Hi Bob. I renamed this thread - 'Code Question' isn't very descriptive.
On 04/11/2018 20:36, Robert Hanson wrote:
> In Jalview2XML I see this:
>
> int entryCount = 1;
>
> do
> {
> jin = jprovider.getJarInputStream();
> for (int i = 0; i < entryCount; i++)
> {
> jarentry = jin.getNextJarEntry();
> }
>
> if (jarentry != null && jarentry.getName().endsWith(".xml"))
> {
> ... entryCount++;
> }
> else if (jarentry != null)
> {
> // Some other file here.
> entryCount++;
> }
> } while (jarentry != null);
>
> What's the reason behind doing that instead of:
>
> int entryCount = 1;
>
> jin = jprovider.getJarInputStream();
> do
> {
> jarentry = jin.getNextJarEntry();
> if (jarentry != null && jarentry.getName().endsWith(".xml"))
> {
> ... entryCount++;
> }
> } while (jarentry != null);
>
> Isn't the first unnecessarily opening and reading completely the jar
> file as many time as there are jar entries?
not as far as I can see ? There's only one call to getJarInputStream
(before the first for loop).
> Why not just read it straight through? So, for example, each URL
> would be opened and read three times for a standard file.
Some readers would close the JarInputStream after handling the entry, so
we implemented a belt'n'braces mechanism here. Remember these are
normally local files, so no harm done...
> Also, can you tell me why a Jalview session file has two models, both
> of which are read, but only one of which is displayed? One has a full
> path to it. The other does not. One is the original? and the other is
> the save? Is that it? But why read both?
Jalview has n+1 'models' in a project: the 'dataset' (all sequences
without gaps, holds features, annotation and coding relationships) -
corresponds to the Dataset alignment returned by
AlignmentI.getDataSet(). The other 'n' are one or more alignment views -
which are grouped by Alignment ID to indicate different views on the
same alignment.
al is klar ? ;)
j.
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