Rectanuglar selection changed to Mouse Button 3 drag

diff --git a/.gitignore b/.gitignore
index 4a81616..2b5afa3 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -13,11 +13,14 @@
 .DS_Store
 /.com.apple.timemachine.supported
 .gitattributes
+.gitignore
 TESTNG
 /jalviewApplet.jar
 /benchmarking/lib
 *.class
 *.patch
+*.diff
+*.orig
 /site
 /site-resources
 /libjs

diff --git a/build.diff b/build.diff
index 8dc92f7..313b266 100644 (file)
--- a/build.diff
+++ b/build.diff
@@ -1,17 +1,17 @@
---- build.gradle       2023-07-02 09:21:09.216542293 +0200
-+++ ../jalview_new/build.gradle        2023-05-15 19:20:46.892861180 +0200
-@@ -45,8 +45,8 @@
+--- build.gradle.orig  2024-05-22 09:14:54.544344630 +0200
++++ build.gradle       2024-05-22 09:45:40.809642258 +0200
+@@ -51,8 +51,8 @@
    id 'java'
    id 'application'
    id 'eclipse'
 -  id "com.diffplug.gradle.spotless" version "3.28.0"
--  id 'com.github.johnrengelman.shadow' version '4.0.3'
-+  id "com.diffplug.spotless" version "6.18.0" //.gradle.spotless" "3.28.0"
-+  id 'com.github.johnrengelman.shadow' version '8.1.1'        // was 4.0.3
-   id 'com.install4j.gradle' version '9.0.6'
-   id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
+-  id 'com.github.johnrengelman.shadow' version '6.0.0'
++  id "com.diffplug.spotless" version "6.18.0"
++  id 'com.github.johnrengelman.shadow' version '8.1.1'
+   id 'com.install4j.gradle' version '10.0.3'
+   id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
    id 'com.palantir.git-version' version '0.13.0' apply false
-@@ -183,6 +183,7 @@
+@@ -193,6 +193,7 @@
    testDir = string("${jalviewDir}/${bareTestSourceDir}")
  
    classesDir = string("${jalviewDir}/${classes_dir}")
@@ -19,7 +19,7 @@
  
    // clover
    useClover = clover.equals("true")
-@@ -547,14 +548,14 @@
+@@ -590,14 +591,14 @@
    main {
      java {
        srcDirs sourceDir
@@ -36,7 +36,7 @@
      compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
  
      runtimeClasspath = compileClasspath
-@@ -564,14 +565,14 @@
+@@ -607,14 +608,14 @@
    clover {
      java {
        srcDirs cloverInstrDir
@@ -53,7 +53,7 @@
      //compileClasspath += files( testClassesDir )
      compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
      compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
-@@ -583,14 +584,14 @@
+@@ -626,14 +627,14 @@
    test {
      java {
        srcDirs testSourceDir
@@ -70,7 +70,7 @@
      compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
      compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
  
-@@ -615,7 +616,7 @@
+@@ -658,7 +659,7 @@
    }
  
    classpath {
@@ -79,7 +79,7 @@
      configurations.each{ c->
        if (c.isCanBeResolved()) {
          minusConfigurations += [c]
-@@ -654,7 +655,7 @@
+@@ -697,7 +698,7 @@
          HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
  
          sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
@@ -88,7 +88,7 @@
            if (it.isDirectory() || ! it.exists()) {
              // don't add dirs to classpath, especially if they don't exist
              return false // groovy "continue" in .any closure
-@@ -674,7 +675,7 @@
+@@ -717,7 +718,7 @@
          }
  
          sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
@@ -97,7 +97,7 @@
            if (it.isDirectory() || ! it.exists()) {
              // don't add dirs to classpath
              return false // groovy "continue" in .any closure
-@@ -1051,7 +1052,7 @@
+@@ -1094,7 +1095,7 @@
  
  clean {
    doFirst {
@@ -106,7 +106,7 @@
    }
  }
  
-@@ -1059,7 +1060,7 @@
+@@ -1102,7 +1103,7 @@
  cleanTest {
    dependsOn cleanClover
    doFirst {
@@ -115,7 +115,7 @@
    }
  }
  
