<classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
<classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
<classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
+ <classpathentry kind="lib" path="lib/forester.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
<name>Jalview Release 2.7</name>
<comment></comment>
<projects>
+ <project>forester</project>
</projects>
<buildSpec>
<buildCommand>
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.7
+org.eclipse.jdt.core.compiler.compliance=1.8
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.source=1.7
+org.eclipse.jdt.core.compiler.source=1.8
+org.eclipse.jdt.core.formatter.align_fields_grouping_blank_lines=2147483647
org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=52
org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=80
org.eclipse.jdt.core.formatter.alignment_for_enum_constants=16
org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=16
+org.eclipse.jdt.core.formatter.alignment_for_expressions_in_for_loop_header=0
org.eclipse.jdt.core.formatter.alignment_for_method_declaration=0
org.eclipse.jdt.core.formatter.alignment_for_multiple_fields=16
+org.eclipse.jdt.core.formatter.alignment_for_parameterized_type_references=0
org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16
org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16
org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration=16
org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration=16
+org.eclipse.jdt.core.formatter.alignment_for_type_arguments=0
+org.eclipse.jdt.core.formatter.alignment_for_type_parameters=0
org.eclipse.jdt.core.formatter.alignment_for_union_type_in_multicatch=16
org.eclipse.jdt.core.formatter.blank_lines_after_imports=1
org.eclipse.jdt.core.formatter.blank_lines_after_package=1
org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=next_line
org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=false
org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false
+org.eclipse.jdt.core.formatter.comment.count_line_length_from_starting_position=false
org.eclipse.jdt.core.formatter.comment.format_block_comments=false
org.eclipse.jdt.core.formatter.comment.format_header=false
org.eclipse.jdt.core.formatter.comment.format_html=true
org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases=true
org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch=false
org.eclipse.jdt.core.formatter.indentation.size=8
+org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_enum_constant=insert
org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field=insert
org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable=insert
org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method=insert
org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false
org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0
org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1
+org.eclipse.jdt.core.formatter.parentheses_positions_in_annotation=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_catch_clause=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_if_while_statement=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_lambda_declaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_method_delcaration=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement=common_lines
+org.eclipse.jdt.core.formatter.parentheses_positions_in_try_clause=common_lines
org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=true
org.eclipse.jdt.core.formatter.tabulation.char=space
org.eclipse.jdt.core.formatter.tabulation.size=2
org.eclipse.jdt.core.formatter.use_on_off_tags=true
org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
+org.eclipse.jdt.core.formatter.wrap_before_assignment_operator=false
org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
+org.eclipse.jdt.core.formatter.wrap_before_conditional_operator=true
org.eclipse.jdt.core.formatter.wrap_before_or_operator_multicatch=true
org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true
+org.eclipse.jdt.core.javaFormatter=org.eclipse.jdt.core.defaultJavaFormatter
eclipse.preferences.version=1
editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
formatter_profile=_Jalview
-formatter_settings_version=12
+formatter_settings_version=13
org.eclipse.jdt.ui.ignorelowercasenames=true
org.eclipse.jdt.ui.importorder=jalview;java;javax;org;com;
org.eclipse.jdt.ui.ondemandthreshold=99
<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
<property name="j2sev" value="1.7+" />
<!-- Java Compilation settings - source and target javac version -->
- <property name="javac.source" value="1.7" />
- <property name="javac.target" value="1.7" />
+ <property name="javac.source" value="1.8" />
+ <property name="javac.target" value="1.8" />
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<offline_allowed />
</information>
<resources>
- <j2se version="1.7+" />
+ <j2se version="1.8+" />
<jar main="true" href="jalview.jar"/>
<fileset dir="${packageDir}">
<exclude name="jalview.jar" />
<jnlpf toFile="${jnlpFile}" />
<!-- add the add-modules j2se attribute for java 9 -->
- <replace file="${jnlpFile}" value="j2se version="1.7+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
- <replacetoken>j2se version="1.7+"</replacetoken>
-
+ <replace file="${jnlpFile}" value="j2se version="1.8+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee"">
+ <replacetoken>j2se version="1.8+"</replacetoken>
</replace>
</target>
<include name="plugin.jar" />
</fileset>
</path>
- <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
<proguard verbose="true" >
<injar file="in.jar" />
--- /dev/null
+#
+# 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
+
+
+Dynamic libraries:
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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
+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)
+
--- /dev/null
+# PLEASE DON'T MOVE ME
+# User Interface Look and Feel
+# ----------------------------
+# Possible values for 'native_ui'
+# 'yes' to use native (system) "look and feel"
+# 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
+# '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
+# Archaeopteryx-style "look and feel" otherwise
+
+native_ui: yes
+
+
+
+# Default Values for Options
+# --------------------------
+# Minimal confidence value to be displayed: 'min_confidence_value':
+# Example: 'min_confidence_value: 50.0' (a commonly used
+# value for bootstrap support)
+#
+# Font family name: 'font_family':
+# Example: 'font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica'
+# It is advisable to use more than one value for font_family (in
+# decreasing order of preference). Font family names have to be
+# comma separated (no spaces). Spaces in font names have to be
+# replaced by underscores (e.g. 'Arial_Unicode_MS').
+#
+# Font size: 'font_size':
+# Example: 'font_size: 10'
+#
+# Screen antialias: 'antialias_screen': values: 'yes'/'no'
+#
+# Show Scale: 'show_scale': values: 'yes'/'no'
+#
+# Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
+#
+# Cladogram display type: 'cladogram_type'
+# Example: 'cladogram_type: non_lined_up'
+# The three possible values are: lined_up
+# non_lined_up
+#
+# Default line width for PDF export: 'pdf_export_line_wdith':
+# Example: 'pdf_export_line_width: 0.5'
+#
+# Show overview: 'show_overview': values: 'yes'/'no'
+#
+# Phylogeny graphics type: 'phylogeny_graphics_type':
+# Example: 'phylogeny_graphics_type: euro_style'
+# The eight possible values are: rectangular
+# euro_style
+# rounded
+# curved
+# triangular
+# convex
+# unrooted
+# circular
+#
+# Node label direction for circular and unrooted type: 'node_label_direction':
+# Example: 'node_label_direction: horizontal'
+# The two possible values are: horizontal
+# radial
+#
+# Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
+#
+# Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
+#
+# Default node shape size: 'default_node_size'
+# Example: 'default_node_size: 6'
+#
+# Default node shape type: 'default_node_shape'
+# Example: 'default_node_shape: '
+# Possible values: circle
+# rectangle
+#
+# Default node shape fill: 'default_node_fill'
+# Example: 'default_node_fill: '
+# Possible values: solid
+# gradient
+# none
+#
+# To determine what data field to return by clicking on "List Node Data": 'list_node_data_field'
+# Possible values: node_name
+# sequence_name
+# gene_name
+# sequence_acc
+# sequence_mol_seq_fasta
+# sequence_symbol
+# taxonomy_scientific_name
+# taxonomy_code
+# domains
+# domains_collapsed
+# seq_annotations
+# go_term_ids
+# user_selected
+#
+# To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in'
+# Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
+# classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
+# Possible values: window (for output to window and buffer)
+# console (for output to console and buffer)
+# buffer_only (for output to buffer only)
+#
+# To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label'
+# Example: 'list_node_data_custom_label: Get_Node_Data'
+#
+# Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
+#
+# Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
+#
+# Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
+#
+# Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no'
+#
+# Number of fraction digits for branch length values: 'branch_length_value_digits'
+#
+# Number of fraction digits for confidence values: 'confidence_value_digits'
+#
+# To turn on/off background color gradient: background_gradient
+# Example: 'background_gradient: yes'
+#
+# To allow/not allow editing (cut, copy, and paste): allow_editing
+# Example: 'allow_editing: yes'
+#
+# To allow/not allow thicker strokes for very small trees: allow_thick_strokes
+# Example: 'allow_thick_strokes: yes'
+#
+# NH/NHX/Nexus file parsing
+# -------------------------
+# To replace underscores with spaces during NH/NHX/Nexus file parsing:
+# 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
+#
+# To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
+# from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
+# possible values are:
+# 'no'
+# 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
+# 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
+# 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
+#
+# Internal node labels are confidence values during NH/NHX/Nexus file parsing:
+# 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
+#
+# phyloXML parsing
+# ----------------
+# To ensure compatibility with all current and future
+# phyloXML applications and to detect malformatted and
+# possibly erroneous data, it is strongly recommended
+# to enable validation of all phyloXML files
+# against the XSD Schema (see: http://www.phyloxml.org/),
+# with:
+# 'validate_against_phyloxml_xsd_schema: true'
+
+
+min_confidence_value: 0.0
+font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
+font_size: 12
+font_size_min: 2
+font_size_max: 20
+antialias_screen: yes
+show_scale: yes
+cladogram_type: non_lined_up
+phylogeny_graphics_type: rectangular
+node_label_direction: horizontal
+show_default_node_shapes_internal: yes
+show_default_node_shapes_external: yes
+show_node_shapes_for_nodes_with_vis_data: yes
+default_node_size: 5
+default_node_shape: rectangle
+default_node_fill: solid
+pdf_export_line_width: 0.5
+show_overview: yes
+overview_width: 120
+overview_height: 120
+overview_placement_type: upper_right
+color_labels_same_as_branch_length_values: no
+display_sequence_relations: no
+show_domain_labels: yes
+line_up_renderable_data: yes
+right_align_domain_architectures: no
+show_seq_annotation_ref_sources: yes
+branch_length_value_digits: 3
+confidence_value_digits: 2
+background_gradient: no
+allow_editing: yes
+allow_thick_strokes: no
+list_node_data_in: window
+list_node_data_field: user_selected
+list_node_data_custom_label:
+# NH/NHX/Nexus file parsing:
+internal_labels_are_confidence_values: no
+replace_underscores_in_nh_parsing: no
+taxonomy_extraction_in_nh_parsing: no
+# phyloXML parsing:
+validate_against_phyloxml_xsd_schema: true
+
+
+# Checkbox Display Selection
+# --------------------------
+# This is used to select which checkboxes to display
+# and what their initial values should be.
