Kira Mourão

JAL-2909 Updated tests

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    • +3
    /src/jalview/datamodel/CigarParser.java
JAL-2909 fixed another insertions bug

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    • +6
    /src/jalview/datamodel/CigarParser.java
JAL-2909 Fixed a bug in the insertions code

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    • +9
    /src/jalview/datamodel/CigarParser.java
JAL-2909 Gaps at start of reads only from start of alignment window

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    • +8
    /src/jalview/datamodel/CigarParser.java
JAL-2909 Wire up coordinates dialog with bam file reader

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    /src/jalview/gui/BamFileOptionsChooser.java
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    /src/jalview/io/AlignmentFileReaderI.java
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    /src/jalview/io/AppletFormatAdapter.java
JAL-2909 Tidy up bam file cigar code

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    /src/jalview/datamodel/CigarParser.java
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    /src/jalview/gui/BamFileOptionsChooser.java
JAL-2909 Bam file parsing with insertions, first pass

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    /src/jalview/datamodel/CigarParser.java
JAL-2909 Changes to htsjdk import control

JAL-2909 Cigar parsing tests

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    /test/jalview/datamodel/CigarParserTest.java
JAL-2909 Partial insertions

All calling code already checks this. Happy to add it in if we think it's safer though?

All calling code already checks this. Happy to add it in if we think it's safer though?

Done.

Done.

JAL-2778 Adjust cursor changes in overview panel

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    /src/jalview/appletgui/OverviewPanel.java
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    /src/jalview/gui/OverviewPanel.java
JAL-2778 Revert back to old synchronisation

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/datamodel/AlignmentI.java
Well I agree that I was wrong to remove the synchronised call, and have put it back. However it’s only indirectly because of iteration - the code in getSequenceAt isn’t itself iterating (although c...

Well I agree that I was wrong to remove the synchronised call, and have put it back. However it’s only indirectly because of iteration - the code in getSequenceAt isn’t itself iterating (although callers do) but the calls to size() and then get() mean that anything changing the size of the list between the calls could break getSequenceAt.

The delay in resolving this was because I was looking to see if a for-each call replacing the current for loop iteration using getSequenceAt would be better. It works fine, and is already synchronised by SynchronizedList so avoids needing further synchronisation, but benchmarking shows that it’s actually slower, at least the way I implemented it.

It does seem a bit pointless to have all the overhead of a SynchronizedList and then still have to manually synchronise every time it’s used - might as well just use a non-thread safe data structure and do the synchronisation manually, but that’s a wider issue…

JAL-2909 Modified classpath

JAL-2909 Insertions almost

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    /lib/htsjdk-2.12.0.jar
JAL-2909 Read in a bam file - but strand/location unaware

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    /src/jalview/io/BamFile.java
JAL-2909 Removed buggy CIGAR parsing code which was not used

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    /src/jalview/datamodel/CigarBase.java
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    /src/jalview/datamodel/SeqCigar.java
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    /test/jalview/datamodel/SeqCigarTest.java
Merge branch 'develop' into feature/JAL-2759

Conflicts:

benchmarking/README

src/jalview/datamodel/Alignment.java

src/jalview/datamodel/AlignmentAnnotation.java

src/jalview/gui/SeqCanvas.java

src/jalview/gui/SeqPanel.java

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    /src/jalview/datamodel/Alignment.java
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    /src/jalview/gui/SeqCanvas.java
JAL-2759 Fix errant RangeElementsIterator (unit tests were failing)

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    /src/jalview/datamodel/HiddenColumns.java
JAL-2759 Rename getBoundedStartIterator

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    /src/jalview/appletgui/ScalePanel.java
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    /src/jalview/datamodel/HiddenColumns.java
ok

ok

JAL-2759 Changes to StartRegionIterator after review

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    /src/jalview/datamodel/HiddenColumns.java
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    /src/jalview/datamodel/StartRegionIterator.java
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    /test/jalview/datamodel/StartRegionIteratorTest.java
ok

ok

JAL-2788 possible adjustments to sequence accesses

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    /src/jalview/datamodel/Alignment.java
JAL-2778 Sequence width benchmark

JAL-2759 Added in JAL-2851 fix

I changed the VisibleColsCollection constructor, though it makes it inconsistent with VisibleSeqsCollection (which actually needs AlignmentI)

I changed the VisibleColsCollection constructor, though it makes it inconsistent with VisibleSeqsCollection (which actually needs AlignmentI)

Renamed to be more generic. This code predates the HiddenColumns changes, and I've now updated it to take a an iterator instead of a list, which has simplified the code. It should be able to take a...

Renamed to be more generic. This code predates the HiddenColumns changes, and I've now updated it to take a an iterator instead of a list, which has simplified the code. It should be able to take a hidden ranges or visible ranges iterator which means it can do duty as either visible or hidden columns iterator (NB iterates over individual columns not ranges).