IMPACT_S

Class ResultsN3DTP

java.lang.Object

IMPACT_S.ResultsN3DTP

public class ResultsN3DTP
extends java.lang.Object

Class to handle necessary computation and data storage for general or final results.
Results from previous tabs and from resources like Jmol and Swiss Model.

Author:

Emanuel Maldonado

See Also:

GUIProtToSwissModel, GUIPDBTool, GUIColorSchemes, GenericJarTask, GUIResultsView

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	bebResults1LocKey Location key for BEB results in field 1, from Codeml tab
static java.lang.String	bebResults2LocKey Location key for BEB results in field 2, from Codeml tab
static java.lang.String	datamonkeySitesLocKey Location key for datamonkey sites files (All methods (Pos/Neg) plus Common Sites (Pos/Neg)) from Datamonkey tab
static java.lang.String	downloadedPDBLocKey Location key for downloaded PDB file from Swiss Model Template Library
static java.lang.String	jmolScriptPathLocKey Location key for produced jmol script from ResultsN3D tab
static java.lang.String	mergedResultsLocKey Location key for merge results in from ResultsN3D tab
static java.lang.String	modelledPDBLocKey Location key for downloaded Modeled PDB file from Swiss Model modes
static java.lang.String	pdbFilePathLocKey Location key for the PDB file selected by user
static java.lang.String	propsByRangeLocKey Location key for properties by range file from TreeSAAP tab
static java.lang.String	propsBySiteLocKey Location key for properties by site file from TreeSAAP tab

Constructor Summary

Constructors

Constructor and Description
ResultsN3DTP(Utilities utilities) Initialize ResultsN3D with empty fields.

Method Summary

Modifier and Type	Method and Description
java.lang.String	createJmolScript(int seloption, int treesaapfield, int bebfield, java.lang.String shape, boolean only, boolean restrict, boolean small) Create Jmol script based on scheme of colors chosen.
java.lang.String[]	getModelledRange() Retrieve the modeled range.
java.util.HashMap<java.lang.String,java.lang.String>	getMRCommonSitesTable() Get Merged Results common sites table.
java.util.HashMap<java.lang.String,java.awt.Color>	getPaintedSites() Get all painted sites after Jmol script is created.
boolean	getPDBFileResRange() Obtain start and end of residue range described in PDB file.
java.lang.String	getPDBFileSequence() Get PDB Sequence from file.
java.lang.String[]	getPDBResRange() Get values previously obtained from PDB file.
java.lang.String	getRLocations(java.lang.String key) Get value for associated key.
java.lang.String	mergeResults(java.lang.String treesaapfile, java.lang.String datamonkeyfile, java.lang.String pamlbebfile) Merge all information from Datamonkey and PAML BEB (in case of positive selection) in any TreeSAAP data files (PBS/PBR).
void	setJmolColorScheme(java.awt.Color[] chColors, java.lang.String[] aanames, int lowerlimit, boolean translucent, boolean labels) Set scheme of colors selected by user.
void	setModelledRange(java.lang.String[] range) Set modeled range obtained from modeling.
void	setRLocations(java.lang.String key, java.lang.String value) Set value for associated key.
void	unsetModelledRange() Unset the use of the modeled range.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

datamonkeySitesLocKey

public static final java.lang.String datamonkeySitesLocKey

Location key for datamonkey sites files (All methods (Pos/Neg) plus Common Sites (Pos/Neg)) from Datamonkey tab

See Also:

Constant Field Values

propsBySiteLocKey

public static final java.lang.String propsBySiteLocKey

Location key for properties by site file from TreeSAAP tab

See Also:

Constant Field Values

propsByRangeLocKey

public static final java.lang.String propsByRangeLocKey

Location key for properties by range file from TreeSAAP tab

See Also:

Constant Field Values

bebResults1LocKey

public static final java.lang.String bebResults1LocKey

Location key for BEB results in field 1, from Codeml tab

See Also:

Constant Field Values

bebResults2LocKey

public static final java.lang.String bebResults2LocKey

Location key for BEB results in field 2, from Codeml tab

See Also:

Constant Field Values

mergedResultsLocKey

public static final java.lang.String mergedResultsLocKey

Location key for merge results in from ResultsN3D tab

See Also:

Constant Field Values

downloadedPDBLocKey

public static final java.lang.String downloadedPDBLocKey

Location key for downloaded PDB file from Swiss Model Template Library

See Also:

Constant Field Values

modelledPDBLocKey

public static final java.lang.String modelledPDBLocKey

Location key for downloaded Modeled PDB file from Swiss Model modes

See Also:

Constant Field Values

jmolScriptPathLocKey

public static final java.lang.String jmolScriptPathLocKey

Location key for produced jmol script from ResultsN3D tab

See Also:

Constant Field Values

pdbFilePathLocKey

public static final java.lang.String pdbFilePathLocKey

Location key for the PDB file selected by user

See Also:

Constant Field Values

Constructor Detail

ResultsN3DTP

public ResultsN3DTP(Utilities utilities)

Initialize ResultsN3D with empty fields.