-@@ -1151,7 +1152,7 @@
+@@ -1194,7 +1195,7 @@
  
  task copyDocs(type: Copy) {
    def inputDir = "${jalviewDir}/${doc_dir}"
@@ -124,7 +124,7 @@
    from(inputDir) {
      include('**/*.txt')
      include('**/*.md')
-@@ -1172,10 +1173,10 @@
+@@ -1215,10 +1216,10 @@
      exclude('**/*.html')
      exclude('**/*.xml')
    }
@@ -137,7 +137,7 @@
  }
  
  
-@@ -1240,15 +1241,15 @@
+@@ -1283,15 +1284,15 @@
        }
        if (inFrontMatter) {
          def m = null
@@ -158,7 +158,7 @@
            map[ m[0][1] ] = m[0][2]
          }
          if (dateOnly && map["date"] != null) {
-@@ -1307,7 +1308,7 @@
+@@ -1350,7 +1351,7 @@
        def inSection = false
        changes.eachLine { line ->
          def m = null
@@ -167,7 +167,7 @@
            if (inSection) {
              changesHugo += "</div>\n\n"
            }
-@@ -1317,7 +1318,7 @@
+@@ -1360,7 +1361,7 @@
            section = section.replaceAll(/[^a-z0-9_\-]/, "")
            changesHugo += "<div class=\"${section}\">\n\n"
            inSection = true
@@ -176,7 +176,7 @@
            def comment = m[0][2].trim()
            if (comment != "") {
              comment = comment.replaceAll('"', "&quot;")
-@@ -1387,7 +1388,7 @@
+@@ -1430,7 +1431,7 @@
    def sectionName = null
    content.eachLine { line ->
      def m = null
@@ -185,7 +185,7 @@
        if (sectionName != null) {
          sections[sectionName] = sectionContent
          sectionName = null
-@@ -1410,7 +1411,7 @@
+@@ -1453,7 +1454,7 @@
  
  task copyHelp(type: Copy) {
    def inputDir = helpSourceDir
@@ -194,7 +194,7 @@
    from(inputDir) {
      include('**/*.txt')
      include('**/*.md')
-@@ -1435,14 +1436,15 @@
+@@ -1478,14 +1479,15 @@
      exclude('**/*.xml')
      exclude('**/*.jhm')
    }
@@ -212,7 +212,7 @@
  task releasesTemplates {
    group "help"
    description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
-@@ -1519,9 +1521,9 @@
+@@ -1562,9 +1564,9 @@
        def lm = null
        def rContentProcessed = ""
        rContent.eachLine { line ->
@@ -224,7 +224,7 @@
            line = "_${lm[0][1].trim()}_"
          }
          rContentProcessed += line + "\n"
-@@ -1579,13 +1581,14 @@
+@@ -1622,13 +1624,14 @@
    outputs.file(whatsnewHtmlFile)
  }
  
@@ -240,7 +240,7 @@
    from(inputDir) {
      include('**/*.txt')
      include('**/*.md')
-@@ -1606,10 +1609,10 @@
+@@ -1649,10 +1652,10 @@
      exclude('**/*.html')
      exclude('**/*.xml')
    }
@@ -253,20 +253,7 @@
  }
  
  task copyChannelResources(type: Copy) {
-@@ -1618,16 +1621,17 @@
-   description = "Copy the channel resources dir to the build resources area"
- 
-   def inputDir = "${channelDir}/${resource_dir}"
--  def outputDir = resourcesBuildDir
-+  def destinationDirectory = resourcesBuildDir
-   from inputDir
--  into outputDir
-+  into destinationDirectory
- 
-   inputs.dir(inputDir)
--  outputs.dir(outputDir)
-+  outputs.dir(destinationDirectory)
- }
+@@ -1683,6 +1686,7 @@
  
  task createBuildProperties(type: WriteProperties) {
    dependsOn copyResources
@@ -274,7 +261,7 @@
    group = "build"
    description = "Create the ${buildProperties} file"
    
