Network

java.lang.Object
- network.Network

```
public class Network
extends java.lang.Object
```
Network is an essential class in Netter. Representing a network both as a collection of Links and as a collection of Nodes. Network's can have temporary states, with links temporaraly removed or added.

Since:

0.0

Version:

1.0

Author:

Joeri Ruyssinck (joeri.ruysssinck@intec.ugent.be)

Constructor Summary

Constructors
Constructor and Description
`Network()` Construct an empty network and inits the members
`Network(Network network)` Copy constructor, will return a copy of the network with new objects
`Network(java.lang.String tsvFile, int numberOfLines)` Creates a network by reading a certain amount of lines from a tsv file.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`addLinkToNetwork(Link link)` Adds a link to the network permanently, returns false if links already exists or if it is a self-regulating link
`boolean`	`addNonCommitalLinkToNetwork(Link a)` Adds a temporary link to the network
`void`	`commit()` Commits network by making all temporary modifications permanent.
`boolean`	`equals(java.lang.Object network)` Overrides equals.
`int`	`getLinkCount()` Returns the amount of nodes in the network (nodes have atleast one link) Ignores temporary changes to the network.
`java.util.ArrayList<Link>`	`getLinks()`
`java.lang.String`	`getName()` Getter for network name
`int`	`getNodeCount()` Returns the amount of nodes in the network (nodes have atleast one link) Ignores temporary changes to the network.
`java.util.LinkedHashSet<Node>`	`getNodes()`
`java.util.ArrayList<Link>`	`getNonCommitalAdded()`
`java.util.ArrayList<Link>`	`getNonCommittalDeleted()`
`int`	`hashCode()` Overwrites hash code for network, network is uniquely defined by name
`boolean`	`isEmpty()` Checks if the network is empty
`void`	`networkToTSV(java.io.File file)` Writes this network to a tsv file in the following format.
`Link`	`removeLinkFromNetwork(int index)` Removes a link at a certain index permanently in the network.
`Link`	`removeLinkFromNetwork(Link e)` Removes the link specified from the network permanently.
`Link`	`removeNonCommitalLinkToNetwork(Link a)` Removes a temporary link from the network
`void`	`revert()` Reverts network to original state.
`void`	`setLinks(java.util.ArrayList<Link> links)`
`void`	`setNodes(java.util.LinkedHashSet<Node> nodes)`
`void`	`sortNetworkNameLink()` Sorts the links by name
`void`	`sortNetworkPredictionRank()` Sorts the links by rank
`void`	`sortOriginalRankInterval(int interval, int startPos, int endPos)` Alters the current ranking by tie-breaking on the original ranking

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - Network
```
public Network()
```
    Construct an empty network and inits the members
  - Network
```
public Network(Network network)
```
    Copy constructor, will return a copy of the network with new objects
    
    Parameters:
    
    network - the network to be copied
  - Network
```
public Network(java.lang.String tsvFile,
               int numberOfLines)
```
    Creates a network by reading a certain amount of lines from a tsv file. File should be formatted, each link separated by newline Each link should be formatted as: source[whitespace]target[whitespace] all other text will be ignored A LinkProperties object will be attached to each link, the ranking position equals the line number Checks that links need to be unique and cannot be self-regulating
    
    Parameters:
    
    tsvFile - string representation of file to read network from
    
    numberOfLines - links/lines to read (for big files)
- Method Detail
  - networkToTSV
```
public void networkToTSV(java.io.File file)
```
    Writes this network to a tsv file in the following format. Each link separated by newline in the order of ranking. Each link formatted as: source[whitespace]target[whitespace]ranking
    
    Parameters:
    
    file - file to write the network to
    
    numberOfLines - links/lines to read (for big files)
  - sortNetworkPredictionRank
```
public void sortNetworkPredictionRank()
```
    Sorts the links by rank
  - sortNetworkNameLink
```
public void sortNetworkNameLink()
```
    Sorts the links by name
  - addLinkToNetwork
```
public boolean addLinkToNetwork(Link link)
```
    Adds a link to the network permanently, returns false if links already exists or if it is a self-regulating link
    
    Parameters:
    
    link - the link to be added
    
    Returns:
    
    true if link was added, false otherwhise
  - removeLinkFromNetwork
```
public Link removeLinkFromNetwork(int index)
```
    Removes a link at a certain index permanently in the network. Use with care if the network is sorted by name.
    
    Parameters:
    
    index - the index at which the link is located
    
    Returns:
    
    The link which was removed
  - removeLinkFromNetwork
```
public Link removeLinkFromNetwork(Link e)
```
    Removes the link specified from the network permanently.
    
    Parameters:
    
    e - the link to remove
    
    Returns:
    
    The link which was removed
  - getNodeCount
```
public int getNodeCount()
```
    Returns the amount of nodes in the network (nodes have atleast one link) Ignores temporary changes to the network.
    
    Returns:
  - getLinkCount
```
public int getLinkCount()
```
    Returns the amount of nodes in the network (nodes have atleast one link) Ignores temporary changes to the network.
    
    Returns:
  - addNonCommitalLinkToNetwork
```
public boolean addNonCommitalLinkToNetwork(Link a)
```
    Adds a temporary link to the network
    
    Returns:
    
    always true
  - removeNonCommitalLinkToNetwork
```
public Link removeNonCommitalLinkToNetwork(Link a)
```
    Removes a temporary link from the network
    
    Returns:
    
    the link which was removed
  - isEmpty
```
public boolean isEmpty()
```
    Checks if the network is empty
    
    Returns:
    
    true if network does not contain links, false otherwhise
  - hashCode
```
public int hashCode()
```
    Overwrites hash code for network, network is uniquely defined by name
    
    Overrides:
    
    hashCode in class java.lang.Object
  - equals
```
public boolean equals(java.lang.Object network)
```
    Overrides equals. Network's are equal if their names are by definition.
    
    Overrides:
    
    equals in class java.lang.Object
  - revert
```
public void revert()
```
    Reverts network to original state. All temporary links which were added or removed will be restored.
  - commit
```
public void commit()
```
    Commits network by making all temporary modifications permanent.
  - sortOriginalRankInterval
```
public void sortOriginalRankInterval(int interval,
                                     int startPos,
                                     int endPos)
```
    Alters the current ranking by tie-breaking on the original ranking
    
    Parameters:
    
    interval - Partition sizes
    
    startPos - Start of the ranking to be resorted
    
    endPos - End of the ranking to be resorted
  - getName
```
public java.lang.String getName()
```
    Getter for network name
    
    Returns:
    
    the name of the network
  - getLinks
```
public java.util.ArrayList<Link> getLinks()
```
  - setLinks
```
public void setLinks(java.util.ArrayList<Link> links)
```
  - getNodes
```
public java.util.LinkedHashSet<Node> getNodes()
```
  - setNodes
```
public void setNodes(java.util.LinkedHashSet<Node> nodes)
```
  - getNonCommittalDeleted
```
public java.util.ArrayList<Link> getNonCommittalDeleted()
```
  - getNonCommitalAdded
```
public java.util.ArrayList<Link> getNonCommitalAdded()
```

Class Network

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Network

Network

Network

Method Detail

networkToTSV

sortNetworkPredictionRank

sortNetworkNameLink

addLinkToNetwork

removeLinkFromNetwork

removeLinkFromNetwork

getNodeCount

getLinkCount

addNonCommitalLinkToNetwork

removeNonCommitalLinkToNetwork

isEmpty

hashCode

equals

revert

commit

sortOriginalRankInterval

getName

getLinks

setLinks

getNodes

setNodes

getNonCommittalDeleted

getNonCommitalAdded