TreeSAAPTP

java.lang.Object
- IMPACT_S.TreeSAAPTP

```
public class TreeSAAPTP
extends java.lang.Object
```
Class for handling TreeSAAP results and input data.

Author:

Emanuel Maldonado

See Also:

GUIResultsView

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`EvpthwyDN` Directory Name for Evpthwy directory
`static java.lang.String`	`EvpthwyLocKey` Location Key for Evpthwy directory
`static java.lang.String`	`NSynSubsFN` File name for NSynSubs file
`static java.lang.String`	`NSynSubsLocKey` Location Key for NSynSubs file
`static java.lang.String`	`SlidingWindowDN` Directory name for Sliding Window
`static java.lang.String`	`SlidingWLocKey` Location Key for SlidingWindow directory
`static java.lang.String`	`SubstsDN` Directory Name for Substs directory
`static java.lang.String`	`SubstsLocKey` Location Key for Substs directory
`static java.lang.String`	`SynSubsFN` File name for SynSubs file
`static java.lang.String`	`SynSubsLocKey` Location Key for SynSubs file
`static java.lang.String`	`ZSigPropFN` File name for Z-SigProp file
`static java.lang.String`	`ZSigPropLocKey` Location Key for Z-SigProp file

Constructor Summary

Constructors
Constructor and Description

TreeSAAPTP(Utilities utilities)
Initialize TreeSAAP Panel resources

Constructors
Constructor and Description
`TreeSAAPTP(Utilities utilities)` Initialize TreeSAAP Panel resources

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`getAllPropsSignifRanges()` For each and every extracted property, get its location (in SlidingWindow) and extract from the corresponding file, all the rows that have columns 6,7 or 8 with values higher than 3.090232 Builds an HashMap having properties absolute paths as keys and a linked list of selected rows as values.
`java.lang.String`	`getMSignifValue()` Get the most significant value (P = 0.001).
`void`	`getMSNSynSubs(java.lang.String nssfile)` Obtain the most significant rows from the NSynSubs file.
`java.util.HashMap<java.lang.String,java.lang.String>`	`getPBSTable()` Get NSynSubs Properties by Site table.
`java.lang.String`	`getPLocation(java.lang.String propname)` Get location of property given its name.
`java.lang.String[]`	`getPropertiesByRange()` From a range list obtained from a property file, find all ranges that match to the most significant row (range) for each property.
`void`	`getPropertiesBySite(boolean incbranches, boolean inccodaa)` Find and retrieve all properties for each site.
`java.lang.String[]`	`getPropertiesFound()` Get listing of properties found in directory Sliding Window.
`int`	`getPropertiesFoundCnt()` Get count of properties found in directory Sliding Window.
`java.lang.String[]`	`getPropertyMostSignif(java.lang.String propname)` Get list of most significant ranges (rows) for given property name.
`java.lang.String`	`getPropertyMostSignifToFile(java.lang.String propname)` Retrieve and write property containing most significant rows to file.
`void`	`getSWProperties()` Retrieve all properties found in Sliding Window directory. Initialize related names and locations.
`java.lang.String`	`getTSLocation(java.lang.String key)` Get TreeSAAP location given key.
`java.lang.String[]`	`getZSPPropertiesNames()` Get names of significant properties whose rows have been extracted from Z-SigProp.
`java.lang.String`	`getZSPSignifRows()` Extract lines from the file Z-SigProp which are most singificant.
`java.lang.String`	`prepareToFile(java.lang.String[] proprange, java.lang.String filepath)` From a list of ranges with properties associated, produce a similar list but with indexes translated to names.
`java.lang.String`	`preprocessTreeSAAPFile(java.lang.String filepath, java.lang.String tag)` This procedure was created to standardize or correct, the csv format found in TreeSAAP files.
`java.lang.String`	`printBranchStatisticsToFile(java.lang.String filename)` Make two tables having separate information of branches information selected by user.
`java.lang.String`	`printMSNSSMap2File(java.lang.String filename)` Print most significant sorted information from NSynSubs to file.
`java.lang.String`	`printPBSMap2File(java.lang.String filename)` Print properties by site information to file.
`java.lang.String`	`printStatisticsToFile(java.lang.String filename)` Print statistical information to file.
`void`	`setRadical(boolean onoff, boolean onlytwo, boolean pos, boolean neg)` Set if to process data for conservative (1,2,3) columns or radical (6,7,8) columns.
`void`	`setTSLocation(java.lang.String key, java.lang.String loc)` Set TreeSAAP location for given key.
`void`	`tryGetSubLocationsE(java.lang.String evpthwydir)` Set top directory for TreeSAAP results.
`void`	`tryGetSubLocationsS(java.lang.String substsdir)` Set top directory for TreeSAAP results.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - EvpthwyDN
```
public static final java.lang.String EvpthwyDN
```
    Directory Name for Evpthwy directory
    
