From: kjvdheide Date: Fri, 17 Nov 2017 13:34:22 +0000 (+0000) Subject: Merge branch 'kjvdh/features/PhylogenyViewer' of X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=91bea2a1185e438bfd52fc1848cf615068016192;hp=7bf767decd23672a1b5eb67974c99f58c54f788f;p=jalview.git Merge branch 'kjvdh/features/PhylogenyViewer' of https://source.jalview.org/git/jalview.git into kjvdh/features/PhylogenyViewer Conflicts: src/jalview/ext/archaeopteryx/AptxBinding.java src/jalview/ext/forester/io/ExternalTreeParserI.java src/jalview/ext/forester/io/ForesterTreeParser.java --- diff --git a/.classpath b/.classpath index b86c3b2..42e9500 100644 --- a/.classpath +++ b/.classpath @@ -70,6 +70,5 @@ - diff --git a/_aptx_jalview_configuration_file.txt b/_aptx_jalview_configuration_file.txt index 03788f9..ec248ac 100644 --- a/_aptx_jalview_configuration_file.txt +++ b/_aptx_jalview_configuration_file.txt @@ -266,7 +266,7 @@ click_to: select_nodes display click_to: get_ext_descendents_data display # Default click-to option (any of the above if set to "display") -default_click_to: display_node_data +default_click_to: select_nodes @@ -283,8 +283,8 @@ display_color: branch 0x000000 display_color: node_box 0x000000 display_color: collapsed 0x000000 display_color: matching_a 0xCC6600 -display_color: matching_b 0x0000CC -display_color: matching_a_and_b 0xCC70CC +display_color: matching_b 0xCC70CC +display_color: matching_a_and_b 0x0000CC display_color: duplication 0xFF00FF display_color: speciation 0xFFFF00 display_color: duplication_or_specation 0xFFAA20 diff --git a/forester b/forester index b977efb..eb22dac 160000 --- a/forester +++ b/forester @@ -1 +1 @@ -Subproject commit b977efb66f2d0b539bd433e80762737925035edc +Subproject commit eb22dac14771c467104f57362e3a624d0140f897 diff --git a/hs_err_pid28190.log b/hs_err_pid28190.log new file mode 100644 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 (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 (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 (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 (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 (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 (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 (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 (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 (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 + + +Dynamic libraries: +0x000000004dd98000 /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa +0x000000004dd98000 /System/Library/Frameworks/Security.framework/Versions/A/Security +0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices +0x000000004dd98000 /usr/lib/libz.1.dylib +0x000000004dd98000 /usr/lib/libSystem.B.dylib 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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 +SIGHUP: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO +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/Aptx.java b/src/jalview/ext/archaeopteryx/Aptx.java new file mode 100644 index 0000000..640dd31 --- /dev/null +++ b/src/jalview/ext/archaeopteryx/Aptx.java @@ -0,0 +1,17 @@ +package jalview.ext.archaeopteryx; + +import jalview.ext.treeviewer.ExternalTreeViewerI; + +import org.forester.archaeopteryx.MainFrame; + +public class Aptx implements ExternalTreeViewerI +{ + private final MainFrame aptxApp; + + public Aptx(MainFrame aptx) + { + aptxApp = aptx; + + + } +} diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java similarity index 89% rename from src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java rename to src/jalview/ext/archaeopteryx/AptxInit.java index 364260e..ce34573 100644 --- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java +++ b/src/jalview/ext/archaeopteryx/AptxInit.