|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object edu.upenn.crimson.Query
public class Query
Contains query info.
Field Summary | |
---|---|
private java.lang.String |
id
This is a unique name for the Query object. |
private int |
leafSelection
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 |
private java.util.HashSet |
leaves
Set of IDs for the leaves to include. |
private int |
levelThresh
Level of the leaves to be selected. |
private java.lang.String |
notes
Notes specific to this Query object. |
private int |
numLeaves
Number of leaves to include when choosen randomly. |
private int |
numPositions
Number of positions (base pairs or codons) to include when choosen randomly. |
private boolean |
onlyStruct
When true, no data will be included in the output file (ie the partitions list will be ignored). |
private java.util.HashSet |
partitions
This set contains the IDs for the partitions to be queried. |
private java.util.HashSet |
positions
Base pair or codon positions to include. |
private boolean |
saved
True when the query object has been saved to the database. |
private long |
seed
Seed for random number generator. |
private int |
sequenceSelection
SEQUENCE SELECTION: 0 = Select All, 1 = Random Codon Selection, 2 = Randon Position Selection, 3 = Manual Codon Selection, 4 = Manual Position Selection, 5 = Select None |
private double |
tempDepthThresh
Temporal depth of the leaves to be selected. |
private java.lang.String |
treeID
This is the ID for the tree object that this query refers to. |
Constructor Summary | |
---|---|
Query(java.lang.String treeID)
Create a new Query object. |
|
Query(java.lang.String treeID,
java.lang.String id)
Create a new Query object. |
Method Summary | |
---|---|
void |
addLeaf(java.lang.String item)
Adds a leaf to the leaf list. |
void |
addPartition(java.lang.String item)
Adds a partitions to the partitions list. |
void |
addPosition(java.lang.String item)
Adds a positions to the positions list. |
void |
addPositions(java.lang.String items)
Adds a ':' separated list of positions to the positions list. |
java.lang.Object |
clone()
Create a shallow clone (just clone the structure, not the Objects) of the existing object. |
java.lang.Object |
clone(java.lang.String id)
Create a shallow clone (just clone the structure, not the Objects) of the existing object. |
static java.lang.Object |
dbLoad(java.util.ArrayList qObj)
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). |
static void |
dbLoadProxy(java.lang.StringBuilder queries)
This routine is only meant to be used by Queries when loading Queries from a database via a proxy. |
java.lang.String |
getID()
Set the ID. |
int |
getLeafSelection()
|
java.lang.String |
getLeafSelectionString()
|
java.util.HashSet |
getLeaves()
|
int |
getLevelThresh()
|
java.lang.String |
getNotes()
|
int |
getNumLeaves()
|
int |
getNumPositions()
|
java.util.HashSet |
getPartitions()
|
java.util.HashSet |
getPositions()
|
long |
getSeed()
|
int |
getSequenceSelection()
|
java.lang.String |
getSequenceSelectionString()
|
double |
getTempDepthThresh()
|
java.lang.String |
getTreeID()
|
boolean |
isOnlyStruct()
|
boolean |
isSaved()
|
void |
setLeafSelection(int leafSelection)
|
void |
setLeaves(java.util.HashSet leaves)
|
void |
setLevelThresh(int levelThresh)
|
void |
setNotes(java.lang.String notes)
|
void |
setNumLeaves(int numLeaves)
|
void |
setNumPositions(int numPositions)
|
void |
setOnlyStruct(boolean onlyStruct)
|
void |
setPartitions(java.util.HashSet partitions)
|
void |
setPositions(java.util.HashSet positions)
|
void |
setSaved(boolean saved)
|
void |
setSeed(long seed)
|
void |
setSequenceSelection(int sequenceSelection)
|
void |
setTempDepthThresh(double tempDepthThresh)
|
boolean |
setTreeID(java.lang.String treeID)
Returns true if treeID set, false otherwise. |
java.lang.String |
toString()
Returns Query information for debugging purposes. |
Methods inherited from class java.lang.Object |
---|
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
---|
private java.lang.String id
private java.lang.String notes
private java.lang.String treeID
private int leafSelection
private int numLeaves
private double tempDepthThresh
private int levelThresh
private java.util.HashSet leaves
private int sequenceSelection
private int numPositions
private java.util.HashSet partitions
private boolean onlyStruct
private java.util.HashSet positions
private long seed
private boolean saved
Constructor Detail |
---|
public Query(java.lang.String treeID)
public Query(java.lang.String treeID, java.lang.String id) throws InvalidIDException
InvalidIDException
Method Detail |
---|
public java.lang.String getID()
public void setNotes(java.lang.String notes)
public java.lang.String getNotes()
public boolean setTreeID(java.lang.String treeID)
public java.lang.String getTreeID()
public void setLeafSelection(int leafSelection)
public int getLeafSelection()
public java.lang.String getLeafSelectionString()
public void setNumLeaves(int numLeaves)
public int getNumLeaves()
public void setTempDepthThresh(double tempDepthThresh)
public double getTempDepthThresh()
public void setLevelThresh(int levelThresh)
public int getLevelThresh()
public void setLeaves(java.util.HashSet leaves)
public java.util.HashSet getLeaves()
public void setSequenceSelection(int sequenceSelection)
public int getSequenceSelection()
public java.lang.String getSequenceSelectionString()
public void setNumPositions(int numPositions)
public int getNumPositions()
public void setPartitions(java.util.HashSet partitions)
public java.util.HashSet getPartitions()
public void setOnlyStruct(boolean onlyStruct)
public boolean isOnlyStruct()
public void setPositions(java.util.HashSet positions)
public java.util.HashSet getPositions()
public void setSeed(long seed)
public long getSeed()
public void setSaved(boolean saved)
public boolean isSaved()
public void addLeaf(java.lang.String item)
public void addPartition(java.lang.String item)
public void addPosition(java.lang.String item)
public void addPositions(java.lang.String items)
public java.lang.Object clone()
clone
in class java.lang.Object
public java.lang.Object clone(java.lang.String id)
public static void dbLoadProxy(java.lang.StringBuilder queries)
public static java.lang.Object dbLoad(java.util.ArrayList qObj)
public java.lang.String toString()
toString
in class java.lang.Object
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |