NexusFile
removeAllRows() - Method in class edu.upenn.crimson.ModelTableModel: Removes all rows from the table.
removeAllRows() - Method in class edu.upenn.crimson.QueryTableModel: Removes all rows from the table.
removeAllRows() - Method in class edu.upenn.crimson.TreeTableModel: Removes all rows from the table.
removeChild(Species) - Method in class edu.upenn.crimson.Species: This will remove the child from the set of children.
removePartition(Partition) - Method in class edu.upenn.crimson.Tree
removeRow(int) - Method in class edu.upenn.crimson.ModelTableModel: Removes the Model that represents the specified row in the table.
removeRow(int) - Method in class edu.upenn.crimson.QueryTableModel: Removes the Query that represents the specified row in the table.
removeRow(int) - Method in class edu.upenn.crimson.TreeTableModel: Removes the Tree that represents the specified row in the table.
removeRows(int[]) - Method in class edu.upenn.crimson.ModelTableModel: Removes the Models that represent the rows specified.
removeRows(int, int) - Method in class edu.upenn.crimson.ModelTableModel: Removes the Models that represent the specified row in the table.
removeRows(int[]) - Method in class edu.upenn.crimson.QueryTableModel: Removes the Queries that represent the rows specified.
removeRows(int, int) - Method in class edu.upenn.crimson.QueryTableModel: Removes the Queries that represent the specified row in the table.
removeRows(int[]) - Method in class edu.upenn.crimson.TreeTableModel: Removes the Trees that represent the rows specified.
removeRows(int, int) - Method in class edu.upenn.crimson.TreeTableModel: Removes the Trees that represent the specified row in the table.
removeSpecies(Species) - Method in class edu.upenn.crimson.Tree
repeat - Variable in class edu.upenn.crimson.gui.QueryEditor
replace(DocumentFilter.FilterBypass, int, int, String, AttributeSet) - Method in class edu.upenn.crimson.gui.GUIUtils.DocumentLengthFilter
resetChildIndex() - Method in class edu.upenn.crimson.Species: This resets the index used by nextChild().
resetCrimsonDefaults() - Static method in class edu.upenn.crimson.CrimsonUtils: RE-set Crimson user defaults.
resetGUIDefaults() - Static method in class edu.upenn.crimson.gui.GUIUtils: RE-set GUI user defaults.
Root - Class in edu.upenn.crimson.gui: Base window for GUI.
Root() - Constructor for class edu.upenn.crimson.gui.Root
root - Variable in class edu.upenn.crimson.Tree: The root Species of the tree.
Root.RootFrame - Class in edu.upenn.crimson.gui
Root.RootFrame() - Constructor for class edu.upenn.crimson.gui.Root.RootFrame
rootFrame - Static variable in class edu.upenn.crimson.gui.Root
run(String, String, boolean, int) - Static method in class edu.upenn.crimson.io.Queries: This will repeatedly run a query, generating a NEXUS file for each run.
run(String, String, boolean, boolean, int, boolean) - Static method in class edu.upenn.crimson.io.Queries: This will perform a tree query, generating a NEXUS file.
runB - Variable in class edu.upenn.crimson.gui.QueryDialog
runB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
runCommand(String) - Static method in class edu.upenn.crimson.gui.Root: This will add the String to the history and then run the command through the console.
runCommand(String, boolean) - Static method in class edu.upenn.crimson.gui.Root: This will add the String to the history and if 'toConsole', then run the command through the console.
runGC() - Static method in class edu.upenn.crimson.CrimsonMain
runPhylip(String, String, int) - Static method in class edu.upenn.crimson.io.Queries: This will perform a tree query, generating a phylip formatted file.
runQuery(String, String, boolean, int) - Static method in class edu.upenn.crimson.gui.QueryUtils: This will run the query.
runQueryDialog(String) - Static method in class edu.upenn.crimson.gui.QueryUtils: This will run the query.
runQueryDialog(String, String, boolean, int) - Static method in class edu.upenn.crimson.gui.QueryUtils
runtime - Static variable in class edu.upenn.crimson.CrimsonMain

