gata.main
Class GATAUtil

java.lang.Object
  gata.main.GATAUtil

public class GATAUtil

extends java.lang.Object

Author:

Nix Master utility class for GATAPlotter. All static.

Field Summary

static java.awt.Color[]

COLORS Color array for tracks, yup I'm lazy

Constructor Summary

GATAUtil()

Method Summary

static java.awt.geom.Line2D.Double[]	ALToLine2DArray(java.util.ArrayList al)
static java.lang.String	ALToString(java.util.ArrayList al)
static int[]	calculateEffectiveMandN(double m, double n, double K, double H) Calculates effective m and n using BLAST parameters, returning int[m', n']
static java.lang.String	calculateEValue(double lambdaNats, double K, int rawS, double effectiveN, double effectiveM)
static boolean	checkFile(java.lang.String par)
static double	convertBitScoreToRaw(double lambdaNats, double K, double bitS)
static int	convertPlusToNumOrientation(java.lang.String orientation)
static double	convertRawScoreToBit(double lambdaNats, double K, double rawS) Converts a raw S score to a bit score given lambda (in nats) and K
static void	deleteFile(java.lang.String fullPathFileName)
static int	DNAStat(java.lang.String seq1, java.lang.String seq2, int match, int misMatch, int gapCreate, int gapExtend)
static void	drawLabels(java.util.ArrayList labels, java.awt.Font font, java.awt.Graphics2D g2)
static void	drawLines(java.awt.geom.Line2D.Double[] lines, java.awt.Graphics2D g2) draws Shapes
static java.util.ArrayList	extractStartEnds(ExonIntron[] exons) Deep copies start stops from ExonIntron objects to an ArrayList
static int[][]	extractStartEndsInts(ExonIntron[] exons)
static java.util.ArrayList	fetchArrayList(java.io.File file)
static double[]	fetchBLASTParams(int match, int misMatch) Returns Lambda and K or null for a given match and misMatch from BLASTN.
static java.util.ArrayList	fetchIntrons(java.util.ArrayList exons) Takes an ArrayList of exon startStop int[2]'s, returns an ArrayList of int[2]'s representing the start,stop for each intron
static java.lang.Object	fetchObject(java.io.File file)
static java.awt.RenderingHints	fetchRenderingHints() Map of hints for high quality/ slow rendering
static int	findHighestInt(int[] ints)
static java.lang.String	genDashes(java.lang.String seq1, java.lang.String seq2)
static int[]	getBaseNumArray(java.lang.String s, int index)
static boolean	isEmpty(java.lang.String text) Method to check if a string is null or empty after trimming
static boolean	isStringEmpty(java.lang.String string)
static java.util.ArrayList	joinSegments(java.util.ArrayList segs) Takes an ArrayList of int[2]'s representing start stop coords kills the dups, and those cotained within another seg, will merge overlapping segments.
static java.util.ArrayList	makeArrowAndButt(int start, int end, int upOrDown, double yCoord, int orientation, double pixPerNt, double ntAtX, double height) Makes an arrow and butt but no base line.
static java.util.ArrayList	makeArrowLine(int start, int end, int upOrDown, double yCoord, int orientation, double pixPerNt, double ntAtX, double height) Makes an arrow line with half arrow up for -1 or down for 1.
static java.awt.geom.GeneralPath	makeArrowLine(int start, int end, int upOrDown, float yCoord, int orientation, float pixPerNt, float ntAtX, float heightArrowButt, float lineThickness) Makes an arrow line with half arrow up for -1 or down for 1.
static javax.swing.JButton	makeButton(java.lang.String text, int size, java.awt.event.ActionListener action, javax.swing.JPanel panel)
static double	makeDoubleInputDialog(java.lang.String title, java.lang.String comment, double suggestion)
static double	makeDoublePercentInputDialog(java.lang.String title, java.lang.String comment, double suggestion)
static javax.swing.JTextField	makeField(javax.swing.JPanel panel, java.lang.String text, javax.swing.JFrame frame, javax.swing.JFileChooser chooser, FileFocusListener focus)
static javax.swing.JTextField	makeFieldSimple(javax.swing.JPanel panel, java.lang.String text)
static int	makeIntInputDialog(java.lang.String title, java.lang.String comment, int suggestion)
static javax.swing.JLabel	makeLabel(javax.swing.JPanel panel, java.lang.String text, int size, int thickness)
static java.util.ArrayList	makeLabel(java.lang.String label, int start, int end, double pixPerNt, double ntAtX, double yCoor)
static java.awt.geom.Line2D.Double	makeLine(int start, int end, double yCoord, double pixPerNt, double ntAtX) Converts an int[2] (startStop) in nucleotides to a Line2D.Double
static java.awt.geom.Rectangle2D.Double	makeRectangle(int start, int end, double startY, double stopY, double pixPerNt, double ntAtX) Returns a rectangle given start stop in nucleotides and y coords in pixels
static java.util.ArrayList	makeSegments(java.util.ArrayList segs, double yCoord, double pixPerNt, double ntAtX) Converts an ArrayList of int[2]'s (startStop) in nucleotides to an ArrayList of Line2D.Double's
static java.util.ArrayList	makeSegmentsInt(int[][] segs, double yCoord, double pixPerNt, double ntAtX) Converts an int[x][2]'s (startStop) in nucleotides to an ArrayList of Line2D.Double's
static Alignment[]	makeSubAligns(LocalAlignment[] locs)
static LocalAlignment[]	mergeLAArrays(LocalAlignment[] a, LocalAlignment[] b)
static java.util.ArrayList	objectArraytoAL(java.lang.Object[] objs) Converts an Object[] to an ArrayList
static int[]	optimizeAlignmentScore(java.lang.String seq1, java.lang.String seq2, int match, int misMatch, int gapCreate, int gapExtend, int scoreCutOff)
static java.lang.String	parseDNAFileName(java.lang.String s)
static void	saveArrayList(java.io.File file, java.util.ArrayList al)
static void	saveObject(java.io.File file, java.lang.Object ob)
static void	setBooleanArray(boolean[] array, boolean value) Takes an array of boolean[] and sets all to the boolean value
static int[]	setButton(javax.swing.JButton but, int x, int y)
static int[]	setChooser(javax.swing.JFileChooser choos, int x, int y, int width)
static int[]	setField(javax.swing.JTextField field, int x, int y, int width)
static void	setFloatArray(float[] array, float value) Takes an array of float[] and sets all to the float value
static int[]	setLabel(javax.swing.JLabel lab, int x, int y)
static void	setScrollPaneScrollBarIncrement(javax.swing.JScrollPane scrollPane, int increment) Sets the scroll bar move increments, vert and horiz, in a scroll pane
static void	showFileChooserDialogBox(javax.swing.JTextField fieldRef, javax.swing.JFrame frame, javax.swing.JFileChooser chooser)
static java.util.ArrayList	sortSegments(java.util.ArrayList segs) Sorts an ArrayList of int[2]'s representing start, end
static java.lang.String	spaces(java.lang.String seq, int number)
static void	throwWarning(javax.swing.JFrame frame, javax.swing.JTextField field, java.lang.String text)
static void	writeString(java.lang.String data, java.lang.String fullPathFileName)

