|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectdasp.model.Alignment
public class Alignment
Field Summary | |
---|---|
protected List<String> |
alignment
|
protected Align |
method
|
protected Map<String,String> |
nameMap
|
protected List<String> |
seqs
|
Constructor Summary | |
---|---|
Alignment()
|
|
Alignment(List<String> sequences,
Align alignmentMethod)
|
Method Summary | |
---|---|
void |
addSequence(String seq)
addSequence can be used to add an addtional sequence to the alignment. |
void |
addSequences(List<String> seqList)
addSequences can be used to add a list of addtional sequences to the alignment. |
void |
deleteSequence(String seq)
deleteSequence can be used to remove a sequence from the alignment. |
void |
doAlign()
|
List<String> |
getAlignment()
Return the alignment itself as a list of strings with dashes inserted to account for insertions. |
String |
getAlignmentAsString()
Return the alignment itself as a string with newlines between sequences and dashes inserted to account for insertions. |
String |
getAlignmentByIndex(int index)
Return the alignment string for just one of the proteins in the alignment. |
String |
getAlignmentByName(String name)
Return the alignment string for just one of the proteins in the alignment. |
String |
getHTMLAlignment()
Return the alignment itself as an HTML-formatted string to account for insertions. |
double |
getIdentity()
Return the % identity for all of the sequences in the alignment. |
double |
getScore()
Return the alignment score that results from the alignment. |
List<String> |
getSequences()
Return all of the sequences as FASTA-formatted strings |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
protected Align method
protected List<String> seqs
protected Map<String,String> nameMap
protected List<String> alignment
Constructor Detail |
---|
public Alignment()
public Alignment(List<String> sequences, Align alignmentMethod)
Method Detail |
---|
public void doAlign()
public void addSequence(String seq)
seq
- the sequence to add as a FASTA-formatted stringpublic void deleteSequence(String seq)
seq
- the sequence to remove as a FASTA-formatted stringpublic void addSequences(List<String> seqList)
seqList
- the sequences to add as a list of FASTA-formatted stringspublic List<String> getSequences()
public double getIdentity()
public double getScore()
public String getAlignmentAsString()
public List<String> getAlignment()
public String getAlignmentByName(String name)
name
- the name of this protein (usually from the fasta file)
public String getAlignmentByIndex(int index)
index
- the index of the desired sequence
public String getHTMLAlignment()
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |