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JAL-2023 avoid writing / loading empty mappings
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 20 Jul 2016 09:00:24 +0000
(10:00 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 20 Jul 2016 09:00:24 +0000
(10:00 +0100)
src/jalview/gui/Jalview2XML.java
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diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
ac85aad
..
1633a5d
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-898,10
+898,10
@@
public class Jalview2XML
for (AlignedCodonFrame acf : jac)
{
AlcodonFrame alc = new AlcodonFrame();
for (AlignedCodonFrame acf : jac)
{
AlcodonFrame alc = new AlcodonFrame();
- vamsasSet.addAlcodonFrame(alc);
if (acf.getProtMappings() != null
&& acf.getProtMappings().length > 0)
{
if (acf.getProtMappings() != null
&& acf.getProtMappings().length > 0)
{
+ boolean hasMap = false;
SequenceI[] dnas = acf.getdnaSeqs();
jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
for (int m = 0; m < pmaps.length; m++)
SequenceI[] dnas = acf.getdnaSeqs();
jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
for (int m = 0; m < pmaps.length; m++)
@@
-911,6
+911,11
@@
public class Jalview2XML
alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
false));
alc.addAlcodMap(alcmap);
alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
false));
alc.addAlcodMap(alcmap);
+ hasMap = true;
+ }
+ if (hasMap)
+ {
+ vamsasSet.addAlcodonFrame(alc);
}
}
// TODO: delete this ? dead code from 2.8.3->2.9 ?
}
}
// TODO: delete this ? dead code from 2.8.3->2.9 ?
@@
-2855,8
+2860,8
@@
public class Jalview2XML
mapping });
}
}
mapping });
}
}
+ al.addCodonFrame(cf);
}
}
- al.addCodonFrame(cf);
}
}
}
}