    See Also:
    
    Constant Field Values
  - ZSigPropFN
```
public static final java.lang.String ZSigPropFN
```
    File name for Z-SigProp file
    
    See Also:
    
    Constant Field Values
  - SlidingWindowDN
```
public static final java.lang.String SlidingWindowDN
```
    Directory name for Sliding Window
    
    See Also:
    
    Constant Field Values
  - EvpthwyLocKey
```
public static final java.lang.String EvpthwyLocKey
```
    Location Key for Evpthwy directory
    
    See Also:
    
    Constant Field Values
  - ZSigPropLocKey
```
public static final java.lang.String ZSigPropLocKey
```
    Location Key for Z-SigProp file
    
    See Also:
    
    Constant Field Values
  - SlidingWLocKey
```
public static final java.lang.String SlidingWLocKey
```
    Location Key for SlidingWindow directory
    
    See Also:
    
    Constant Field Values
  - SubstsDN
```
public static final java.lang.String SubstsDN
```
    Directory Name for Substs directory
    
    See Also:
    
    Constant Field Values
  - NSynSubsFN
```
public static final java.lang.String NSynSubsFN
```
    File name for NSynSubs file
    
    See Also:
    
    Constant Field Values
  - SynSubsFN
```
public static final java.lang.String SynSubsFN
```
    File name for SynSubs file
    
    See Also:
    
    Constant Field Values
  - SubstsLocKey
```
public static final java.lang.String SubstsLocKey
```
    Location Key for Substs directory
    
    See Also:
    
    Constant Field Values
  - NSynSubsLocKey
```
public static final java.lang.String NSynSubsLocKey
```
    Location Key for NSynSubs file
    
    See Also:
    
    Constant Field Values
  - SynSubsLocKey
```
public static final java.lang.String SynSubsLocKey
```
    Location Key for SynSubs file
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - TreeSAAPTP
```
public TreeSAAPTP(Utilities utilities)
```
    Initialize TreeSAAP Panel resources
    
    Parameters:
    
    utilities - object from the class Utilities.
- Method Detail
  - setRadical
```
public void setRadical(boolean onoff,
                       boolean onlytwo,
                       boolean pos,
                       boolean neg)
```
    Set if to process data for conservative (1,2,3) columns or radical (6,7,8) columns.
    
    Parameters:
    
    onoff - true for radical, false otherwise.
    
    onlytwo - if true uses only two categories (1,2 or 7,8, according to previous parameter); three otherwise,
    
    pos - get or not positive values.
    
    neg - get or not negative values.
  - getTSLocation
```
public java.lang.String getTSLocation(java.lang.String key)
```
    Get TreeSAAP location given key.
    
    Parameters:
    
    key - the key for the location.
    
    Returns:
    
    the corresponding key location.
  - setTSLocation
```
public void setTSLocation(java.lang.String key,
                          java.lang.String loc)
```
    Set TreeSAAP location for given key.
    
    Parameters:
    
    key - the key for the location.
    
    loc - the location associated to this key.
  - getMSignifValue
```
public java.lang.String getMSignifValue()
```
    Get the most significant value (P = 0.001).
    
    Returns:
    
    string representation of this value.
    
    See Also:
    
    msignificant
  - tryGetSubLocationsE
```
public void tryGetSubLocationsE(java.lang.String evpthwydir)
```
    Set top directory for TreeSAAP results. Search and set subdirectories and files that match requirements.
    
