JAL-2805 loads of file reorganizing, interfaces expanded

diff --git a/.classpath b/.classpath
index b86c3b2..42e9500 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -70,6 +70,5 @@
        <classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
        <classpathentry kind="lib" path="lib/groovy-all-2.4.6-indy.jar"/>
        <classpathentry combineaccessrules="false" kind="src" path="/forester"/>
-       <classpathentry combineaccessrules="false" kind="src" path="/forester_applications"/>
        <classpathentry kind="output" path="classes"/>
 </classpath>

diff --git a/hs_err_pid28190.log b/hs_err_pid28190.log
new file mode 100644 (file)
index 0000000..976d063
--- /dev/null
+++ b/hs_err_pid28190.log
@@ -0,0 +1,642 @@
+#
+# A fatal error has been detected by the Java Runtime Environment:
+#
+#  SIGSEGV (0xb) at pc=0x0000000129be645f, pid=28190, tid=0x000000000000eb07
+#
+# JRE version: Java(TM) SE Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01)
+# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.144-b01 mixed mode bsd-amd64 compressed oops)
+# Problematic frame:
+# C  [libawt_lwawt.dylib+0x1c45f]  OGLSD_SetScratchSurface+0x49
+#
+# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
+#
+# If you would like to submit a bug report, please visit:
+#   http://bugreport.java.com/bugreport/crash.jsp
+# The crash happened outside the Java Virtual Machine in native code.
+# See problematic frame for where to report the bug.
+#
+
+---------------  T H R E A D  ---------------
+
+Current thread (0x00007fb7d6a28000):  JavaThread "Java2D Queue Flusher" daemon [_thread_in_native, id=60167, stack(0x000070000a322000,0x000070000a422000)]
+
+siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000000002
+
+Registers:
+RAX=0x0000000129c06d0e, RBX=0x0000000000000002, RCX=0x0000000000000047, RDX=0x0000000129c07258
+RSP=0x000070000a421730, RBP=0x000070000a421750, RSI=0x00007fb7dc2381e0, RDI=0x00007fb7d6a281f8
+R8 =0x00000000000002d5, R9 =0x000000000190822f, R10=0x000000010e0ee8f8, R11=0x000000010e6e8100
+R12=0x0000000000000000, R13=0x000070000a4218e8, R14=0x00007fb7d6a281f8, R15=0x00007fb7d6a28000
+RIP=0x0000000129be645f, EFLAGS=0x0000000000010202, ERR=0x0000000000000004
+  TRAPNO=0x000000000000000e
+
+Top of Stack: (sp=0x000070000a421730)
+0x000070000a421730:   00007fb7dc2381e0 0000000000000000
+0x000070000a421740:   00007fb7d6a5d610 00007fb7d6a28000
+0x000070000a421750:   000070000a4217d0 0000000129c06d36
+0x000070000a421760:   00007fb7d648b700 0000000200000001
+0x000070000a421770:   0000000000000000 000070000a421800
+0x000070000a421780:   0000000000000000 0000000000000000
+0x000070000a421790:   000070000a4217d0 00007fb7d6a5d620
+0x000070000a4217a0:   00000000005effd0 00007fb7d6a281f8
+0x000070000a4217b0:   000000016d2bc370 0000000000000000
+0x000070000a4217c0:   000070000a421968 00007fb7d6a28000
+0x000070000a4217d0:   000070000a421820 000000010e0ee96a
+0x000070000a4217e0:   00000006c00a3af8 000000010d138a00
+0x000070000a4217f0:   0000000000000064 0000000000000000
+0x000070000a421800:   0000000000000064 00007fb7d648b1e8
+0x000070000a421810:   000070000a421870 000000010cf501e8
+0x000070000a421820:   000070000a421940 000000010e6e86fc
+0x000070000a421830:   0000000000000001 00007fb7d648bea0
+0x000070000a421840:   00000006c00a3b00 00007fb7d6a28000
+0x000070000a421850:   00007fb7d6a28000 00000001258fda00
+0x000070000a421860:   000070000a421968 00007fb7d6a28000
+0x000070000a421870:   000070000a4218c0 000000010e2f2968
+0x000070000a421880:   00000006c00a3af8 000000010e5aafe6
+0x000070000a421890:   000070000a421940 000000010e6e815c
+0x000070000a4218a0:   000000012f278bb4 000070000a4218e8
+0x000070000a4218b0:   000000012f278c30 0000000000000000
+0x000070000a4218c0:   000070000a421940 000000010dbaf2bd
+0x000070000a4218d0:   000070000a421940 000000010dbaf2bd
+0x000070000a4218e0:   000000010dbaf2bd 00000006c00a3af8
+0x000070000a4218f0:   0000000000000001 00000006c00a3b80
+0x000070000a421900:   000070000a4218f0 000000012e64d689
+0x000070000a421910:   000070000a421968 000000012e64d820
+0x000070000a421920:   0000000000000000 000000012e64d790 
+
+Instructions: (pc=0x0000000129be645f)
+0x0000000129be643f:   c0 e9 82 00 00 00 48 8b 5e 10 48 85 db 75 0e bf
+0x0000000129be644f:   01 00 00 00 48 8d 15 67 7b 03 00 eb d6 49 89 fe
+0x0000000129be645f:   4c 8b 3b 30 c0 e8 21 a6 02 00 49 8b 3f 49 89 c4
+0x0000000129be646f:   48 8b 35 aa 02 06 00 30 c0 e8 51 a7 02 00 48 85 
+
+Register to memory mapping:
+
+RAX=0x0000000129c06d0e: Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer+0x612 in /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libawt_lwawt.dylib at 0x0000000129bca000
+RBX=0x0000000000000002 is an unknown value
+RCX=0x0000000000000047 is an unknown value
+RDX=0x0000000129c07258: Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer+0xb5c in /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libawt_lwawt.dylib at 0x0000000129bca000
+RSP=0x000070000a421730 is pointing into the stack for thread: 0x00007fb7d6a28000
+RBP=0x000070000a421750 is pointing into the stack for thread: 0x00007fb7d6a28000
+RSI=0x00007fb7dc2381e0 is an unknown value
+RDI=0x00007fb7d6a281f8 is an unknown value
+R8 =0x00000000000002d5 is an unknown value
+R9 =0x000000000190822f is an unknown value
+R10=0x000000010e0ee8f8 is at entry_point+56 in (nmethod*)0x000000010e0ee750
+R11=0x000000010e6e8100 is at entry_point+0 in (nmethod*)0x000000010e6e7f90
+R12=0x0000000000000000 is an unknown value
+R13=0x000070000a4218e8 is pointing into the stack for thread: 0x00007fb7d6a28000
+R14=0x00007fb7d6a281f8 is an unknown value
+R15=0x00007fb7d6a28000 is a thread
+
+
+Stack: [0x000070000a322000,0x000070000a422000],  sp=0x000070000a421730,  free space=1021k
+Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
+C  [libawt_lwawt.dylib+0x1c45f]  OGLSD_SetScratchSurface+0x49
+C  [libawt_lwawt.dylib+0x3cd36]  Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer+0x63a
+J 4748  sun.java2d.opengl.OGLRenderQueue.flushBuffer(JI)V (0 bytes) @ 0x000000010e0ee96a [0x000000010e0ee8c0+0xaa]
+J 3668 C1 sun.java2d.opengl.OGLRenderQueue.flushBuffer()V (41 bytes) @ 0x000000010e6e86fc [0x000000010e6e84a0+0x25c]
+J 3667 C1 sun.java2d.opengl.OGLRenderQueue.access$100(Lsun/java2d/opengl/OGLRenderQueue;)V (5 bytes) @ 0x000000010e6e815c [0x000000010e6e8100+0x5c]
+j  sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run()V+81
+v  ~StubRoutines::call_stub
+V  [libjvm.dylib+0x2ee70a]
+V  [libjvm.dylib+0x2eeeae]
+V  [libjvm.dylib+0x2ef05a]
+V  [libjvm.dylib+0x3497b1]
+V  [libjvm.dylib+0x56c0b3]
+V  [libjvm.dylib+0x56d7a0]
+V  [libjvm.dylib+0x48baee]
+C  [libsystem_pthread.dylib+0x393b]  _pthread_body+0xb4
+C  [libsystem_pthread.dylib+0x3887]  _pthread_body+0x0
+C  [libsystem_pthread.dylib+0x308d]  thread_start+0xd
+C  0x0000000000000000
+
+Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
+J 4748  sun.java2d.opengl.OGLRenderQueue.flushBuffer(JI)V (0 bytes) @ 0x000000010e0ee8f8 [0x000000010e0ee8c0+0x38]
+J 3668 C1 sun.java2d.opengl.OGLRenderQueue.flushBuffer()V (41 bytes) @ 0x000000010e6e86fc [0x000000010e6e84a0+0x25c]
+J 3667 C1 sun.java2d.opengl.OGLRenderQueue.access$100(Lsun/java2d/opengl/OGLRenderQueue;)V (5 bytes) @ 0x000000010e6e815c [0x000000010e6e8100+0x5c]
+j  sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run()V+81
+v  ~StubRoutines::call_stub
+
+---------------  P R O C E S S  ---------------
+
+Java Threads: ( => current thread )
+  0x00007fb7d92c2000 JavaThread "class jalview.workers.ConservationThread" [_thread_in_Java, id=84243, stack(0x000070000acc0000,0x000070000adc0000)]
+  0x00007fb7d6c86000 JavaThread "Image Fetcher 0" daemon [_thread_blocked, id=46819, stack(0x000070000abbd000,0x000070000acbd000)]
+  0x00007fb7d6996800 JavaThread "LoadFileThread" [_thread_blocked, id=71699, stack(0x000070000aaba000,0x000070000abba000)]
+  0x00007fb7d935c800 JavaThread "TimerQueue" daemon [_thread_blocked, id=81411, stack(0x000070000b14f000,0x000070000b24f000)]
+  0x00007fb7d6bc7800 JavaThread "DestroyJavaVM" [_thread_blocked, id=7171, stack(0x0000700008b54000,0x0000700008c54000)]
+  0x00007fb7d9213800 JavaThread "pool-1-thread-1" [_thread_blocked, id=70863, stack(0x000070000a934000,0x000070000aa34000)]
+  0x00007fb7d7389000 JavaThread "ConsoleTextAppendThread" daemon [_thread_blocked, id=69379, stack(0x000070000a831000,0x000070000a931000)]
+  0x00007fb7d7388000 JavaThread "ConsoleReader2Thread" daemon [_thread_blocked, id=68867, stack(0x000070000a72e000,0x000070000a82e000)]
+  0x00007fb7d7387800 JavaThread "ConsoleReader1Thread" daemon [_thread_blocked, id=68363, stack(0x000070000a62b000,0x000070000a72b000)]
+  0x00007fb7d7344800 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=62987, stack(0x000070000a528000,0x000070000a628000)]
+  0x00007fb7d7313800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=62479, stack(0x000070000a425000,0x000070000a525000)]
+=>0x00007fb7d6a28000 JavaThread "Java2D Queue Flusher" daemon [_thread_in_native, id=60167, stack(0x000070000a322000,0x000070000a422000)]
+  0x00007fb7da830800 JavaThread "AWT-Shutdown" [_thread_blocked, id=32287, stack(0x0000700009f10000,0x000070000a010000)]
+  0x00007fb7d69c8800 JavaThread "AppKit Thread" daemon [_thread_in_native, id=775, stack(0x00007fff54a39000,0x00007fff55239000)]
+  0x00007fb7d8065800 JavaThread "Service Thread" daemon [_thread_blocked, id=20995, stack(0x0000700009c87000,0x0000700009d87000)]
+  0x00007fb7d6800800 JavaThread "C1 CompilerThread3" daemon [_thread_blocked, id=20483, stack(0x0000700009b84000,0x0000700009c84000)]
+  0x00007fb7d8044800 JavaThread "C2 CompilerThread2" daemon [_thread_blocked, id=19971, stack(0x0000700009a81000,0x0000700009b81000)]
+  0x00007fb7d7044000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=19459, stack(0x000070000997e000,0x0000700009a7e000)]
+  0x00007fb7d7011000 JavaThread "C2 CompilerThread0" daemon [_thread_in_native, id=18947, stack(0x000070000987b000,0x000070000997b000)]
+  0x00007fb7d702a800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=18435, stack(0x0000700009778000,0x0000700009878000)]
+  0x00007fb7d802a000 JavaThread "Finalizer" daemon [_thread_blocked, id=14595, stack(0x0000700009675000,0x0000700009775000)]
+  0x00007fb7d8027000 JavaThread "Reference Handler" daemon [_thread_blocked, id=14083, stack(0x0000700009572000,0x0000700009672000)]
+
+Other Threads:
+  0x00007fb7d9012800 VMThread [stack: 0x000070000946f000,0x000070000956f000] [id=13571]
+  0x00007fb7d8076000 WatcherThread [stack: 0x0000700009d8a000,0x0000700009e8a000] [id=21507]
+
+VM state:not at safepoint (normal execution)
+
+VM Mutex/Monitor currently owned by a thread: None
+
+Heap:
+ PSYoungGen      total 86528K, used 20241K [0x000000076ab00000, 0x0000000774800000, 0x00000007c0000000)
+  eden space 75776K, 15% used [0x000000076ab00000,0x000000076b683258,0x000000076f500000)
+  from space 10752K, 78% used [0x000000076f600000,0x000000076fe413f8,0x0000000770080000)
+  to   space 42496K, 0% used [0x0000000771e80000,0x0000000771e80000,0x0000000774800000)
+ ParOldGen       total 209920K, used 31492K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
+  object space 209920K, 15% used [0x00000006c0000000,0x00000006c1ec11e8,0x00000006ccd00000)
+ Metaspace       used 37085K, capacity 37796K, committed 38016K, reserved 1083392K
+  class space    used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
+
+Card table byte_map: [0x000000010ae5a000,0x000000010b65b000] byte_map_base: 0x000000010785a000
