- Jalview's alignment related arguments are linked together using a linked ID. In all of the basic usage examples this linked ID is assigned using a default formula of JALVIEW:n where n starts at 0 and increments every time there is an --opened file (or a first use of --append) or the --new argument is used.
+ Jalview's alignment related arguments are linked together using a linked ID. In all of the basic usage examples this linked ID is assigned using a default formula of JALVIEW:n where n starts at 0 and increments every time there is an ‑‑opened file (or a first use of ‑‑append) or the ‑‑new argument is used.
- When another alignment related argument is used (without a specified linked ID), it is assigned this default linked ID. When the --all argument is used, following alignment related arguments are applied to all of the linked IDs (made so far).
+ When another alignment related argument is used (without a specified linked ID), it is assigned this default linked ID. When the ‑‑all argument is used, following alignment related arguments are applied to all of the linked IDs (made so far).
@@ -67,7 +67,7 @@
- A specified linked ID will also take precedence over a wildcard or --all set linked ID. e.g.
+ A specified linked ID will also take precedence over a wildcard or ‑‑all set linked ID. e.g.
jalview --open[myID] examples/uniref50.fa --all --colour taylor --colour[myID] gecos-blossom@@ -75,18 +75,18 @@ -
{n}, {++n}, [*]){n}, {++n}, [*], {m}, {++m})In the basic usage document we have a list of special strings that get replaced in output filename values with parts of input filename values.
- There is also an incrementor integer value {n} that can be put into both linked IDs and filenames and works across different linked IDs. Whenever you use {n} in a linked ID or filename value it is replaced with the current value of n. The initial value is 0, and it can be incremented by using the argument --npp or --n++, or using a another special substitution {++n} in either a linked ID or filename value which increments the value and is replaced with the new incremented value of n.
+ There is also an incrementor integer value {n} that can be put into both linked IDs and filenames and works across different linked IDs. Whenever you use {n} in a linked ID or filename value it is replaced with the current value of n. The initial value is 0, and it can be incremented by using the argument ‑‑npp or ‑‑n++, or using a another special substitution {++n} in either a linked ID or filename value which increments the value and is replaced with the new incremented value of n.
- In the same way that the --all argument enables (some) following arguments to apply to all opened alignments so far, the special linked ID * will also apply an individual argument to all opened linked IDs (in fact when you use the --all argument it simply changes the default linked ID to *).
+ In the same way that the ‑‑all argument enables (some) following arguments to apply to all opened alignments so far, the special linked ID * will also apply an individual argument to all opened linked IDs (in fact when you use the ‑‑all argument it simply changes the default linked ID to *).
jalview --open[myId1] fileA.fa --open[myId2] fileB.fa --open[myId3] fileC.fa --colour[*] taylor --all --image tmp/image-{++n}.png --headless
@@ -97,8 +97,10 @@
because all of the command line arguments are read and sorted into their linked IDs before starting to be processed, and the [myId3] specified linked ID takes precedence over the [*] wildcard linked ID.
-
+
+ All of the substitutions talked about so far are evaluated in the argument parsing process. If in some cases (almost certainly involving structure images!) you find {n} is not incrementing when you think it should, when specifying ‑‑structureimage filenames you can also use {m} and {++m}, along with {structuredirname}, {structurebasename} and {structureextension} which are substituted at the point of use. {m} is just a plain counter starting at 0.
+
- One benefit of this is seen above in the --image argument, the special "alloutput" wildcard filename *.png will not be expanded by the shell, so does not need to be escaped or surrounded with quotation marks.
+ One benefit of this is seen above in the ‑‑image argument, the special "alloutput" wildcard filename *.png will not be expanded by the shell, so does not need to be escaped or surrounded with quotation marks.
@@ -150,7 +152,7 @@
- Some arguments (such as --scale=n) are used to modify the behaviour of other "primary" arguments (such as --image=filename). These arguments can alternatively be specifed as sub-value modifiers of the values given to the primary argument. If specified as a sub-value modifier, this modifier takes precedence over any following linked argument if given. e.g
+ Some arguments (such as ‑‑scale=n) are used to modify the behaviour of other "primary" arguments (such as ‑‑image=filename). These arguments can alternatively be specifed as sub-value modifiers of the values given to the primary argument. If specified as a sub-value modifier, this modifier takes precedence over any following linked argument if given. e.g
jalview --open=[colour=zappo]examples/*.fa@@ -166,7 +168,7 @@
- You can specify multiple sub-value modifiers separating them with a comma (','). If you wish to specify a "boolean" argument, such as --wrap or --nowrap then simply use the argument name without a value, like this:
+ You can specify multiple sub-value modifiers separating them with a comma (','). If you wish to specify a "boolean" argument, such as ‑‑wrap or ‑‑nowrap then simply use the argument name without a value, like this:
jalview --open=[colour=gecos-flower,wrap,noannotations,features=examples/plantfdx.features]examples/plantfdx.fa