biggests.gui
Class ThreadPostProcessing

java.lang.Object
  extended by java.lang.Thread
      extended by biggests.gui.ThreadPostProcessing
All Implemented Interfaces:
java.lang.Runnable

public class ThreadPostProcessing
extends java.lang.Thread

Title: Post-Processing Thread

Description: Implements a thread to apply post-processing algorithms, such as filtering and sorting of biclusters based on well known metrics. Also informs a ProgressBarFrame about the progress of the post-processing operations.

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.


Nested Class Summary
 
Nested classes/interfaces inherited from class java.lang.Thread
java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler
 
Field Summary
 
Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY
 
Constructor Summary
ThreadPostProcessing(smadeira.biclustering.Biclustering biclustering, javax.swing.tree.TreePath selectionPath, PanelPostProcessing panel)
          Creates a new post-processing thread, to post-process a group of biclusters.
 
Method Summary
 smadeira.biclustering.Biclustering filter_CONSTANT_PATTERN(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with a constant pattern and a % of overlapping conditions below two given thresholds.
 smadeira.biclustering.Biclustering filter_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Filters the biclusters of the given biclusters' group (BiclusteringInDiscretizedMatrix) for which the pattern p-value with columns is not significant.
 smadeira.biclustering.Biclustering filter_PATTERN_PVALUE_NOT_SIGNIFICANT(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Filters the biclusters of the given biclusters' group (BiclusteringInDiscretizedMatrix) for which the pattern p-value is not significant.
 smadeira.biclustering.Biclustering filter_TRIVIAL(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs trivial biclusters filtering algorithm.
 smadeira.biclustering.Biclustering filterBy_ACV_ARV_Thresholds(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with ACV and ARV below two given thresholds.
 smadeira.biclustering.Biclustering filterBy_ACV_Threshold(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with an ACV below a given threshold.
 smadeira.biclustering.Biclustering filterBy_ARV_Threshold(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with an ARV below a given threshold.
 smadeira.biclustering.Biclustering filterBy_MSR_Threshold(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with a MSR below a given threshold.
 smadeira.biclustering.Biclustering filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_MSR_Thresholds(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with a number of conditions, a number of genes, ACV, ARV and MSR below five given thresholds.
 smadeira.biclustering.Biclustering filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_Thresholds(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with a number of conditions, a number of genes, ACV and ARV below four given thresholds.
 smadeira.biclustering.Biclustering filterBy_NR_CONDITIONS(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with less than a given number of conditions.
 smadeira.biclustering.Biclustering filterBy_NR_GENES_NR_CONDITIONS(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with less than a given number of genes and a given number of conditions.
 smadeira.biclustering.Biclustering filterBy_NR_GENES(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with less than a given number of genes.
 smadeira.biclustering.Biclustering filterBy_OVERLAPPING_GENES_CONDITIONS_Thresholds(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with a % of overlapping genes and a % of overlapping conditions below two given thresholds.
 smadeira.biclustering.Biclustering filterBy_OVERLAPPING_GENES_Threshold(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with a % of overlapping genes below a given threshold.
 smadeira.biclustering.Biclustering filterBy_SIZE_ARV_ACV_Thresholds(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with size, ACV and ARV below three given thresholds.
 smadeira.biclustering.Biclustering filterBy_SIZE_Threshold(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs filtering of biclusters with size below a given threshold.
 void run()
          Overrides Thread's run method.
 smadeira.biclustering.Biclustering sortBy_ACV(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their ACV.
 smadeira.biclustering.Biclustering sortBy_ARV_ACV_DIFF(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by the difference of their ARV and ACV (ARV-ACV).
 smadeira.biclustering.Biclustering sortBy_ARV_MSR_DIFF(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by the difference of their ARV and MSR (ARV-MSR).
 smadeira.biclustering.Biclustering sortBy_ARV(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their ARV.
 smadeira.biclustering.Biclustering sortBy_BEST_GO_BONFERRONI_PVALUE(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their best GO Bonferroni corrected p-values in ascending order.
 smadeira.biclustering.Biclustering sortBy_BEST_GO_PVALUE(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their best GO p-values in ascending order.
 smadeira.biclustering.Biclustering sortBy_MSR(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their MSR.
 smadeira.biclustering.Biclustering sortBy_NR_CONDITIONS(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their number of conditions.
 smadeira.biclustering.Biclustering sortBy_NR_GENES(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their number of genes.
 smadeira.biclustering.Biclustering sortBy_PATTERN_PVALUE(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their pattern p-value in ascending order.
 smadeira.biclustering.Biclustering sortBy_PATTERN_WITH_COLUMNS_PVALUE(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their pattern with columns p-value in ascending order.
 smadeira.biclustering.Biclustering sortBy_SIZE(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their sizes.
 smadeira.biclustering.Biclustering sortBy_VARIANCE(smadeira.biclustering.Biclustering biclustering, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles)
          Performs sorting of biclusters by their variances.
 