+
+Marking Bits: (ParMarkBitMap*) 0x000000010d4f35d0
+ Begin Bits: [0x000000011d0fd000, 0x00000001210fd000)
+ End Bits:   [0x00000001210fd000, 0x00000001250fd000)
+
+Polling page: 0x000000010aa87000
+
+CodeCache: size=245760Kb used=15978Kb max_used=15978Kb free=229781Kb
+ bounds [0x000000010dba7000, 0x000000010eb57000, 0x000000011cba7000]
+ total_blobs=5726 nmethods=5006 adapters=631
+ compilation: enabled
+
+Compilation events (10 events):
+Event: 1054.326 Thread 0x00007fb7d8044800 nmethod 5621 0x000000010eb34b10 code [0x000000010eb34c60, 0x000000010eb34cd8]
+Event: 1054.327 Thread 0x00007fb7d6800800 5622       3       javax.swing.DefaultButtonModel::isArmed (15 bytes)
+Event: 1054.327 Thread 0x00007fb7d6800800 nmethod 5622 0x000000010eb343d0 code [0x000000010eb34540, 0x000000010eb346f0]
+Event: 1054.346 Thread 0x00007fb7d6800800 5623 %     3       jalview.schemes.ResidueProperties::buildAmbiguityCodonSet @ 657 (878 bytes)
+Event: 1054.350 Thread 0x00007fb7d6800800 nmethod 5623% 0x000000010eb34d90 code [0x000000010eb357e0, 0x000000010eb3e3f8]
+Event: 1054.351 Thread 0x00007fb7d6800800 5624       3       jalview.schemes.ResidueProperties::buildAmbiguityCodonSet (878 bytes)
+Event: 1054.363 Thread 0x00007fb7d6800800 nmethod 5624 0x000000010eb45590 code [0x000000010eb45fc0, 0x000000010eb4e878]
+Event: 1054.363 Thread 0x00007fb7d6800800 5625       3       java.io.FileInputStream::finalize (22 bytes)
+Event: 1054.363 Thread 0x00007fb7d6800800 nmethod 5625 0x000000010eb33f50 code [0x000000010eb340c0, 0x000000010eb34348]
+Event: 1054.364 Thread 0x00007fb7d7011000 5626 %     4       jalview.schemes.ResidueProperties::buildAmbiguityCodonSet @ 575 (878 bytes)
+
+GC Heap History (10 events):
+Event: 8.499 GC heap before
+{Heap before GC invocations=3 (full 1):
+ PSYoungGen      total 76288K, used 65536K [0x000000076ab00000, 0x0000000770000000, 0x00000007c0000000)
+  eden space 65536K, 100% used [0x000000076ab00000,0x000000076eb00000,0x000000076eb00000)
+  from space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
+  to   space 10752K, 0% used [0x000000076f580000,0x000000076f580000,0x0000000770000000)
+ ParOldGen       total 121856K, used 7919K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
+  object space 121856K, 6% used [0x00000006c0000000,0x00000006c07bbd10,0x00000006c7700000)
+ Metaspace       used 32188K, capacity 32772K, committed 33024K, reserved 1077248K
+  class space    used 4214K, capacity 4351K, committed 4352K, reserved 1048576K
+Event: 8.510 GC heap after
+Heap after GC invocations=3 (full 1):
+ PSYoungGen      total 76288K, used 10746K [0x000000076ab00000, 0x0000000770d80000, 0x00000007c0000000)
+  eden space 65536K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076eb00000)
+  from space 10752K, 99% used [0x000000076f580000,0x000000076fffe850,0x0000000770000000)
+  to   space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
+ ParOldGen       total 121856K, used 24160K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
+  object space 121856K, 19% used [0x00000006c0000000,0x00000006c17980a8,0x00000006c7700000)
+ Metaspace       used 32188K, capacity 32772K, committed 33024K, reserved 1077248K
+  class space    used 4214K, capacity 4351K, committed 4352K, reserved 1048576K
+}
+Event: 28.095 GC heap before
+{Heap before GC invocations=4 (full 1):
+ PSYoungGen      total 76288K, used 76282K [0x000000076ab00000, 0x0000000770d80000, 0x00000007c0000000)
+  eden space 65536K, 100% used [0x000000076ab00000,0x000000076eb00000,0x000000076eb00000)
+  from space 10752K, 99% used [0x000000076f580000,0x000000076fffe850,0x0000000770000000)
+  to   space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
+ ParOldGen       total 121856K, used 24160K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
+  object space 121856K, 19% used [0x00000006c0000000,0x00000006c17980a8,0x00000006c7700000)
+ Metaspace       used 34471K, capacity 35178K, committed 35456K, reserved 1079296K
+  class space    used 4439K, capacity 4626K, committed 4736K, reserved 1048576K
+Event: 28.111 GC heap after
+Heap after GC invocations=4 (full 1):
+ PSYoungGen      total 76288K, used 10746K [0x000000076ab00000, 0x0000000770b00000, 0x00000007c0000000)
+  eden space 65536K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076eb00000)
+  from space 10752K, 99% used [0x000000076eb00000,0x000000076f57e870,0x000000076f580000)
+  to   space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
+ ParOldGen       total 121856K, used 49145K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
+  object space 121856K, 40% used [0x00000006c0000000,0x00000006c2ffe560,0x00000006c7700000)
+ Metaspace       used 34471K, capacity 35178K, committed 35456K, reserved 1079296K
+  class space    used 4439K, capacity 4626K, committed 4736K, reserved 1048576K
+}
+Event: 28.286 GC heap before
+{Heap before GC invocations=5 (full 1):
+ PSYoungGen      total 76288K, used 21665K [0x000000076ab00000, 0x0000000770b00000, 0x00000007c0000000)
+  eden space 65536K, 16% used [0x000000076ab00000,0x000000076b5a9db8,0x000000076eb00000)
+  from space 10752K, 99% used [0x000000076eb00000,0x000000076f57e870,0x000000076f580000)
+  to   space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
+ ParOldGen       total 121856K, used 49145K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
+  object space 121856K, 40% used [0x00000006c0000000,0x00000006c2ffe560,0x00000006c7700000)
+ Metaspace       used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
+  class space    used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
+Event: 28.293 GC heap after
+Heap after GC invocations=5 (full 1):
+ PSYoungGen      total 87552K, used 10724K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
