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java.lang.Objectmodel.SequenceImpl
public class SequenceImpl
Implementation of the Sequence Interface.
Constructor Summary | |
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SequenceImpl(SequenceImpl seq)
Copy Constructor |
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SequenceImpl(java.lang.String name,
java.lang.String sequence)
Constructor for the sequence implementation. |
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SequenceImpl(java.lang.String name,
java.lang.String sequence,
int start,
int end)
Constructor for the sequence implementation, where sequence is given as string |
Method Summary | |
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int |
findPosition(int i)
Finds the i'th position in the sequence, skipping the gaps. |
java.awt.Color |
getClusterColor()
Returns the cluster sequence color. |
int |
getEnd()
Returns the end position of the sequence. |
int |
getLength()
Returns the sequence length. |
char |
getLetterAt(int i)
Returns the letter (amino acid) at a certain position. |
java.lang.String |
getName()
Returns the sequence name. |
char[] |
getSequence()
Returns the sequence as char array. |
char[] |
getSequence(int start,
int end)
Returns the sequence (for start and end position) as char array. |
java.lang.String |
getSequenceAsString()
Returns the sequence as a string. |
int |
getStart()
Returns the sequence start position of the sequence. |
boolean |
isClusterEnd()
is cluster end boolean. |
boolean |
isClusterStart()
Is cluster start boolean. |
void |
setClusterColor(java.awt.Color clusterColor)
Sets the cluster sequence color. |
void |
setClusterEnd(boolean clusterEnd)
Set the cluster end boolean. |
void |
setClusterStart(boolean clusterStart)
Set the cluster start boolean. |
void |
setEnd(int end)
Sets the end position of the sequence. |
void |
setName(java.lang.String name)
Sets the sequence name. |
void |
setSequence(char[] sequence)
Sets the sequence as char array. |
void |
setSequence(java.lang.String sequence)
Sets the sequence as string. |
void |
setStart(int start)
Sets the start position of the sequence. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SequenceImpl(SequenceImpl seq)
seq
- public SequenceImpl(java.lang.String name, java.lang.String sequence, int start, int end)
name
- sequence
- start
- end
- public SequenceImpl(java.lang.String name, java.lang.String sequence)
name
- sequence
- Method Detail |
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public char getLetterAt(int i)
getLetterAt
in interface Sequence
public int getStart()
getStart
in interface Sequence
public int findPosition(int i)
i
-
public void setStart(int start)
setStart
in interface Sequence
public int getEnd()
getEnd
in interface Sequence
public void setEnd(int end)
setEnd
in interface Sequence
public int getLength()
getLength
in interface Sequence
public java.lang.String getName()
getName
in interface Sequence
public void setName(java.lang.String name)
setName
in interface Sequence
public char[] getSequence(int start, int end)
getSequence
in interface Sequence
public void setSequence(java.lang.String sequence)
setSequence
in interface Sequence
public void setSequence(char[] sequence)
sequence
- public java.lang.String getSequenceAsString()
getSequenceAsString
in interface Sequence
public char[] getSequence()
getSequence
in interface Sequence
public java.awt.Color getClusterColor()
public void setClusterColor(java.awt.Color clusterColor)
clusterColor
- public boolean isClusterStart()
public void setClusterStart(boolean clusterStart)
clusterStart
- boolean.public boolean isClusterEnd()
public void setClusterEnd(boolean clusterEnd)
clusterEnd
- Boolean
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