com.pacbio.secondary.vis.io.motifs

Class MotifsReader

java.lang.Object

com.pacbio.secondary.vis.io.motifs.MotifsReader

public class MotifsReader
extends java.lang.Object

reads motifs_summary.csv into motifs database

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	fileName
protected static java.lang.String	MOTIFS_CENTERPOS_TAG
protected java.util.ArrayList<MotifData>	motifs_db
protected static java.lang.String	MOTIFS_FRACTION_TAG
protected static java.lang.String	MOTIFS_GROUP_TAG
protected static java.lang.String	MOTIFS_MEANCOVERAGE_TAG
protected static java.lang.String	MOTIFS_MEANIPDRATIO_TAG
protected static java.lang.String	MOTIFS_MEANSCORE_TAG
protected static java.lang.String	MOTIFS_NDETECTED_TAG
protected static java.lang.String	MOTIFS_NGENOME_TAG
protected static java.lang.String	MOTIFS_OBJSCORE_TAG
protected static java.lang.String	MOTIFS_PARTNER_TAG
protected static java.lang.String	MOTIFS_STRING_TAG

Constructor Summary

Constructors

Constructor and Description
MotifsReader()

Method Summary

Methods

Modifier and Type	Method and Description
java.util.ArrayList<MotifData>	getMotifsDB()
int	loadFromFile(java.io.File file, VioletApp app)
int	loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
int	readElements(VioletApp app, java.io.Reader reader)

Methods inherited from class java.lang.Object

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

Field Detail

MOTIFS_STRING_TAG

protected static final java.lang.String MOTIFS_STRING_TAG

See Also:

Constant Field Values

MOTIFS_CENTERPOS_TAG

protected static final java.lang.String MOTIFS_CENTERPOS_TAG

See Also:

Constant Field Values

MOTIFS_FRACTION_TAG

protected static final java.lang.String MOTIFS_FRACTION_TAG

See Also:

Constant Field Values

MOTIFS_NDETECTED_TAG

protected static final java.lang.String MOTIFS_NDETECTED_TAG

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Constant Field Values

MOTIFS_NGENOME_TAG

protected static final java.lang.String MOTIFS_NGENOME_TAG

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Constant Field Values

MOTIFS_GROUP_TAG

protected static final java.lang.String MOTIFS_GROUP_TAG

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Constant Field Values

MOTIFS_PARTNER_TAG

protected static final java.lang.String MOTIFS_PARTNER_TAG

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Constant Field Values

MOTIFS_MEANSCORE_TAG

protected static final java.lang.String MOTIFS_MEANSCORE_TAG

See Also:

Constant Field Values

MOTIFS_MEANIPDRATIO_TAG

protected static final java.lang.String MOTIFS_MEANIPDRATIO_TAG

See Also:

Constant Field Values

MOTIFS_MEANCOVERAGE_TAG

protected static final java.lang.String MOTIFS_MEANCOVERAGE_TAG

See Also:

Constant Field Values

MOTIFS_OBJSCORE_TAG

protected static final java.lang.String MOTIFS_OBJSCORE_TAG

See Also:

Constant Field Values

fileName

protected java.lang.String fileName

motifs_db

protected java.util.ArrayList<MotifData> motifs_db

Constructor Detail

MotifsReader

public MotifsReader()

Method Detail

loadFromFile

public int loadFromFile(java.io.File file,
               VioletApp app)
                 throws java.io.IOException,
                        FileFormatException

Parameters:

file -

app -

Throws:

java.io.IOException

FileFormatException

loadFromReader

public int loadFromReader(java.io.Reader reader,
                 java.lang.String file_name,
                 VioletApp app)
                   throws java.io.IOException,
                          FileFormatException

Throws:

java.io.IOException

FileFormatException

readElements

public int readElements(VioletApp app,
               java.io.Reader reader)
                 throws java.io.IOException,
                        FileFormatException

Throws:

java.io.IOException

FileFormatException

getMotifsDB

public java.util.ArrayList<MotifData> getMotifsDB()