-@@ -1651,6 +1655,7 @@
+@@ -1706,6 +1710,7 @@
  
  task buildIndices(type: JavaExec) {
    dependsOn copyHelp
@@ -282,7 +269,7 @@
    classpath = sourceSets.main.compileClasspath
    main = "com.sun.java.help.search.Indexer"
    workingDir = "${helpBuildDir}/${help_dir}"
-@@ -1678,15 +1683,25 @@
+@@ -1733,7 +1738,7 @@
    dependsOn buildResources
    dependsOn copyDocs
    dependsOn copyHelp
@@ -291,33 +278,30 @@
    dependsOn convertMdFiles
    dependsOn buildIndices
  }
- 
- 
-+// random block of dependencies
+@@ -1742,6 +1747,14 @@
  compileJava.dependsOn prepare
  run.dependsOn compileJava
- //run.dependsOn prepare
-+compileTestJava.dependsOn compileJava //
-+compileTestJava.dependsOn buildIndices //
-+processResources.dependsOn copyChannelResources //
-+processResources.dependsOn copyResources //
-+processResources.dependsOn createBuildProperties //
-+processResources.dependsOn copyDocs //
-+processResources.dependsOn convertMdFiles //
-+processResources.dependsOn copyHelp //
-+processResources.dependsOn buildIndices //
- 
- 
- //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
-@@ -1731,6 +1746,7 @@
- }
+ compileTestJava.dependsOn compileJava
++compileTestJava.dependsOn buildIndices
++processResources.dependsOn copyChannelResources
++processResources.dependsOn copyResources
++processResources.dependsOn createBuildProperties
++processResources.dependsOn copyDocs
++processResources.dependsOn convertMdFiles
++processResources.dependsOn copyHelp
++processResources.dependsOn buildIndices
+ 
+ 
+ 
+@@ -2037,6 +2050,7 @@
+ /* END of test tasks results summary */
  
  
 +/*
  task compileLinkCheck(type: JavaCompile) {
    options.fork = true
    classpath = files("${jalviewDir}/${utils_dir}")
-@@ -1765,6 +1781,7 @@
+@@ -2071,6 +2085,7 @@
    inputs.dir(helpBuildDir)
    outputs.file(helpLinksCheckerOutFile)
  }
@@ -325,7 +309,7 @@
  
  
  // import the pubhtmlhelp target
-@@ -1779,10 +1796,14 @@
+@@ -2085,10 +2100,14 @@
    }
  }
  
@@ -341,7 +325,7 @@
  
    manifest {
      attributes "Main-Class": main_class,
-@@ -1792,8 +1813,8 @@
+@@ -2098,8 +2117,8 @@
      "Implementation-Version": JALVIEW_VERSION
    }
  
@@ -352,7 +336,7 @@
    archiveFileName = rootProject.name+".jar"
    duplicatesStrategy "EXCLUDE"
  
-@@ -1804,11 +1825,11 @@
+@@ -2110,11 +2129,11 @@
    exclude "**/*.jar"
    exclude "**/*.jar.*"
  
@@ -366,8 +350,8 @@
  }
  
  
-@@ -1867,7 +1888,7 @@
- 
+@@ -2207,7 +2226,7 @@
+   // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead
    mainClassName = shadow_jar_main_class
    mergeServiceFiles()
 -  classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -375,7 +359,7 @@
    minimize()
  }
  
-@@ -2922,10 +2943,10 @@
+@@ -3388,10 +3407,10 @@
  
    def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
    inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
@@ -388,7 +372,7 @@
  }
  
