Fix: refactor implementation and design smells#1088
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cassandrabeaton wants to merge 1 commit intobiojava:masterfrom
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Fix: refactor implementation and design smells#1088cassandrabeaton wants to merge 1 commit intobiojava:masterfrom
cassandrabeaton wants to merge 1 commit intobiojava:masterfrom
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… and structure modules
josemduarte
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Apr 8, 2024
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josemduarte
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Thanks. Please see some comments below
| // Use structural alignment to match the subunit clusters | ||
| if (c1.get(i).mergeStructure(c2.get(j),cParams)) { | ||
| SubunitClusterMerge subunitClusterMerge = new SubunitClusterMerge(c1.get(i)); | ||
| if (subunitClusterMerge.mergeStructure(c2.get(j),cParams)) { |
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In my opinion it was more readable before, as you could see the i/j merging in a single line. Would you have a strong reason for this change?
| public PdbPairsMessage(){ | ||
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| method = PdbPairXMLConverter.DEFAULT_METHOD_NAME; | ||
| method = FatCatRigid.algorithmName; |
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I think it was intended to point to DEFAULT_METHOD_NAME. Then there's a constant that's specific for the default.
| SubunitClusterMerge subunitClusterMerge = new SubunitClusterMerge(clusters.get(c1)); | ||
| if (params.isUseEntityIdForSeqIdentityDetermination() && | ||
| clusters.get(c1).mergeIdenticalByEntityId(clusters.get(c2))) { | ||
| subunitClusterMerge.mergeIdenticalByEntityId(clusters.get(c2))) { |
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I would have the same comment here as above. I don't see this improves readability. And same for a few other cases below.
| * i.e. it is between symmetry-related molecules (with same chain identifier) | ||
| * @return | ||
| */ | ||
| public boolean isSymRelated() { |
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The Pair class is general and intended for any kind of pair (note the generic type T). This would break that generality.
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This is a fix for several code smells discovered in the code.
Tests are passing for all fixes. Test class TestSubunitClusterMerge was created for the new extracted class mentioned in #4.