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; @@ -20,7 +22,7 @@ import org.forester.phylogeny.PhylogenyNode; * @author kjvanderheide * */ -public final class ArchaeopteryxInit +public final class AptxInit { /** * Test method, should generally not be used as it does not bind the tree to @@ -54,7 +56,7 @@ public final class ArchaeopteryxInit public static MainFrame createInstance( final TreeBuilder calculatedTree) // very dense method, to be split up { - ExternalTreeBuilderI aptxTreeBuilder = new ArchaeopteryxTreeBuilder( + ExternalTreeBuilderI aptxTreeBuilder = new AptxTreeBuilder( calculatedTree); Phylogeny aptxTree = aptxTreeBuilder.buildTree(); @@ -87,7 +89,7 @@ public final class ArchaeopteryxInit final Map alignMappedToNodes, final Map nodesMappedToAlign) { - return new AptxBinding(aptxApp, jalviewAlignViewport, + return new JalviewBinding(aptxApp, jalviewAlignViewport, alignMappedToNodes, nodesMappedToAlign); } @@ -97,6 +99,8 @@ public final class ArchaeopteryxInit int width = 400; int height = 550; aptxApp.setMinimumSize(new Dimension(width, height)); + // aptxApp.setFont(Desktop.instance.getFont()); + // aptxApp.getMainPanel().setFont(Desktop.instance.getFont()); Desktop.addInternalFrame(aptxApp, "Archaeopteryx Tree View", true, width, height, true, true); diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java similarity index 94% rename from src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java rename to src/jalview/ext/archaeopteryx/AptxTreeBuilder.java index f010450..7b03d5c 100644 --- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java +++ b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.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; @@ -25,7 +26,7 @@ import org.forester.phylogeny.data.Sequence; * @author kjvanderheide * */ -public class ArchaeopteryxTreeBuilder +public class AptxTreeBuilder implements ExternalTreeBuilderI { protected final SequenceI[] sequences; @@ -44,7 +45,7 @@ public class ArchaeopteryxTreeBuilder private final Map nodesWithAlignment; - public ArchaeopteryxTreeBuilder(final TreeBuilder calculatedTree) + public AptxTreeBuilder(final TreeBuilder calculatedTree) { jalviewTree = calculatedTree; sequences = jalviewTree.getSequences(); @@ -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/AptxTreePanel.java b/src/jalview/ext/archaeopteryx/AptxTreePanel.java new file mode 100644 index 0000000..631ff15 --- /dev/null +++ b/src/jalview/ext/archaeopteryx/AptxTreePanel.java @@ -0,0 +1,14 @@ +package jalview.ext.archaeopteryx; + +import jalview.ext.treeviewer.ExternalTreePanelI; + +public class AptxTreePanel implements ExternalTreePanelI +{ + private final org.forester.archaeopteryx.TreePanel treeView; + + public AptxTreePanel(org.forester.archaeopteryx.TreePanel aptxTreePanel) + { + treeView = aptxTreePanel; + + } +} diff --git a/src/jalview/ext/archaeopteryx/AptxBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java similarity index 97% rename from src/jalview/ext/archaeopteryx/AptxBinding.java rename to src/jalview/ext/archaeopteryx/JalviewBinding.java index 24f75bc..ee349b6 100644 --- 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 { 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 alignMappedToNodes, final Map nodesMappedToAlign) @@ -177,15 +178,17 @@ public final class AptxBinding @Override public void showMatchingChildSequences(final PhylogenyNode parentNode) { - final List childNodes = PhylogenyMethods + List childNodes = PhylogenyMethods .getAllDescendants(parentNode); for (PhylogenyNode childNode : childNodes) { + SequenceI matchingSequence = nodesBoundToSequences.get(childNode); if (matchingSequence != null) { treeSelectionChanged(matchingSequence); + } } @@ -224,7 +227,6 @@ public final class AptxBinding { this.parentAvport = parentAvport; } - // av.setCurrentTree(tree); // // /* @@ -298,7 +300,6 @@ public final class AptxBinding // PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); // repaint(); // } - } 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..adea693 100644 --- 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 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); @@ -77,6 +79,8 @@ public class AptxNodeAssociation } + + public Map getAlignmentWithNodes() { return alignmentWithNodes; diff --git a/src/jalview/ext/archaeopteryx/Tree.java b/src/jalview/ext/archaeopteryx/Tree.java new file mode 100644 index 0000000..884a359 --- /dev/null +++ b/src/jalview/ext/archaeopteryx/Tree.java @@ -0,0 +1,50 @@ +package jalview.ext.archaeopteryx; + +import jalview.ext.treeviewer.ExternalTreeI; +import jalview.ext.treeviewer.ExternalTreeNodeI; + +import org.forester.phylogeny.Phylogeny; + +public class Tree implements ExternalTreeI +{ + private final Phylogeny tree; + + public Tree(Phylogeny aptxTree) + { + tree = aptxTree; + } + + @Override + public Phylogeny getOriginalTree() + { + return tree; + + } + + @Override + public ExternalTreeNodeI getRoot() + { + ExternalTreeNodeI root = new TreeNode(tree.getRoot()); + return root; + } + + @Override + public void setTreeName(String name) + { + tree.setName(name); + + } + + @Override + public ExternalTreeNodeI getNodeWithName(String name) + { + return new TreeNode(tree.getNode(name)); + + } + + @Override + public String[] getAllLeafNames() + { + return tree.getAllExternalNodeNames(); + } +} diff --git a/src/jalview/ext/archaeopteryx/TreeNode.java b/src/jalview/ext/archaeopteryx/TreeNode.java new file mode 100644 index 0000000..8e06d6c --- /dev/null +++ b/src/jalview/ext/archaeopteryx/TreeNode.java @@ -0,0 +1,38 @@ +package jalview.ext.archaeopteryx; + +import jalview.ext.treeviewer.ExternalTreeNodeI; + +import java.util.List; + +import org.forester.phylogeny.PhylogenyNode; + +public class TreeNode implements ExternalTreeNodeI +{ + private final PhylogenyNode node; + + public TreeNode(PhylogenyNode aptxNode) + { + node = aptxNode; + } + + @Override + public PhylogenyNode getOriginalNode() + { + return node; + } + + @Override + public String getNodeName() + { + return node.getName(); + } + + @Override + public List 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 --- 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 --- 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 88% rename from src/jalview/ext/forester/io/ForesterTreeParser.java rename to src/jalview/ext/forester/io/TreeParser.java index 411f5a2..54f79bc 100644 --- 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.ArchaeopteryxInit; +import jalview.ext.archaeopteryx.AptxInit; +import jalview.ext.archaeopteryx.JalviewBinding; +import jalview.ext.archaeopteryx.LoadedTreeAssociation; +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 +public class TreeParser implements ExternalTreeParserI { 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 } - public ForesterTreeParser(final File treeFile) throws IOException + public TreeParser(final File treeFile) throws IOException { final String possibleError = ForesterUtil.isReadableFile(treeFile); if (possibleError != null) @@ -58,15 +59,16 @@ public class ForesterTreeParser implements ExternalTreeParserI "_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); + AptxInit.bindFrameToJalview(aptx); return 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 --- 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/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 --- 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 * Tree node object that the tree viewer requires. */ -interface ExternalTreeBuilderI +public interface ExternalTreeBuilderI { public T buildTree(N treeRoot); diff --git a/src/jalview/ext/treeviewer/ExternalTreeI.java b/src/jalview/ext/treeviewer/ExternalTreeI.java new file mode 100644 index 0000000..0184227 --- /dev/null +++ b/src/jalview/ext/treeviewer/ExternalTreeI.java @@ -0,0 +1,15 @@ +package jalview.ext.treeviewer; + +public interface ExternalTreeI +{ + public void setTreeName(String name); + + public T getOriginalTree(); + + public ExternalTreeNodeI getRoot(); + + public ExternalTreeNodeI getNodeWithName(String name); + + public String[] getAllLeafNames(); + +} diff --git a/src/jalview/ext/treeviewer/ExternalTreeNodeI.java b/src/jalview/ext/treeviewer/ExternalTreeNodeI.java