  
-@@ -3033,13 +3054,13 @@
+@@ -3499,13 +3518,13 @@
    dependsOn jalviewjsTransferUnzipAllLibs
    def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
    inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
@@ -405,7 +389,7 @@
      null
    }
    preserve {
-@@ -3058,13 +3079,13 @@
+@@ -3524,13 +3543,13 @@
    dependsOn buildResources
  
    def inputFiles = fileTree(dir: resourcesBuildDir)
@@ -422,7 +406,7 @@
      null
    }
    preserve {
-@@ -3077,13 +3098,13 @@
+@@ -3543,13 +3562,13 @@
  
  task jalviewjsSyncSiteResources (type: Sync) {
    def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
@@ -439,7 +423,7 @@
      null
    }
    preserve {
-@@ -3097,13 +3118,13 @@
+@@ -3563,13 +3582,13 @@
  task jalviewjsSyncBuildProperties (type: Sync) {
    dependsOn createBuildProperties
    def inputFiles = [file(buildProperties)]
@@ -456,7 +440,7 @@
      null
    }
    preserve {
-@@ -3322,7 +3343,7 @@
+@@ -3788,7 +3807,7 @@
    def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
    def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
    def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
@@ -465,7 +449,7 @@
    def prefixFile = "${jsDir}/core/coretop2.js"
    def suffixFile = "${jsDir}/core/corebottom2.js"
  
-@@ -3366,8 +3387,8 @@
+@@ -3832,8 +3851,8 @@
      }
      def list = fileTree(dir: j2sDir, includes: filelist)
  
@@ -476,7 +460,7 @@
  
      jalviewjsCoreClasslists += [
        'jsfile': jsfile,
-@@ -3385,8 +3406,8 @@
+@@ -3851,8 +3870,8 @@
    // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
    def stevesoftClasslistName = "_stevesoft"
    def stevesoftClasslist = [
@@ -487,7 +471,7 @@
      'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
      'name': stevesoftClasslistName
    ]
-@@ -3419,8 +3440,8 @@
+@@ -3885,8 +3904,8 @@
      ]
    )
    def allClasslist = [
@@ -498,7 +482,7 @@
      'list': allJsFiles,
      'name': allClasslistName
    ]
-@@ -3473,11 +3494,11 @@
+@@ -3939,11 +3958,11 @@
    dependsOn jalviewjsBuildAllCores
    def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
    def inputFile = file(inputFileName)
@@ -512,7 +496,7 @@
      cl['outputfile'] = outputFile
      outputFiles += outputFile
    }
-@@ -3496,13 +3517,13 @@
+@@ -3962,13 +3981,13 @@
    dependsOn jalviewjsBuildAllCores
    dependsOn jalviewjsPublishCoreTemplates
    def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")

diff --git a/build.gradle b/build.gradle
index 6df3ec9..f89a53a 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -51,8 +51,8 @@ plugins {
   id 'java'
   id 'application'
   id 'eclipse'
-  id "com.diffplug.gradle.spotless" version "3.28.0"
-  id 'com.github.johnrengelman.shadow' version '6.0.0'
+  id "com.diffplug.spotless" version "6.18.0"
+  id 'com.github.johnrengelman.shadow' version '8.1.1'
   id 'com.install4j.gradle' version '10.0.3'
   id 'com.dorongold.task-tree' version '2.1.1' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
   id 'com.palantir.git-version' version '0.13.0' apply false
@@ -193,6 +193,7 @@ ext {
   testDir = string("${jalviewDir}/${bareTestSourceDir}")
 
   classesDir = string("${jalviewDir}/${classes_dir}")
+  destinationDirectory = file(classesDir)
 
   // clover
   useClover = clover.equals("true")
@@ -590,14 +591,14 @@ sourceSets {
   main {
     java {
       srcDirs sourceDir
-      outputDir = file(classesDir)
+      destinationDirectory = file(classesDir)
     }
 
     resources {
       srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
-    compileClasspath = files(sourceSets.main.java.outputDir)
+    compileClasspath = files(sourceSets.main.java.destinationDirectory)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -607,14 +608,14 @@ sourceSets {
   clover {
     java {
       srcDirs cloverInstrDir
-      outputDir = cloverClassesDir
+      destinationDirectory = cloverClassesDir
     }
 
