From a953c1c155ccad106ef9f011861a925bb63de905 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 8 Aug 2008 15:49:39 +0000
Subject: [PATCH] optimise reading in data
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8514 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/plot/UserDataAlgorithm.java | 35 ++++++++++---------
1 file changed, 19 insertions(+), 16 deletions(-)
diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
index 6356ad91d..bb596c477 100644
--- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java,v 1.4 2008-05-15 09:57:31 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java,v 1.5 2008-08-08 15:49:39 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -31,6 +31,7 @@ import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.ReadFormatException;
import java.io.*;
+import java.util.regex.Pattern;
/**
* Objects of this class have one useful method - getValues (), which takes a
@@ -39,7 +40,7 @@ import java.io.*;
* set in the constructor.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: UserDataAlgorithm.java,v 1.4 2008-05-15 09:57:31 tjc Exp $
+ * @version $Id: UserDataAlgorithm.java,v 1.5 2008-08-08 15:49:39 tjc Exp $
**/
public class UserDataAlgorithm extends BaseAlgorithm
@@ -52,12 +53,12 @@ public class UserDataAlgorithm extends BaseAlgorithm
/**
* The maximum value in the data array.
**/
- private float data_max = -9999999;
+ private float data_max = Float.MAX_VALUE;
/**
* The minimum value in the data array.
**/
- private float data_min = 9999999;
+ private float data_min = Float.MAX_VALUE;
/**
* The average calculated by readData ().
@@ -98,6 +99,7 @@ public class UserDataAlgorithm extends BaseAlgorithm
data = new float [strand.getSequenceLength ()][tokens.size ()];
readData (pushback_reader);
+ pushback_reader.close();
}
/**
@@ -108,24 +110,25 @@ public class UserDataAlgorithm extends BaseAlgorithm
{
String line = null;
int count = 0;
-
+ final int seqLength = getStrand ().getSequenceLength ();
+ final Pattern patt = Pattern.compile("\\s+");
+
while ((line = pushback_reader.readLine ()) != null)
{
-
- if (count >= getStrand ().getSequenceLength ())
+ if (count >= seqLength)
throw new ReadFormatException ("too many values in input file");
- final StringVector tokens = StringVector.getStrings (line, " ");
- //final int read_base;
+ //final StringVector tokens = StringVector.getStrings (line, " ");
- if (tokens.size () == data[0].length)
+ String tokens[] = patt.split(line); //line.split("\\s+");
+ if (tokens.length == data[0].length)
{
- for (int i = 0 ; i < tokens.size () ; ++i)
+ for (int i = 0 ; i < tokens.length ; ++i)
{
try
{
- float value =
- Float.valueOf ((String)tokens.elementAt (i)).floatValue ();
+ float value = Float.parseFloat(tokens[i]);
+ //Float.valueOf ((String)tokens.elementAt (i)).floatValue ();
if(logTransform)
value = (float) Math.log(value+1);
@@ -143,18 +146,18 @@ public class UserDataAlgorithm extends BaseAlgorithm
catch (NumberFormatException e)
{
throw new ReadFormatException ("cannot understand this number: " +
- tokens.elementAt (i) + " - " +
+ tokens[i] + " - " +
e.getMessage ());
}
}
}
else
- throw new ReadFormatException ("line has the wrong number of fields");
+ throw new ReadFormatException ("line has the wrong number of fields:\n"+line);
++count;
}
- average_value /= data[0].length * getStrand ().getSequenceLength ();
+ average_value /= data[0].length * seqLength;
}
/**
--
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