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java.lang.Objectbiggests.tree.NodeInfo
public class NodeInfo
Title: Node Information Object
Description: Contains information about the content of a specific node in the dataset tree.
Copyright: Copyright (C) 2007 Joana Gonçalves This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Field Summary | |
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static int |
BICLUSTER_GROUP
The bicluster group node object type. |
static int |
BICLUSTER_SINGLE
The single bicluster node object type. |
static int |
DISCRETIZED
The discretized node object type. |
static int |
ORIGINAL
The original node object type. |
static int |
POSTPROCESSED_GROUP
The post-processed group node object type. |
static int |
POSTPROCESSED_SINGLE
The post-processed single node object type. |
static int |
PREPROCESSED
The preprocessed node object type. |
static long |
serialVersionUID
|
static boolean |
SYMBOLS
The symbol values matrix data type. |
static boolean |
VALUES
The float values matrix data type. |
Constructor Summary | |
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NodeInfo(smadeira.biclustering.NodeObjectInterface nodeObject,
int nodeObjectType,
javax.swing.tree.TreePath selectionPath,
DatasetTree tree,
NodeInfo parent,
java.util.ArrayList<java.lang.String> infoStrings,
java.util.ArrayList<java.lang.String> infoStyles)
Constructs an object of type NodeInfo (with all the information about
a certain node, including a pointer for the node object itself. |
|
NodeInfo(smadeira.biclustering.NodeObjectInterface nodeObject,
int nodeObjectType,
javax.swing.tree.TreePath selectionPath,
DatasetTree tree,
NodeInfo parent,
java.util.ArrayList<java.lang.String> infoStrings,
java.util.ArrayList<java.lang.String> infoStyles,
int index)
Constructs an object of type NodeInfo (with all the information about
a certain node, including a pointer for the node object itself. |
Method Summary | |
---|---|
protected void |
addStylesToDocument(javax.swing.text.StyledDocument doc)
Adds a set of common styles to StyledDocument doc |
int |
findInfoString(java.lang.String s)
Finds a specific information string. |
boolean |
getDataType()
Returns the node object data type value. |
int |
getFakeID()
Returns the ID of the post-processed bicluster. |
int |
getId()
Returns the number id of the NodeInfo |
javax.swing.text.StyledDocument |
getInfo()
Returns a styled document containing information about this node. |
java.util.ArrayList<java.lang.String> |
getInfoStrings()
Returns information strings. |
java.util.ArrayList<java.lang.String> |
getInfoStyles()
Returns information styles. |
java.lang.String |
getName()
Returns the name of this node information object. |
smadeira.biclustering.NodeObjectInterface |
getNodeObject()
Returns the node object associated with the current node information object. |
int |
getNodeObjectType()
Returns the node object type. |
NodeInfo |
getParentNodeInfo()
Returns parent node information object. |
boolean |
isGeneID()
Returns genes' names type. |
void |
setInfoStrings(java.util.ArrayList<java.lang.String> strings)
Sets information strings. |
void |
setInfoStyles(java.util.ArrayList<java.lang.String> styles)
Sets information styles. |
java.lang.String |
toString()
Overrides the default toString method. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final long serialVersionUID
public static final int ORIGINAL
public static final int PREPROCESSED
public static final int DISCRETIZED
public static final int BICLUSTER_GROUP
public static final int BICLUSTER_SINGLE
public static final int POSTPROCESSED_GROUP
public static final int POSTPROCESSED_SINGLE
public static final boolean VALUES
public static final boolean SYMBOLS
Constructor Detail |
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public NodeInfo(smadeira.biclustering.NodeObjectInterface nodeObject, int nodeObjectType, javax.swing.tree.TreePath selectionPath, DatasetTree tree, NodeInfo parent, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles, int index) throws InvalidNodeObjectTypeException
NodeInfo
(with all the information about
a certain node, including a pointer for the node object itself.
nodeObject
- NodeObjectInterface the node objectnodeObjectType
- int the type of the node object:NodeInfo.ORIGINAL
NodeInfo.PREPROCESSED
NodeInfo.DISCRETIZED
NodeInfo.BICLUSTER_GROUP
NodeInfo.BICLUSTER_SINGLE
NodeInfo.POSTPROCESSED_GROUP
NodeInfo.POSTPROCESSED_SINGLE
selectionPath
- TreePath the selected pathtree
- DatasetTree the dataset treeparent
- the parent NodeInfo
of this NodeInfo
object's
parent group (only for post-processed biclusters NodeInfo
objects)infoStrings
- the information String[]
infoStyles
- the styles String[]
index
- int
the index of the bicluster in the array
of biclusters (it applies only to post-processed biclusters
InvalidNodeObjectTypeException
- if the type of the node object is not validpublic NodeInfo(smadeira.biclustering.NodeObjectInterface nodeObject, int nodeObjectType, javax.swing.tree.TreePath selectionPath, DatasetTree tree, NodeInfo parent, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles) throws InvalidNodeObjectTypeException
NodeInfo
(with all the information about
a certain node, including a pointer for the node object itself.
nodeObject
- NodeObjectInterface the node objectnodeObjectType
- int the type of the node object:NodeInfo.ORIGINAL
NodeInfo.PREPROCESSED
NodeInfo.DISCRETIZED
NodeInfo.BICLUSTER_GROUP
NodeInfo.BICLUSTER_SINGLE
NodeInfo.POSTPROCESSED_GROUP
NodeInfo.POSTPROCESSED_SINGLE
selectionPath
- TreePath the selected pathtree
- DatasetTree the dataset treeparent
- the parent NodeInfo
of this NodeInfo
objectinfoStrings
- the information String[]
infoStyles
- the styles String[]
InvalidNodeObjectTypeException
- if the type of the node object is not validMethod Detail |
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public java.lang.String getName()
String
name of this node information objectpublic int getId()
NodeInfo
object.
- Returns:
- int the number id
public int getNodeObjectType()
NodeInfo.ORIGINAL
NodeInfo.PREPROCESSED
NodeInfo.DISCRETIZED
NodeInfo.BICLUSTER_GROUP
NodeInfo.BICLUSTER_SINGLE
NodeInfo.POSTPROCESSED_GROUP
NodeInfo.POSTPROCESSED_SINGLE
public boolean getDataType()
NodeInfo.VALUES
NodeInfo.SYMBOLS
public boolean isGeneID()
true
- genes' names are gene IDs (gene ontology names)false
- genes' names are probeset IDs (IDs used in the mRNA measurements
public smadeira.biclustering.NodeObjectInterface getNodeObject()
public NodeInfo getParentNodeInfo()
public java.util.ArrayList<java.lang.String> getInfoStrings()
public java.util.ArrayList<java.lang.String> getInfoStyles()
public int getFakeID()
public void setInfoStrings(java.util.ArrayList<java.lang.String> strings)
strings
- information ArrayList
public void setInfoStyles(java.util.ArrayList<java.lang.String> styles)
styles
- information ArrayList
stylespublic javax.swing.text.StyledDocument getInfo() throws javax.swing.text.BadLocationException
javax.swing.text.BadLocationException
- if strings or styles could not be foundpublic int findInfoString(java.lang.String s)
s
- the information String
to look for
protected void addStylesToDocument(javax.swing.text.StyledDocument doc)
StyledDocument
doc
doc
- the StyledDocument
to add styles topublic java.lang.String toString()
toString
method. Returns a formatted
string with the name to display in the corresponding dataset tree node.
toString
in class java.lang.Object
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