S

save - Variable in class edu.upenn.crimson.gui.FieldEditDialog
save(Model) - Static method in class edu.upenn.crimson.io.Models: This will publish the specified model to the MODELS table in the current database.
saved - Variable in class edu.upenn.crimson.Query: True when the query object has been saved to the database.
saveFileChooser(String, String, FileFilter) - Static method in class edu.upenn.crimson.gui.GUIUtils: Create a file chooser for saving files.
saveFileChooser() - Method in class edu.upenn.crimson.gui.ViewHTML: Use a JFileChooser the get the file info for saving HTML to a file.
saveFileChooser() - Static method in class edu.upenn.crimson.io.HTMLFile: Use a JFileChooser the get the file info for saving HTML to a file.
saveInputStream(InputStream) - Static method in class edu.upenn.crimson.io.HTMLFile
saveInputStream(InputStream, String, boolean) - Static method in class edu.upenn.crimson.io.HTMLFile
saveQuery() - Method in class edu.upenn.crimson.gui.QueryEditor: This will save the changes to the query.
saveText(String, boolean) - Method in class edu.upenn.crimson.gui.ViewHTML: Save the html text to a file.
saveText(String) - Static method in class edu.upenn.crimson.io.HTMLFile: Save the html text to a file.
saveText(String, String, boolean) - Static method in class edu.upenn.crimson.io.HTMLFile: Save the html text to a file.
saveURL(URL) - Static method in class edu.upenn.crimson.io.HTMLFile
saveURL(URL, String, boolean) - Static method in class edu.upenn.crimson.io.HTMLFile
seed - Variable in class edu.upenn.crimson.Query: Seed for random number generator.
seedTF - Variable in class edu.upenn.crimson.gui.QueryEditor
selectAllB - Variable in class edu.upenn.crimson.gui.QueryEditor
selectB - Variable in class edu.upenn.crimson.gui.ObjectSelectorDialog
selectHistory - Variable in class edu.upenn.crimson.gui.Root.RootFrame
selectModelB - Variable in class edu.upenn.crimson.gui.QueryEditor
SEQUENCE_SELECTION - Variable in class edu.upenn.crimson.gui.QueryEditor
sequenceCB - Variable in class edu.upenn.crimson.gui.QueryEditor
sequenceSelection - Variable in class edu.upenn.crimson.Query: SEQUENCE SELECTION: 0 = Select All, 1 = Random Codon Selection, 2 = Randon Position Selection, 3 = Manual Codon Selection, 4 = Manual Position Selection, 5 = Select None
SERVER - Static variable in class edu.upenn.crimson.CrimsonUtils: String containing server connection information.
setConnection(Connection) - Static method in class edu.upenn.crimson.CrimsonMain: Set the DBConnection.
setDatabase(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Set the DATABASE flag.
setDBType(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Set the DB_TYPE flag.
setDBType() - Static method in class edu.upenn.crimson.gui.GUIUtils
setDBType - Variable in class edu.upenn.crimson.gui.Root.RootFrame
setDBType(String) - Static method in class edu.upenn.crimson.io.SQL: Set the type of database (oracle or mysql).
setDetails(String) - Method in class edu.upenn.crimson.Model: Sets the value of the details field.
setDetails(String, boolean) - Method in class edu.upenn.crimson.Model: Sets the value of the details field.
setID(String) - Method in class edu.upenn.crimson.Species: The species ID is forced to be upper case.
setLeafSelection(int) - Method in class edu.upenn.crimson.Query
setLeaves(HashSet) - Method in class edu.upenn.crimson.Query
setLevel(int) - Method in class edu.upenn.crimson.Species
setLevelThresh(int) - Method in class edu.upenn.crimson.Query
setModelID(Model) - Method in class edu.upenn.crimson.Partition: Sets the ID for the model underlying this partition.
setModelID(Model) - Method in class edu.upenn.crimson.Tree: Sets the ID for the model underlying this tree.
setNewick(String) - Method in class edu.upenn.crimson.Tree: This will update the newick string stored in the database.
setNotes(String) - Method in class edu.upenn.crimson.Model: Sets the value of the notes field.
setNotes(String, boolean) - Method in class edu.upenn.crimson.Model: Sets the value of the notes field.
setNotes(String) - Method in class edu.upenn.crimson.Partition: Updates the notes field in the partition object and the PARTITIONS table.
setNotes(String) - Method in class edu.upenn.crimson.Query
setNotes(String) - Method in class edu.upenn.crimson.Tree: Updates the local notes field and the TREES table.
setNumLeaves(int) - Method in class edu.upenn.crimson.Query
setNumPositions(int) - Method in class edu.upenn.crimson.Query
setOnlyStruct(boolean) - Method in class edu.upenn.crimson.Query
setParent(Species) - Method in class edu.upenn.crimson.Species
setPartitions(HashSet) - Method in class edu.upenn.crimson.Query
setPort(int) - Static method in class edu.upenn.crimson.CrimsonUtils: Set the PORT flag.
setPositions(HashSet) - Method in class edu.upenn.crimson.Query
setRandomSeed(long) - Static method in class edu.upenn.crimson.CrimsonUtils: The seed is initially set to the system time.