+# Format: 'name: display|nodisplay yes|no'
+# Note: if an option is not displayed, it will not be enabled
+#
+# For the following use '?' to let Archaeopteryx decide (depending on tree):
+# - 'phylogram'
+# - 'write_confidence_values'
+# - 'write_events'
+
+phylogram: display ?
+rollover: display yes
+color_according_to_sequence: display no
+color_according_to_species: display no
+color_according_to_annotation: display no
+show_node_names: display yes
+show_seq_names: display yes
+show_seq_symbols: display yes
+show_seq_acc: display no
+show_gene_names: display yes
+show_taxonomy_code: display yes
+show_taxonomy_scientific_names: display yes
+show_taxonomy_rank: display no
+show_taxonomy_common_names: display no
+show_taxonomy_images: display no
+show_annotations: display no
+write_confidence_values: display ?
+write_branch_length_values: display yes
+write_events: display ?
+use_visual_styles: display yes
+width_branches: display no
+show_domain_architectures: display no
+show_msa: display no
+show_binary_characters: display no
+show_binary_character_counts: display no
+display_internal_data: display yes
+dynamically_hide_data: display yes
+show_relation_confidence: display no
+show_properties: display no
+show_vector_data: display no
+
+
+
+# Combo-box Display Selection
+# ---------------------------
+# Format: 'name: display/nodisplay'
+click_to: display_node_data display
+click_to: collapse_uncollapse display
+click_to: uncollapse_all display
+click_to: reroot display
+click_to: subtree display
+click_to: swap display
+click_to: order_subtree display
+click_to: sort_descendants display
+click_to: color_subtree display
+click_to: change_node_font display
+click_to: color_node_font display
+click_to: open_seq_web display
+click_to: open_pdb_web display
+click_to: open_tax_web display
+click_to: blast display
+click_to: cut_subtree display
+click_to: copy_subtree display
+click_to: paste_subtree display
+click_to: delete display
+click_to: add_new_node display
+click_to: edit_node_data display
+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: select_nodes
+
+
+
+# Default Tree Display Colors
+# ---------------------------
+
+display_color: background 0xFFFFFF
+display_color: background_gradient_bottom 0xFFFFFF
+display_color: sequence 0x111111
+display_color: taxonomy 0x8D8D8D
+display_color: confidence 0xAEAEAE
+display_color: branch_length 0x3A3A3A
+display_color: branch 0x000000
+display_color: node_box 0x000000
+display_color: collapsed 0x000000
+display_color: matching_a 0xCC6600
+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
+display_color: domain_label 0x939393
+display_color: domain_base 0x505050
+display_color: binary_domain_combinations 0x4169FF
+display_color: annotation 0xFFCC00
+display_color: overview 0x828282
+
+
+
+# GUI (graphical user interface) Colors
+# -------------------------------------
+#
+# These are ignored if native (system) "look and feel"
+# is being used ('native_ui: yes').
+
+gui_background_color: 0x202020
+gui_checkbox_text_color: 0xDCDCDC
+gui_checkbox_and_button_active_color: 0xFF0000
+gui_button_text_color: 0xFFFFFF
+gui_button_background_color: 0x404040
+gui_menu_background_color: 0x000000
+gui_menu_text_color: 0xFFFFFF
+gui_button_border_color: 0x000000
+
+
+# Vector Data Display Colors and Sizes
+# ------------------------------------
+vector_data_min_color: 0x0000FF
+vector_data_max_color: 0xFFFF00
+vector_data_mean_color: 0x000000
+vector_data_width: 120
+vector_data_height: 12
+
+
+# Settings Specific for Archaeopteryx Applets (E and A)
+# -----------------------------------------------------
+# To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
+
+midpoint_reroot: yes
+
+
+
+# Settings Specific for ArchaeopteryxE Applets
+# --------------------------------------------
+# To hide controls and menus: 'hide_controls_and_menus: yes'
+# To use tabbed display : 'use_tabbed_display: yes'
+
+hide_controls_and_menus: no
+use_tabbed_display: yes
+
+
+
+# Settings For Phylogenetic Inference
+# -----------------------------------
+# EXPERIMENTAL: DO NOT USE!!
