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java.lang.Objectfr.umlv.gramofone.graphs.MyPattern
public class MyPattern
Manage a motif
| Field Summary | |
|---|---|
static java.lang.String |
NONAMEPATTERN
|
| Constructor Summary | |
|---|---|
MyPattern()
|
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MyPattern(java.util.List<java.lang.String> proteins)
Build a pattern from a list of proteins (the name of the pattern wil be NONAMEPATTERN) |
|
MyPattern(MyPattern pattern)
Build a motif from a motif (copy) |
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MyPattern(java.lang.String patternFastaFile)
Initialize a pattern from a FASTA file ! |
|
MyPattern(java.lang.String name,
java.util.List<java.lang.String> proteins)
Build a pattern from a list of proteins with a given name for this pattern |
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| Method Summary | |
|---|---|
int |
getColor(java.lang.String id)
Return the color associated to the protein id in the motif |
int |
getColorfulSize()
Return the number of different colors in the motif |
java.util.Set<java.lang.Integer> |
getColors()
Return a set with the different colors used in the motif |
java.lang.String |
getName()
return the name of the motif |
int |
getOccurence(int id)
Return the occurences of the protein id in the motif |
java.util.Set<java.lang.String> |
getPattern()
Get all the proteins in the pattern |
java.lang.String |
getPatternText()
Return a String representing the pattern |
java.util.HashSet<java.lang.String> |
getProteinsFromColor(int color)
Get the protein who got this color |
int |
getTotalMotifSize()
return the size of the motif (with repetitions) |
protected static java.util.List<java.lang.String> |
parseFastaFile(java.lang.String patternFastaFile)
Return a list of proteins in a Fasta file |
protected void |
removeProteins(java.util.Set<java.lang.String> proteins)
Remove a set of proteins in the motif (used in apriori deletions) |
protected void |
toMultiSet(Homologies homologies)
Convert the original pattern set as a multiset : proteins in the pattern which are homologs now use the same color |
| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
|---|
public static java.lang.String NONAMEPATTERN
| Constructor Detail |
|---|
public MyPattern(MyPattern pattern)
pattern - public MyPattern()
public MyPattern(java.util.List<java.lang.String> proteins)
proteins -
public MyPattern(java.lang.String name,
java.util.List<java.lang.String> proteins)
name - proteins - public MyPattern(java.lang.String patternFastaFile)
patternFastaFile - | Method Detail |
|---|
protected static java.util.List<java.lang.String> parseFastaFile(java.lang.String patternFastaFile)
patternFastaFile -
public int getTotalMotifSize()
public int getColorfulSize()
public java.lang.String getName()
public java.util.Set<java.lang.String> getPattern()
public java.lang.String getPatternText()
public int getColor(java.lang.String id)
id -
public java.util.HashSet<java.lang.String> getProteinsFromColor(int color)
color - the color of the protein
public int getOccurence(int id)
public java.util.Set<java.lang.Integer> getColors()
protected void removeProteins(java.util.Set<java.lang.String> proteins)
proteins - protected void toMultiSet(Homologies homologies)
homologies - to know homologs
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