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resolve 1:many mappings from feature sequence ID to alignment sequence(s) with same ID
author
jprocter
<Jim Procter>
Fri, 18 Jul 2008 15:05:30 +0000
(15:05 +0000)
committer
jprocter
<Jim Procter>
Fri, 18 Jul 2008 15:05:30 +0000
(15:05 +0000)
src/jalview/io/FeaturesFile.java
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diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
03a7a83
..
3e0314a
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-148,7
+148,7
@@
public class FeaturesFile extends AlignFile
}
\r
continue;
\r
}
\r
}
\r
continue;
\r
}
\r
-
\r
+ String seqId="";
\r
while (st.hasMoreElements())
\r
{
\r
\r
while (st.hasMoreElements())
\r
{
\r
\r
@@
-156,8
+156,8
@@
public class FeaturesFile extends AlignFile
{
\r
// Still possible this is an old Jalview file,
\r
// which does not have type colours at the beginning
\r
{
\r
// Still possible this is an old Jalview file,
\r
// which does not have type colours at the beginning
\r
- token = st.nextToken();
\r
- seq = align.findName(token, true);
\r
+ seqId = token = st.nextToken();
\r
+ seq = align.findName(seqId, true);
\r
if (seq != null)
\r
{
\r
desc = st.nextToken();
\r
if (seq != null)
\r
{
\r
desc = st.nextToken();
\r
@@
-205,7
+205,10
@@
public class FeaturesFile extends AlignFile
}
\r
\r
seq.addSequenceFeature(sf);
\r
}
\r
\r
seq.addSequenceFeature(sf);
\r
-
\r
+ while ((seq=align.findName(seq, seqId, true))!=null)
\r
+ {
\r
+ seq.addSequenceFeature(new SequenceFeature(sf));
\r
+ }
\r
break;
\r
}
\r
}
\r
break;
\r
}
\r
}
\r
@@
-231,11
+234,12
@@
public class FeaturesFile extends AlignFile
\r
if (!token.equals("ID_NOT_SPECIFIED"))
\r
{
\r
\r
if (!token.equals("ID_NOT_SPECIFIED"))
\r
{
\r
- seq = align.findName(token, true);
\r
+ seq = align.findName(seqId=token, true);
\r
st.nextToken();
\r
}
\r
else
\r
{
\r
st.nextToken();
\r
}
\r
else
\r
{
\r
+ seqId=null;
\r
try
\r
{
\r
index = Integer.parseInt(st.nextToken());
\r
try
\r
{
\r
index = Integer.parseInt(st.nextToken());
\r
@@
-266,8
+270,6
@@
public class FeaturesFile extends AlignFile
\r
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
\r
\r
\r
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
\r
\r
- seq.addSequenceFeature(sf);
\r
-
\r
if (groupLink != null && removeHTML)
\r
{
\r
sf.addLink(groupLink);
\r
if (groupLink != null && removeHTML)
\r
{
\r
sf.addLink(groupLink);
\r
@@
-281,6
+283,12
@@
public class FeaturesFile extends AlignFile
\r
parseDescriptionHTML(sf, removeHTML);
\r
\r
\r
parseDescriptionHTML(sf, removeHTML);
\r
\r
+ seq.addSequenceFeature(sf);
\r
+
\r
+ while (seqId!=null && (seq=align.findName(seq, seqId, false))!=null)
\r
+ {
\r
+ seq.addSequenceFeature(new SequenceFeature(sf));
\r
+ }
\r
// If we got here, its not a GFFFile
\r
GFFFile = false;
\r
}
\r
// If we got here, its not a GFFFile
\r
GFFFile = false;
\r
}
\r