Bugs item #3452300, was opened at 2011-12-06 03:40
Message generated for change (Tracker Item Submitted) made by cpudney
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Chris Pudney (cpudney)
Assigned to: Nobody/Anonymous (nobody)
Summary: copyPeakListRowProperties() should deep copy PeakIdenties
Initial Comment:
PeakUtils.copyPeakListRowProperties() contains the following code:
// Copy all peak identities, if these are not already present
for (PeakIdentity identity : source.getPeakIdentities()) {
if (!containsIdentity(target, identity))
target.addPeakIdentity(identity, false);
}
This creates shallow copies of the source PeakListRow's identities in the
target PeakListRow.
This is probably not what is wanted.
For example, if you use the Duplicate Peak List Rows filter and then edit an
identity in the resulting peak list, the changes are also reflected in the
corresponding identity from the original peak list.
A possible fix would be to add a clone() method to the PeakIdentity interface
that all PeakIdentity implementations must implement:
public PeakIdentity clone();
and use this in copyPeakListRowProperties:
for (PeakIdentity identity : source.getPeakIdentities()) {
target.addPeakIdentity(identity.clone(), false);
}
Implementations might be difficult for some PeakIdentity implementations
though, e.g. AdductIdentity & ComplexIdentity, which refer to peak list rows.
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