JAL-3806 fix and test for one-to-many sequence mapping case

[jalview.git] / doc / building.md

diff --git a/doc/building.md b/doc/building.md
index ad19979..497e722 100644 (file)
--- a/doc/building.md
+++ b/doc/building.md
@@ -9,7 +9,7 @@ git clone http://source.jalview.org/git/jalview.git
 cd jalview
 gradle shadowJar
 # run
 cd jalview
 gradle shadowJar
 # run

-java -jar build/libs/jalview-all-11.jar
+java -jar build/libs/jalview-all-*-j11.jar

 
 # and/or create launcher
 gradle getdown
 
 # and/or create launcher
 gradle getdown

@@ -26,7 +26,7 @@ java -jar getdown-launcher.jar . jalview
 The method here is described in terms of using a command line.  You can easily do this on linux or in a Terminal window in macOS.  You can do it in Windows.
 
 * Java 11 compliant JDK
 The method here is described in terms of using a command line.  You can easily do this on linux or in a Terminal window in macOS.  You can do it in Windows.
 
 * Java 11 compliant JDK

-* gradle 5.2 or above
+* gradle 5.2 or above *(NB gradle 6.6 and above currently produces NullPointerExceptions during the build. This is non-fatal and does not affect the build. Use gradle 6.5.1 to avoid this)*

 * git
 
 > The versions and installation methods here are just suggestions (which we have tested 
 * git
 
 > The versions and installation methods here are just suggestions (which we have tested 

@@ -248,20 +248,23 @@ and all of the supporting libraries in `j11lib/*.jar` merged into one `.jar` arc
 file.  A default launching class (`MAIN-CLASS: jalview.bin.Launcher`) is specified in the `.jar` 
 manifest file (`META/MANIFEST.MF`) so a start class doesn't need to be specified.
 
 file.  A default launching class (`MAIN-CLASS: jalview.bin.Launcher`) is specified in the `.jar` 
 manifest file (`META/MANIFEST.MF`) so a start class doesn't need to be specified.
 

-Build the shadow jar file in `build/lib/jalview-all-11.jar` with
+Build the shadow jar file in `build/libs/jalview-all-VERSION-j11.jar` with

 
 ```bash
 gradle shadowJar
 ```
 
 ```bash
 gradle shadowJar
 ```

-and run it with
+
+__NB__ `VERSION` will be replaced with a version number or "`DEVELOPMENT`" depending on how the branch is set up.
+
+Run it with

 
 ```bash
 
 ```bash

-java -jar build/lib/jalview-all-11.jar
+java -jar build/libs/jalview-all-VERSION-j11.jar

 ```
 
 Because no arguments are required, most OSes will associate a `.jar` file with the 
 `java` application (if this has been installed through the OS and not just a local 
 ```
 
 Because no arguments are required, most OSes will associate a `.jar` file with the 
 `java` application (if this has been installed through the OS and not just a local 

-unzip) as a `-jar` argument so you may find you can launch `jalview-all-11.jar` 
+unzip) as a `-jar` argument so you may find you can launch `jalview-all-VERSION-j11.jar` 

 just by double-clicking on it)!
 
 > The `shadowJar` task is not a requirement for any other task, so to build the shadow 
 just by double-clicking on it)!
 
 > The `shadowJar` task is not a requirement for any other task, so to build the shadow 

@@ -276,8 +279,8 @@ although without the many and compelling benefits of the `getdown` launcher.
 We have made significant customisations to the `getdown` launcher which you can find 
 in `getdown/src/getdown`.
 
 We have made significant customisations to the `getdown` launcher which you can find 
 in `getdown/src/getdown`.
 

-> You don't need to build this afresh as the required `gradle-core.jar` 
-and `gradle-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then 
+> You don't need to build this afresh as the required `getdown-core.jar` 
+and `getdown-launcher.jar` files are already distributed in `j11lib` and `getdown/lib` but if you want to, then 

 you'll need a working Maven and also a Java 8 JDK.  Ensure the Java 8 `javac` is forefront 
 in your path and do
 >
 you'll need a working Maven and also a Java 8 JDK.  Ensure the Java 8 `javac` is forefront 
 in your path and do
 >

