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BioinformaticDataCompression
QcmpCompressionLibrary
Commits
e4292e00
Commit
e4292e00
authored
5 years ago
by
Vojtech Moravec
Browse files
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Report Huffman symbol frequencies in verbose mode on decompression.
parent
3804d8d7
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Changes
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2 changed files
src/main/java/azgracompress/compression/CompressorDecompressorBase.java
+16
-0
16 additions, 0 deletions
...azgracompress/compression/CompressorDecompressorBase.java
src/main/java/azgracompress/huffman/Huffman.java
+29
-9
29 additions, 9 deletions
src/main/java/azgracompress/huffman/Huffman.java
with
45 additions
and
9 deletions
src/main/java/azgracompress/compression/CompressorDecompressorBase.java
+
16
−
0
View file @
e4292e00
...
@@ -6,6 +6,8 @@ import azgracompress.huffman.Huffman;
...
@@ -6,6 +6,8 @@ import azgracompress.huffman.Huffman;
import
azgracompress.io.OutBitStream
;
import
azgracompress.io.OutBitStream
;
import
java.io.DataOutputStream
;
import
java.io.DataOutputStream
;
import
java.util.Iterator
;
import
java.util.Map
;
public
abstract
class
CompressorDecompressorBase
{
public
abstract
class
CompressorDecompressorBase
{
public
static
final
int
LONG_BYTES
=
8
;
public
static
final
int
LONG_BYTES
=
8
;
...
@@ -30,6 +32,20 @@ public abstract class CompressorDecompressorBase {
...
@@ -30,6 +32,20 @@ public abstract class CompressorDecompressorBase {
protected
Huffman
createHuffmanCoder
(
final
int
[]
symbols
,
final
long
[]
frequencies
)
{
protected
Huffman
createHuffmanCoder
(
final
int
[]
symbols
,
final
long
[]
frequencies
)
{
Huffman
huffman
=
new
Huffman
(
symbols
,
frequencies
);
Huffman
huffman
=
new
Huffman
(
symbols
,
frequencies
);
huffman
.
buildHuffmanTree
();
huffman
.
buildHuffmanTree
();
if
(
options
.
isVerbose
())
{
StringBuilder
sb
=
new
StringBuilder
();
sb
.
append
(
"Huffman symbols and their probabilities:\n"
);
Iterator
<
Map
.
Entry
<
Integer
,
Double
>>
it
=
huffman
.
getSymbolProbabilityMap
().
entrySet
().
iterator
();
while
(
it
.
hasNext
())
{
final
Map
.
Entry
<
Integer
,
Double
>
pair
=
(
Map
.
Entry
<
Integer
,
Double
>)
it
.
next
();
sb
.
append
(
String
.
format
(
"%d: %.10f\n"
,
pair
.
getKey
(),
pair
.
getValue
()));
}
System
.
out
.
println
(
sb
.
toString
());
}
return
huffman
;
return
huffman
;
}
}
...
...
This diff is collapsed.
Click to expand it.
src/main/java/azgracompress/huffman/Huffman.java
+
29
−
9
View file @
e4292e00
package
azgracompress.huffman
;
package
azgracompress.huffman
;
import
java.util.ArrayList
;
import
java.util.*
;
import
java.util.HashMap
;
import
java.util.PriorityQueue
;
public
class
Huffman
{
public
class
Huffman
{
HuffmanNode
root
=
null
;
private
HuffmanNode
root
=
null
;
HashMap
<
Integer
,
boolean
[]>
symbolCodes
;
private
HashMap
<
Integer
,
boolean
[]>
symbolCodes
;
final
int
[]
symbols
;
private
HashMap
<
Integer
,
Double
>
symbolProbabilityMap
;
final
long
[]
symbolFrequencies
;
private
final
int
[]
symbols
;
private
final
long
[]
symbolFrequencies
;
public
Huffman
(
int
[]
symbols
,
long
[]
symbolFrequencies
)
{
public
Huffman
(
int
[]
symbols
,
long
[]
symbolFrequencies
)
{
assert
(
symbols
.
length
==
symbolFrequencies
.
length
)
:
"Array lengths mismatch"
;
assert
(
symbols
.
length
==
symbolFrequencies
.
length
)
:
"Array lengths mismatch"
;
...