+  eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
+  from space 10752K, 99% used [0x0000000770080000,0x0000000770af9260,0x0000000770b00000)
+  to   space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
+ ParOldGen       total 121856K, used 50465K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
+  object space 121856K, 41% used [0x00000006c0000000,0x00000006c3148700,0x00000006c7700000)
+ Metaspace       used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
+  class space    used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
+}
+Event: 28.293 GC heap before
+{Heap before GC invocations=6 (full 2):
+ PSYoungGen      total 87552K, used 10724K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
+  eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
+  from space 10752K, 99% used [0x0000000770080000,0x0000000770af9260,0x0000000770b00000)
+  to   space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
+ ParOldGen       total 121856K, used 50465K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
+  object space 121856K, 41% used [0x00000006c0000000,0x00000006c3148700,0x00000006c7700000)
+ Metaspace       used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
+  class space    used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
+Event: 28.336 GC heap after
+Heap after GC invocations=6 (full 2):
+ PSYoungGen      total 87552K, used 0K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
+  eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
+  from space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
+  to   space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
+ ParOldGen       total 209920K, used 22383K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
+  object space 209920K, 10% used [0x00000006c0000000,0x00000006c15dbcc8,0x00000006ccd00000)
+ Metaspace       used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
+  class space    used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
+}
+Event: 1054.355 GC heap before
+{Heap before GC invocations=7 (full 2):
+ PSYoungGen      total 87552K, used 76800K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
+  eden space 76800K, 100% used [0x000000076ab00000,0x000000076f600000,0x000000076f600000)
+  from space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
+  to   space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
+ ParOldGen       total 209920K, used 22383K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
+  object space 209920K, 10% used [0x00000006c0000000,0x00000006c15dbcc8,0x00000006ccd00000)
+ Metaspace       used 37084K, capacity 37796K, committed 38016K, reserved 1083392K
+  class space    used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
+Event: 1054.361 GC heap after
+Heap after GC invocations=7 (full 2):
+ PSYoungGen      total 86528K, used 8452K [0x000000076ab00000, 0x0000000774800000, 0x00000007c0000000)
+  eden space 75776K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f500000)
+  from space 10752K, 78% used [0x000000076f600000,0x000000076fe413f8,0x0000000770080000)
+  to   space 42496K, 0% used [0x0000000771e80000,0x0000000771e80000,0x0000000774800000)
+ ParOldGen       total 209920K, used 31492K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
+  object space 209920K, 15% used [0x00000006c0000000,0x00000006c1ec11e8,0x00000006ccd00000)
+ Metaspace       used 37084K, capacity 37796K, committed 38016K, reserved 1083392K
+  class space    used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
+}
+
+Deoptimization events (10 events):
+Event: 1012.924 Thread 0x00007fb7d7344800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010e9f3390 method=java.awt.LightweightDispatcher.processMouseEvent(Ljava/awt/event/MouseEvent;)Z @ 52
+Event: 1047.684 Thread 0x00007fb7d7344800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010dd0e4a4 method=java.awt.font.FontRenderContext.equals(Ljava/awt/font/FontRenderContext;)Z @ 53
+Event: 1054.165 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010dd0ceac method=java.awt.EventQueue.setCurrentEventAndMostRecentTimeImpl(Ljava/awt/AWTEvent;)V @ 16
+Event: 1054.205 Thread 0x00007fb7d6996800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010e197614 method=java.util.regex.Matcher.search(I)Z @ 86
+Event: 1054.205 Thread 0x00007fb7d6996800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010e197614 method=java.util.regex.Matcher.search(I)Z @ 86
+Event: 1054.298 Thread 0x00007fb7d6996800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010eacccb4 method=sun.java2d.loops.SurfaceType.pixelFor(ILjava/awt/image/ColorModel;)I @ 6
+Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010e19b9d4 method=java.awt.Component.isShowing()Z @ 20
+Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010ea97958 method=javax.swing.RepaintManager.addDirtyRegion0(Ljava/awt/Container;IIII)V @ 53
+Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010ea60790 method=javax.swing.RepaintManager.addDirtyRegion0(Ljava/awt/Container;IIII)V @ 53
+Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010ea46b30 method=javax.swing.RepaintManager.addDirtyRegion0(Ljava/awt/Container;IIII)V @ 53
+
+Internal exceptions (10 events):
+Event: 23.206 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': com/sun/org/glassfish/hk2/osgiresourcelocator/ServiceLoader> (0x000000076e381ed8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
+Event: 23.208 Thread 0x00007fb7d98fb800 Exception <a 'java/io/FileNotFoundException'> (0x000000076e3d4c68) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
+Event: 23.492 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': com/sun/org/glassfish/hk2/osgiresourcelocator/ServiceLoader> (0x000000076e616378) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
