Serialized Form

Package phylonet.app.model.datum

Class phylonet.app.model.datum.ADatum extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.String id

Class phylonet.app.model.datum.BatchDatum extends ADatum implements Serializable

Serialized Fields

dataBatch

java.util.List<E> dataBatch

Class phylonet.app.model.datum.HGTDatum extends ADatum implements Serializable

Serialized Fields

hgt

RiataHgt hgt

Class phylonet.app.model.datum.NetworkDatum extends ADatum implements Serializable

Serialized Fields

network

Network<T> network

Class phylonet.app.model.datum.SequenceAlignmentDatum extends ADatum implements Serializable

Serialized Fields

sa

SequenceAlignment sa

Class phylonet.app.model.datum.TreeDatum extends ADatum implements Serializable

Serialized Fields

tree

Tree tree

Class phylonet.app.model.datum.TreeWithBranchLengthsDatum extends TreeDatum implements Serializable

Package phylonet.app.tool

Class phylonet.app.tool.AParamsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

accepted

boolean accepted

cancelButton

javax.swing.JButton cancelButton

OKButton

javax.swing.JButton OKButton

parametersPanel

javax.swing.JPanel parametersPanel

Class phylonet.app.tool.APhyloTool extends javax.swing.AbstractAction implements Serializable

Serialized Fields

paramsDialog

AParamsDialog paramsDialog

parentController

PhyloNetAppController parentController

menuText

java.lang.String menuText

toolTipText

java.lang.String toolTipText

Class phylonet.app.tool.AResultsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

logText

java.lang.String logText

resultsPanel

javax.swing.JPanel resultsPanel

buttonPanel

javax.swing.JPanel buttonPanel

exportButton

javax.swing.JButton exportButton

okButton

javax.swing.JButton okButton

Class phylonet.app.tool.InvalidParameterException extends java.lang.RuntimeException implements Serializable

Package phylonet.app.tool.charnet

Class phylonet.app.tool.charnet.CharnetClusterResultsDialog extends CharnetResultsDialog implements Serializable

Class phylonet.app.tool.charnet.CharnetParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

networkBox

PhyloComboBox networkBox

treesButton

javax.swing.JRadioButton treesButton

tripartitionsButton

javax.swing.JRadioButton tripartitionsButton

clustersButton

javax.swing.JRadioButton clustersButton

Class phylonet.app.tool.charnet.CharnetResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.charnet.CharnetTool extends APhyloTool implements Serializable

Class phylonet.app.tool.charnet.CharnetTreeResultsDialog extends CharnetResultsDialog implements Serializable

Class phylonet.app.tool.charnet.CharnetTripartitionResultsDialog extends CharnetResultsDialog implements Serializable

Package phylonet.app.tool.cmpnets

Class phylonet.app.tool.cmpnets.CmpnetsParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

network1Box

PhyloComboBox network1Box

network2Box

PhyloComboBox network2Box

treesButton

javax.swing.JRadioButton treesButton

tripartitionsButton

javax.swing.JRadioButton tripartitionsButton

clustersButton

javax.swing.JRadioButton clustersButton

Class phylonet.app.tool.cmpnets.CmpnetsResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.cmpnets.CmpnetsTool extends APhyloTool implements Serializable

Package phylonet.app.tool.component

Class phylonet.app.tool.component.BrowseButton extends javax.swing.JButton implements Serializable

Class phylonet.app.tool.component.ExtendableComboBoxList extends javax.swing.JPanel implements Serializable

Serialized Fields

combos

java.util.List<E> combos

addButton

javax.swing.JButton addButton

Class phylonet.app.tool.component.ExtendableNodeSetsList extends javax.swing.JPanel implements Serializable

Serialized Fields

fields

java.util.List<E> fields

Class phylonet.app.tool.component.PhyloComboBox extends javax.swing.JComboBox implements Serializable

Serialized Fields

criterion

DataCriterion criterion

model

PhyloNetAppModel model

Class phylonet.app.tool.component.PhyloTextArea extends javax.swing.JTextArea implements Serializable

Class phylonet.app.tool.component.PhyloTextField extends javax.swing.JTextField implements Serializable