Methods inherited from class java.lang.Thread
activeCount, checkAccess, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

ThreadPostProcessing

public ThreadPostProcessing(smadeira.biclustering.Biclustering biclustering,
                            javax.swing.tree.TreePath selectionPath,
                            PanelPostProcessing panel)
Creates a new post-processing thread, to post-process a group of biclusters.

Parameters:
biclustering - Biclustering the group of biclusters to post-process
selectionPath - the selected TreePath in the dataset tree, which contains the biclustering object
panel - the PanelPostProcessing which makes the user interface with post-processing options
Method Detail

run

public void run()
Overrides Thread's run method. Performs the actual work of this thread, that is, applies post-processing algorithms to the group of biclusters in biclustering attribute.

Specified by:
run in interface java.lang.Runnable
Overrides:
run in class java.lang.Thread

filter_TRIVIAL

public smadeira.biclustering.Biclustering filter_TRIVIAL(smadeira.biclustering.Biclustering biclustering,
                                                         java.util.ArrayList<java.lang.String> infoStrings,
                                                         java.util.ArrayList<java.lang.String> infoStyles)
                                                  throws java.lang.Exception
Performs trivial biclusters filtering algorithm.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_NR_GENES

public smadeira.biclustering.Biclustering filterBy_NR_GENES(smadeira.biclustering.Biclustering biclustering,
                                                            java.util.ArrayList<java.lang.String> infoStrings,
                                                            java.util.ArrayList<java.lang.String> infoStyles)
                                                     throws java.lang.Exception
Performs filtering of biclusters with less than a given number of genes. Reads the number of genes from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_NR_CONDITIONS

public smadeira.biclustering.Biclustering filterBy_NR_CONDITIONS(smadeira.biclustering.Biclustering biclustering,
                                                                 java.util.ArrayList<java.lang.String> infoStrings,
                                                                 java.util.ArrayList<java.lang.String> infoStyles)
                                                          throws java.lang.Exception
Performs filtering of biclusters with less than a given number of conditions. Reads the number of conditions from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_NR_GENES_NR_CONDITIONS

public smadeira.biclustering.Biclustering filterBy_NR_GENES_NR_CONDITIONS(smadeira.biclustering.Biclustering biclustering,
                                                                          java.util.ArrayList<java.lang.String> infoStrings,
                                                                          java.util.ArrayList<java.lang.String> infoStyles)
                                                                   throws java.lang.Exception
Performs filtering of biclusters with less than a given number of genes and a given number of conditions. Reads these numbers from the corresponding input text fields located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_ACV_Threshold

public smadeira.biclustering.Biclustering filterBy_ACV_Threshold(smadeira.biclustering.Biclustering biclustering,
                                                                 java.util.ArrayList<java.lang.String> infoStrings,
                                                                 java.util.ArrayList<java.lang.String> infoStyles)
                                                          throws java.lang.Exception
Performs filtering of biclusters with an ACV below a given threshold. Reads the threshold from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_ARV_Threshold