+
+default_number_of_bootstrap_resamples: 100
+mafft_local: /bin/mafft
+fastme_local: /bin/fastme
+raxml_local: /bin/raxml
+
+
+
+# Sequence colors
+# ---------------
+# Format: species_color: sequencename hexcolor
+sequence_color: Tubulin-alpha 0xEE0000
+sequence_color: Tubulin-beta 0x00EE00
+
+
+# Species colors
+# --------------
+# Format: species_color: speciesname hexcolor
+species_color: BRAFL 0x00FFFF
+species_color: SPHGR 0x9620F0
+species_color: STRPU 0x9620F0
+species_color: CIOIN 0xFF1CAE
+species_color: CIOSA 0xFF2CAE
+species_color: BOVIN 0x5C3317
+species_color: CANFA 0x8B2323
+species_color: HUMAN 0xFF2400
+species_color: PANTR 0xCC2400
+species_color: MOUSE 0xFF7F00
+species_color: RAT 0xFFEF00
+species_color: MONDO 0xEE9A49
+species_color: ORNAN 0xCD853F
+species_color: XENLA 0x6BAA23
+species_color: XENTR 0x6BAA23
+species_color: CHICK 0xFFC125
+species_color: FUGRU 0x0000FF
+species_color: BRARE 0x0000DD
+species_color: DANRE 0x0000BB
+species_color: TETNG 0x0000AA
+species_color: ORYLA 0x000088
+species_color: GASAC 0x000066
+species_color: CAEEL 0x666699
+species_color: CAEBR 0xB0B0B0
+species_color: DROME 0x663366
+species_color: DROPS 0x996699
+species_color: APIME 0x7A7700
+species_color: AEDAE 0x8C5900
+species_color: TRICA 0x918E00
+species_color: NEMVE 0x0066CC
+species_color: HYDAT 0x3399FF
+species_color: HYDVU 0x3399FF
+species_color: LUBBA 0xF7B5CB
+species_color: GEOCY 0xF5A0BD
+species_color: AMPQE 0x009966
+species_color: SUBDO 0xC790B9
+species_color: MONBE 0xFC0FC0
+species_color: DICPU 0xFFCC33
+species_color: DICDI 0xFFCC00
+species_color: ENTHI 0x5959AB
+species_color: ARATH 0x00FF00
+species_color: POPTR 0x006400
+species_color: VITVI 0x00CD00
+species_color: GLYMA 0x00FF7F
+species_color: ORYSA 0x008B00
+species_color: ORYSJ 0x008C00
+species_color: SORBI 0x00EE76
+species_color: SELMO 0x238E23
+species_color: PHYPA 0x09F911
+species_color: OSTLU 0x7FFF00
+species_color: OSTTA 0x7FFF00
+species_color: OSTRC 0x7FFF00
+species_color: MICPU 0x66CD00
+species_color: MIC99 0x66CD00
+species_color: CHLRE 0xB3EE3A
+species_color: VOLCA 0xC0FF3E
+species_color: CHLSP 0x6B8E23
+species_color: CYAME 0xD02090
+species_color: YEAST 0xAAAAAA
+species_color: BACFR 0xFF0000
+species_color: BACTN 0xFFFF00
+species_color: MYXXD 0x0000FF
+species_color: STIAU 0x00FFFF
+species_color: BACOV 0x8C5900
+species_color: BACUN 0x66CD00
+species_color: PORGI 0x918E00
+# rank: Class
+species_color: Mammalia 0xFF0000
+species_color: mammals 0xFF0000
+# rank: Phylum
+species_color: Chordata 0x8470FF
+species_color: Echinodermata 0x6495ED
+species_color: Hemichordata 0x7EC0EE
+species_color: Arthropoda 0x7AC5CD
+species_color: Nematoda 0x7171C6
+species_color: Tardigrada 0x388E8E
+species_color: Annelida 0xC67171
+species_color: Mollusca 0x00F5FF
+species_color: Ctenophora 0xBBFFFF
+species_color: Cnidaria 0xFF83FA
+species_color: Placozoa 0xEED2EE
+species_color: Porifera 0xFF3E96
+species_color: Microsporidia 0x8B8378
+species_color: Ascomycota 0xFF6347
+species_color: Basidiomycota 0xFFD700
+species_color: Chlorophyta 0x00C78C
+species_color: Streptophyta 0x00C957
+# rank: Kingdom
+species_color: Viridiplantae 0x00FF00
+species_color: plants 0x00FF00
+species_color: Metazoa 0x0000FF
+species_color: animals 0x0000FF
+species_color: Fungi 0xFF9912
+# rank: Superkingdom
+species_color: Viruses 0xFFD700
+species_color: Bacteria 0x00FF00
+species_color: Archaea 0x0000FF
+species_color: Eukaryota 0xFF0000
+species_color: eukaryotes 0xFF0000
+
+
+
+# Domain colors
+# -------------
+domain_color: Cofilin_ADF 0xFC0FC0
+domain_color: TIR 0x900000
+domain_color: NACHT 0x202020
+domain_color: CARD 0xFF0000
+domain_color: Peptidase_C14 0x00FF00
+domain_color: Death 0x0000FF
+domain_color: DED 0x00FFFF
+domain_color: BIR 0xCCFF33
+domain_color: PAAD_DAPIN 0x9999CC
+domain_color: NB-ARC 0x500050
+domain_color: WD40 0x888888
+domain_color: RVT_1 0x999900
+domain_color: CBM_48 0xFF0000
+domain_color: Alpha-amylase 0x0000FF
+domain_color: Alpha-amylase_C 0x0080FF
+domain_color: CBM_48 0xFF0000
+domain_color: Alpha-amylase 0x0000FF
+domain_color: Alpha-amylase_C 0x0080FF
+domain_color: GDE_N 0x009000
+domain_color: GDE_C 0x00FF00
+domain_color: hGDE_N 0x990099
+domain_color: GDE_N_bis 0x007000
+domain_color: hGDE_central 0xFF8000
+domain_color: hGDE_amylase 0x0000EE
+domain_color: hDGE_amylase 0x0000EE
+
+
+
+# Annotation colors
+# -----------------
+annotation_color: dehydrogenase 0x0000FF
+annotation_color: kinase 0xFF00FF
+annotation_color: protease 0x009900
+annotation_color: transcription 0xAAAA00
+
+
+# END
\ No newline at end of file
label.neighbour_joining_identity = Neighbour Joining Using % Identity
label.choose_calculation = Choose Calculation
label.treecalc_title = {0} Using {1}
+label.aptx_title = Archaeopteryx Tree View
+label.aptx_title_append = of {0}
label.tree_calc_av = Average Distance
label.tree_calc_nj = Neighbour Joining
label.select_score_model = Select score model
label.mark_unassociated_leaves = Mark Unassociated Leaves
label.fit_to_window = Fit To Window
label.newick_format = Newick Format
-label.select_newick_like_tree_file = Select a newick-like tree file
+label.select_tree_file = Select a tree file
+label.treebase_study = TreeBASE Study
+label.treebase = TreeBASE
+label.treefam = TreeFam
+label.tree_of_life = Tree of Life
label.colours = Colours
label.view_mapping = View Mapping
label.wireframe = Wireframe
label.selected_region_to_tree_may_only_contain_residues_or_gaps = The selected region to create a tree may\nonly contain residues or gaps.\nTry using the Pad function in the edit menu,\nor one of the multiple sequence alignment web services.
label.sequences_selection_not_aligned = Sequences in selection are not aligned
label.problem_reading_tree_file = Problem reading tree file
+label.tabs_detected_archaeopteryx = Warning, multiple trees detected in a single tree viewer instance. This will cause problems!
label.possible_problem_with_tree_file = Possible problem with tree file
+label.aptx_config_not_found = Warning: tree viewer configuration file not found, continue anyway? (this WILL cause the viewer to look different)
+label.tree_url_example = Please enter a complete URL, for example \"http://www.jalview.org/examples/ferredoxin.nw\"
+label.from_database = From Database...
+label.load_tree_url = Tree from URL
label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation.
label.translation_failed = Translation Failed
label.error_when_translating_sequences_submit_bug_report = Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.
label.input_alignment = Input Alignment
label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
label.vamsas_document_import_failed = Vamsas Document Import Failed
-label.couldnt_locate = Couldn't locate {0}
+label.couldnt_locate = Could not locate {0}
label.url_not_found = URL not found
label.new_sequence_url_link = New sequence URL link
label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view
label.share_data_vamsas_applications = Share data with other vamsas applications
label.connect_to = Connect to
label.join_existing_vamsas_session = Join an existing vamsas session
-label.from_url = from URL
+label.from_url = From URL
label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment
label.sort_with_new_tree = Sort With New Tree
-label.from_textbox = from Textbox
+label.from_textbox = From Textbox
label.window = Window
label.preferences = Preferences
label.tools = Tools
label.loading_file = Loading File: {0}
label.edit_params = Edit {0}
label.as_percentage = As Percentage
+error.database_id_has_letters = Database identifier ({0}) should contain only digits
+error.phyloxml_validation = phyloXML XSD-based validation is turned off (enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file)
error.not_implemented = Not implemented
error.no_such_method_as_clone1_for = No such method as clone1 for {0}
error.null_from_clone1 = Null from clone1!
exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})
+exception.invalid_matrix_identifier = Sequence identifier {0} not found in distance matrix.
exception.browser_not_found = Exception in finding browser: {0}
exception.browser_unable_to_locate = Unable to locate browser: {0}
exception.invocation_target_exception_creating_aedesc = InvocationTargetException while creating AEDesc: {0}
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
import jalview.util.QuickSort;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
/**
* Routines for manipulating the order of a multiple sequence alignment TODO:
static TreeModel lastTree = null;
+ static TreeI lastExternalTree = null;
+
static boolean sortTreeAscending = true;
/*
List<SequenceI> algn;
synchronized (algn = align.getSequences())
{
- List<SequenceI> tmp = new ArrayList<SequenceI>();
+ List<SequenceI> tmp = new ArrayList<>();
for (int i = 0; i < seqs.length; i++)
{
{
// MAINTAINS ORIGNAL SEQUENCE ORDER,
// ORDERS BY GROUP SIZE
- List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
+ List<SequenceGroup> groups = new ArrayList<>();
if (groups.hashCode() != lastGroupHash)
{
// NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
// /////////////////////////////////////////////
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
for (int i = 0; i < groups.size(); i++)
{
// tmp2 = tmp.retainAll(mask);
// return tmp2.addAll(mask.removeAll(tmp2))
- ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ ArrayList<SequenceI> seqs = new ArrayList<>();
int i, idx;
boolean[] tmask = new boolean[mask.size()];
{
int nSeq = align.getHeight();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
+ List<SequenceI> tmp = new ArrayList<>();
- tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
+ tmp = _sortByTree(tree.getTopNode(), tmp);
if (tmp.size() != nSeq)
{
return tmp;
}
+
+
+ private static List<SequenceI> getOrderByTree(TreeI aptxTree,
+ Map<TreeNodeI, SequenceI> nodesWithBoundSeqs)
+ {
+ List<SequenceI> seqsByTreeOrder = new ArrayList<>();
+ if (!aptxTree.isEmpty())
+ {
+ for (final Iterator<TreeNodeI> iter = aptxTree
+ .iterateInPreOrder(); iter.hasNext();)
+ {
+ TreeNodeI treeNode = iter.next();
+ seqsByTreeOrder.add(nodesWithBoundSeqs.get(treeNode));
+ }
+
+ }
+ return seqsByTreeOrder;
+
+
+ }
+
/**
* Sorts the alignment by a given tree
*
}
/**
+ * Sorts the alignment by a given tree from Archaeopteryx
+ *
+ * @param align
+ * alignment to order
+ * @param tree
+ * tree which has
+ */
+ public static void sortByTree(AlignmentI align,
+ Map<TreeNodeI, SequenceI> nodesBoundToSequences,
+ TreeI treeI) throws IllegalArgumentException
+ {
+ List<SequenceI> tmp = getOrderByTree(treeI, nodesBoundToSequences);
+
+ if (!tmp.isEmpty())
+ {
+ if (lastExternalTree != treeI)
+ {
+ sortTreeAscending = true;
+ lastExternalTree = treeI;
+ }
+ else
+ {
+ sortTreeAscending = !sortTreeAscending;
+ }
+
+ if (sortTreeAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
+ }
+ else
+ {
+ throw new IllegalArgumentException();
+ }
+ }
+
+ /**
* DOCUMENT ME!
*
* @param align
* @return DOCUMENT ME!