Package phylonet.app.tool.countcoal

Class phylonet.app.tool.countcoal.CountCoalParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

treeBox1

PhyloComboBox treeBox1

treeBox2

PhyloComboBox treeBox2

Class phylonet.app.tool.countcoal.CountCoalResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.countcoal.CountCoalTool extends APhyloTool implements Serializable

Package phylonet.app.tool.inferst

Class phylonet.app.tool.inferst.InferSTParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

geneTreeComboList

ExtendableComboBoxList geneTreeComboList

currentlySelectedInferenceMethod

InferenceMethod currentlySelectedInferenceMethod

currentMethodSpecificParametersPanel

InferenceMethodParametersSubpanel currentMethodSpecificParametersPanel

mdcDpRootedRadio

javax.swing.JRadioButton mdcDpRootedRadio

mdcDpRootedSubpanel

MdcDpSubpanel mdcDpRootedSubpanel

mdcDpRootedTimeRadio

javax.swing.JRadioButton mdcDpRootedTimeRadio

mdcDpRootedTimeSubpanel

MdcDpRootedTimeSubpanel mdcDpRootedTimeSubpanel

mdcDpUnrootedRadio

javax.swing.JRadioButton mdcDpUnrootedRadio

mdcDpUnrootedSubpanel

MdcDpSubpanel mdcDpUnrootedSubpanel

mdcIlpRadio

javax.swing.JRadioButton mdcIlpRadio

mdcIlpPanel

MdcIlpSubpanel mdcIlpPanel

mdcIlpTimeRadio

javax.swing.JRadioButton mdcIlpTimeRadio

mdcIlpTimePanel

MdcIlpTimeSubpanel mdcIlpTimePanel

glassRadio

javax.swing.JRadioButton glassRadio

glassSubpanel

GlassTreeSubpanel glassSubpanel

glassMatrixRadio

javax.swing.JRadioButton glassMatrixRadio

glassMatrixSubpanel

GlassMatrixSubpanel glassMatrixSubpanel

majorityRadio

javax.swing.JRadioButton majorityRadio

majorityPanel

MajoritySubpanel majorityPanel

democraticRadio

javax.swing.JRadioButton democraticRadio

democraticSubpanel

NoParametersSubpanel democraticSubpanel

Class phylonet.app.tool.inferst.InferStResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.inferst.InferSTTool extends APhyloTool implements Serializable

Package phylonet.app.tool.inferst.subpanel

Class phylonet.app.tool.inferst.subpanel.GlassMatrixSubpanel extends InferenceMethodParametersSubpanel implements Serializable

Serialized Fields

distanceMatrixFileField

javax.swing.JTextField distanceMatrixFileField

Class phylonet.app.tool.inferst.subpanel.GlassTreeSubpanel extends InferenceMethodParametersSubpanel implements Serializable

Serialized Fields

taxonFileField

javax.swing.JTextField taxonFileField

useTaxonMapBox

javax.swing.JCheckBox useTaxonMapBox

Class phylonet.app.tool.inferst.subpanel.InferenceMethodParametersSubpanel extends javax.swing.JPanel implements Serializable

Class phylonet.app.tool.inferst.subpanel.MajoritySubpanel extends InferenceMethodParametersSubpanel implements Serializable

Serialized Fields

taxonFileField

javax.swing.JTextField taxonFileField

useTaxonMapBox

javax.swing.JCheckBox useTaxonMapBox

Class phylonet.app.tool.inferst.subpanel.MdcDpRootedTimeSubpanel extends InferenceMethodParametersSubpanel implements Serializable

Serialized Fields

taxonFileField

javax.swing.JTextField taxonFileField

useTaxonMapBox

javax.swing.JCheckBox useTaxonMapBox

Class phylonet.app.tool.inferst.subpanel.MdcDpSubpanel extends InferenceMethodParametersSubpanel implements Serializable