public smadeira.biclustering.Biclustering filterBy_ARV_Threshold(smadeira.biclustering.Biclustering biclustering,
                                                                 java.util.ArrayList<java.lang.String> infoStrings,
                                                                 java.util.ArrayList<java.lang.String> infoStyles)
                                                          throws java.lang.Exception
Performs filtering of biclusters with an ARV below a given threshold. Reads the threshold from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_ACV_ARV_Thresholds

public smadeira.biclustering.Biclustering filterBy_ACV_ARV_Thresholds(smadeira.biclustering.Biclustering biclustering,
                                                                      java.util.ArrayList<java.lang.String> infoStrings,
                                                                      java.util.ArrayList<java.lang.String> infoStyles)
                                                               throws java.lang.Exception
Performs filtering of biclusters with ACV and ARV below two given thresholds. Reads the thresholds from the corresponding input text fields located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_MSR_Threshold

public smadeira.biclustering.Biclustering filterBy_MSR_Threshold(smadeira.biclustering.Biclustering biclustering,
                                                                 java.util.ArrayList<java.lang.String> infoStrings,
                                                                 java.util.ArrayList<java.lang.String> infoStyles)
                                                          throws java.lang.Exception
Performs filtering of biclusters with a MSR below a given threshold. Reads the threshold from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_SIZE_Threshold

public smadeira.biclustering.Biclustering filterBy_SIZE_Threshold(smadeira.biclustering.Biclustering biclustering,
                                                                  java.util.ArrayList<java.lang.String> infoStrings,
                                                                  java.util.ArrayList<java.lang.String> infoStyles)
                                                           throws java.lang.Exception
Performs filtering of biclusters with size below a given threshold. Reads the threshold from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_SIZE_ARV_ACV_Thresholds

public smadeira.biclustering.Biclustering filterBy_SIZE_ARV_ACV_Thresholds(smadeira.biclustering.Biclustering biclustering,
                                                                           java.util.ArrayList<java.lang.String> infoStrings,
                                                                           java.util.ArrayList<java.lang.String> infoStyles)
                                                                    throws java.lang.Exception
Performs filtering of biclusters with size, ACV and ARV below three given thresholds. Reads the thresholds from the corresponding input text fields located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_Thresholds

public smadeira.biclustering.Biclustering filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_Thresholds(smadeira.biclustering.Biclustering biclustering,
                                                                                             java.util.ArrayList<java.lang.String> infoStrings,
                                                                                             java.util.ArrayList<java.lang.String> infoStyles)
                                                                                      throws java.lang.Exception
Performs filtering of biclusters with a number of conditions, a number of genes, ACV and ARV below four given thresholds. Reads the thresholds from the corresponding input text fields located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_MSR_Thresholds

public smadeira.biclustering.Biclustering filterBy_NR_CONDITIONS_NR_GENES_ARV_ACV_MSR_Thresholds(smadeira.biclustering.Biclustering biclustering,
                                                                                                 java.util.ArrayList<java.lang.String> infoStrings,
                                                                                                 java.util.ArrayList<java.lang.String> infoStyles)
                                                                                          throws java.lang.Exception
Performs filtering of biclusters with a number of conditions, a number of genes, ACV, ARV and MSR below five given thresholds. Reads the thresholds from the corresponding input text fields located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_OVERLAPPING_GENES_Threshold

public smadeira.biclustering.Biclustering filterBy_OVERLAPPING_GENES_Threshold(smadeira.biclustering.Biclustering biclustering,
                                                                               java.util.ArrayList<java.lang.String> infoStrings,
                                                                               java.util.ArrayList<java.lang.String> infoStyles)
                                                                        throws java.lang.Exception
Performs filtering of biclusters with a % of overlapping genes below a given threshold. Reads the threshold from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filterBy_OVERLAPPING_GENES_CONDITIONS_Thresholds

public smadeira.biclustering.Biclustering filterBy_OVERLAPPING_GENES_CONDITIONS_Thresholds(smadeira.biclustering.Biclustering biclustering,
                                                                                           java.util.ArrayList<java.lang.String> infoStrings,
                                                                                           java.util.ArrayList<java.lang.String> infoStyles)
                                                                                    throws java.lang.Exception
Performs filtering of biclusters with a % of overlapping genes and a % of overlapping conditions below two given thresholds. Reads the thresholds from the corresponding input text fields located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filter_CONSTANT_PATTERN

