git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Set startRes 0 for switch to wrap view
[jalview.git]
/
src
/
jalview
/
datamodel
/
BinarySequence.java
diff --git
a/src/jalview/datamodel/BinarySequence.java
b/src/jalview/datamodel/BinarySequence.java
index
7d03404
..
49e3543
100755
(executable)
--- a/
src/jalview/datamodel/BinarySequence.java
+++ b/
src/jalview/datamodel/BinarySequence.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
@@
-49,7
+49,7
@@
public class BinarySequence extends Sequence
public void encode()
\r
{
\r
// Set all matrix to 0
\r
public void encode()
\r
{
\r
// Set all matrix to 0
\r
- dbinary = new double[getSequence().length() * 21];
\r
+ dbinary = new double[getSequence().length * 21];
\r
\r
int nores = 21;
\r
\r
\r
int nores = 21;
\r
\r
@@
-58,15
+58,13
@@
public class BinarySequence extends Sequence
dbinary[i] = 0.0;
\r
}
\r
\r
dbinary[i] = 0.0;
\r
}
\r
\r
- for (int i = 0; i < getSequence().length(); i++)
\r
+ for (int i = 0; i < getSequence().length; i++)
\r
{
\r
int aanum = 20;
\r
\r
try
\r
{
\r
{
\r
int aanum = 20;
\r
\r
try
\r
{
\r
- aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
\r
- .substring(i,
\r
- i + 1))).intValue();
\r
+ aanum = ResidueProperties.aaIndex[getCharAt(i)];
\r
}
\r
catch (NullPointerException e)
\r
{
\r
}
\r
catch (NullPointerException e)
\r
{
\r
@@
-88,22
+86,20
@@
public class BinarySequence extends Sequence
public void blosumEncode()
\r
{
\r
// Set all matrix to 0
\r
public void blosumEncode()
\r
{
\r
// Set all matrix to 0
\r
- dbinary = new double[getSequence().length() * 21];
\r
+ dbinary = new double[getSequence().length * 21];
\r
\r
int nores = 21;
\r
\r
//for (int i = 0; i < dbinary.length; i++) {
\r
// dbinary[i] = 0.0;
\r
//}
\r
\r
int nores = 21;
\r
\r
//for (int i = 0; i < dbinary.length; i++) {
\r
// dbinary[i] = 0.0;
\r
//}
\r
- for (int i = 0; i < getSequence().length(); i++)
\r
+ for (int i = 0; i < getSequence().length; i++)
\r
{
\r
int aanum = 20;
\r
\r
try
\r
{
\r
{
\r
int aanum = 20;
\r
\r
try
\r
{
\r
- aanum = ((Integer) ResidueProperties.getAAHash().get(getSequence()
\r
- .substring(i,
\r
- i + 1))).intValue();
\r
+ aanum = ResidueProperties.aaIndex[getCharAt(i)];
\r
}
\r
catch (NullPointerException e)
\r
{
\r
}
\r
catch (NullPointerException e)
\r
{
\r