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.clover.java.outputDir )
+    compileClasspath = files( sourceSets.clover.java.destinationDirectory )
     //compileClasspath += files( testClassesDir )
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
     compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
@@ -626,14 +627,14 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file(testClassesDir)
+      destinationDirectory = file(testClassesDir)
     }
 
     resources {
       srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
-    compileClasspath = files( sourceSets.test.java.outputDir )
+    compileClasspath = files( sourceSets.test.java.destinationDirectory )
     compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
@@ -658,7 +659,7 @@ eclipse {
   }
 
   classpath {
-    //defaultOutputDir = sourceSets.main.java.outputDir
+    //defaultOutputDir = sourceSets.main.java.destinationDirectory
     configurations.each{ c->
       if (c.isCanBeResolved()) {
         minusConfigurations += [c]
@@ -697,7 +698,7 @@ eclipse {
         HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
 
         sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
-          //don't want to add outputDir as eclipse is using its own output dir in bin/main
+          //don't want to add destinationDirectory as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath, especially if they don't exist
             return false // groovy "continue" in .any closure
@@ -717,7 +718,7 @@ eclipse {
         }
 
         sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.any {
-          //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+          //no longer want to add destinationDirectory as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
             // don't add dirs to classpath
             return false // groovy "continue" in .any closure
@@ -1094,7 +1095,7 @@ compileTestJava {
 
 clean {
   doFirst {
-    delete sourceSets.main.java.outputDir
+    delete sourceSets.main.java.destinationDirectory
   }
 }
 
@@ -1102,7 +1103,7 @@ clean {
 cleanTest {
   dependsOn cleanClover
   doFirst {
-    delete sourceSets.test.java.outputDir
+    delete sourceSets.test.java.destinationDirectory
   }
 }
 
@@ -1194,7 +1195,7 @@ def convertMdToHtml (FileTree mdFiles, File cssFile) {
 
 task copyDocs(type: Copy) {
   def inputDir = "${jalviewDir}/${doc_dir}"
-  def outputDir = "${docBuildDir}/${doc_dir}"
+  def destinationDirectory = "${docBuildDir}/${doc_dir}"
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1215,10 +1216,10 @@ task copyDocs(type: Copy) {
     exclude('**/*.html')
     exclude('**/*.xml')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 
@@ -1283,15 +1284,15 @@ def mdFileComponents(File mdFile, def dateOnly=false) {
       }
       if (inFrontMatter) {
         def m = null
-        if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
+        if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2})/) {
           map["date"] = new Date().parse("yyyy-MM-dd HH:mm:ss", m[0][1])
-        } else if (m = line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
+        } else if (m == line =~ /^date:\s*(\d{4}-\d{2}-\d{2})/) {
           map["date"] = new Date().parse("yyyy-MM-dd", m[0][1])
-        } else if (m = line =~ /^channel:\s*(\S+)/) {
+        } else if (m == line =~ /^channel:\s*(\S+)/) {
           map["channel"] = m[0][1]
-        } else if (m = line =~ /^version:\s*(\S+)/) {
+        } else if (m == line =~ /^version:\s*(\S+)/) {
           map["version"] = m[0][1]
-        } else if (m = line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
+        } else if (m == line =~ /^\s*([^:]+)\s*:\s*(\S.*)/) {
           map[ m[0][1] ] = m[0][2]
         }
         if (dateOnly && map["date"] != null) {
@@ -1350,7 +1351,7 @@ task hugoTemplates {
       def inSection = false
       changes.eachLine { line ->
         def m = null
-        if (m = line =~ /^##([^#].*)$/) {
+        if (m == line =~ /^##([^#].*)$/) {
           if (inSection) {
             changesHugo += "</div>\n\n"
           }
@@ -1360,7 +1361,7 @@ task hugoTemplates {
           section = section.replaceAll(/[^a-z0-9_\-]/, "")
           changesHugo += "<div class=\"${section}\">\n\n"
           inSection = true
-        } else if (m = line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
+        } else if (m == line =~ /^(\s*-\s*)<!--([^>]+)-->(.*?)(<br\/?>)?\s*$/) {
           def comment = m[0][2].trim()
           if (comment != "") {
             comment = comment.replaceAll('"', "&quot;")
@@ -1430,7 +1431,7 @@ def getMdSections(String content) {
   def sectionName = null
   content.eachLine { line ->
     def m = null
-    if (m = line =~ /^##([^#].*)$/) {
+    if (m == line =~ /^##([^#].*)$/) {
       if (sectionName != null) {
         sections[sectionName] = sectionContent
         sectionName = null
@@ -1453,7 +1454,7 @@ def getMdSections(String content) {
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${helpBuildDir}/${help_dir}"
+  def destinationDirectory = "${helpBuildDir}/${help_dir}"
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1478,14 +1479,15 @@ task copyHelp(type: Copy) {
     exclude('**/*.xml')
     exclude('**/*.jhm')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
   outputs.files(helpFile)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 
+/*
 task releasesTemplates {
   group "help"
   description "Recreate whatsNew.html and releases.html from markdown files and templates in help"
@@ -1562,9 +1564,9 @@ task releasesTemplates {
       def lm = null
       def rContentProcessed = ""
       rContent.eachLine { line ->
-        if (lm = line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
+        if (lm == line =~ /^(\s*-)(\s*<!--[^>]*?-->)(.*)$/) {
           line = "${lm[0][1]}${lm[0][3]}${lm[0][2]}"
-      } else if (lm = line =~ /^###([^#]+.*)$/) {
+      } else if (lm == line =~ /^###([^#]+.*)$/) {
           line = "_${lm[0][1].trim()}_"
         }
         rContentProcessed += line + "\n"
@@ -1622,13 +1624,14 @@ task releasesTemplates {
   outputs.file(whatsnewHtmlFile)
 }
 