public smadeira.biclustering.Biclustering filter_CONSTANT_PATTERN(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering,
                                                                  java.util.ArrayList<java.lang.String> infoStrings,
                                                                  java.util.ArrayList<java.lang.String> infoStyles)
                                                           throws java.lang.Exception
Performs filtering of biclusters with a constant pattern and a % of overlapping conditions below two given thresholds. Reads the thresholds from the corresponding input text fields located in postProcessingPanel. This method is suited only for biclusters extracted from discretized epression matrices.

Parameters:
biclustering - BiclusteringInDiscretizedMatrix the group of biclusters to filter
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new filtered group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be filtered

filter_PATTERN_PVALUE_NOT_SIGNIFICANT

public smadeira.biclustering.Biclustering filter_PATTERN_PVALUE_NOT_SIGNIFICANT(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering,
                                                                                java.util.ArrayList<java.lang.String> infoStrings,
                                                                                java.util.ArrayList<java.lang.String> infoStyles)
                                                                         throws java.lang.Exception
Filters the biclusters of the given biclusters' group (BiclusteringInDiscretizedMatrix) for which the pattern p-value is not significant.

Parameters:
biclustering - BiclusteringInDiscretizedMatrix (the biclusters' group)
infoStrings - ArrayList information strings
infoStyles - ArrayList styles for information strings
Returns:
Biclustering biclustering object after filtering
Throws:
java.lang.Exception

filter_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT

public smadeira.biclustering.Biclustering filter_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering,
                                                                                        java.util.ArrayList<java.lang.String> infoStrings,
                                                                                        java.util.ArrayList<java.lang.String> infoStyles)
                                                                                 throws java.lang.Exception
Filters the biclusters of the given biclusters' group (BiclusteringInDiscretizedMatrix) for which the pattern p-value with columns is not significant.

Parameters:
biclustering - BiclusteringInDiscretizedMatrix (the biclusters' group)
infoStrings - ArrayList information strings
infoStyles - ArrayList styles for information strings
Returns:
Biclustering biclustering object after filtering
Throws:
java.lang.Exception

sortBy_ACV

public smadeira.biclustering.Biclustering sortBy_ACV(smadeira.biclustering.Biclustering biclustering,
                                                     java.util.ArrayList<java.lang.String> infoStrings,
                                                     java.util.ArrayList<java.lang.String> infoStyles)
                                              throws java.lang.Exception
Performs sorting of biclusters by their ACV. Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_ARV

public smadeira.biclustering.Biclustering sortBy_ARV(smadeira.biclustering.Biclustering biclustering,
                                                     java.util.ArrayList<java.lang.String> infoStrings,
                                                     java.util.ArrayList<java.lang.String> infoStyles)
                                              throws java.lang.Exception
Performs sorting of biclusters by their ARV. Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_MSR

public smadeira.biclustering.Biclustering sortBy_MSR(smadeira.biclustering.Biclustering biclustering,
                                                     java.util.ArrayList<java.lang.String> infoStrings,
                                                     java.util.ArrayList<java.lang.String> infoStyles)
                                              throws java.lang.Exception
Performs sorting of biclusters by their MSR. Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_ARV_ACV_DIFF

public smadeira.biclustering.Biclustering sortBy_ARV_ACV_DIFF(smadeira.biclustering.Biclustering biclustering,
                                                              java.util.ArrayList<java.lang.String> infoStrings,
                                                              java.util.ArrayList<java.lang.String> infoStyles)
                                                       throws java.lang.Exception
Performs sorting of biclusters by the difference of their ARV and ACV (ARV-ACV). Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_ARV_MSR_DIFF

