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update modification state flag according to parsing activity
author
jprocter
<Jim Procter>
Wed, 15 Dec 2010 14:51:08 +0000
(14:51 +0000)
committer
jprocter
<Jim Procter>
Wed, 15 Dec 2010 14:51:08 +0000
(14:51 +0000)
src/jalview/io/packed/ParsePackedSet.java
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diff --git
a/src/jalview/io/packed/ParsePackedSet.java
b/src/jalview/io/packed/ParsePackedSet.java
index
20b2061
..
787a88f
100644
(file)
--- a/
src/jalview/io/packed/ParsePackedSet.java
+++ b/
src/jalview/io/packed/ParsePackedSet.java
@@
-76,6
+76,7
@@
public class ParsePackedSet
// deuniquify and construct/merge additional dataset entries if
// necessary.
context.addAlignment(al);
// deuniquify and construct/merge additional dataset entries if
// necessary.
context.addAlignment(al);
+ context.updateSetModified(true);
rslt.add(al);
deuniquify = true;
}
rslt.add(al);
deuniquify = true;
}
@@
-101,8
+102,8
@@
public class ParsePackedSet
{
br = new BufferedReader(src.getReader());
}
{
br = new BufferedReader(src.getReader());
}
- new jalview.io.AnnotationFile().parseAnnotationFrom(
- context.getLastAlignment(), br);
+ context.updateSetModified(new jalview.io.AnnotationFile()
+ .parseAnnotationFrom(context.getLastAlignment(), br));
} catch (Exception e)
{
} catch (Exception e)
{
@@
-123,16
+124,17
@@
public class ParsePackedSet
}
if (dta.getType().equals(JvDataType.FEATURES))
{
}
if (dta.getType().equals(JvDataType.FEATURES))
{
- // check the context has a place to store feature rendering definitions, if not, create one.
- if (context.featureColours==null)
+ // check the context has a place to store feature rendering definitions,
+ // if not, create one.
+ if (context.featureColours == null)
{
context.featureColours = new Hashtable();
}
try
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
{
context.featureColours = new Hashtable();
}
try
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
- ff.parse(context.getLastAlignment(), context.featureColours,
- false);
+ context.updateSetModified(ff.parse(context.getLastAlignment(),
+ context.featureColours, false));
} catch (Exception e)
{
errmsg = ("Failed to parse the Features file associated with the alignment.");
} catch (Exception e)
{
errmsg = ("Failed to parse the Features file associated with the alignment.");
@@
-155,6
+157,7
@@
public class ParsePackedSet
context.addTreeFromFile(nf);
rslt.add(nf);
context.addTreeFromFile(nf);
rslt.add(nf);
+ context.updateSetModified(true);
}
} catch (Exception e)
{
}
} catch (Exception e)
{
@@
-248,6
+251,11
@@
public class ParsePackedSet
// to buffers.
// import with deuniquify info, and compare results to input.
// to buffers.
// import with deuniquify info, and compare results to input.
+ } else {
+ if (context.getLastAlignmentSet().isModified())
+ {
+ System.err.println("Initial alignment set was modified and any associated views should be updated.");
+ }
}
}
}
}
}
}