From 3eca2c1e7ccfc5014f2a268f04180ec87c094bb6 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 3 Mar 2006 11:34:26 +0000
Subject: [PATCH] uniprot version no. fix
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4130 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/editor/FastaTextPane.java | 27 +++++++++++++++++--
uk/ac/sanger/artemis/editor/HitInfo.java | 21 +++++++++++++--
2 files changed, 44 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/editor/FastaTextPane.java b/uk/ac/sanger/artemis/editor/FastaTextPane.java
index 55b034223..9ff581903 100644
--- a/uk/ac/sanger/artemis/editor/FastaTextPane.java
+++ b/uk/ac/sanger/artemis/editor/FastaTextPane.java
@@ -231,7 +231,17 @@ public class FastaTextPane extends JScrollPane
currentID = line.substring(1,ind);
int indDot;
if( (indDot = currentID.indexOf(".")) > 5)
- currentID= currentID.substring(0,indDot);
+ {
+ String version = currentID.substring(indDot+1);
+ try
+ {
+ int version_no = Integer.parseInt(version);
+ // version number looks like uniprot so strip this
+ if(version_no < 50)
+ currentID= currentID.substring(0,indDot);
+ }
+ catch(NumberFormatException nfe){}
+ }
}
int ind2 = currentID.indexOf(":");
@@ -416,7 +426,19 @@ public class FastaTextPane extends JScrollPane
int indDot;
if( (indDot = currentID.indexOf(".")) > 5)
- currentID= currentID.substring(0,indDot);
+ {
+ String version = currentID.substring(indDot+1);
+ try
+ {
+ int version_no = Integer.parseInt(version);
+ // version number looks like uniprot so strip this
+ if(version_no < 50)
+ currentID= currentID.substring(0,indDot);
+ }
+ catch(NumberFormatException nfe){}
+
+ // HERE currentID= currentID.substring(0,indDot);
+ }
if(hi != null)
hi.setEndPosition(textPosition);
@@ -431,6 +453,7 @@ public class FastaTextPane extends JScrollPane
if(ind1 > -1)
{
ind2 = line.indexOf(";",ind1);
+
hi.setScore(line.substring(ind1+6,ind2));
ind1 = ind2+1;
diff --git a/uk/ac/sanger/artemis/editor/HitInfo.java b/uk/ac/sanger/artemis/editor/HitInfo.java
index c2af1258d..c5aacf725 100644
--- a/uk/ac/sanger/artemis/editor/HitInfo.java
+++ b/uk/ac/sanger/artemis/editor/HitInfo.java
@@ -117,7 +117,16 @@ public class HitInfo
// uniprot fasta headers
// >pac.sv id desc
//
- id = id.substring(0,indDot);
+ String version = id.substring(indDot+1);
+ try
+ {
+ int version_no = Integer.parseInt(version);
+ // version number looks like uniprot so strip this
+ if(version_no < 50)
+ id = id.substring(0,indDot);
+ }
+ catch(NumberFormatException nfe){}
+
acc = id;
}
}
@@ -177,7 +186,15 @@ public class HitInfo
// uniprot fasta headers
// >pac.sv id desc
//
- id = id.substring(0,indDot);
+ String version = id.substring(indDot+1);
+ try
+ {
+ int version_no = Integer.parseInt(version);
+ // version number looks like uniprot so strip this
+ if(version_no < 50)
+ id = id.substring(0,indDot);
+ }
+ catch(NumberFormatException nfe){}
acc = id;
}
}
--
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