diff --git a/uk/ac/sanger/artemis/io/MSPcrunchStreamFeature.java b/uk/ac/sanger/artemis/io/MSPcrunchStreamFeature.java
index fd0cfb07354a5958d63cd1afcffa995122e0f40a..09931200ac35a202bbe7ab644bafb06558ea25cf 100644
--- a/uk/ac/sanger/artemis/io/MSPcrunchStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/MSPcrunchStreamFeature.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/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) {
- 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) {
+
+ 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_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 =