setRoot(Species) - Method in class edu.upenn.crimson.Tree: The root's label will be set to "_Root" if there is currently no label.
setSaved(boolean) - Method in class edu.upenn.crimson.Query
setSeed(long) - Method in class edu.upenn.crimson.Query
setSequenceSelection(int) - Method in class edu.upenn.crimson.Query
setServer(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Set the SERVER flag.
setShowAllFiles(boolean) - Static method in class edu.upenn.crimson.gui.GUIUtils: Set the SHOW_ALL_FILES flag.
setStemLength(double) - Method in class edu.upenn.crimson.Species
setSystemProperty(String, String) - Static method in class edu.upenn.crimson.CrimsonMain
setTempDepth(double) - Method in class edu.upenn.crimson.Species
setTempDepth_Level(double, int) - Method in class edu.upenn.crimson.Species: This will set the temporal depth and level at the same time.
setTempDepthThresh(double) - Method in class edu.upenn.crimson.Query
setText(String) - Method in class edu.upenn.crimson.gui.ViewHTML.HTMLEditorPane
setTmpDir(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Set the TMP_DIR variable.
setToList(HashSet) - Static method in class edu.upenn.crimson.CrimsonUtils: This will return the elements of a HashSet as a ':' delimited string.
setTreeID(String) - Method in class edu.upenn.crimson.Query: Returns true if treeID set, false otherwise.
setup(Object, int) - Method in class edu.upenn.crimson.gui.ViewHTML
setUseFileExtensions(boolean) - Static method in class edu.upenn.crimson.gui.GUIUtils: Set the USE_FILE_EXTENSIONS flag.
setUsername(String) - Static method in class edu.upenn.crimson.CrimsonUtils: Set the USERNAME flag.
setVerbose(int) - Static method in class edu.upenn.crimson.CrimsonUtils: Set the VERBOSE flag.
shortStringNeedsQuotes(String) - Static method in class edu.upenn.crimson.io.NexusFile: From Mark Holder handles strings of len 1 or 0 only.
shortStrNeedsQuotePattern - Static variable in class edu.upenn.crimson.io.NexusFile: From Mark Holder
show() - Static method in class edu.upenn.crimson.gui.ModelManager: Only allow one instance of PanelFrame.
show() - Static method in class edu.upenn.crimson.gui.QueryManager: Only allow one instance of PanelFrame.
show() - Static method in class edu.upenn.crimson.gui.Root
show() - Static method in class edu.upenn.crimson.gui.TreeManager: Only allow one instance of PanelFrame.
SHOW_ALL_FILES - Static variable in class edu.upenn.crimson.gui.GUIUtils: By using global static variables, these values will persist across instances of the open/save fileChoosers.
showAllFiles() - Static method in class edu.upenn.crimson.gui.GUIUtils
showMessages - Static variable in class edu.upenn.crimson.gui.Root: Flag whether to display messages in the 'messages' panel.
sizeOf() - Static method in class edu.upenn.crimson.CrimsonMain: A simple class to experiment with your JVM's garbage collector and memory sizes for various data types.
Species - Class in edu.upenn.crimson: A single species object.
Species(int, Tree) - Constructor for class edu.upenn.crimson.Species
Species(String, Tree) - Constructor for class edu.upenn.crimson.Species
Species(String, double, int, Tree) - Constructor for class edu.upenn.crimson.Species
SPECIES_CHUNK - Static variable in class edu.upenn.crimson.io.Queries: When writing data to a NEXUS file ('run()'), this is the number of species queried per SQL statement.
speciesList - Variable in class edu.upenn.crimson.Tree: Array containing references to all species in the tree.
SQL - Class in edu.upenn.crimson.io: Most SQL commands are contained here, to facilitate portability to different databases.
SQL() - Constructor for class edu.upenn.crimson.io.SQL
sqlToArray(String) - Static method in class edu.upenn.crimson.io.Database: This will execute SQL queries of the database.
sqlToClob(String) - Static method in class edu.upenn.crimson.io.Database: This will execute SQL queries of the database.
sqlToHash(String) - Static method in class edu.upenn.crimson.io.Database: This will execute SQL queries of the database.
startProgressBar(String) - Static method in class edu.upenn.crimson.gui.Root: This will turn on the progress bar.
statsB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
statsTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
statsTree(String) - Static method in class edu.upenn.crimson.gui.TreeUtils: This will display the tree statistics.
statusBar - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
statusBar - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
statusBar - Variable in class edu.upenn.crimson.gui.Root.RootFrame
statusBar - Static variable in class edu.upenn.crimson.gui.Root
statusBar - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
stemLength - Variable in class edu.upenn.crimson.Species: Length from parent to this species (default = 1.0).
stopProgressBar() - Static method in class edu.upenn.crimson.gui.Root: This will turn off the progress bar.

