Package org.snpeff.stats
Class CountByType
- java.lang.Object
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- org.snpeff.stats.CountByType
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- All Implemented Interfaces:
java.io.Serializable
public class CountByType extends java.lang.Object implements java.io.Serializable
Counters indexed by 'type' (type is a generic string that can mean anything)- Author:
- pcingola
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
TOTAL_TYPE
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Constructor Summary
Constructors Constructor Description CountByType()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description long
addScore(java.lang.String type, double score)
Add score for a typeboolean
contains(java.lang.String key)
long
get(java.lang.String type)
How many counts of this type?java.lang.String
getColorHtml(java.lang.String type)
Background color used for table (heatmap)long
getCount(java.lang.String type)
Count for this typedouble
getScore(java.lang.String type)
Score for this typelong
getTotalCount()
java.util.List<java.lang.String>
getTypeList()
List all types (alphabetically sorted) We need it as a getter for summary page (freemarker)boolean
hasCount(java.lang.String type)
boolean
hasData()
boolean
hasScore(java.lang.String type)
long
inc(java.lang.String type)
long
inc(java.lang.String type, int increment)
Increment counter for a given typeboolean
isEmpty()
Is this emptyjava.util.Set<java.lang.String>
keySet()
java.util.List<java.lang.String>
keysRanked(boolean reverse)
List all types (sorted by count)java.util.List<java.lang.String>
keysSorted()
List all types (alphabetically sorted)long
max()
Maximum countlong
min()
Minimum countdouble
percent(java.lang.String type)
Percentage by typejava.util.Map<java.lang.String,java.lang.Integer>
ranks(boolean reverse)
A map: key -> rank(counts)void
remove(java.lang.String type)
Remove this entry typevoid
setScore(java.lang.String type, double score)
long
sum()
Sum all counts.java.lang.String
toString()
java.lang.String
toString(boolean showScores)
java.lang.String
toString(java.lang.String type)
java.lang.String
toStringLine()
java.lang.String
toStringSort()
java.lang.String
toStringTop(int n)
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Field Detail
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TOTAL_TYPE
public static final java.lang.String TOTAL_TYPE
- See Also:
- Constant Field Values
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Method Detail
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addScore
public long addScore(java.lang.String type, double score)
Add score for a type
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contains
public boolean contains(java.lang.String key)
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get
public long get(java.lang.String type)
How many counts of this type?
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getColorHtml
public java.lang.String getColorHtml(java.lang.String type)
Background color used for table (heatmap)- Returns:
- An html coded color
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getCount
public long getCount(java.lang.String type)
Count for this type
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getScore
public double getScore(java.lang.String type)
Score for this type
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getTotalCount
public long getTotalCount()
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getTypeList
public java.util.List<java.lang.String> getTypeList()
List all types (alphabetically sorted) We need it as a getter for summary page (freemarker)
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hasCount
public boolean hasCount(java.lang.String type)
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hasData
public boolean hasData()
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hasScore
public boolean hasScore(java.lang.String type)
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inc
public long inc(java.lang.String type)
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inc
public long inc(java.lang.String type, int increment)
Increment counter for a given type
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isEmpty
public boolean isEmpty()
Is this empty
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keySet
public java.util.Set<java.lang.String> keySet()
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keysRanked
public java.util.List<java.lang.String> keysRanked(boolean reverse)
List all types (sorted by count)
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keysSorted
public java.util.List<java.lang.String> keysSorted()
List all types (alphabetically sorted)
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max
public long max()
Maximum count
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min
public long min()
Minimum count
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percent
public double percent(java.lang.String type)
Percentage by type
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ranks
public java.util.Map<java.lang.String,java.lang.Integer> ranks(boolean reverse)
A map: key -> rank(counts)
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remove
public void remove(java.lang.String type)
Remove this entry type
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setScore
public void setScore(java.lang.String type, double score)
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sum
public long sum()
Sum all counts.
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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toString
public java.lang.String toString(boolean showScores)
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toString
public java.lang.String toString(java.lang.String type)
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toStringLine
public java.lang.String toStringLine()
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toStringSort
public java.lang.String toStringSort()
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toStringTop
public java.lang.String toStringTop(int n)
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