Methods inherited from class java.lang.Object

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

Field Detail

COLORS

public static final java.awt.Color[] COLORS

Color array for tracks, yup I'm lazy

Constructor Detail

GATAUtil

public GATAUtil()

Method Detail

setBooleanArray

public static void setBooleanArray(boolean[] array,
                                   boolean value)

Takes an array of boolean[] and sets all to the boolean value

setFloatArray

public static void setFloatArray(float[] array,
                                 float value)

Takes an array of float[] and sets all to the float value

setScrollPaneScrollBarIncrement

public static void setScrollPaneScrollBarIncrement(javax.swing.JScrollPane scrollPane,
                                                   int increment)

Sets the scroll bar move increments, vert and horiz, in a scroll pane

makeDoublePercentInputDialog

public static double makeDoublePercentInputDialog(java.lang.String title,
                                                  java.lang.String comment,
                                                  double suggestion)

makeDoubleInputDialog

public static double makeDoubleInputDialog(java.lang.String title,
                                           java.lang.String comment,
                                           double suggestion)

makeIntInputDialog

public static int makeIntInputDialog(java.lang.String title,
                                     java.lang.String comment,
                                     int suggestion)

throwWarning

public static void throwWarning(javax.swing.JFrame frame,
                                javax.swing.JTextField field,
                                java.lang.String text)

setButton

public static int[] setButton(javax.swing.JButton but,
                              int x,
                              int y)

makeButton

public static javax.swing.JButton makeButton(java.lang.String text,
                                             int size,
                                             java.awt.event.ActionListener action,
                                             javax.swing.JPanel panel)

