Class AAindexStreamReader
java.lang.Object
org.biojava.bio.proteomics.aaindex.AAindexStreamReader
- All Implemented Interfaces:
SymbolPropertyTableIterator
Iterator over
AAindex
objects that
are stored in a stream in the AAindex1 file format. The format
of such an Amino Acid Index Database file is described in the
AAindex manual
. The nextTable()
method returns objects of type
AAindex
. See this class also for
further informations. To hold an AAindex1 file in memory for random access
use the SimpleSymbolPropertyTableDB
class:
SimpleSymbolPropertyTableDB db = new SimpleSymbolPropertyTableDB(
new AAindexStreamReader(new FileReader("aaindex1")));
AAindex hydrophobicity = (AAindex) db.table("CIDH920105");
SymbolList symbols = ProteinTools.createProtein(
"ARNDCEQGHILKMFPSTWYV");
double hp = 0.0;
for (int i = 1; i invalid input: '<'= symbols.length(); i++) {
hp += hydrophobicity.getDoubleValue(symbols.symbolAt(i));
}
System.out.println("Average hydrophobicity: " + Double.toString(
hp / symbols.length()));
References:
Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000).
Tomii, K. and Kanehisa, M.; Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996).
Nakai, K., Kidera, A., and Kanehisa, M.; Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng. 2, 93-100 (1988)
- Version:
- $Revision$
- Author:
- Martin Szugat
-
Constructor Summary
ConstructorsConstructorDescriptionAAindexStreamReader
(BufferedReader reader) Initializes the iterator.AAindexStreamReader
(Reader reader) Initializes the iterator. -
Method Summary
Modifier and TypeMethodDescriptionboolean
eof()
Checks if the end of the file or stream is reached.boolean
hasNext()
Checks if there is a furtherSymbolPropertyTable
object.Returns the nextSymbolPropertyTable
object.
-
Constructor Details
-
AAindexStreamReader
Initializes the iterator.- Parameters:
reader
- reader over a stream in the AAindex file format.- Throws:
IOException
- if the stream could not be read.NullPointerException
- ifreader
isnull
.
-
AAindexStreamReader
Initializes the iterator.- Parameters:
reader
- buffered reader over a stream in the AAindex file format.- Throws:
IOException
- if the stream could not be read.NullPointerException
- ifreader
isnull
.
-
-
Method Details
-
eof
Checks if the end of the file or stream is reached.- Returns:
true
if the end of the file is reached,false
otherwise.
-
hasNext
Checks if there is a furtherSymbolPropertyTable
object.- Specified by:
hasNext
in interfaceSymbolPropertyTableIterator
- Returns:
true
if a call to theSymbolPropertyTableIterator.nextTable()
method is valid,false
otherwise.
-
nextTable
Returns the nextSymbolPropertyTable
object.- Specified by:
nextTable
in interfaceSymbolPropertyTableIterator
- Returns:
- a symbol property table
- Throws:
BioException
- if the next symbol property table could not be retrieved.
-