From 2b6ae047456ecb0c470985ab65919c40de7f2c19 Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 13 Jun 2019 10:10:11 +0100
Subject: [PATCH] JAL-3295 Can now compile/run/debug in Eclipse with Java 1.8.
 Change JAVA_VERSION in gradle.properties

---
 build.gradle      |   25 ++++++++++++++-----------
 gradle.properties |    6 ++----
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/build.gradle b/build.gradle
index 1441e7d..3876753 100644
--- a/build.gradle
+++ b/build.gradle
@@ -55,7 +55,7 @@ ext {
   // TODO: consider allowing this expression to  be overridden by -P arg
   getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION
   getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
-  getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
+  //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
   getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
   getdownLauncher = jalviewDir + '/' + getdown_launcher
   getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/'
@@ -111,7 +111,6 @@ sourceSets {
 
     resources {
       srcDirs "$jalviewDir/$resourceDir"
-      srcDirs "$jalviewDir/$libDistDir"
     }
 
     jar.destinationDir = file("$jalviewDir/$packageDir")
@@ -156,8 +155,7 @@ sourceSets {
     } else {
       compileClasspath += files(sourceSets.main.java.outputDir)
     }
-    //compileClasspath += sourceSets.main.compileClasspath
-    //compileClasspath += files( sourceSets.main.resources.srcDirs)
+    
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
 
@@ -216,15 +214,18 @@ eclipse {
         }
         cp.entries.removeAll(removeTheseToo)
         
+        print ("CP="+cp.inspect())
+        
         cp.entries += new Output("bin/main")
         cp.entries += new Library(fileReference(helpParentDir))
         cp.entries += new Library(fileReference(resourceDir))
         
         HashMap<String, Boolean> addedLibPath = new HashMap<>();
-        def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath
-        sourceSets.main.compileClasspath.each{
-          //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
-          //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+        
+        // changing from sourcesets.main.classpath to specific Java version lib
+        //sourceSets.main.compileClasspath.each{
+        fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").each {
+          //don't want to add outputDir as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath
             return
@@ -242,7 +243,9 @@ eclipse {
           }
         }
 
-        sourceSets.test.compileClasspath.each{
+        // changing from sourcesets.main.classpath to specific Java version lib
+        //sourceSets.test.compileClasspath.each{
+        fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]).each {
           //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
           //no longer want to add outputDir as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
@@ -303,8 +306,8 @@ eclipse {
 
   jdt {
     // for the IDE, use java 11 compatibility
-    sourceCompatibility = JAVA_VERSION
-    targetCompatibility = JAVA_VERSION
+    sourceCompatibility = compile_source_compatibility
+    targetCompatibility = compile_target_compatibility
     javaRuntimeName = eclipse_java_runtime_name
 
     file {
diff --git a/gradle.properties b/gradle.properties
index 1189f12..f5c6f49 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,5 +1,6 @@
 jalviewDir = .
 
+#JAVA_VERSION = 1.8
 JAVA_VERSION = 11
 JALVIEW_VERSION = DEVELOPMENT
 INSTALLATION = Source
@@ -15,9 +16,6 @@ jalview_keydig = SHA1
 
 testngGroups = Functional
 
-javac_source = 11
-javac_target = 11
-
 j8libDir = j8lib
 j11libDir = j11lib
 resourceDir = resources
@@ -50,7 +48,7 @@ getdown_local = false
 getdown_website_dir = getdown/website
 getdown_resource_dir = resource
 getdown_app_dir = dist
-getdown_j11lib_dir = j11lib
+#getdown_j11lib_dir = j11lib
 getdown_files_dir = getdown/files
 getdown_launcher = getdown/lib/getdown-launcher.jar
 getdown_core = getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
-- 
1.7.10.2