*/
private static List<SequenceI> _sortByTree(SequenceNode node,
- List<SequenceI> tmp, List<SequenceI> seqset)
+ List<SequenceI> tmp)
{
if (node == null)
{
}
else
{
- _sortByTree(left, tmp, seqset);
- _sortByTree(right, tmp, seqset);
+ _sortByTree(left, tmp);
+ _sortByTree(right, tmp);
}
return tmp;
}
+
+
// Ordering Objects
// Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
// appropriate order
--- /dev/null
+package jalview.analysis;
+
+public enum TreeAlgorithm
+{
+ NEIGHBOUR_JOINING("NJ", "Neighbour Joining"),
+ AVERAGE_DISTANCE("AV", "Average Distance (UPGMA)"),
+ MAXIMUM_PARSIMONY("MP", ("Maximum Parsimony")),
+ MAXIMUM_LIKELIHOOD("ML", "Maximum Likelihood"),
+ BAYESIAN("BY", "Bayesian Inference");
+
+ private final String abbreviation;
+
+ private final String name;
+
+ TreeAlgorithm(String abbreviatedName, String fullName)
+ {
+ this.abbreviation = abbreviatedName;
+ this.name = fullName;
+ }
+
+ public String getAbbreviation()
+ {
+ return abbreviation;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+}
double maxDistValue;
- double maxheight;
+ double maxHeight;
int ycount;
Vector<SequenceNode> node;
- private AlignmentView seqStrings;
+ protected ScoreModelI scoreModel;
+
+ protected SimilarityParamsI scoreParams;
+
+ private AlignmentViewport avport;
+
+ private AlignmentView seqStrings; // redundant? (see seqData)
/**
* Constructor
SimilarityParamsI scoreParameters)
{
int start, end;
+ avport = av;
boolean selview = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 1;
seqStrings = av.getAlignmentView(selview);
{
if (nd == null)
{
- return maxheight;
+ return maxHeight;
}
if ((nd.left() == null) && (nd.right() == null))
{
nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
- if (nd.height > maxheight)
+ if (nd.height > maxHeight)
{
return nd.height;
}
else
{
- return maxheight;
+ return maxHeight;
}
}
else
}
else
{
- maxheight = 0;
+ maxHeight = 0;
nd.height = (float) 0.0;
}
- maxheight = findHeight((SequenceNode) (nd.left()));
- maxheight = findHeight((SequenceNode) (nd.right()));
+ maxHeight = findHeight((SequenceNode) (nd.left()));
+ maxHeight = findHeight((SequenceNode) (nd.right()));
}
- return maxheight;
+ return maxHeight;
}
/**
*/
protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
{
- distances = sm.findDistances(seqData, scoreOptions);
+
+ this.scoreModel = sm;
+ this.scoreParams = scoreOptions;
+
+ distances = scoreModel.findDistances(seqData, scoreParams);
makeLeaves();
protected void init(AlignmentView seqView, int start, int end)
{
- this.node = new Vector<SequenceNode>();
+ this.node = new Vector<>();
if (seqView != null)
{
this.seqData = seqView;
*/
void makeLeaves()
{
- clusters = new Vector<BitSet>();
+ clusters = new Vector<>();
for (int i = 0; i < noseqs; i++)
{
sn.setElement(sequences[i]);
sn.setName(sequences[i].getName());
node.addElement(sn);
+
BitSet bs = new BitSet();
bs.set(i);
clusters.addElement(bs);
return seqStrings;
}
+ public MatrixI getDistances()
+ {
+ return distances;
+ }
+
+ public ScoreModelI getScoreModel()
+ {
+ return scoreModel;
+ }
+
+ public SimilarityParamsI getScoreParams()
+ {
+ return scoreParams;
+ }
+
+ public AlignmentViewport getAvport()
+ {
+ return avport;
+ }
+
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($Version-Rel$)
+ * Copyright (C) $Year-Rel$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.gui.AlignViewport;
+
+/**
+ * @author kjvanderheide
+ *
+ */
+public class TreeCalculator extends Thread// add threading
+{
+ SimilarityParamsI similarityParams;
+
+ String treeType;
+
+ String scoreModelName; // if tree computed
+
+ /**
+ *
+ * @param treeAlgo
+ * @param substitutionMatrix
+ * @param calculateParams
+ */
+ public TreeCalculator(String treeAlgo, String substitutionMatrix,
+ SimilarityParamsI calculateParams)
+ {
+ this.treeType = treeAlgo;
+ this.scoreModelName = substitutionMatrix;
+ this.similarityParams = calculateParams;
+ }
+
+ /**
+ *
+ * @param alignViewport
+ * @return
+ */
+ public TreeBuilder makeTree(AlignViewport alignViewport)
+ {
+ ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,
+ alignViewport.getAlignPanel());
+
+ TreeBuilder builtTree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
+ ? new NJTree(alignViewport, sm, similarityParams)
+ : new AverageDistanceTree(alignViewport, sm, similarityParams);
+
+ return builtTree;
+
+ }
+
+ public SimilarityParamsI getSimilarityParams()
+ {
+ return similarityParams;
+ }
+
+ public void setSimilarityParams(SimilarityParamsI similarityParams)
+ {
+ this.similarityParams = similarityParams;
+ }
+
+ public String getTreeType()
+ {
+ return treeType;
+ }
+
+ public void setTreeType(String treeType)
+ {
+ this.treeType = treeType;
+ }
+
+ public String getScoreModelName()
+ {
+ return scoreModelName;
+ }
+
+ public void setScoreModelName(String scoreModelName)
