kea.programs.pintail
Class PintailUtil
java.lang.Object
kea.programs.pintail.PintailUtil
- All Implemented Interfaces:
- Constants
public class PintailUtil
- extends java.lang.Object
- implements Constants
- Version:
- 1.0.
- Author:
- Kevin Ashelford.
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 |
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)