kea.programs.pintail
Class PintailUtil

java.lang.Object
  extended by kea.programs.pintail.PintailUtil
All Implemented Interfaces:
Constants

public class PintailUtil
extends java.lang.Object
implements Constants

Version:
1.0.
Author:
Kevin Ashelford.

Field Summary
 
Fields inherited from interface kea.programs.pintail.Constants
BACKGROUND_COLOUR, BOLD_FONT, CUT_OFF_TYPE, CV_UPPER_LIMIT, DEFAULT_STEP_SIZE, DEFAULT_WINDOW_SIZE, ECOLI, ECOLI_LABEL, ERROR_BAR_SIZE, ERROR_Y_AXIS_END, ERROR_Y_AXIS_START, FIRST_SEQUENCE_NAME, FOREGROUND_COLOUR, GREATER_THAN, HEADING_FONT, HIGH_MEAN, HTML_END, HTML_START, LARGE_BOLD_FONT, LESS_THAN, LOW_MEAN, MAC_OSX_CLUSTAL_PATH, MAX_STEP_SIZE, MAX_WINDOW_SIZE, MIN_STEP_SIZE, MIN_WINDOW_SIZE, MODEL, NULL_VALUE, OBSERVED_SCORES_MEAN_CUT_OFF, QUANTILE_TYPE, RC_LOWER_LIMIT, RC_UPPER_LIMIT, SD_UPPER_LIMIT, SECOND_SEQUENCE_NAME, STEP_SIZE_USED_TO_CALCULATE_MODEL, TEXT_FONT, TITLE_FONT, TOO_HIGH_MEAN_FOR_ACCURATE_CONCLUSION, UNUSUALLY_HIGH_MEAN, UNUSUALLY_LARGE_SEQUENCE, WIN_CLUSTAL_PATH, WIN_XP_CLUSTAL_PATH, WINDOW_SIZE_USED_TO_CALCULATE_MODEL, X_AXIS_END, X_AXIS_START, Y_AXIS_END, Y_AXIS_START
 
Method Summary
static boolean badSequences(java.awt.Window owner, java.lang.String sequence1, java.lang.String sequence2)
           
static java.lang.String convertToSimpleConsensusString(java.lang.String consensus)
           
static java.lang.String editConsensusString(java.lang.String consensus, java.lang.String alignedEcoli)
           
static float[] generateExpectedScores(float[] model, int window, int step, float mean, int lengthTrimmedFromStart, int lengthTrimmedFromEnd)
           
static float[] generateObservedScores(int window, int step, java.lang.String consensus)
           
static kea.programs.plot.CoordinateCollection scoresCoordinateCollection(float[] scores, int profileStep, int window, java.lang.String title, int start)
           
static kea.programs.plot.CoordinateCollection straightLineCoordinateCollection(float gradient, float intercept, java.lang.String title)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

convertToSimpleConsensusString

public static java.lang.String convertToSimpleConsensusString(java.lang.String consensus)

editConsensusString

public static java.lang.String editConsensusString(java.lang.String consensus,
                                                   java.lang.String alignedEcoli)

generateObservedScores

public static float[] generateObservedScores(int window,
                                             int step,
                                             java.lang.String consensus)

generateExpectedScores

public static float[] generateExpectedScores(float[] model,
                                             int window,
                                             int step,
                                             float mean,
                                             int lengthTrimmedFromStart,
                                             int lengthTrimmedFromEnd)

straightLineCoordinateCollection

public static kea.programs.plot.CoordinateCollection straightLineCoordinateCollection(float gradient,
                                                                                      float intercept,
                                                                                      java.lang.String title)

scoresCoordinateCollection

public static kea.programs.plot.CoordinateCollection scoresCoordinateCollection(float[] scores,
                                                                                int profileStep,
                                                                                int window,
                                                                                java.lang.String title,
                                                                                int start)

badSequences

public static boolean badSequences(java.awt.Window owner,
                                   java.lang.String sequence1,
                                   java.lang.String sequence2)