@@ -285,9 +288,9 @@ in your path and do
 >cd getdown/src/getdown
 >mvn clean package -Dgetdown.host.whitelist="jalview.org,*.jalview.org"
 >```
 >cd getdown/src/getdown
 >mvn clean package -Dgetdown.host.whitelist="jalview.org,*.jalview.org"
 >```

-> and you will find the required `.jar` files in `core/target/gradle-core-XXX.jar` 
-and `launcher/target/gradle-launcher-XXX.jar`.  The `gradle-core.jar` should then be copied 
-to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `gradle-launcher.jar` only 
+> and you will find the required `.jar` files in `core/target/getdown-core-XXX.jar` 
+and `launcher/target/getdown-launcher-XXX.jar`.  The `getdown-core.jar` should then be copied 
+to all three of the `j8lib`, `j11lib` and `getdown/lib` folders, whilst the `getdown-launcher.jar` only 

 needs to be copied to `getdown/lib`.
 >
 >The `mvn` command should ideally include the `-Dgetdown.host.whitelist=*.jalview.org` setting. 
 needs to be copied to `getdown/lib`.
 >
 >The `mvn` command should ideally include the `-Dgetdown.host.whitelist=*.jalview.org` setting. 

@@ -318,6 +321,7 @@ java -jar getdown/files/11/getdown-launcher.jar getdown/files/11/ jalview
 getdown, and the final argument, "`jalview`", is a getdown application id (only "`jalview`" 
 is defined here).
 
 getdown, and the final argument, "`jalview`", is a getdown application id (only "`jalview`" 
 is defined here).
 

+The command line sequence for building and relocating the getdown artifacts can be executed as a script via `getdown/src/getdown/mvn_cmd`. Please make sure this script is kept up to date should the getdown build instructions change.

 
 ### Running tests
 
 
 ### Running tests
 

@@ -536,7 +540,7 @@ We develop in Eclipse, and support settings to develop and save Jalview source c
 in our preferred style.  We also support running the Jalview application, debugging 
 and running tests with TestNG from within Eclipse.
 
 in our preferred style.  We also support running the Jalview application, debugging 
 and running tests with TestNG from within Eclipse.
 

-To get Jalview set up as a project in Eclipse, we recommend using at least the 2019-12 
+To get Jalview set up as a project in Eclipse, we recommend using at least the 2020-03

 version of Eclipse IDE for Java Developers which you can download from the Eclipse 
 website: <https://www.eclipse.org/downloads/>.  Since Eclipse 2020-03 you are encouraged to use the Eclipse Installer (see the Eclipse Downloads page).
 In the installer, when given a choice of packages for Eclipse you should choose the "Eclipse IDE for Enterprise Java Developers" package.
 version of Eclipse IDE for Java Developers which you can download from the Eclipse 
 website: <https://www.eclipse.org/downloads/>.  Since Eclipse 2020-03 you are encouraged to use the Eclipse Installer (see the Eclipse Downloads page).
 In the installer, when given a choice of packages for Eclipse you should choose the "Eclipse IDE for Enterprise Java Developers" package.

@@ -560,7 +564,7 @@ Search for and install:
 1. TestNG for Eclipse (optional -- only needed if you want to run tests from Eclipse)
 
 > At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace 
 1. TestNG for Eclipse (optional -- only needed if you want to run tests from Eclipse)
 
 > At time of writing, TestNG for Eclipse does not show up in the Eclipse Marketplace 

-as the latest released version does not install in Eclipse 2019-03.
+as the latest released version does not install in Eclipse 2020-03.

 However, you can install a working release of TestNG for Eclipse by going to
 >
 Help->Install New Software...
 However, you can install a working release of TestNG for Eclipse by going to
 >
 Help->Install New Software...

@@ -600,6 +604,14 @@ You can now import Jalview.
 
 If you have already downloaded Jalview using `git clone` then you can import this folder into Eclipse directly.
 
 
 If you have already downloaded Jalview using `git clone` then you can import this folder into Eclipse directly.
 

+__Before importing the cloned git repo you must create the Eclipse project files.__ You can do this by either running
+
+`gradle eclipse`
+
+or
+
+Unzipping the file `utils/eclipse/eclipse_startup_files.zip` in the base repo directory (`jalview`)
+

 It is important to import 
 Jalview as a Gradle project (not as a Java project), so go to
 
 It is important to import 
 Jalview as a Gradle project (not as a Java project), so go to