Serialized Fields

taxonMapField

javax.swing.JTextField taxonMapField

useTaxonMapBox

javax.swing.JCheckBox useTaxonMapBox

taxonMapBrowseButton

BrowseButton taxonMapBrowseButton

taxonMapLabel

javax.swing.JLabel taxonMapLabel

propField

javax.swing.JTextField propField

exhaustBox

javax.swing.JCheckBox exhaustBox

exploreBox

javax.swing.JCheckBox exploreBox

propLabel

javax.swing.JLabel propLabel

Class phylonet.app.tool.inferst.subpanel.MdcIlpSubpanel extends InferenceMethodParametersSubpanel implements Serializable

Serialized Fields

cplexFieldWithoutTime

javax.swing.JTextField cplexFieldWithoutTime

Class phylonet.app.tool.inferst.subpanel.MdcIlpTimeSubpanel extends InferenceMethodParametersSubpanel implements Serializable

Serialized Fields

cplexFieldWithTime

javax.swing.JTextField cplexFieldWithTime

deepCoalWeightsField

javax.swing.JTextField deepCoalWeightsField

noCoalWeightsField

javax.swing.JTextField noCoalWeightsField

Class phylonet.app.tool.inferst.subpanel.NoParametersSubpanel extends InferenceMethodParametersSubpanel implements Serializable

Package phylonet.app.tool.lca

Class phylonet.app.tool.lca.LCAParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

treeBox

PhyloComboBox treeBox

nodeSetsList

ExtendableNodeSetsList nodeSetsList

prefixField

javax.swing.JTextField prefixField

Class phylonet.app.tool.lca.LCAResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.lca.LCATool extends APhyloTool implements Serializable

Package phylonet.app.tool.mast

Class phylonet.app.tool.mast.MASTParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

treeBox1

PhyloComboBox treeBox1

treeBox2

PhyloComboBox treeBox2

checkBox

javax.swing.JCheckBox checkBox

Class phylonet.app.tool.mast.MASTResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.mast.MastTool extends APhyloTool implements Serializable

Package phylonet.app.tool.netpars

Class phylonet.app.tool.netpars.NetparsParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

networkBox

PhyloComboBox networkBox

sequenceBox

PhyloComboBox sequenceBox

blockSizeField

javax.swing.JTextField blockSizeField

Class phylonet.app.tool.netpars.NetparsResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.netpars.NetparsTool extends APhyloTool implements Serializable

Package phylonet.app.tool.recomp

Class phylonet.app.tool.recomp.RECOMPParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

sequenceListBox

PhyloComboBox sequenceListBox

windowSizeField

javax.swing.JTextField windowSizeField

stepSizeField

javax.swing.JTextField stepSizeField

rfDistanceMeasureButton

javax.swing.JRadioButton rfDistanceMeasureButton

sprDistanceMeasureButton

javax.swing.JRadioButton sprDistanceMeasureButton

parsimonyFunctionButton

javax.swing.JRadioButton parsimonyFunctionButton

avgMaxDistanceFunctionButton

javax.swing.JRadioButton avgMaxDistanceFunctionButton

avgMinDistanceFunctionButton

javax.swing.JRadioButton avgMinDistanceFunctionButton

percentIntersectionFunctionButton

javax.swing.JRadioButton percentIntersectionFunctionButton

paupExecutableField

javax.swing.JTextField paupExecutableField

paupBrowseButton

BrowseButton paupBrowseButton

popSizeField

javax.swing.JTextField popSizeField

iterationsField

javax.swing.JTextField iterationsField

levelsField

javax.swing.JTextField levelsField

Class phylonet.app.tool.recomp.RECOMPResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.recomp.RecompTool extends APhyloTool implements Serializable

Package phylonet.app.tool.rf

Class phylonet.app.tool.rf.RFParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

treeBox1

PhyloComboBox treeBox1

treeBox2

PhyloComboBox treeBox2

Class phylonet.app.tool.rf.RFResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.rf.RFTool extends APhyloTool implements Serializable

Package phylonet.app.tool.riatahgt

Class phylonet.app.tool.riatahgt.RiataHGTParamsDialog extends AParamsDialog implements Serializable

Serialized Fields

speciesTreeBox

PhyloComboBox speciesTreeBox

geneTreeBox

PhyloComboBox geneTreeBox

prefixField

javax.swing.JTextField prefixField

refineBox

javax.swing.JCheckBox refineBox

collapseBox

javax.swing.JCheckBox collapseBox

Class phylonet.app.tool.riatahgt.RiataHGTResultsDialog extends AResultsDialog implements Serializable

