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java.lang.Objectedu.upenn.gloDB.AbstractFeature
public abstract class AbstractFeature
AbstractFeature.
Field Summary | |
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protected java.lang.String |
attributes
This is similar to "qualifiers" in GenBank. |
protected java.lang.String |
source
The contig that underlies the positions. |
Constructor Summary | |
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AbstractFeature(Sequence source)
Set the source when the Feature is created. |
Method Summary | |
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void |
addAttribute(java.lang.String value)
Add an attribute (key/value pair). |
void |
addAttribute(java.lang.String key,
java.lang.String value)
Add an attribute. |
boolean |
containsAttribute(java.lang.String key)
Returns true if attribute 'key' exists. |
void |
delAttribute(java.lang.String key)
Remove an attribute. |
java.lang.String |
getAttribute(java.lang.String key)
Get value for attribute 'key'. |
java.lang.String |
getAttributes()
Get the attributes. |
java.util.HashMap |
getAttributesMap()
Get the attributes as HashMap. |
Sequence |
getSource()
Returns the underlying Sequence object. |
java.lang.String |
getSourceID()
Returns the underlying Sequence object's ID. |
int |
getType()
Returns Feature type (see GloDBUtils) |
void |
setAttributes(java.util.HashMap attribMap)
Set the attributes using a HashMap. |
void |
setAttributes(java.lang.String attributes)
Set the attributes. |
java.lang.String |
toString()
Returns description and Feature information. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface edu.upenn.gloDB.Feature |
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compareTo, contains, contains, equals, flip, getData, getDataFormatted, getMax, getMin, getStart, getStop, length, overlap, overlaps, toStringFull, toStringMin |
Field Detail |
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protected java.lang.String source
protected java.lang.String attributes
Constructor Detail |
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public AbstractFeature(Sequence source)
Method Detail |
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public int getType()
public void setAttributes(java.lang.String attributes)
setAttributes
in interface Feature
attributes
- a String of Feature attributespublic void setAttributes(java.util.HashMap attribMap)
setAttributes
in interface Feature
attribMap
- a HashMap of Feature attributespublic java.lang.String getAttributes()
getAttributes
in interface Feature
public Sequence getSource()
getSource
in interface Feature
public java.lang.String getSourceID()
getSourceID
in interface Feature
public void addAttribute(java.lang.String key, java.lang.String value)
public void addAttribute(java.lang.String value)
public void delAttribute(java.lang.String key)
public boolean containsAttribute(java.lang.String key)
containsAttribute
in interface Feature
public java.util.HashMap getAttributesMap()
getAttributesMap
in interface Feature
public java.lang.String getAttribute(java.lang.String key)
getAttribute
in interface Feature
public java.lang.String toString()
toString
in interface Feature
toString
in class java.lang.Object
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