T

table - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame: List of all queries in current database.
table - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame: List of all queries in current database.
table - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame: List of all trees in current database.
tableExists(String) - Static method in class edu.upenn.crimson.io.Database: Test if the table exists in the current database.
tableExists(String) - Static method in class edu.upenn.crimson.io.SQL: This code will return the table name, if the table exists in the database.
tableModel - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
tableModel - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
tableModel - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
tempDepth - Variable in class edu.upenn.crimson.Species: Length from root to this species.
tempDepthS - Variable in class edu.upenn.crimson.gui.QueryEditor
tempDepthSM - Variable in class edu.upenn.crimson.gui.QueryEditor
tempDepthThresh - Variable in class edu.upenn.crimson.Query: Temporal depth of the leaves to be selected.
testConn(String, String, String, String, String, String) - Static method in class edu.upenn.crimson.CrimsonMain: This method can be used to test encryption and checksum connection schemes.
testConnection() - Static method in class edu.upenn.crimson.io.Database: This will perform a simple query of the database to test if the database connection is functional.
testDB - Variable in class edu.upenn.crimson.gui.Root.RootFrame
testProxy(String, String, String, String, String) - Static method in class edu.upenn.crimson.CrimsonMain
TEXT - Static variable in class edu.upenn.crimson.gui.ViewHTML
textArea - Variable in class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel
textFields - Variable in class edu.upenn.crimson.gui.FieldEditDialog
thisDialog - Variable in class edu.upenn.crimson.gui.FieldEditDialog
thisDialog - Variable in class edu.upenn.crimson.gui.ObjectSelectorDialog
thisDialog - Variable in class edu.upenn.crimson.gui.QueryDialog
thisFrame - Variable in class edu.upenn.crimson.gui.ModelEditor
thisFrame - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
thisFrame - Variable in class edu.upenn.crimson.gui.QueryEditor.NotesPanel
thisFrame - Variable in class edu.upenn.crimson.gui.QueryEditor
thisFrame - Variable in class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel
thisFrame - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
thisFrame - Variable in class edu.upenn.crimson.gui.TreeManager.NotesPanel
thisFrame - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
thisFrame - Variable in class edu.upenn.crimson.gui.TreeUtils.NewickViewer
thisFrame - Variable in class edu.upenn.crimson.gui.ViewHTML
thisThreshType - Variable in class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel
thisTree - Variable in class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel
TMP_DIR - Static variable in class edu.upenn.crimson.CrimsonUtils: String containing the location of the temporary dataloader files.
toggleShowMessages - Variable in class edu.upenn.crimson.gui.Root.RootFrame
toNewick() - Method in class edu.upenn.crimson.Tree: This will print out this species and all children as a newick formatted tree.
toNewick(boolean) - Method in class edu.upenn.crimson.Tree: This will print out this species and all children as a newick formatted tree.
toNewick(boolean, boolean) - Method in class edu.upenn.crimson.Tree: This will output this species and all children as a newick formatted tree.
toString() - Method in class edu.upenn.crimson.io.Models: Returns the non-CLOB columns in the MODELS table.
toString() - Method in class edu.upenn.crimson.io.Partitions: Returns the data in the PARTITIONS table.
toString() - Method in class edu.upenn.crimson.io.Queries: Returns the non-Clob columns in the QUERIES table.
toString() - Method in class edu.upenn.crimson.io.Trees: Returns the non-Blob columns in the TREES table.