    Parameters:
    
    evpthwydir - the Evpthwy (Evolutionary Pathway) directory absolute path.
  - tryGetSubLocationsS
```
public void tryGetSubLocationsS(java.lang.String substsdir)
```
    Set top directory for TreeSAAP results. Search and set subdirectories and files that match requirements.
    
    Parameters:
    
    substsdir - the Substs (Substitutions) directory absolute path.
  - getSWProperties
```
public void getSWProperties()
```
    Retrieve all properties found in Sliding Window directory.
    Initialize related names and locations.
  - getPropertiesFound
```
public java.lang.String[] getPropertiesFound()
```
    Get listing of properties found in directory Sliding Window.
    
    Returns:
    
    array of properties; or null if not found.
  - getPropertiesFoundCnt
```
public int getPropertiesFoundCnt()
```
    Get count of properties found in directory Sliding Window.
    
    Returns:
    
    count of properties; or -1 if not found.
  - getPLocation
```
public java.lang.String getPLocation(java.lang.String propname)
```
    Get location of property given its name.
    
    Parameters:
    
    propname - property name without extension (txt)
    
    Returns:
    
    location property path; or null if there is none.
  - getZSPSignifRows
```
public java.lang.String getZSPSignifRows()
```
    Extract lines from the file Z-SigProp which are most singificant. I.E having a star in third column and falling in category 6,7 or 8.
    
    Returns:
    
    path of Z-SigProp file significant rows, saved to a temporary file.
  - getZSPPropertiesNames
```
public java.lang.String[] getZSPPropertiesNames()
```
    Get names of significant properties whose rows have been extracted from Z-SigProp.
    
    Returns:
    
    extracted names; or null if not initialized.
    
    See Also:
    
    getZSPSignifRows()
  - getAllPropsSignifRanges
```
public void getAllPropsSignifRanges()
```
    For each and every extracted property, get its location (in SlidingWindow) and extract from the corresponding file, all the rows that have columns 6,7 or 8 with values higher than 3.090232
    Builds an HashMap having properties absolute paths as keys and a linked list of selected rows as values.
    
    See Also:
    
    getZSPSignifRows(), getZSPPropertiesNames()
  - getPropertyMostSignif
```
public java.lang.String[] getPropertyMostSignif(java.lang.String propname)
```
    Get list of most significant ranges (rows) for given property name.
    
    Parameters:
    
    propname - property name.
    
    Returns:
    
    list of rows; or null if no rows where found.
  - getPropertyMostSignifToFile
```
public java.lang.String getPropertyMostSignifToFile(java.lang.String propname)
```
    Retrieve and write property containing most significant rows to file.
    
    Parameters:
    
    propname - property name to search for.
    
    Returns:
    
    property file absolute path; or null if property does not exist or produces no results.
  - getPropertiesByRange
```
public java.lang.String[] getPropertiesByRange()
```
    From a range list obtained from a property file, find all
    ranges that match to the most significant row (range) for each property. This way obtaining the corresponding property, that falls into that range. Properties are described as indexes in same order as the extracted names.
    
    Returns:
    
    a list of ranges that have properties associated. This list has the following format for each row:
    from,to:p1;...;pn
    -range separated from properties by colon
    -each property separated by semicolon.
    -range separated by comma.; or null if not found.
    
    See Also:
    
    getZSPPropertiesNames(), getPropertyMostSignif(java.lang.String), getRangeList()
  - prepareToFile
```
public java.lang.String prepareToFile(java.lang.String[] proprange,
                                      java.lang.String filepath)
```
    From a list of ranges with properties associated, produce
    a similar list but with indexes translated to names. The file being written is in proper CSV format.
    
    Parameters:
    
    proprange - list of ranges with properties associated.
    
    filepath - the path of the file where to save content.
    
    Returns:
    
    file absolute path containing same list given as argument,
    but with property indexes translated into names.
    
    See Also:
    
    getPropertiesByRange()
  - preprocessTreeSAAPFile
```
public java.lang.String preprocessTreeSAAPFile(java.lang.String filepath,
                                               java.lang.String tag)
```
    This procedure was created to standardize or correct, the csv format found in TreeSAAP files. This procedure can be applied to the Z-SigProp file and any file (property) from the SlidingWindow directory.
    Each case has its own specificities, so the second argument indicates which is being treated. This is specified by Z-SigProp file name or SlidingWindow directory name.
    