+*/
 
 task copyResources(type: Copy) {
   group = "build"
   description = "Copy (and make text substitutions in) the resources dir to the build area"
 
   def inputDir = resourceDir
-  def outputDir = resourcesBuildDir
+  def destinationDirectory = resourcesBuildDir
   from(inputDir) {
     include('**/*.txt')
     include('**/*.md')
@@ -1649,10 +1652,10 @@ task copyResources(type: Copy) {
     exclude('**/*.html')
     exclude('**/*.xml')
   }
-  into outputDir
+  into destinationDirectory
 
   inputs.dir(inputDir)
-  outputs.dir(outputDir)
+  outputs.dir(destinationDirectory)
 }
 
 task copyChannelResources(type: Copy) {
@@ -1683,6 +1686,7 @@ task copyChannelResources(type: Copy) {
 
 task createBuildProperties(type: WriteProperties) {
   dependsOn copyResources
+  dependsOn copyChannelResources
   group = "build"
   description = "Create the ${buildProperties} file"
   
@@ -1706,6 +1710,7 @@ task createBuildProperties(type: WriteProperties) {
 
 task buildIndices(type: JavaExec) {
   dependsOn copyHelp
+  //dependsOn releasesTemplates
   classpath = sourceSets.main.compileClasspath
   main = "com.sun.java.help.search.Indexer"
   workingDir = "${helpBuildDir}/${help_dir}"
@@ -1733,7 +1738,7 @@ task prepare {
   dependsOn buildResources
   dependsOn copyDocs
   dependsOn copyHelp
-  dependsOn releasesTemplates
+  //dependsOn releasesTemplates
   dependsOn convertMdFiles
   dependsOn buildIndices
 }
@@ -1742,6 +1747,14 @@ task prepare {
 compileJava.dependsOn prepare
 run.dependsOn compileJava
 compileTestJava.dependsOn compileJava
+compileTestJava.dependsOn buildIndices
+processResources.dependsOn copyChannelResources
+processResources.dependsOn copyResources
+processResources.dependsOn createBuildProperties
+processResources.dependsOn copyDocs
+processResources.dependsOn convertMdFiles
+processResources.dependsOn copyHelp
+processResources.dependsOn buildIndices
 
