Fix container inefficiency in GenericFastaHeaderParser.java

[cinsttool]

Hi,

We find that there exist container inefficiency in GenericFastaHeaderParser.java.

In particular, at lines 96 and 97 in GenericFastaHeaderParser.java, the for loop keep allocating the data array and transform container object values to array, which incurs redundant memory allocation and container operations.

We discovered the above containers inefficiencies by our tool cinst. The patch is submitted. Could you please check and accept it? We have tested the patch on our PC. The patched program works well.

[cinsttool]

We cannot figure out why the CI is failing because the error still occurs even after we undo the patch.

[aalhossary]

The PR looks good to me.
The error log is

Error:  org.biojava.nbio.structure.io.TestQuaternaryStructureProviders.test5LDH  Time elapsed: 1.061 s  <<< FAILURE!
java.lang.AssertionError: Bioassembly 3 for PDB id 5LDH should fail with a StructureException!
	at org.biojava.nbio.structure.io.TestQuaternaryStructureProviders.test5LDH(TestQuaternaryStructureProviders.java:69)
Error:  org.biojava.nbio.structure.io.TestQuaternaryStructureProviders.testGetNrBioAssemblies5LDH  Time elapsed: 0.042 s  <<< FAILURE!
java.lang.AssertionError: There should be 4 bioassemblies for 5LDH, see github issue #230 expected:<4> but was:<1>
	at org.biojava.nbio.structure.io.TestQuaternaryStructureProviders.testGetNrBioAssemblies5LDH(TestQuaternaryStructureProviders.java:104)

Which does not look relevant here.

[josemduarte]

LGTM thanks

The test problems is unrelated. I'll push a fix to master.

[josemduarte]

Could you merge master into your branch to trigger the tests again?

[cinsttool]

We could not pass the biojava-integrationtest.

The error log is

2024-04-10T16:06:21.2084227Z 15:56:19 [main] WARN  org.biojava.nbio.core.util.FileDownloadUtils - could not find expected file size for resource http://prodata.swmed.edu/ecod/distributions/ecod.develop204.domains.txt.
2024-04-10T16:06:21.2092790Z 16:06:21 [main] WARN  org.biojava.nbio.structure.ecod.EcodFactory - Could not get Ecod version, or file is corrupted
2024-04-10T16:06:21.2094379Z java.net.SocketTimeoutException: Connect timed out

Maybe http://prodata.swmed.edu/ecod/distributions/ecod.develop204.domains.txt is unavailable.

[josemduarte]

Maybe http://prodata.swmed.edu/ecod/distributions/ecod.develop204.domains.txt is unavailable.

Indeed, it looks like it has been down for many days now. Which is odd. It's a popular resource and there's even a very recent publication about it (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011586). I'll see if I can contact them.

[cinsttool]

Maybe http://prodata.swmed.edu/ecod/distributions/ecod.develop204.domains.txt is unavailable.

Hi, we have found that this file is re-available.

[josemduarte]

Thanks... tests are passing finally!