Uses of Class
org.peace_tools.data.ESTList

Packages that use ESTList

org.peace_tools.core.dataset	Contains the classes associated with the data set wizard.
org.peace_tools.data	Contains the classes that provide data for the various views in the GUI.
org.peace_tools.views	Contains the classes that provide views for the various data objects in the GUI.

Uses of ESTList in org.peace_tools.core.dataset

Fields in org.peace_tools.core.dataset declared as ESTList

private ESTList

DataSetWizard.estList The list of ESTs associated with this data set.

Methods in org.peace_tools.core.dataset that return ESTList

ESTList

DataSetWizard.getESTList() This method can be used to obtain the ESTs associated with this data set.

Methods in org.peace_tools.core.dataset with parameters of type ESTList

void	DataSetWizard.setESTList(ESTList estList) Set the list of ESTs associated with this data set.

Uses of ESTList in org.peace_tools.data

Fields in org.peace_tools.data declared as ESTList

private ESTList	ESTTableModel.estList Reference to the list of fragments that is actually exposed by this table model.
private ESTList	MSTTreeModel.estList The list of ESTs for which this MST was constructed.
private ESTList	ClusterTreeTableModel.estList Reference to the EST file that contains the cluster data to be adapted and interfaced by this model.
private ESTList	OverlapModel.estList Reference to the EST file that contains the fragment data that is to be adapted and presented by this model.

Methods in org.peace_tools.data that return ESTList

ESTList	ESTTableModel.getESTList() Obtain the list of ESTs associated with this model.
ESTList	MSTTreeModel.getESTList() Obtain the list of ESTs for which this MST was generated.
ESTList	ClusterTreeTableModel.getESTList() Obtain the list of ESTs associated with this model.
ESTList	OverlapModel.getESTList() Obtain the list of ESTs associated with this model.
ESTList	DataStore.getFASTA(java.lang.String fileName, java.awt.Component parent) Method to load/get a given FASTA file.
static ESTList	ESTList.loadESTs(java.io.File fastaFile) Load ESTs from a given FASTA file and build a new ESTList.
static ESTList	ESTList.loadESTs(java.lang.String fileName, java.io.InputStream is) Load ESTs from a stream that provides FASTA data.

Methods in org.peace_tools.data with parameters of type ESTList

protected void	ClusterNode.classify(ESTList estList, javax.swing.ProgressMonitor pm) Method to compute classification statistics for this cluster node.
void	ClusterFile.classify(ESTList estList, javax.swing.ProgressMonitor pm) Method to recompute (as needed) the classification of ESTs in clusters.
static OverlapModel	OverlapModel.create(ClusterFile clusters, ESTList ests, MST mst, MSTClusterData wsEntry) The constructor.
void	ClusterNode.write(ESTList estList, java.io.PrintStream os) Method to dump the EST data out in FASTA file format.

Constructors in org.peace_tools.data with parameters of type ESTList

ClusterTreeTableModel(ClusterFile clusters, ESTList ests, MSTClusterData wsEntry)
The constructor.

ESTTableModel(ESTList estList)
The default constructor.

MSTTreeModel(MST mst, ESTList estList, MSTData wsEntry)
The default constructor.

OverlapModel(ClusterFile clusters, ESTList ests, MSTClusterData wsEntry)
The constructor.

Uses of ESTList in org.peace_tools.views

Fields in org.peace_tools.views declared as ESTList

private ESTList

ClusterSummaryView.estList The set of ESTs that the clusters correspond to.

Constructors in org.peace_tools.views with parameters of type ESTList

ClusterSummaryView(MainFrame frame, ClusterFile clusterFile, ESTList estList, MSTClusterData wsEntry)
The default constructor.