 
 
@@ -2037,6 +2050,7 @@ private static void printResults(allResults) {
 /* END of test tasks results summary */
 
 
+/*
 task compileLinkCheck(type: JavaCompile) {
   options.fork = true
   classpath = files("${jalviewDir}/${utils_dir}")
@@ -2071,6 +2085,7 @@ task linkCheck(type: JavaExec) {
   inputs.dir(helpBuildDir)
   outputs.file(helpLinksCheckerOutFile)
 }
+*/
 
 
 // import the pubhtmlhelp target
@@ -2085,10 +2100,14 @@ task cleanPackageDir(type: Delete) {
   }
 }
 
+// block of dependencies
+//compileTestJava.dependsOn compileLinkCheck //
+//copyChannelResources.dependsOn compileLinkCheck //
+//convertMdFiles.dependsOn compileLinkCheck //
 
 jar {
   dependsOn prepare
-  dependsOn linkCheck
+  dependsOn //linkCheck
 
   manifest {
     attributes "Main-Class": main_class,
@@ -2098,8 +2117,8 @@ jar {
     "Implementation-Version": JALVIEW_VERSION
   }
 
-  def outputDir = "${jalviewDir}/${package_dir}"
-  destinationDirectory = file(outputDir)
+  def destinationDirectory = "${jalviewDir}/${package_dir}"
+  destinationDirectory = file(destinationDirectory)
   archiveFileName = rootProject.name+".jar"
   duplicatesStrategy "EXCLUDE"
 
@@ -2110,11 +2129,11 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir(sourceSets.main.java.outputDir)
+  inputs.dir(sourceSets.main.java.destinationDirectory)
   sourceSets.main.resources.srcDirs.each{ dir ->
     inputs.dir(dir)
   }
-  outputs.file("${outputDir}/${archiveFileName}")
+  outputs.file("${destinationDirectory}/${archiveFileName}")
 }
 
 
@@ -2207,7 +2226,7 @@ shadowJar {
   // this mainClassName is mandatory but gets ignored due to manifest created in doFirst{}. Set the Main-Class as an attribute in launcherJar instead
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
-  classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
+  archiveClassifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
   minimize()
 }
 
@@ -3388,10 +3407,10 @@ task jalviewjsEclipseCopyDropins(type: Copy) {
 
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
   inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
-  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
 }
 
 
@@ -3499,13 +3518,13 @@ task jalviewjsSyncAllLibs (type: Sync) {
   dependsOn jalviewjsTransferUnzipAllLibs
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
   inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3524,13 +3543,13 @@ task jalviewjsSyncResources (type: Sync) {
   dependsOn buildResources
 
   def inputFiles = fileTree(dir: resourcesBuildDir)
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3543,13 +3562,13 @@ task jalviewjsSyncResources (type: Sync) {
 
 task jalviewjsSyncSiteResources (type: Sync) {
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3563,13 +3582,13 @@ task jalviewjsSyncSiteResources (type: Sync) {
 task jalviewjsSyncBuildProperties (type: Sync) {
   dependsOn createBuildProperties
   def inputFiles = [file(buildProperties)]
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {
@@ -3788,7 +3807,7 @@ task jalviewjsBuildAllCores {
   def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
   def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
   def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
   def prefixFile = "${jsDir}/core/coretop2.js"
   def suffixFile = "${jsDir}/core/corebottom2.js"
 
@@ -3832,8 +3851,8 @@ task jalviewjsBuildAllCores {
     }
     def list = fileTree(dir: j2sDir, includes: filelist)
 