@@ -29,8 +28,6 @@ public class Huffman {
...
@@ -29,8 +28,6 @@ public class Huffman {
parentB
.
getProbability
()));
parentB
.
getProbability
()));
assert
(
parentA
.
getProbability
()
<=
parentB
.
getProbability
());
assert
(
parentA
.
getProbability
()
<=
parentB
.
getProbability
());
}
}
assert
(
parentA
!=
null
&&
parentB
!=
null
);
parentA
.
setBit
(
1
);
parentA
.
setBit
(
1
);
parentB
.
setBit
(
0
);
parentB
.
setBit
(
0
);
...
@@ -81,6 +78,7 @@ public class Huffman {
...
@@ -81,6 +78,7 @@ public class Huffman {
}
}
private
PriorityQueue
<
HuffmanNode
>
buildPriorityQueue
()
{
private
PriorityQueue
<
HuffmanNode
>
buildPriorityQueue
()
{
symbolProbabilityMap
=
new
HashMap
<>(
symbols
.
length
);
double
totalFrequency
=
0.0
;
double
totalFrequency
=
0.0
;
for
(
final
long
symbolFrequency
:
symbolFrequencies
)
{
for
(
final
long
symbolFrequency
:
symbolFrequencies
)
{
totalFrequency
+=
symbolFrequency
;
totalFrequency
+=
symbolFrequency
;
...
@@ -90,6 +88,7 @@ public class Huffman {
...
@@ -90,6 +88,7 @@ public class Huffman {
for
(
int
sIndex
=
0
;
sIndex
<
symbols
.
length
;
sIndex
++)
{
for
(
int
sIndex
=
0
;
sIndex
<
symbols
.
length
;
sIndex
++)
{
final
double
symbolProbability
=
(
double
)
symbolFrequencies
[
sIndex
]
/
totalFrequency
;
final
double
symbolProbability
=
(
double
)
symbolFrequencies
[
sIndex
]
/
totalFrequency
;
symbolProbabilityMap
.
put
(
symbols
[
sIndex
],
symbolProbability
);
queue
.
add
(
new
HuffmanNode
(
symbols
[
sIndex
],
symbolProbability
,
symbolFrequencies
[
sIndex
]));
queue
.
add
(
new
HuffmanNode
(
symbols
[
sIndex
],
symbolProbability
,
symbolFrequencies
[
sIndex
]));
}
}
...
@@ -104,4 +103,25 @@ public class Huffman {
...
@@ -104,4 +103,25 @@ public class Huffman {
public
HuffmanNode
getRoot
()
{
public
HuffmanNode
getRoot
()
{
return
root
;
return
root
;
}
}
public
HashMap
<
Integer
,
Double
>
getSymbolProbabilityMap
()
{
return
createSortedHashMap
(
symbolProbabilityMap
);
}
private
HashMap
<
Integer
,
Double
>
createSortedHashMap
(
HashMap
<
Integer
,
Double
>
map
)
{
List
<
Map
.
Entry
<
Integer
,
Double
>>
list
=
new
LinkedList
<
Map
.
Entry
<
Integer
,
Double
>>(
map
.
entrySet
());
//Custom Comparator
list
.
sort
(
new
Comparator
<
Map
.
Entry
<
Integer
,
Double
>>()
{
@Override
public
int
compare
(
Map
.
Entry
<
Integer
,
Double
>
t0
,
Map
.
Entry
<
Integer
,
Double
>
t1
)
{
return
-(
t0
.
getValue
().
compareTo
(
t1
.
getValue
()));
}
});
//copying the sorted list in HashMap to preserve the iteration order
HashMap
<
Integer
,
Double
>
sortedHashMap
=
new
LinkedHashMap
<
Integer
,
Double
>();
for
(
Map
.
Entry
<
Integer
,
Double
>
entry
:
list
)
{
sortedHashMap
.
put
(
entry
.
getKey
(),
entry
.
getValue
());
}
return
sortedHashMap
;
}
}
}
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