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Commit fc45b931 authored by tjc's avatar tjc
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memory optimise 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3773 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 12e4b60e
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uk/ac/sanger/artemis/io/MSPcrunchStreamFeature.java
+ 97
− 67
View file @ fc45b931
......@@ -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/io/MSPcrunchStreamFeature.java,v 1.3 2005-10-11 14:20:31 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/MSPcrunchStreamFeature.java,v 1.4 2005-10-13 12:21:24 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
......@@ -33,7 +33,7 @@ import java.io.*;
* A StreamFeature that thinks it is a MSPcrunch feature.
*
* @author Kim Rutherford
* @version $Id: MSPcrunchStreamFeature.java,v 1.3 2005-10-11 14:20:31 tjc Exp $
* @version $Id: MSPcrunchStreamFeature.java,v 1.4 2005-10-13 12:21:24 tjc Exp $
**/
public class MSPcrunchStreamFeature
......@@ -110,37 +110,76 @@ public class MSPcrunchStreamFeature
throws ReadFormatException {
super (null);
final StringVector line_bits = StringVector.getStrings (line, " ");
// final StringVector line_bits = StringVector.getStrings (line, " ");
if (line_bits.size () < 7) {
int index = 0;
int lastIndex = 0;
int count = 1;
while( (index = line.indexOf(" ", index)) > -1)
{
count++;
index++;
}
if(count > 8)
count = 9;
else if(count < 7)
throw new ReadFormatException ("invalid MSPcrunch line (not enough " +
"fields): " + line);
final String line_bits[] = new String[count];
count = 0;
index = 0;
while( (index = line.indexOf(" ", index)) > -1 &&
count < line_bits.length-1)
{
line_bits[count] = line.substring(lastIndex, index);
count++;
index++;
lastIndex = index;
}
if(lastIndex < line.length())
{
line_bits[count] = line.substring(lastIndex);
count++;
}
try {
int query_start = Integer.valueOf ((String)line_bits.elementAt (2)).intValue ();
int query_end = Integer.valueOf ((String)line_bits.elementAt (3)).intValue ();
try
{
int query_start = Integer.valueOf (line_bits[2]).intValue ();
int query_end = Integer.valueOf (line_bits[3]).intValue ();
final boolean crunch_x;
final boolean complement_flag;
if (line_bits.elementAt (1).equals ("(+1)")) {
if (line_bits[1].equals ("(+1)"))
{
crunch_x = true;
complement_flag = false;
} else {
if (line_bits.elementAt (1).equals ("(-1)")) {
}
else
{
if (line_bits[1].equals ("(-1)"))
{
crunch_x = true;
complement_flag = true;
} else {
if (((String)line_bits.elementAt (1)).charAt (0) == '.' ||
Character.isDigit (((String)line_bits.elementAt (1)).charAt (0))) {
}
else
{
if (line_bits[1].charAt (0) == '.' ||
Character.isDigit (line_bits[1].charAt (0)))
{
crunch_x = false;
if (query_start > query_end) {
if (query_start > query_end)
complement_flag = true;
} else {
else
complement_flag = false;
}
} else {
else
{
final String message =
"invalid MSPcrunch line - column 3 should be a " +
"number, (-1) or (+1): " + line;
......@@ -150,61 +189,50 @@ public class MSPcrunchStreamFeature
}
if (query_start > query_end) {
if(query_start > query_end)
{
final int tmp = query_end;
query_end = query_start;
query_start = tmp;
}
final String score = (String)line_bits.elementAt (0);
final String percent_id;
if(crunch_x)
line_bits[1] = null;
if (crunch_x) {
percent_id = null;
} else {
percent_id = (String)line_bits.elementAt (1);
}
final Qualifier query_id_qualifier;
final String query_id;
final String subject_start;
final String subject_end;
final String subject_id;
final String description;
if (crunch_x) {
query_id = "unknown";
subject_start = (String)line_bits.elementAt (4);
subject_end = (String)line_bits.elementAt (5);
subject_id = (String)line_bits.elementAt (6);
if(crunch_x)
{
query_id_qualifier = new Qualifier ("query_id", "unknown");
subject_start = line_bits[4];
subject_end = line_bits[5];
subject_id = line_bits[6];
final StringBuffer desc_buffer = new StringBuffer ();
for (int i = 7 ; i < line_bits.size () ; ++i) {
desc_buffer.append ((String)line_bits.elementAt (i));
if (i < line_bits.size () - 1) {
for (int i = 7 ; i < line_bits.length ; ++i)
{
desc_buffer.append (line_bits[i]);
if(i < line_bits.length - 1)
desc_buffer.append (" ");
}
}
description = desc_buffer.toString ();
} else {
query_id = (String)line_bits.elementAt (4);
subject_start = (String)line_bits.elementAt (5);
subject_end = (String)line_bits.elementAt (6);
subject_id = (String)line_bits.elementAt (7);
final StringBuffer desc_buffer = new StringBuffer ();
for (int i = 8 ; i < line_bits.size () ; ++i) {
desc_buffer.append ((String)line_bits.elementAt (i));
if (i < line_bits.size () - 1) {
desc_buffer.append (" ");
}
}
description = desc_buffer.toString ();
else
{
query_id_qualifier = new Qualifier ("query_id", line_bits[4]);
subject_start = line_bits[5];
subject_end = line_bits[6];
subject_id = line_bits[7];
description = line_bits[8];
}
final Qualifier blast_score_qualifier =
new Qualifier ("blast_score", score);
final Qualifier query_id_qualifier =
new Qualifier ("query_id", query_id);
new Qualifier ("blast_score", line_bits[0]);
final Qualifier subject_start_qualifier =
new Qualifier ("subject_start", subject_start);
......@@ -217,13 +245,14 @@ public class MSPcrunchStreamFeature
setQualifier (blast_score_qualifier);
if (percent_id != null) {
if(line_bits[1] != null)
{
// score qualifier must be 1-100
final Qualifier score_qualifier =
new Qualifier ("score", percent_id);
new Qualifier ("score", line_bits[1]);
final Qualifier percent_id_qualifier =
new Qualifier ("percent_id", percent_id);
new Qualifier ("percent_id", line_bits[1]);
setQualifier (score_qualifier);
setQualifier (percent_id_qualifier);
......@@ -244,17 +273,18 @@ public class MSPcrunchStreamFeature
setKey (key);
final StringVector note_values = new StringVector ();
note_values.add ("hit to " + subject_id + " " + subject_start +
".." + subject_end + " score: " + score +
(percent_id == null ?
"" :
" percent id: " + percent_id) +
" " + description);
final Qualifier note_qualifier = new Qualifier ("note", note_values);
// final StringVector note_values = new StringVector ();
// note_values.add (description);
//
// This is more memory intensive than just using the description:
// note_values.add ("hit to " + subject_id + " " + subject_start +
// ".." + subject_end + " score: " + line_bits[0] +
// (line_bits[1] == null ?
// "" :
// " percent id: " + line_bits[1]) +
// " " + description);
final Qualifier note_qualifier = new Qualifier ("note", description);
setQualifier (note_qualifier);
final RangeVector ranges =
......
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