gnu: Rename Java packages to match new naming specification.

* gnu/packages/bioinformatics.scm (htsjdk): Rename to...
(java-htsjdk): ...this.
(ngs-java): Rename to...
(java-ngs): ...this.
(ncbi-vdb)[arguments,inputs]: Use new name.
* gnu/packages/java.scm (swt): Rename to...
(java-swt): ...this.
* gnu/packages/music.scm (tuxguitar)[make-flags,inputs,arguments]: Use
new name of package "swt".

gnu/packages/bioinformatics.scm

@@ -2144,9 +2144,9 @@ HMMs).")
 from high-throughput sequencing assays.")
     (license license:gpl3+)))
 
-(define-public htsjdk
+(define-public java-htsjdk
   (package
-    (name "htsjdk")
+    (name "java-htsjdk")
     (version "1.129")
     (source (origin
               (method url-fetch)
@@ -3081,9 +3081,9 @@ any particular back-end implementation, and supports use of multiple back-ends
 simultaneously.")
     (license license:public-domain)))
 
-(define-public ngs-java
+(define-public java-ngs
   (package (inherit ngs-sdk)
-    (name "ngs-java")
+    (name "java-ngs")
     (arguments
      `(,@(substitute-keyword-arguments
              `(#:modules ((guix build gnu-build-system)
@@ -3146,7 +3146,7 @@ simultaneously.")
                     (string-append "--with-ngs-sdk-prefix="
                                    (assoc-ref inputs "ngs-sdk"))
                     (string-append "--with-ngs-java-prefix="
-                                   (assoc-ref inputs "ngs-java"))
+                                   (assoc-ref inputs "java-ngs"))
                     (string-append "--with-hdf5-prefix="
                                    (assoc-ref inputs "hdf5"))))))
         (alist-cons-after
@@ -3172,7 +3172,7 @@ simultaneously.")
     (inputs
      `(("libxml2" ,libxml2)
        ("ngs-sdk" ,ngs-sdk)
-       ("ngs-java" ,ngs-java)
+       ("java-ngs" ,java-ngs)
        ("libmagic" ,file)
        ("hdf5" ,hdf5)))
     (native-inputs `(("perl" ,perl)))

gnu/packages/java.scm

@@ -51,9 +51,9 @@
   #:use-module (gnu packages texinfo)
   #:use-module ((srfi srfi-1) #:select (fold alist-delete)))
 
-(define-public swt
+(define-public java-swt
   (package
-    (name "swt")
+    (name "java-swt")
     (version "4.4.2")
     (source (origin
               (method url-fetch)

gnu/packages/music.scm

@@ -775,7 +775,7 @@ is subjective.")
                           (string-append "PREFIX="
                                          (assoc-ref %outputs "out"))
                           (string-append "SWT_PATH="
-                                         (assoc-ref %build-inputs "swt")
+                                         (assoc-ref %build-inputs "java-swt")
                                          "/share/java/swt.jar"))
        #:tests? #f ;no "check" target
        #:parallel-build? #f ;not supported
@@ -790,11 +790,11 @@ is subjective.")
                (string-append "GCJFLAGS=-fsource=1.4 -fPIC " rest))
               (("PROPERTIES\\?=")
                (string-append "PROPERTIES?= -Dswt.library.path="
-                              (assoc-ref inputs "swt") "/lib"))
+                              (assoc-ref inputs "java-swt") "/lib"))
               (("\\$\\(GCJ\\) -o") "$(GCJ) $(LDFLAGS) -o"))
             #t)))))
     (inputs
-     `(("swt" ,swt)))
+     `(("java-swt" ,java-swt)))
     (native-inputs
      `(("gcj" ,gcj)
        ("pkg-config" ,pkg-config)))