-    def jsfile = "${outputDir}/core${name}.js"
-    def zjsfile = "${outputDir}/core${name}.z.js"
+    def jsfile = "${destinationDirectory}/core${name}.js"
+    def zjsfile = "${destinationDirectory}/core${name}.z.js"
 
     jalviewjsCoreClasslists += [
       'jsfile': jsfile,
@@ -3851,8 +3870,8 @@ task jalviewjsBuildAllCores {
   // _stevesoft core. add any cores without a classlist here (and the inputs and outputs)
   def stevesoftClasslistName = "_stevesoft"
   def stevesoftClasslist = [
-    'jsfile': "${outputDir}/core${stevesoftClasslistName}.js",
-    'zjsfile': "${outputDir}/core${stevesoftClasslistName}.z.js",
+    'jsfile': "${destinationDirectory}/core${stevesoftClasslistName}.js",
+    'zjsfile': "${destinationDirectory}/core${stevesoftClasslistName}.z.js",
     'list': fileTree(dir: j2sDir, include: "com/stevesoft/pat/**/*.js"),
     'name': stevesoftClasslistName
   ]
@@ -3885,8 +3904,8 @@ task jalviewjsBuildAllCores {
     ]
   )
   def allClasslist = [
-    'jsfile': "${outputDir}/core${allClasslistName}.js",
-    'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
+    'jsfile': "${destinationDirectory}/core${allClasslistName}.js",
+    'zjsfile': "${destinationDirectory}/core${allClasslistName}.z.js",
     'list': allJsFiles,
     'name': allClasslistName
   ]
@@ -3939,11 +3958,11 @@ task jalviewjsPublishCoreTemplates {
   dependsOn jalviewjsBuildAllCores
   def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
   def inputFile = file(inputFileName)
-  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
 
   def outputFiles = []
   jalviewjsCoreClasslists.each { cl ->
-    def outputFile = "${outputDir}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
+    def outputFile = "${destinationDirectory}/${jalviewjsJalviewTemplateName}_${cl.name}.html"
     cl['outputfile'] = outputFile
     outputFiles += outputFile
   }
@@ -3962,13 +3981,13 @@ task jalviewjsSyncCore (type: Sync) {
   dependsOn jalviewjsBuildAllCores
   dependsOn jalviewjsPublishCoreTemplates
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
-  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
+  def destinationDirectory = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
-  into outputDir
+  into destinationDirectory
   def outputFiles = []
   rename { filename ->
-    outputFiles += "${outputDir}/${filename}"
+    outputFiles += "${destinationDirectory}/${filename}"
     null
   }
   preserve {

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 346e3fa..ee08d60 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -601,7 +601,7 @@ public class CalculationChooser extends JPanel
     ScoreModels scoreModels = ScoreModels.getInstance();
     for (ScoreModelI sm : scoreModels.getModels())
     {
-      if (!forPasimap && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
+      if ((!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
               || sm.isSecondaryStructure() && ssPresent))
               
       {

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 042f178..3a2089b 100755 (executable)
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -506,6 +506,7 @@ public class RotatableCanvas extends JPanel
     {
       rotate(-1f, 0f);
     }
+    /*
     else if (evt.getKeyChar() == 's')
     {
       // Cache.warn("DEBUG: Rectangle selection");
@@ -515,6 +516,7 @@ public class RotatableCanvas extends JPanel
        {
        rectSelect(rectx1, recty1, rectx2, recty2);
        }
+    */
     }
 
     repaint();
@@ -630,10 +632,14 @@ public class RotatableCanvas extends JPanel
     int yDelta = yPos - mouseY;
 
     // Check if this is a rectangle drawing drag
-    if ((evt.getModifiersEx() & InputEvent.BUTTON2_DOWN_MASK) != 0)
+    if ((evt.getModifiersEx() & InputEvent.BUTTON3_DOWN_MASK) != 0)
     {
        rectx2 = evt.getX();
        recty2 = evt.getY();
+       if ((rectx2 != -1) && (recty2 != -1))
+       {
+         rectSelect(rectx1, recty1, rectx2, recty2);
+       }
     }
     else
     {
@@ -641,11 +647,9 @@ public class RotatableCanvas extends JPanel
 
       mouseX = xPos;
       mouseY = yPos;
-
       // findWidths();
-
-      repaint();
     }
+      repaint();
   }
 
   @Override