showFileChooserDialogBox

public static void showFileChooserDialogBox(javax.swing.JTextField fieldRef,
                                            javax.swing.JFrame frame,
                                            javax.swing.JFileChooser chooser)

checkFile

public static boolean checkFile(java.lang.String par)

makeField

public static javax.swing.JTextField makeField(javax.swing.JPanel panel,
                                               java.lang.String text,
                                               javax.swing.JFrame frame,
                                               javax.swing.JFileChooser chooser,
                                               FileFocusListener focus)

makeFieldSimple

public static javax.swing.JTextField makeFieldSimple(javax.swing.JPanel panel,
                                                     java.lang.String text)

makeLabel

public static javax.swing.JLabel makeLabel(javax.swing.JPanel panel,
                                           java.lang.String text,
                                           int size,
                                           int thickness)

setChooser

public static int[] setChooser(javax.swing.JFileChooser choos,
                               int x,
                               int y,
                               int width)

setField

public static int[] setField(javax.swing.JTextField field,
                             int x,
                             int y,
                             int width)

setLabel

public static int[] setLabel(javax.swing.JLabel lab,
                             int x,
                             int y)

deleteFile

public static void deleteFile(java.lang.String fullPathFileName)

convertRawScoreToBit

public static double convertRawScoreToBit(double lambdaNats,
                                          double K,
                                          double rawS)

Converts a raw S score to a bit score given lambda (in nats) and K

convertBitScoreToRaw

public static double convertBitScoreToRaw(double lambdaNats,
                                          double K,
                                          double bitS)

calculateEValue

public static java.lang.String calculateEValue(double lambdaNats,
                                               double K,
                                               int rawS,
                                               double effectiveN,
                                               double effectiveM)

calculateEffectiveMandN

public static int[] calculateEffectiveMandN(double m,
                                            double n,
                                            double K,
                                            double H)

Calculates effective m and n using BLAST parameters, returning int[m', n']

DNAStat

public static int DNAStat(java.lang.String seq1,
                          java.lang.String seq2,
                          int match,
                          int misMatch,
                          int gapCreate,
                          int gapExtend)

findHighestInt

public static int findHighestInt(int[] ints)

genDashes

public static java.lang.String genDashes(java.lang.String seq1,
                                         java.lang.String seq2)

getBaseNumArray

public static int[] getBaseNumArray(java.lang.String s,
                                    int index)

makeSubAligns

public static Alignment[] makeSubAligns(LocalAlignment[] locs)

mergeLAArrays

public static LocalAlignment[] mergeLAArrays(LocalAlignment[] a,
                                             LocalAlignment[] b)

optimizeAlignmentScore

public static int[] optimizeAlignmentScore(java.lang.String seq1,
                                           java.lang.String seq2,
                                           int match,
                                           int misMatch,
                                           int gapCreate,
                                           int gapExtend,
                                           int scoreCutOff)

parseDNAFileName

public static java.lang.String parseDNAFileName(java.lang.String s)

spaces

public static java.lang.String spaces(java.lang.String seq,
                                      int number)

writeString

public static void writeString(java.lang.String data,
                               java.lang.String fullPathFileName)

fetchRenderingHints

public static java.awt.RenderingHints fetchRenderingHints()

Map of hints for high quality/ slow rendering

drawLabels

public static void drawLabels(java.util.ArrayList labels,
                              java.awt.Font font,
                              java.awt.Graphics2D g2)

makeLabel

public static java.util.ArrayList makeLabel(java.lang.String label,
                                            int start,
                                            int end,
                                            double pixPerNt,
                                            double ntAtX,
                                            double yCoor)

ALToLine2DArray

public static java.awt.geom.Line2D.Double[] ALToLine2DArray(java.util.ArrayList al)

drawLines

public static void drawLines(java.awt.geom.Line2D.Double[] lines,
                             java.awt.Graphics2D g2)

draws Shapes

makeSegments

public static java.util.ArrayList makeSegments(java.util.ArrayList segs,
                                               double yCoord,
                                               double pixPerNt,
                                               double ntAtX)

Converts an ArrayList of int[2]'s (startStop) in nucleotides to an ArrayList of Line2D.Double's

makeSegmentsInt

public static java.util.ArrayList makeSegmentsInt(int[][] segs,
                                                  double yCoord,
                                                  double pixPerNt,
                                                  double ntAtX)