toString() - Method in class edu.upenn.crimson.Model: Returns Model information formatted for JLists.
toString() - Method in class edu.upenn.crimson.Partition: Returns Partition information.
toString() - Method in class edu.upenn.crimson.Query: Returns Query information for debugging purposes.
toString() - Method in class edu.upenn.crimson.Species
toString() - Method in class edu.upenn.crimson.Tree: This will print lots of specs about the tree.
toStringFull() - Method in class edu.upenn.crimson.Model: Returns Model information for debugging purposes.
toStringFull() - Method in class edu.upenn.crimson.Species
tree - Variable in class edu.upenn.crimson.gui.QueryEditor
tree - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame: Reference to the Tree selected.
Tree - Class in edu.upenn.crimson: A rooted tree that is composed of Species objects.
Tree(String) - Constructor for class edu.upenn.crimson.Tree
Tree(String, boolean) - Constructor for class edu.upenn.crimson.Tree
Tree(String, Species, Model, String, int, int, boolean, boolean, int, int, double, double, double, double) - Constructor for class edu.upenn.crimson.Tree: Trees should not be instantiated by the user, using this routine.
treeCB - Variable in class edu.upenn.crimson.gui.QueryEditor
treeID - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
treeID - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame: The ID for the Tree selected.
treeID - Variable in class edu.upenn.crimson.Partition: This is the tree structure for this partition.
treeID - Variable in class edu.upenn.crimson.Query: This is the ID for the tree object that this query refers to.
treeIterator() - Static method in class edu.upenn.crimson.ObjectHandles: Returns a iterator over all Trees in treePool.
treeLeavesL - Variable in class edu.upenn.crimson.gui.QueryEditor
treeLengthL - Variable in class edu.upenn.crimson.gui.QueryEditor
treeLevelB - Variable in class edu.upenn.crimson.gui.QueryEditor
treeList - Static variable in class edu.upenn.crimson.ObjectHandles: This is a duplicate list of Trees in the treePool.
TreeManager - Class in edu.upenn.crimson.gui: Browse existing Trees.
TreeManager() - Constructor for class edu.upenn.crimson.gui.TreeManager
TreeManager.NotesPanel - Class in edu.upenn.crimson.gui: Edit notes field.
TreeManager.NotesPanel(Tree) - Constructor for class edu.upenn.crimson.gui.TreeManager.NotesPanel
TreeManager.NotesPanel(Partition) - Constructor for class edu.upenn.crimson.gui.TreeManager.NotesPanel
TreeManager.NotesPanel(Tree, Partition) - Constructor for class edu.upenn.crimson.gui.TreeManager.NotesPanel
TreeManager.PanelFrame - Class in edu.upenn.crimson.gui
TreeManager.PanelFrame() - Constructor for class edu.upenn.crimson.gui.TreeManager.PanelFrame
treeMaxLevelL - Variable in class edu.upenn.crimson.gui.QueryEditor
treeMaxTempDepthL - Variable in class edu.upenn.crimson.gui.QueryEditor
treePartitionsL - Variable in class edu.upenn.crimson.gui.QueryEditor
treePool - Static variable in class edu.upenn.crimson.ObjectHandles: The HashMap of all existing Trees.
Trees - Class in edu.upenn.crimson.io: Functions related to the TREES table.
Trees() - Constructor for class edu.upenn.crimson.io.Trees
trees - Variable in class edu.upenn.crimson.TreeTableModel: Stores the Trees that are in the table.
treeSelector() - Static method in class edu.upenn.crimson.gui.TreeUtils: Present a dialog box for selecting a particular Tree.
treeTableModel - Static variable in class edu.upenn.crimson.ObjectHandles: This is a duplicate list of Trees in the treePool.
TreeTableModel - Class in edu.upenn.crimson: TreeTableModel.
TreeTableModel() - Constructor for class edu.upenn.crimson.TreeTableModel
treeTempDepthB - Variable in class edu.upenn.crimson.gui.QueryEditor
TreeUtils - Class in edu.upenn.crimson.gui: Static methods used throughout the GUI for Tree objects.
TreeUtils() - Constructor for class edu.upenn.crimson.gui.TreeUtils
TreeUtils.NewickViewer - Class in edu.upenn.crimson.gui
TreeUtils.NewickViewer(String) - Constructor for class edu.upenn.crimson.gui.TreeUtils.NewickViewer