    Parameters:
    
    filepath - the absolute path of the file to be treated.
    
    tag - the tag used to distinguish each case. View the See Also section.
    
    Returns:
    
    the new file absolute path to the treated file. This new file is identified by having same name has the original,
    but with "_view_version.csv" appended, with any previously found extension removed.
    
    See Also:
    
    ZSigPropFN, SlidingWindowDN
  - getMSNSynSubs
```
public void getMSNSynSubs(java.lang.String nssfile)
```
    Obtain the most significant rows from the NSynSubs file. Results are collected based on user selected options and placed in an HashMap. Categories ((1,2),3) or (6,(7,8)) for either positive or negative values.
    
    Parameters:
    
    nssfile - absolute path for the NSynSubs file.
  - printMSNSSMap2File
```
public java.lang.String printMSNSSMap2File(java.lang.String filename)
```
    Print most significant sorted information from NSynSubs to file.
    
    Parameters:
    
    filename - where to write information.
    
    Returns:
    
    the absolute file path.
    
    See Also:
    
    getMSNSynSubs(java.lang.String), sortValues(java.lang.String[], boolean)
  - getPropertiesBySite
```
public void getPropertiesBySite(boolean incbranches,
                                boolean inccodaa)
```
    Find and retrieve all properties for each site. Requires previous extraction of Most Significant rows from NSynSubs file. Results are placed in an HashMap. Finally builds the statistics data, from this resulting data, which is stored in a different HashMap.
    
    Parameters:
    
    incbranches - whether or not to include branches information in the results.
    
    inccodaa - whether or not to include codons and amino-acids information in the results.
    
    See Also:
    
    getMSNSynSubs(java.lang.String)
  - printBranchStatisticsToFile
```
public java.lang.String printBranchStatisticsToFile(java.lang.String filename)
```
    Make two tables having separate information of branches information selected by user. These tables contain information on the number of properties, either unique or totaling per node.
    
    Parameters:
    
    filename - base file path.
    
    Returns:
    
    two file paths or files: one for branches node-&node; another for node-&species.
  - printStatisticsToFile
```
public java.lang.String printStatisticsToFile(java.lang.String filename)
```
    Print statistical information to file. This information (choices) depends on the file built in properties by site. This file name is the same as given as argument, but with ".stat.csv" as extension.
    
    Parameters:
    
    filename - properties by site absolute file path.
    
    Returns:
    
    file absolute path for the statistics file.
    
    See Also:
    
    getPropertiesBySite(boolean, boolean), buildStatistics(int)
  - printPBSMap2File
```
public java.lang.String printPBSMap2File(java.lang.String filename)
```
    Print properties by site information to file.
    
    Parameters:
    
    filename - file where to write PBS information.
    
    Returns:
    
    file absolute path.
  - getPBSTable
```
public java.util.HashMap<java.lang.String,java.lang.String> getPBSTable()
```
    Get NSynSubs Properties by Site table.
    
    Returns:
    
    PBS table.

Class TreeSAAPTP

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

EvpthwyDN

ZSigPropFN

SlidingWindowDN

EvpthwyLocKey

ZSigPropLocKey

SlidingWLocKey

SubstsDN

NSynSubsFN

SynSubsFN

SubstsLocKey

NSynSubsLocKey

SynSubsLocKey

Constructor Detail

TreeSAAPTP

Method Detail

setRadical

getTSLocation

setTSLocation

getMSignifValue

tryGetSubLocationsE

tryGetSubLocationsS

getSWProperties

getPropertiesFound

getPropertiesFoundCnt

getPLocation

getZSPSignifRows

getZSPPropertiesNames

getAllPropsSignifRanges

getPropertyMostSignif

getPropertyMostSignifToFile

getPropertiesByRange

prepareToFile

preprocessTreeSAAPFile

getMSNSynSubs

printMSNSSMap2File

getPropertiesBySite

printBranchStatisticsToFile

printStatisticsToFile

printPBSMap2File

getPBSTable