Parameters:

utilities - object from the class Utilities.

Method Detail

getRLocations

public java.lang.String getRLocations(java.lang.String key)

Get value for associated key.

Parameters:

key - from class specific values.

Returns:

value value associated to given key.

setRLocations

public void setRLocations(java.lang.String key,
                          java.lang.String value)

Set value for associated key.

Parameters:

key - from class specific values.

value - value associated to given key.

setModelledRange

public void setModelledRange(java.lang.String[] range)

Set modeled range obtained from modeling. The range consists of an array of two positions were
the first refers to the range lower limit and the second to the upper limit.

Parameters:

range - modeled range [lower,upper]

See Also:

getModelledRange()

unsetModelledRange

public void unsetModelledRange()

Unset the use of the modeled range. The class field holding the ranges values are set to null,
and the flag signaling its use is set to false.

See Also:

setModelledRange(java.lang.String[])

getModelledRange

public java.lang.String[] getModelledRange()

Retrieve the modeled range.

Returns:

modeled range array consisting of two positions; or null if has not been set.

See Also:

setModelledRange(java.lang.String[])

mergeResults

public java.lang.String mergeResults(java.lang.String treesaapfile,
                                     java.lang.String datamonkeyfile,
                                     java.lang.String pamlbebfile)

Merge all information from Datamonkey and PAML BEB (in case of positive selection) in any TreeSAAP data files (PBS/PBR).

Parameters:

treesaapfile - treesaap file: PBR or PBS.

datamonkeyfile - datamonkey file: common sites or any model (SLAC; FEL; REL; MEME or FUBAR)

pamlbebfile - paml beb file: from Model 2 or 8.

Returns:

file location for saved merge results.

setJmolColorScheme

public void setJmolColorScheme(java.awt.Color[] chColors,
                               java.lang.String[] aanames,
                               int lowerlimit,
                               boolean translucent,
                               boolean labels)

Set scheme of colors selected by user. And Amino Acids names.
Each parameter matches each other in its position/index.

Parameters:

chColors - user chosen colors.

aanames - amino acids names in same order as the colors.

lowerlimit - scheme specific option only for TreeSAAP (User) Type III, defined by user. Use value ≤ 0 if not needed.

translucent - use translucent for other residues color (not fitting the main colors: fallback color).

labels - true to select the use of labels.

getPaintedSites

public java.util.HashMap<java.lang.String,java.awt.Color> getPaintedSites()

Get all painted sites after Jmol script is created.

Returns:

all painted sites.

createJmolScript

public java.lang.String createJmolScript(int seloption,
                                         int treesaapfield,
                                         int bebfield,
                                         java.lang.String shape,
                                         boolean only,
                                         boolean restrict,
                                         boolean small)

Create Jmol script based on scheme of colors chosen.

Parameters:

seloption - scheme selected.

treesaapfield - once there are two fields for TreeSAAP results, one of them must be chosen, for some options to be used: treesaapfield = 1 or 2;

bebfield - once there are two fields for BEB results, one of them must be chosen, for some options to be used: bebfield = 1 or 2;

shape - the rendering shape to be applied.

only - if the shape is to be presented solely.

restrict - if the colored residues are shown as being the only molecules. Other non-painted molecules/residues are not shown.

small - true to select the size of residues to be small.

Returns:

path of script created.

getMRCommonSitesTable

public java.util.HashMap<java.lang.String,java.lang.String> getMRCommonSitesTable()

Get Merged Results common sites table.

Returns:

common sites hashtable.

getPDBFileResRange

public boolean getPDBFileResRange()

Obtain start and end of residue range described in PDB file.

Returns:

true if residue range was found; false if for some reason could not.
Makes a first try in the fourth column, and a second try (if the first was unsuccessful), in the fifth column of the PDB file.

See Also:

getPDBResRange()

getPDBResRange

public java.lang.String[] getPDBResRange()

Get values previously obtained from PDB file. If obtention was unsuccessful, array contains string "0" in both positions;

Returns:

array of two values: 0:from and 1:to.

See Also:

getPDBFileResRange()

getPDBFileSequence

public java.lang.String getPDBFileSequence()

Get PDB Sequence from file. If SQRES section does not exist, tries to get from ATOM section.

Returns:

Amino-acid sequence from PDB file.

See Also:

getPDBSequenceSQRES(), getPDBSequenceATOM()