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java.lang.Objectedu.upenn.gloDB.io.GFFTrack
public class GFFTrack
Import/Export Track data from/to GFF files.
File format (each column is separated by a tab character '\t'):
seqname | source | feature | start | end | score | strand | frame | [attributes] |
SEQ1 | EMBL | splice5 | 172 | 173 | . | + | . | |
SEQ1 | netgene | splice5 | 172 | 173 | 0.94 | + | . | |
SEQ1 | genie | sp5-20 | 163 | 182 | 2.3 | + | . | |
SEQ2 | grail | ATG | 17 | 19 | 2.1 | - | 0 | |
seq1 | BLASTX | similarity | 101 | 235 | 87.1 | + | 0 | Target "HBA_HUMAN" 11 55 ; E_value 0.0003 |
dJ102G20 | GD_mRNA | coding_exon | 7105 | 7201 | . | - | 2 | Sequence "dJ102G20.C1.1" |
X | gadfly | exon | 3118 | 3280 | . | - | . | genegrp=CG3038; transgrp=CG3038-RB; name=CG3038:1 |
X | gadfly | exon | 2850 | 3016 | . | - | . | genegrp=CG3038; transgrp=CG3038-RB; name=CG3038:2 |
Nested Class Summary | |
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private class |
GFFTrack.GFFFilter
GFF specific FileFilter. |
Field Summary | |
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private java.lang.String |
DESC
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private java.lang.String[] |
EXT
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private javax.swing.filechooser.FileFilter |
fileFilter
|
private int |
ID
|
Constructor Summary | |
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GFFTrack()
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Method Summary | |
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java.lang.String |
format(java.lang.String id)
Format all Features into a GFF like string. |
java.lang.String |
getDesc()
Get a description of the file type. |
java.lang.String[] |
getExt()
Get an array of file extensions. |
javax.swing.filechooser.FileFilter |
getFileFilter()
Get a FileFilter for use in the GUI. |
int |
getID()
Get the file ID. |
Track |
load(java.lang.String filename)
Load all Features in the GFF file into a single Track and return the resulting Track object. |
Track |
load(java.lang.String filename,
java.lang.String sourceID)
Load all Features in the GFF file into a single Track and return the resulting Track object. |
void |
save(java.lang.String id)
Save the Track to a file based on it's ID. |
void |
save(java.lang.String id,
java.lang.String filename,
boolean overwrite)
Save all Features in a GFF file. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private final int ID
private final java.lang.String DESC
private final java.lang.String[] EXT
private final javax.swing.filechooser.FileFilter fileFilter
Constructor Detail |
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public GFFTrack()
Method Detail |
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public int getID()
DataFile
getID
in interface DataFile
public java.lang.String getDesc()
DataFile
getDesc
in interface DataFile
public java.lang.String[] getExt()
DataFile
getExt
in interface DataFile
public javax.swing.filechooser.FileFilter getFileFilter()
DataFile
getFileFilter
in interface DataFile
public Track load(java.lang.String filename)
load
in interface TrackFile
public Track load(java.lang.String filename, java.lang.String sourceID)
load
in interface TrackFile
public void save(java.lang.String id)
save
in interface TrackFile
public void save(java.lang.String id, java.lang.String filename, boolean overwrite)
save
in interface TrackFile
public java.lang.String format(java.lang.String id)
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