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JAL-2226 new method to search for annotation matching particular description as well...
[jalview.git]
/
src
/
jalview
/
io
/
VamsasAppDatastore.java
diff --git
a/src/jalview/io/VamsasAppDatastore.java
b/src/jalview/io/VamsasAppDatastore.java
index
adf4447
..
2fc526b
100644
(file)
--- a/
src/jalview/io/VamsasAppDatastore.java
+++ b/
src/jalview/io/VamsasAppDatastore.java
@@
-338,10
+338,8
@@
public class VamsasAppDatastore
if (vbound.getV_parent() != null
&& dataset != vbound.getV_parent())
{
if (vbound.getV_parent() != null
&& dataset != vbound.getV_parent())
{
- throw new Error(MessageManager.getString(
- "error.implementation_error_cannot_map_alignment_sequences"));
- // This occurs because the dataset for the alignment we are
- // trying to
+ throw new Error(
+ "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
}
}
}
}
}
}
@@
-2248,7
+2246,7
@@
public class VamsasAppDatastore
Float val = null;
try
{
Float val = null;
try
{
- val = new Float(props[p].getContent());
+ val = Float.valueOf(props[p].getContent());
} catch (Exception e)
{
Cache.log.warn("Failed to parse threshold property");
} catch (Exception e)
{
Cache.log.warn("Failed to parse threshold property");
@@
-2537,7
+2535,7
@@
public class VamsasAppDatastore
int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
{
int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
{
- posList.add(new Integer(p));
+ posList.add(Integer.valueOf(p));
}
}
}
}
}
}
@@
-2548,7
+2546,7
@@
public class VamsasAppDatastore
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
- posList.add(new Integer(pos));
+ posList.add(Integer.valueOf(pos));
}
}
}
}
}
}