+Event: 23.495 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': javax/servlet/ServletContext> (0x000000076e69f500) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 23.718 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': com/sun/org/glassfish/hk2/osgiresourcelocator/ServiceLoader> (0x000000076e722190) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
+Event: 23.719 Thread 0x00007fb7d98fb800 Exception <a 'java/io/FileNotFoundException'> (0x000000076e772ab8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
+Event: 23.847 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': com/sun/org/glassfish/hk2/osgiresourcelocator/ServiceLoader> (0x000000076e9b3cd8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
+Event: 23.850 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': javax/servlet/ServletContext> (0x000000076ea3ab10) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 28.222 Thread 0x00007fb7d68ba800 Exception <a 'java/io/FileNotFoundException'> (0x000000076b08b318) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
+Event: 1047.684 Thread 0x00007fb7d7344800 Implicit null exception at 0x000000010dd0e2c2 to 0x000000010dd0e48d
+
+Events (10 events):
+Event: 1054.333 loading class jalview/schemes/RNAHelicesColour
+Event: 1054.333 loading class jalview/schemes/RNAHelicesColour done
+Event: 1054.334 loading class jalview/schemes/TCoffeeColourScheme
+Event: 1054.334 loading class jalview/schemes/TCoffeeColourScheme done
+Event: 1054.335 loading class jalview/schemes/Consensus
+Event: 1054.335 loading class jalview/schemes/Consensus done
+Event: 1054.335 loading class jalview/api/analysis/PairwiseScoreModelI
+Event: 1054.335 loading class jalview/api/analysis/PairwiseScoreModelI done
+Event: 1054.355 Executing VM operation: ParallelGCFailedAllocation
+Event: 1054.361 Executing VM operation: ParallelGCFailedAllocation done
+
+
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+
+VM Arguments:
+jvm_args: -Dfile.encoding=UTF-8 
+java_command: jalview.bin.Jalview
+java_class_path (initial): /Users/kjvanderheide/Documents/Jalview development/classes:/Users/kjvanderheide/Documents/Jalview development/lib/activation.jar:/Users/kjvanderheide/Documents/Jalview development/lib/axis.jar:/Users/kjvanderheide/Documents/Jalview development/lib/commons-discovery.jar:/Users/kjvanderheide/Documents/Jalview development/lib/jaxrpc.jar:/Users/kjvanderheide/Documents/Jalview development/lib/jhall.jar:/Users/kjvanderheide/Documents/Jalview development/lib/mail.jar:/Users/kjvanderheide/Documents/Jalview development/lib/regex.jar:/Users/kjvanderheide/Documents/Jalview development/lib/saaj.jar:/Users/kjvanderheide/Documents/Jalview development/lib/wsdl4j.jar:/Users/kjvanderheide/Documents/Jalview development/lib/xercesImpl.jar:/Users/kjvanderheide/Documents/Jalview development/lib/castor-1.1-cycle-xml.jar:/Users/kjvanderheide/Documents/Jalview development/lib/JGoogleAnalytics_0.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/vamsas-client.jar:/Users/kjvanderheide/Documents/Jalview development/lib/commons-logging-1.1.1.jar:/Users/kjvanderheide/Documents/Jalview development/lib/apache-mime4j-0.6.jar:/Users/kjvanderheide/Documents/Jalview development/lib/httpclient-4.0.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/httpcore-4.0.1.jar:/Users/kjvanderheide/Documents/Jalview development/lib/httpmime-4.0.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/miglayout-4.0-swing.jar:/Users/kjvanderheide/Documents/Jalview development/lib/jswingreader-0.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/commons-codec-1.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/jdas-1.0.4.jar:/Users/kjvanderheide/Documents/Jalview development/lib/spring-core-3.0.5.RELEASE.jar:/Users/kjvanderheide/Documents/Jalview development/lib/spring-web-3.0.5.RELEASE.jar:/Users/kjvanderheide/Documents/Jalview development/lib:/Users/kjvanderheide/Documents/Jalview development/lib/jabaws-min-client-2.2.0.jar:/Users/kjvanderhe
+Launcher Type: SUN_STANDARD
+
+Environment Variables:
+PATH=/usr/bin:/bin:/usr/sbin:/sbin
+SHELL=/bin/bash
+
+Signal Handlers:
+SIGSEGV: [libjvm.dylib+0x5b26e5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_ONSTACK|SA_RESTART|SA_SIGINFO
+SIGBUS: [libjvm.dylib+0x5b26e5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGFPE: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGPIPE: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGXFSZ: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGILL: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
+SIGUSR2: [libjvm.dylib+0x488c1e], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
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+SIGINT: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGTERM: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGQUIT: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+
+
+---------------  S Y S T E M  ---------------
+
+OS:Bsduname:Darwin 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
+rlimit: STACK 8192k, CORE 0k, NPROC 709, NOFILE 10240, AS infinity
+load average:1.63 2.07 2.13
+
+CPU:total 8 (initial active 8) (4 cores per cpu, 2 threads per core) family 6 model 70 stepping 1, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, rtm, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2
+
+Memory: 4k page, physical 16777216k(1152628k free)
+
+/proc/meminfo:
+
+
+vm_info: Java HotSpot(TM) 64-Bit Server VM (25.144-b01) for bsd-amd64 JRE (1.8.0_144-b01), built on Jul 21 2017 22:07:42 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
+
+time: Wed Nov 15 14:06:19 2017
+elapsed time: 1054 seconds (0d 0h 17m 34s)
+

