edu.mssm.crover.util
Class Motif

java.lang.Object
  extended by edu.mssm.crover.util.Motif

public class Motif
extends java.lang.Object

Created by IntelliJ IDEA. User: Lei Shi Date: Dec 19, 2003 Time: 3:16:05 PM To change this template use Options | File Templates.


Field Summary
static java.lang.String NOTFOUND
           
 
Constructor Summary
Motif(AnnotatedBioSequence s)
           
 
Method Summary
 void calSA()
           
 void calSS()
           
 void calSSC()
           
 java.lang.String[] getExtendedMotif(int width)
           
 java.lang.String getExtendedMotif(int position, int width)
           
static java.lang.String getExtendedMotif(Sequence sequence, int position, int width)
           
static java.lang.String getExtendedMotif(Sequence sequence, java.lang.String motif, java.lang.String residue, int width)
           
 int[] getIndex()
           
static int getMotifedResiduePosition(Sequence sequence, java.lang.String motif, java.lang.String residue)
           
 double[] getSA()
           
 Sequence getSequence()
           
 double[][] getSS()
           
 double[][] getSSC()
           
static Motif getTestMotif()
           
 boolean positiveIndex(int position)
           
 void printExtendedSegment(java.io.PrintWriter motifout, int width)
           
static int residueCount(java.lang.String motif, java.lang.String residue)
           
 void setSegment(java.lang.String inputmotif)
           
 void setSequence(AnnotatedBioSequence inputsequence)
           
 java.io.File toFasta(java.io.File location)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

NOTFOUND

public static final java.lang.String NOTFOUND
See Also:
Constant Field Values
Constructor Detail

Motif

public Motif(AnnotatedBioSequence s)
Method Detail

setSequence

public void setSequence(AnnotatedBioSequence inputsequence)

setSegment

public void setSegment(java.lang.String inputmotif)

getSequence

public Sequence getSequence()

printExtendedSegment

public void printExtendedSegment(java.io.PrintWriter motifout,
                                 int width)

getMotifedResiduePosition

public static int getMotifedResiduePosition(Sequence sequence,
                                            java.lang.String motif,
                                            java.lang.String residue)

residueCount

public static int residueCount(java.lang.String motif,
                               java.lang.String residue)

getIndex

public int[] getIndex()

positiveIndex

public boolean positiveIndex(int position)

getExtendedMotif

public java.lang.String[] getExtendedMotif(int width)

getExtendedMotif

public java.lang.String getExtendedMotif(int position,
                                         int width)

toFasta

public java.io.File toFasta(java.io.File location)
                     throws java.io.IOException
Throws:
java.io.IOException

calSA

public void calSA()
           throws java.lang.InterruptedException,
                  java.io.IOException
Throws:
java.lang.InterruptedException
java.io.IOException

getSA

public double[] getSA()
               throws java.lang.InterruptedException,
                      java.io.IOException
Throws:
java.lang.InterruptedException
java.io.IOException

calSS

public void calSS()
           throws java.lang.InterruptedException,
                  java.io.IOException
Throws:
java.lang.InterruptedException
java.io.IOException

getSS

public double[][] getSS()
                 throws java.lang.InterruptedException,
                        java.io.IOException
Throws:
java.lang.InterruptedException
java.io.IOException

calSSC

public void calSSC()
            throws java.lang.InterruptedException,
                   java.io.IOException
Throws:
java.lang.InterruptedException
java.io.IOException

getSSC

public double[][] getSSC()
                  throws java.lang.InterruptedException,
                         java.io.IOException
Throws:
java.lang.InterruptedException
java.io.IOException

getExtendedMotif

public static java.lang.String getExtendedMotif(Sequence sequence,
                                                int position,
                                                int width)

getExtendedMotif

public static java.lang.String getExtendedMotif(Sequence sequence,
                                                java.lang.String motif,
                                                java.lang.String residue,
                                                int width)

getTestMotif

public static Motif getTestMotif()


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