new file mode 100644 index 0000000..34f45bd --- /dev/null +++ b/src/jalview/ext/treeviewer/ExternalTreeNodeI.java @@ -0,0 +1,12 @@ +package jalview.ext.treeviewer; + +import java.util.List; + +public interface ExternalTreeNodeI +{ + public N getOriginalNode(); + + public String getNodeName(); + + public List getChildren(); +} diff --git a/src/jalview/ext/treeviewer/ExternalTreePanelI.java b/src/jalview/ext/treeviewer/ExternalTreePanelI.java new file mode 100644 index 0000000..c488683 --- /dev/null +++ b/src/jalview/ext/treeviewer/ExternalTreePanelI.java @@ -0,0 +1,6 @@ +package jalview.ext.treeviewer; + +public interface ExternalTreePanelI +{ + +} 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 7804fb8..defd744 100644 --- 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 --- a/src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java +++ b/src/jalview/ext/treeviewer/ExternalTreeViewerBindingI.java @@ -18,7 +18,7 @@ * along with Jalview. If not, see . * 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 * Tree node object. */ -interface ExternalTreeViewerBindingI +public interface ExternalTreeViewerBindingI extends ActionListener, MouseListener, SelectionListener, SelectionSource { diff --git a/src/jalview/ext/treeviewer/ExternalTreeViewerI.java b/src/jalview/ext/treeviewer/ExternalTreeViewerI.java new file mode 100644 index 0000000..20c47f6 --- /dev/null +++ b/src/jalview/ext/treeviewer/ExternalTreeViewerI.java @@ -0,0 +1,6 @@ +package jalview.ext.treeviewer; + +public interface ExternalTreeViewerI +{ + +} diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 1c19eb1..71f240b 100644 --- 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.SupportedTreeFileFilter; +import jalview.ext.forester.io.TreeParser; +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.loadTreeFile(viewport); diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 11ee1a0..30a9b3d 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -28,7 +28,7 @@ import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; import jalview.datamodel.SequenceGroup; -import jalview.ext.archaeopteryx.ArchaeopteryxInit; +import jalview.ext.archaeopteryx.AptxInit; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -497,7 +497,7 @@ public class CalculationChooser extends JPanel substitutionMatrix, params); TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport()); - ArchaeopteryxInit.createInstance(calculatedTree); + AptxInit.createInstance(calculatedTree); TreeModel tree = new TreeModel(calculatedTree); openTreePanel(tree, treeAlgo, substitutionMatrix); diff --git a/test/jalview/ext/archaeopteryx/AptxJalviewSequenceTreeTest.java b/test/jalview/ext/archaeopteryx/AptxJalviewSequenceTreeTest.java index 569855c..e7324eb 100644 --- a/test/jalview/ext/archaeopteryx/AptxJalviewSequenceTreeTest.java +++ b/test/jalview/ext/archaeopteryx/AptxJalviewSequenceTreeTest.java @@ -60,7 +60,7 @@ public class AptxJalviewSequenceTreeTest extends TreeViewTest @BeforeClass(dependsOnMethods = { "setUpTree" }) public void createTreeView() { - treeView = ArchaeopteryxInit.createInstance(jalviewTree); + treeView = AptxInit.createInstance(jalviewTree); aptx = (MainFrame) treeView; // still pretty ugly treePanel = aptx.getMainPanel().getCurrentTreePanel(); diff --git a/test/jalview/ext/archaeopteryx/AptxPhylogenyTreeTest.java b/test/jalview/ext/archaeopteryx/AptxPhylogenyTreeTest.java index 921150c..9d62eb1 100644 --- a/test/jalview/ext/archaeopteryx/AptxPhylogenyTreeTest.java +++ b/test/jalview/ext/archaeopteryx/AptxPhylogenyTreeTest.java @@ -61,7 +61,7 @@ public class AptxPhylogenyTreeTest extends TreeViewTest @BeforeClass(dependsOnMethods = { "setUpJalview", "setUpTree" }) public void createTreeView() { - treeView = ArchaeopteryxInit.createUnboundInstance(inputTree); + treeView = AptxInit.createUnboundInstance(inputTree); aptx = (MainFrame) treeView; // pretty ugly treePanel = aptx.getMainPanel().getCurrentTreePanel(); tree = treePanel.getPhylogeny();