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java.lang.Objectdasp.algorithms.ClustalAlign
public class ClustalAlign
Constructor Summary | |
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ClustalAlign()
Will need to store the alignment or files the alignemnt is saved to? |
Method Summary | |
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double |
align(List<String> sequences)
align actually performs the alignment. |
List<String> |
getAlignment()
Return the alignment itself with each sequence as a single string and with dashes inserted to account for insertions. |
double |
getASPscore(String alnFile,
int numSequences)
Return the ASP score as defined in Cammer et al for this alignment. |
String |
getHTMLAlignment(List<String> alignment)
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. |
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 ClustalAlign()
Method Detail |
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public double align(List<String> sequences)
align
in interface Align
model
- the data model we're using
public double getASPscore(String alnFile, int numSequences)
getASPscore
in interface Align
public double getIdentity()
getIdentity
in interface Align
public List<String> getAlignment()
getAlignment
in interface Align
public String getHTMLAlignment(List<String> alignment)
getHTMLAlignment
in interface Align
alignment
- the string alignment
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