Class phylonet.app.tool.riatahgt.RIATAHGTTool extends APhyloTool implements Serializable

Package phylonet.app.view

Class phylonet.app.view.PhyloNetAppView extends javax.swing.JFrame implements Serializable

Serialized Fields

datumViews

java.util.Set<E> datumViews

mainPanel

javax.swing.JPanel mainPanel

importTreeMenuItem

javax.swing.JMenuItem importTreeMenuItem

importTreeWithBranchLengthsMenuItem

javax.swing.JMenuItem importTreeWithBranchLengthsMenuItem

importSequenceAlignmentMenuItem

javax.swing.JMenuItem importSequenceAlignmentMenuItem

importNetworkMenuItem

javax.swing.JMenuItem importNetworkMenuItem

clearWorkspaceMenuItem

javax.swing.JMenuItem clearWorkspaceMenuItem

saveWorkspaceMenuItem

javax.swing.JMenuItem saveWorkspaceMenuItem

loadWorkspaceMenuItem

javax.swing.JMenuItem loadWorkspaceMenuItem

quitMenuItem

javax.swing.JMenuItem quitMenuItem

calculateMenu

javax.swing.JMenu calculateMenu

Package phylonet.app.view.datum

Class phylonet.app.view.datum.ADatumView extends javax.swing.JFrame implements Serializable

Serialized Fields

thumbnailView

DatumThumbnailView thumbnailView

menuBar

javax.swing.JMenuBar menuBar

fileMenu

javax.swing.JMenu fileMenu

closeMenuItem

javax.swing.JMenuItem closeMenuItem

deleteDatumMenuItem

javax.swing.JMenuItem deleteDatumMenuItem

renameDatumMenuItem

javax.swing.JMenuItem renameDatumMenuItem

exportDatumMenuItem

javax.swing.JMenuItem exportDatumMenuItem

Class phylonet.app.view.datum.BatchDatumView extends ADatumView implements Serializable

Serialized Fields

batchDatum

BatchDatum batchDatum

Class phylonet.app.view.datum.DatumThumbnailView extends javax.swing.JPanel implements Serializable

Serialized Fields

button

javax.swing.JButton button

nameLabel

javax.swing.JLabel nameLabel

Class phylonet.app.view.datum.HGTDatumView extends ADatumView implements Serializable

Serialized Fields

hgtDatum

HGTDatum hgtDatum

_species_tree

STITree<D> _species_tree

_tc

TreeCanvas _tc

_scenarios

javax.swing.JTree _scenarios

saveImageMenuItem

javax.swing.JMenuItem saveImageMenuItem

Class phylonet.app.view.datum.NetworkDatumView extends ADatumView implements Serializable

Serialized Fields

networkDatum

NetworkDatum networkDatum

Class phylonet.app.view.datum.SequenceAlignmentDatumView extends ADatumView implements Serializable

Serialized Fields

sequenceListDatum

SequenceAlignmentDatum sequenceListDatum

Class phylonet.app.view.datum.TreeDatumView extends ADatumView implements Serializable

Serialized Fields

treeDatum

TreeDatum treeDatum

treeCanvas

TreeCanvas treeCanvas

countNodesMenuItem

javax.swing.JMenuItem countNodesMenuItem

Package phylonet.cmdline.tool

Class phylonet.cmdline.tool.ToolException extends java.lang.RuntimeException implements Serializable

Class phylonet.cmdline.tool.ToolInitializationException extends java.lang.RuntimeException implements Serializable

Package phylonet.network.io

Class phylonet.network.io.ExNewickException extends java.lang.Exception implements Serializable

serialVersionUID: 1L

Package phylonet.network.model

Package phylonet.network.model.bni

Class phylonet.network.model.bni.BniNetNode extends java.lang.Object implements Serializable

Serialized Fields

_data

java.lang.Object _data

_name

java.lang.String _name

_children

java.util.List<E> _children

_parents

java.util.List<E> _parents

_gammas

java.util.List<E> _gammas

_parent_distances

java.util.List<E> _parent_distances

Class phylonet.network.model.bni.BniNetwork extends java.lang.Object implements Serializable