Converts an int[x][2]'s (startStop) in nucleotides to an ArrayList of Line2D.Double's

makeLine

public static java.awt.geom.Line2D.Double makeLine(int start,
                                                   int end,
                                                   double yCoord,
                                                   double pixPerNt,
                                                   double ntAtX)

Converts an int[2] (startStop) in nucleotides to a Line2D.Double

makeRectangle

public static java.awt.geom.Rectangle2D.Double makeRectangle(int start,
                                                             int end,
                                                             double startY,
                                                             double stopY,
                                                             double pixPerNt,
                                                             double ntAtX)

Returns a rectangle given start stop in nucleotides and y coords in pixels

makeArrowAndButt

public static java.util.ArrayList makeArrowAndButt(int start,
                                                   int end,
                                                   int upOrDown,
                                                   double yCoord,
                                                   int orientation,
                                                   double pixPerNt,
                                                   double ntAtX,
                                                   double height)

Makes an arrow and butt but no base line. Half arrow/butt up for -1 or down for 1. Start and end are really just 5 ' and 3' coordinates, start should always be less than end. Orientation is 1 for + (arrow pointing right), -1 for - (left). yCoord is for the y-coordinate to draw the main line. Returns an ArrayList of Line2D.doubles.

makeArrowLine

public static java.util.ArrayList makeArrowLine(int start,
                                                int end,
                                                int upOrDown,
                                                double yCoord,
                                                int orientation,
                                                double pixPerNt,
                                                double ntAtX,
                                                double height)

Makes an arrow line with half arrow up for -1 or down for 1. Start and end are really just 5 ' and 3' coordinates, start should always be less than end. Orientation is 1 for + (arrow pointing right), -1 for - (left). yCoord is for the y-coordinate to draw the main line. Returns an ArrayList of Line2D.doubles.

makeArrowLine

public static java.awt.geom.GeneralPath makeArrowLine(int start,
                                                      int end,
                                                      int upOrDown,
                                                      float yCoord,
                                                      int orientation,
                                                      float pixPerNt,
                                                      float ntAtX,
                                                      float heightArrowButt,
                                                      float lineThickness)

Makes an arrow line with half arrow up for -1 or down for 1. Start and end are really just 5 ' and 3' coordinates, start should always be less than end. Orientation is 1 for + (arrow pointing right), -1 for - (left). yCoord is for the y-coordinate to draw the main line. Line thickness is needed to calculate whether to draw an arrow or not, for short segments. Will always return a line of at least 1 pixel.

fetchBLASTParams

public static double[] fetchBLASTParams(int match,
                                        int misMatch)

Returns Lambda and K or null for a given match and misMatch from BLASTN. Some combinations of match/misMatch are not computed by BLASTN!

saveArrayList

public static void saveArrayList(java.io.File file,
                                 java.util.ArrayList al)

saveObject

public static void saveObject(java.io.File file,
                              java.lang.Object ob)

isStringEmpty

public static boolean isStringEmpty(java.lang.String string)

fetchArrayList

public static java.util.ArrayList fetchArrayList(java.io.File file)

fetchObject

public static java.lang.Object fetchObject(java.io.File file)

isEmpty

public static boolean isEmpty(java.lang.String text)

Method to check if a string is null or empty after trimming

objectArraytoAL

public static java.util.ArrayList objectArraytoAL(java.lang.Object[] objs)

Converts an Object[] to an ArrayList

extractStartEnds

public static java.util.ArrayList extractStartEnds(ExonIntron[] exons)

Deep copies start stops from ExonIntron objects to an ArrayList

extractStartEndsInts

public static int[][] extractStartEndsInts(ExonIntron[] exons)

convertPlusToNumOrientation

public static int convertPlusToNumOrientation(java.lang.String orientation)

fetchIntrons

public static java.util.ArrayList fetchIntrons(java.util.ArrayList exons)

Takes an ArrayList of exon startStop int[2]'s, returns an ArrayList of int[2]'s representing the start,stop for each intron

ALToString

public static java.lang.String ALToString(java.util.ArrayList al)

sortSegments

public static java.util.ArrayList sortSegments(java.util.ArrayList segs)

Sorts an ArrayList of int[2]'s representing start, end

joinSegments

public static java.util.ArrayList joinSegments(java.util.ArrayList segs)

Takes an ArrayList of int[2]'s representing start stop coords kills the dups, and those cotained within another seg, will merge overlapping segments.