U

ultrametric - Variable in class edu.upenn.crimson.Tree: True when all leaves have the same temporal depth: (minTempDepth = maxTempDepth)
uniformSampleByLevel(int, int) - Method in class edu.upenn.crimson.Tree: Returns the random, uniform sampling of species from each subtree demarkated by the level value.
uniformSampleByTempDepth(double, int) - Method in class edu.upenn.crimson.Tree: Returns the random, uniform sampling of species from each subtree demarkated by the temporal depth value.
unselectAllB - Variable in class edu.upenn.crimson.gui.QueryEditor
unselectModelB - Variable in class edu.upenn.crimson.gui.QueryEditor
updateNumPositionsSM() - Method in class edu.upenn.crimson.gui.QueryEditor: Update numPositions spinner bounds, bounded by sequence length.
URL - Static variable in class edu.upenn.crimson.gui.ViewHTML
USE_FILE_EXTENSIONS - Static variable in class edu.upenn.crimson.gui.GUIUtils
usedMemory() - Static method in class edu.upenn.crimson.CrimsonMain
useFileExtensions() - Static method in class edu.upenn.crimson.gui.GUIUtils
userDefaults - Static variable in class edu.upenn.crimson.CrimsonMain: User established properties.
USERNAME - Static variable in class edu.upenn.crimson.CrimsonUtils: String containing username for database connection.

V

VERBOSE - Static variable in class edu.upenn.crimson.CrimsonUtils: Amount of detailed feedback: 2 = lots, 1 = no warnings (default), 0 = no feedback.
view3DTree - Variable in class edu.upenn.crimson.gui.Root.RootFrame
view3DTree(String) - Static method in class edu.upenn.crimson.gui.TreeUtils: This will view the tree specified by TreeSelector().
viewAPI - Variable in class edu.upenn.crimson.gui.Root.RootFrame
viewB - Variable in class edu.upenn.crimson.gui.ModelManager.PanelFrame
viewB - Variable in class edu.upenn.crimson.gui.QueryManager.PanelFrame
viewB - Variable in class edu.upenn.crimson.gui.TreeManager.PanelFrame
ViewHTML - Class in edu.upenn.crimson.gui: Browse HTML file or text.
ViewHTML(URL) - Constructor for class edu.upenn.crimson.gui.ViewHTML
ViewHTML(String) - Constructor for class edu.upenn.crimson.gui.ViewHTML
ViewHTML(InputStream) - Constructor for class edu.upenn.crimson.gui.ViewHTML
ViewHTML.HTMLEditorPane - Class in edu.upenn.crimson.gui: This class is meant to wrap the JEditorPane because the JEditorPane munges up the HTML source when it stores the text.
ViewHTML.HTMLEditorPane() - Constructor for class edu.upenn.crimson.gui.ViewHTML.HTMLEditorPane
ViewHTML.HTMLFilter - Class in edu.upenn.crimson.gui: HTML FileFilter.
ViewHTML.HTMLFilter() - Constructor for class edu.upenn.crimson.gui.ViewHTML.HTMLFilter
ViewHTML.Hyperactive - Class in edu.upenn.crimson.gui
ViewHTML.Hyperactive() - Constructor for class edu.upenn.crimson.gui.ViewHTML.Hyperactive
viewModel(String) - Static method in class edu.upenn.crimson.gui.ModelUtils: This will display the specified model.
viewModel - Variable in class edu.upenn.crimson.gui.Root.RootFrame
viewQuery(String) - Static method in class edu.upenn.crimson.gui.QueryUtils: This will display the specified query.
viewQuery - Variable in class edu.upenn.crimson.gui.Root.RootFrame
viewS - Variable in class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel
viewSM - Variable in class edu.upenn.crimson.gui.QueryEditor.ViewDistributePanel

W

WALRUS - Static variable in class edu.upenn.crimson.CrimsonMain: Connect to Walrus.
WARNING - Static variable in class edu.upenn.crimson.CrimsonUtils
weightedSampleByLevel(int, int) - Method in class edu.upenn.crimson.Tree: Returns the random, weighted sampling of species from each subtree demarkated by the level value.
weightedSampleByTempDepth(double, int) - Method in class edu.upenn.crimson.Tree: Returns the random, weighted sampling of species from each subtree demarkated by the temporal depth value.
writeClob(String, String, String, String) - Static method in class edu.upenn.crimson.io.Database: This will store 'value' as a CLOB in 'id'.
writeClobSet(String, String, String, HashSet) - Static method in class edu.upenn.crimson.io.Database: This will store 'value' as a CLOB in 'id'.
writeDataClob(String, String, String, String) - Static method in class edu.upenn.crimson.io.Database: This will store 'value' as a CLOB in the PART_DATA table.
writeString(String, boolean, String) - Static method in class edu.upenn.crimson.io.FileIO: Write string to file.

_

_runGC() - Static method in class edu.upenn.crimson.CrimsonMain

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