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
index 364260e..602d472 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
@@ -2,6 +2,8 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.ExternalTreeBuilderI;
+import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
 import jalview.gui.Desktop;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -87,7 +89,7 @@ public final class ArchaeopteryxInit
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
-    return new AptxBinding(aptxApp, jalviewAlignViewport,
+    return new JalviewBinding(aptxApp, jalviewAlignViewport,
             alignMappedToNodes, nodesMappedToAlign);
   }
 

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
index f010450..7a2ee64 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -2,8 +2,9 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.ForesterDataConversions;
+import jalview.ext.forester.DataConversions;
 import jalview.ext.forester.ForesterMatrix;
+import jalview.ext.treeviewer.ExternalTreeBuilderI;
 import jalview.util.MessageManager;
 
 import java.util.HashMap;
@@ -83,7 +84,7 @@ public class ArchaeopteryxTreeBuilder
 
     for (SequenceI sequence : sequences)
     {
-      Sequence seq = ForesterDataConversions
+      Sequence seq = DataConversions
               .createForesterSequence(sequence, true);
       PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
 

diff --git a/src/jalview/ext/archaeopteryx/AptxBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
similarity index 96%
rename from src/jalview/ext/archaeopteryx/AptxBinding.java
rename to src/jalview/ext/archaeopteryx/JalviewBinding.java
index d82f660..19a66f8 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -4,6 +4,7 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
 import jalview.gui.PaintRefresher;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
@@ -28,7 +29,7 @@ import org.forester.phylogeny.PhylogenyNode;
  * @author kjvanderheide
  *
  */
-public final class AptxBinding
+public final class JalviewBinding
         implements ExternalTreeViewerBindingI<PhylogenyNode>
 {
   private org.forester.archaeopteryx.TreePanel treeView;
@@ -56,7 +57,7 @@ public final class AptxBinding
    *          map with tree nodes and matching sequences used to calculate the
    *          tree as key, value pair respectively.
    */
-  public AptxBinding(final MainFrame archaeopteryx,
+  public JalviewBinding(final MainFrame archaeopteryx,
           final AlignmentViewport jalviewAlignmentViewport,
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
@@ -179,6 +180,7 @@ public final class AptxBinding
   {
     final List<PhylogenyNode> childNodes = PhylogenyMethods
             .getAllDescendants(parentNode);
+    // final BranchColor branchColor = new BranchColor();
 
     for (PhylogenyNode childNode : childNodes)
     {
@@ -186,6 +188,7 @@ public final class AptxBinding
       if (matchingSequence != null)
       {
         treeSelectionChanged(matchingSequence);
+
       }
     }
 

diff --git a/src/jalview/ext/archaeopteryx/AptxNodeAssociation.java b/src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java
similarity index 91%
rename from src/jalview/ext/archaeopteryx/AptxNodeAssociation.java
rename to src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java
index b1dc106..3255c69 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxNodeAssociation.java
+++ b/src/jalview/ext/archaeopteryx/LoadedTreeAssociation.java
@@ -2,7 +2,9 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.ForesterDataConversions;
+import jalview.ext.forester.DataConversions;
+import jalview.ext.treeviewer.ExternalLoadedTreeAssociationI;
+import jalview.ext.treeviewer.ExternalTreeBuilderI;
 
 import java.util.HashMap;
 import java.util.List;
@@ -11,7 +13,7 @@ import java.util.Map;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 
-public class AptxNodeAssociation
+public class LoadedTreeAssociation
         implements ExternalLoadedTreeAssociationI
 {
   SequenceI[] alignSequences;
@@ -22,7 +24,7 @@ public class AptxNodeAssociation
 
   Map<PhylogenyNode, SequenceI> nodesWithAlignment;
 