public smadeira.biclustering.Biclustering sortBy_ARV_MSR_DIFF(smadeira.biclustering.Biclustering biclustering,
                                                              java.util.ArrayList<java.lang.String> infoStrings,
                                                              java.util.ArrayList<java.lang.String> infoStyles)
                                                       throws java.lang.Exception
Performs sorting of biclusters by the difference of their ARV and MSR (ARV-MSR). Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_NR_GENES

public smadeira.biclustering.Biclustering sortBy_NR_GENES(smadeira.biclustering.Biclustering biclustering,
                                                          java.util.ArrayList<java.lang.String> infoStrings,
                                                          java.util.ArrayList<java.lang.String> infoStyles)
                                                   throws java.lang.Exception
Performs sorting of biclusters by their number of genes. Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_NR_CONDITIONS

public smadeira.biclustering.Biclustering sortBy_NR_CONDITIONS(smadeira.biclustering.Biclustering biclustering,
                                                               java.util.ArrayList<java.lang.String> infoStrings,
                                                               java.util.ArrayList<java.lang.String> infoStyles)
                                                        throws java.lang.Exception
Performs sorting of biclusters by their number of conditions. Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_SIZE

public smadeira.biclustering.Biclustering sortBy_SIZE(smadeira.biclustering.Biclustering biclustering,
                                                      java.util.ArrayList<java.lang.String> infoStrings,
                                                      java.util.ArrayList<java.lang.String> infoStyles)
                                               throws java.lang.Exception
Performs sorting of biclusters by their sizes. Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_VARIANCE

public smadeira.biclustering.Biclustering sortBy_VARIANCE(smadeira.biclustering.Biclustering biclustering,
                                                          java.util.ArrayList<java.lang.String> infoStrings,
                                                          java.util.ArrayList<java.lang.String> infoStyles)
                                                   throws java.lang.Exception
Performs sorting of biclusters by their variances. Checks which order (ascending or descending) should be applied by accessing the selected property of ascending and descending radio buttons located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_BEST_GO_PVALUE

public smadeira.biclustering.Biclustering sortBy_BEST_GO_PVALUE(smadeira.biclustering.Biclustering biclustering,
                                                                java.util.ArrayList<java.lang.String> infoStrings,
                                                                java.util.ArrayList<java.lang.String> infoStyles)
                                                         throws java.lang.Exception
Performs sorting of biclusters by their best GO p-values in ascending order.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_BEST_GO_BONFERRONI_PVALUE

public smadeira.biclustering.Biclustering sortBy_BEST_GO_BONFERRONI_PVALUE(smadeira.biclustering.Biclustering biclustering,
                                                                           java.util.ArrayList<java.lang.String> infoStrings,
                                                                           java.util.ArrayList<java.lang.String> infoStyles)
                                                                    throws java.lang.Exception
Performs sorting of biclusters by their best GO Bonferroni corrected p-values in ascending order.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_PATTERN_PVALUE

public smadeira.biclustering.Biclustering sortBy_PATTERN_PVALUE(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering,
                                                                java.util.ArrayList<java.lang.String> infoStrings,
                                                                java.util.ArrayList<java.lang.String> infoStyles)
                                                         throws java.lang.Exception
Performs sorting of biclusters by their pattern p-value in ascending order. Retrieves the Markov chain order from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted

sortBy_PATTERN_WITH_COLUMNS_PVALUE

public smadeira.biclustering.Biclustering sortBy_PATTERN_WITH_COLUMNS_PVALUE(smadeira.biclustering.BiclusteringInDiscretizedMatrix biclustering,
                                                                             java.util.ArrayList<java.lang.String> infoStrings,
                                                                             java.util.ArrayList<java.lang.String> infoStyles)
                                                                      throws java.lang.Exception
Performs sorting of biclusters by their pattern with columns p-value in ascending order. Retrieves the Markov chain order from the corresponding input text field located in postProcessingPanel.

Parameters:
biclustering - Biclustering the group of biclusters to sort
infoStrings - ArrayList the set of information strings for the group of biclusters
infoStyles - the set of styles for the information strings of the biclusters' group
Returns:
Biclustering the new sorted group of biclusters
Throws:
java.lang.Exception - if the group of biclusters cannot be sorted