Serialized Fields

_root

BniNetNode<T> _root

Package phylonet.riatahgt

Class phylonet.riatahgt.HgtEvent extends java.lang.Object implements Serializable

Serialized Fields

_dest

TNode _dest

_src

TNode _src

_bad

boolean _bad

_violated

boolean _violated

_decomp_nodes

java.util.List<E> _decomp_nodes

_primary_node

TNode _primary_node

Class phylonet.riatahgt.HgtScenario extends java.lang.Object implements Serializable

Serialized Fields

_events

java.util.List<E> _events

Class phylonet.riatahgt.RiataHgt extends java.lang.Object implements Serializable

Serialized Fields

_result_tree

STITree<D> _result_tree

_collapsed

boolean _collapsed

_refined

boolean _refined

_rh

phylonet.riatahgt.SingleRiataHgt _rh

_ermh

phylonet.riatahgt.MultipleRiataHgt _ermh

_species_original

Tree _species_original

_species_copy

MutableTree _species_copy

_gene_copy

MutableTree _gene_copy

_counted_primary_nodes

java.util.List<E> _counted_primary_nodes

_prefix

java.lang.String _prefix

_chain_prefix

java.lang.String _chain_prefix

Package phylonet.riatahgt.viewer

Class phylonet.riatahgt.viewer.RiataViewerFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

_species_tree

STITree<D> _species_tree

_tc

TreeCanvas _tc

_scenarios

javax.swing.JTree _scenarios

_stree

STITree<D> _stree

_tree_model_root

javax.swing.tree.DefaultMutableTreeNode _tree_model_root

Class phylonet.riatahgt.viewer.TreeCanvas extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

_tree

STITree<D> _tree

_high_layer

java.util.Hashtable<K,V> _high_layer

_low_layer

java.util.Hashtable<K,V> _low_layer

_layer

java.util.Hashtable<K,V> _layer

_x_pos

java.util.Hashtable<K,V> _x_pos

_y_pos

java.util.Hashtable<K,V> _y_pos

_ideal_height

int _ideal_height

_ideal_width

int _ideal_width

_edges

java.util.LinkedList<E> _edges

Package phylonet.sequence.model

Class phylonet.sequence.model.SequenceAlignment extends java.lang.Object implements Serializable

Serialized Fields

_length

int _length

_size

int _size

_taxa

java.lang.String[] _taxa

_sequences

java.lang.String[] _sequences

Class phylonet.sequence.model.SequenceException extends java.lang.Exception implements Serializable

Package phylonet.tree.io

Class phylonet.tree.io.ParseException extends java.lang.Exception implements Serializable

serialVersionUID: 1L

Package phylonet.tree.model

Package phylonet.tree.model.sti

Class phylonet.tree.model.sti.STINode extends java.lang.Object implements Serializable

Serialized Fields

_data

java.lang.Object _data

_tree

STITree<D> _tree

_valid

boolean _valid

_id

int _id

_name

java.lang.String _name

_parent

STINode<D> _parent

_children

java.util.LinkedList<E> _children

_distance

double _distance

Class phylonet.tree.model.sti.STITree extends java.lang.Object implements Serializable

Serialized Fields

_name

java.lang.String _name

_nodes

java.util.Hashtable<K,V> _nodes

_node_set

java.util.HashSet<E> _node_set

_name2node

java.util.Hashtable<K,V> _name2node

_root

STINode<D> _root

_is_rooted

boolean _is_rooted

_next_node_id

int _next_node_id

_leaf_count

int _leaf_count

Package phylonet.tree.view.swing

Class phylonet.tree.view.swing.NewickViewer extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

_tview

TreeView _tview

_newickstring

javax.swing.JTextField _newickstring

_render_btn

javax.swing.JButton _render_btn

Class phylonet.tree.view.swing.TreeView extends javax.swing.JComponent implements Serializable

serialVersionUID: 4719960494198238254L

Serialized Fields

_tree

Tree _tree

_style

TreeView.TreeStyle _style

_max_depth

double _max_depth

_leafname_width

int _leafname_width

_need_update

boolean _need_update