-  public AptxNodeAssociation(SequenceI[] alignmentSequences,
+  public LoadedTreeAssociation(SequenceI[] alignmentSequences,
           Phylogeny aptxTree)
   {
     alignSequences = alignmentSequences;
@@ -61,7 +63,7 @@ public class AptxNodeAssociation
       nodeSequence = algnIds.findIdMatch(nodeSequenceName);
       if (nodeSequence != null)
       {
-        org.forester.phylogeny.data.Sequence foresterNodeSeq = ForesterDataConversions
+        org.forester.phylogeny.data.Sequence foresterNodeSeq = DataConversions
                 .createForesterSequence(nodeSequence, true);
         treeNode.getNodeData().setSequence(foresterNodeSeq);
 

diff --git a/src/jalview/ext/archaeopteryx/Tree.java b/src/jalview/ext/archaeopteryx/Tree.java
new file mode 100644 (file)
index 0000000..de5f32a
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/Tree.java
@@ -0,0 +1,36 @@
+package jalview.ext.archaeopteryx;
+
+import jalview.ext.treeviewer.ExternalTree;
+import jalview.ext.treeviewer.ExternalTreeNode;
+
+import org.forester.phylogeny.Phylogeny;
+
+public class Tree implements ExternalTree
+{
+  private final Phylogeny tree;
+
+  public Tree(Phylogeny aptxTree)
+  {
+    tree = aptxTree;
+  }
+
+  @Override
+  public Phylogeny getOriginalTree()
+  {
+    return tree;
+  }
+
+  @Override
+  public ExternalTreeNode getRoot()
+  {
+    ExternalTreeNode root = new TreeNode(tree.getRoot());
+    return root;
+  }
+
+  @Override
+  public void setTreeName(String name)
+  {
+    tree.setName(name);
+
+  }
+}

diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java
new file mode 100644 (file)
index 0000000..6c2dbed
--- /dev/null
+++ b/src/jalview/ext/archaeopteryx/TreeNode.java
@@ -0,0 +1,31 @@
+package jalview.ext.archaeopteryx;
+
+import jalview.ext.treeviewer.ExternalTreeNode;
+
+import java.util.List;
+
+import org.forester.phylogeny.PhylogenyNode;
+
+public class TreeNode implements ExternalTreeNode
+{
+  private final PhylogenyNode node;
+
+  public TreeNode(PhylogenyNode aptxNode)
+  {
+    node = aptxNode;
+  }
+
+  @Override
+  public String getNodeName()
+  {
+    return node.getName();
+  }
+
+  @Override
+  public List<ExternalTreeNode> getChildren()
+  {
+    // return node.getDescendants();
+    return null;
+  }
+
+}

diff --git a/src/jalview/ext/forester/ForesterDataConversions.java b/src/jalview/ext/forester/DataConversions.java
similarity index 98%
rename from src/jalview/ext/forester/ForesterDataConversions.java
rename to src/jalview/ext/forester/DataConversions.java
index 6168820..b084382 100644 (file)
--- a/src/jalview/ext/forester/ForesterDataConversions.java
+++ b/src/jalview/ext/forester/DataConversions.java
@@ -6,7 +6,7 @@ import jalview.math.MatrixI;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 
-public final class ForesterDataConversions
+public final class DataConversions
 {
   public static org.forester.phylogeny.data.Sequence createForesterSequence(
           final SequenceI jalviewSequence, final boolean sequenceIsAligned)

diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index 6c60622..a12dc1d 100644 (file)
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -166,7 +166,7 @@ public class ForesterMatrix implements DistanceMatrix
           final MatrixI jalviewInputMatrix,
           final SequenceI[] matrixSequences)
   {
-    return ForesterDataConversions.createForesterDistanceMatrix(
+    return DataConversions.createForesterDistanceMatrix(
             jalviewInputMatrix, matrixSequences);
 
   }
@@ -175,7 +175,7 @@ public class ForesterMatrix implements DistanceMatrix
           final MatrixI jalviewInputMatrix,
           final String[] matrixIdentifiers)
   {
-    return ForesterDataConversions.createForesterDistanceMatrix(
+    return DataConversions.createForesterDistanceMatrix(
             jalviewInputMatrix, matrixIdentifiers);
 
   }

diff --git a/src/jalview/ext/forester/io/ForesterTreeParser.java b/src/jalview/ext/forester/io/TreeParser.java
similarity index 78%
rename from src/jalview/ext/forester/io/ForesterTreeParser.java
rename to src/jalview/ext/forester/io/TreeParser.java
index 85960e0..2c08e99 100644 (file)
--- a/src/jalview/ext/forester/io/ForesterTreeParser.java
+++ b/src/jalview/ext/forester/io/TreeParser.java
@@ -1,8 +1,9 @@
 package jalview.ext.forester.io;
 
-import jalview.ext.archaeopteryx.AptxBinding;
-import jalview.ext.archaeopteryx.AptxNodeAssociation;
+import jalview.ext.archaeopteryx.JalviewBinding;
+import jalview.ext.archaeopteryx.LoadedTreeAssociation;
 import jalview.ext.archaeopteryx.ArchaeopteryxInit;
+import jalview.ext.treeviewer.ExternalTreeParserI;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
@@ -15,13 +16,13 @@ import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.archaeopteryx.MainFrame;
 import org.forester.util.ForesterUtil;
 
-public class ForesterTreeParser implements ExternalTreeParserI<MainFrame>
+public class TreeParser implements ExternalTreeParserI<MainFrame>
 {
   private final String filePath;
 
   private final File file;
 
-  public ForesterTreeParser(final String treeFilePath)
+  public TreeParser(final String treeFilePath)
   {
     final String possibleError = ForesterUtil.isReadableFile(treeFilePath);
     if (possibleError != null)
@@ -37,7 +38,7 @@ public class ForesterTreeParser implements ExternalTreeParserI<MainFrame>
 
   }
 
-  public ForesterTreeParser(final File treeFile) throws IOException
+  public TreeParser(final File treeFile) throws IOException
   {
     final String possibleError = ForesterUtil.isReadableFile(treeFile);
     if (possibleError != null)
@@ -58,12 +59,12 @@ public class ForesterTreeParser implements ExternalTreeParserI<MainFrame>
         "_aptx_jalview_configuration_file", filePath };
     MainFrame aptx = Archaeopteryx.main(AptxArgs);
 
-    AptxNodeAssociation bindAptxNodes = new AptxNodeAssociation(
+    LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
             viewport.getAlignment().getSequencesArray(),
             aptx.getMainPanel().getCurrentTreePanel().getPhylogeny());
 
     bindAptxNodes.associateLeavesToSequences();
-    new AptxBinding(aptx, viewport, bindAptxNodes.getAlignmentWithNodes(),
+    new JalviewBinding(aptx, viewport, bindAptxNodes.getAlignmentWithNodes(),
             bindAptxNodes.getNodesWithAlignment());
 
     ArchaeopteryxInit.bindFrameToJalview(aptx);

diff --git a/src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java b/src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java
similarity index 72%
rename from src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java
rename to src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java
index cf58e46..83ffac6 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java
+++ b/src/jalview/ext/treeviewer/ExternalLoadedTreeAssociationI.java
@@ -1,4 +1,4 @@
-package jalview.ext.archaeopteryx;
+package jalview.ext.treeviewer;
 
 /**
  * Interface for associating the leaves of a loaded in (not calculated) tree to
@@ -8,7 +8,7 @@ package jalview.ext.archaeopteryx;
  *
  * 
  */
-interface ExternalLoadedTreeAssociationI
+public interface ExternalLoadedTreeAssociationI
 {
   public void associateLeavesToSequences();
 }

diff --git a/src/jalview/ext/treeviewer/ExternalTree.java b/src/jalview/ext/treeviewer/ExternalTree.java
new file mode 100644 (file)
index 0000000..02b4a0a
--- /dev/null
+++ b/src/jalview/ext/treeviewer/ExternalTree.java
@@ -0,0 +1,11 @@
+package jalview.ext.treeviewer;
+
+public interface ExternalTree
+{
+  public void setTreeName(String name);
+
+  public <T> T getOriginalTree();
+
+  public ExternalTreeNode getRoot();
+
+}

diff --git a/src/jalview/ext/archaeopteryx/ExternalTreeBuilderI.java b/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java
similarity index 93%
rename from src/jalview/ext/archaeopteryx/ExternalTreeBuilderI.java
rename to src/jalview/ext/treeviewer/ExternalTreeBuilderI.java
index d30be0e..27659d7 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ExternalTreeBuilderI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeBuilderI.java
@@ -1,4 +1,4 @@
-package jalview.ext.archaeopteryx;
+package jalview.ext.treeviewer;
 
 import jalview.datamodel.SequenceI;
 
@@ -16,7 +16,7 @@ import java.util.Map;
  * @param <N>
  *          Tree node object that the tree viewer requires.
  */
-interface ExternalTreeBuilderI<T, N>
+public interface ExternalTreeBuilderI<T, N>
 {
   public T buildTree(N treeRoot);
 

diff --git a/src/jalview/ext/treeviewer/ExternalTreeNode.java b/src/jalview/ext/treeviewer/ExternalTreeNode.java
new file mode 100644 (file)
index 0000000..8d6f3b8
--- /dev/null
+++ b/src/jalview/ext/treeviewer/ExternalTreeNode.java
@@ -0,0 +1,10 @@
+package jalview.ext.treeviewer;
+
+import java.util.List;
+
+public interface ExternalTreeNode
+{
+  public String getNodeName();
+
+  public List<ExternalTreeNode> getChildren();
+}

diff --git a/src/jalview/ext/treeviewer/ExternalTreePanel.java b/src/jalview/ext/treeviewer/ExternalTreePanel.java
new file mode 100644 (file)
index 0000000..e736410
--- /dev/null
+++ b/src/jalview/ext/treeviewer/ExternalTreePanel.java
@@ -0,0 +1,6 @@
+package jalview.ext.treeviewer;
+
+public interface ExternalTreePanel
+{
+
+}

diff --git a/src/jalview/ext/forester/io/ExternalTreeParserI.java b/src/jalview/ext/treeviewer/ExternalTreeParserI.java
similarity index 91%
rename from src/jalview/ext/forester/io/ExternalTreeParserI.java
rename to src/jalview/ext/treeviewer/ExternalTreeParserI.java
index e1210d1..ee466e8 100644 (file)
--- a/src/jalview/ext/forester/io/ExternalTreeParserI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeParserI.java
@@ -1,4 +1,4 @@
-package jalview.ext.forester.io;
+package jalview.ext.treeviewer;
 
 import jalview.viewmodel.AlignmentViewport;
 

diff --git a/src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java b/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java
similarity index 96%
rename from src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java
rename to src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java
index 8acbbf0..57b71f2 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java
@@ -18,7 +18,7 @@
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-package jalview.ext.archaeopteryx;
+package jalview.ext.treeviewer;
 
 import jalview.datamodel.SequenceI;
 import jalview.structure.SelectionListener;
@@ -40,7 +40,7 @@ import java.awt.event.MouseListener;
  * @param <N>
  *          Tree node object.
  */
-interface ExternalTreeViewerBindingI<N>
+public interface ExternalTreeViewerBindingI<N>
         extends ActionListener, MouseListener, SelectionListener,
         SelectionSource
 {

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fa3f489..5dbfb41 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -60,9 +60,9 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.io.ExternalTreeParserI;
-import jalview.ext.forester.io.ForesterTreeParser;
+import jalview.ext.forester.io.TreeParser;
 import jalview.ext.forester.io.SupportedTreeFileFilter;
+import jalview.ext.treeviewer.ExternalTreeParserI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
@@ -3771,6 +3771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         @Override
         public void actionPerformed(ActionEvent e)
         {
+          // adapt to Aptx
           tp.sortByTree_actionPerformed();
           addHistoryItem(tp.sortAlignmentIn(alignPanel));
 
@@ -3903,7 +3904,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       NewickFile fin = null;
       try
       {
-        ExternalTreeParserI<?> treeParser = new ForesterTreeParser(
+        ExternalTreeParserI<?> treeParser = new TreeParser(
                 filePath);
         treeParser.loadTree(viewport);