+ {
+ this.scoreModelName = scoreModelName;
+ }
+
+
+
+
+}
public TreeModel(SequenceI[] seqs, AlignmentView odata,
NewickFile treefile)
{
- this(seqs, treefile.getTree(), treefile.HasDistances(),
- treefile.HasBootstrap(), treefile.HasRootDistance());
+ this(seqs, treefile.getTree(), treefile.hasDistances(),
+ treefile.hasBootstrap(), treefile.hasRootDistance());
seqData = odata;
associateLeavesToSequences(seqs);
Vector<SequenceNode> leaves = findLeaves(top);
- int i = 0;
int namesleft = seqs.length;
- SequenceNode j;
- SequenceI nam;
- String realnam;
- Vector<SequenceI> one2many = new Vector<SequenceI>();
+ SequenceI nodeSequence;
+ String nodeSequenceName;
+ Vector<SequenceI> one2many = new Vector<>();
// int countOne2Many = 0;
- while (i < leaves.size())
+
+ for (SequenceNode sn : leaves)
{
- j = leaves.elementAt(i++);
- realnam = j.getName();
- nam = null;
+ nodeSequenceName = sn.getName();
+ nodeSequence = null;
if (namesleft > -1)
{
- nam = algnIds.findIdMatch(realnam);
+ nodeSequence = algnIds.findIdMatch(nodeSequenceName);
}
- if (nam != null)
+ if (nodeSequence != null)
{
- j.setElement(nam);
- if (one2many.contains(nam))
+ sn.setElement(nodeSequence);
+ if (one2many.contains(nodeSequence))
{
// countOne2Many++;
// if (jalview.bin.Cache.log.isDebugEnabled())
}
else
{
- one2many.addElement(nam);
+ one2many.addElement(nodeSequence);
namesleft--;
}
}
else
{
- j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
- j.setPlaceholder(true);
+ sn.setElement(new Sequence(nodeSequenceName, "THISISAPLACEHLDER"));
+ sn.setPlaceholder(true);
}
}
// if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
*/
public Vector<SequenceNode> findLeaves(SequenceNode nd)
{
- Vector<SequenceNode> leaves = new Vector<SequenceNode>();
+ Vector<SequenceNode> leaves = new Vector<>();
findLeaves(nd, leaves);
return leaves;
}
*/
public List<SequenceNode> groupNodes(float threshold)
{
- List<SequenceNode> groups = new ArrayList<SequenceNode>();
+ List<SequenceNode> groups = new ArrayList<>();
_groupNodes(groups, getTopNode(), threshold);
return groups;
}
updateRunning = true;
}
- Thread thread = new Thread(this);
+ Thread thread = new Thread(this, "OverviewUpdate");
thread.start();
repaint();
updateRunning = false;
MessageManager.getString("label.principal_component_analysis"),
475, 400);
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "PCACalc");
worker.start();
}
ScoreModelI scoreModel = ScoreModels.getInstance()
.getDefaultModel(false);
pcaModel.setScoreModel(scoreModel);
- new Thread(this).start();
+ new Thread(this, "PCARecalc").start();
}
}
else if (evt.getSource() == protSetting)
ScoreModelI scoreModel = ScoreModels.getInstance()
.getDefaultModel(true);
pcaModel.setScoreModel(scoreModel);
- new Thread(this).start();
+ new Thread(this, "PCARecalc").start();
}
}
}
frame.addWindowListener(this);
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "RedundancyCalc");
worker.start();
}
{
// Set default view, paying lip service to any overriding tree view
// parameter settings
- boolean showDist = newtree.HasDistances()
+ boolean showDist = newtree.hasDistances()
&& av.applet.getDefaultParameter("showTreeDistances",
- newtree.HasDistances());
- boolean showBoots = newtree.HasBootstrap()
+ newtree.hasDistances());
+ boolean showBoots = newtree.hasBootstrap()
&& av.applet.getDefaultParameter("showTreeBootstraps",
- newtree.HasBootstrap());
+ newtree.hasBootstrap());
distanceMenu.setState(showDist);
bootstrapMenu.setState(showBoots);
treeCanvas.setShowBootstrap(showBoots);
*/
package jalview.bin;
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import javax.swing.UIManager;
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
/**
* Main class for Jalview Application <br>
* <br>
running--;
}
}
- }).start();
+ }, "FeatureFetcher").start();
}
public synchronized boolean allFinished()
}
try
{
- Map<String, Object> vbinding = new HashMap<String, Object>();
+ Map<String, Object> vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
+ nickname + "|" + url);
if (source == null)
{
- source = new Vector<String>();
+ source = new Vector<>();
}
source.addElement(nickname);
}
System.out.println("adding source '" + data + "'");
if (source == null)
{
- source = new Vector<String>();
+ source = new Vector<>();
}
source.addElement(data);
}
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import jalview.ext.treeviewer.TreeControlsI;
+
+import org.forester.archaeopteryx.ControlPanel;
+
+public class AptxControlPanel implements TreeControlsI
+{
+ ControlPanel aptxCp;
+
+ protected AptxControlPanel(ControlPanel aptxControlPanel)
+ {
+ aptxCp = aptxControlPanel;
+
+ }
+
+ @Override
+ public void defaultSettings()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void displayEntireTree()
+ {
+ aptxCp.showWhole();
+
+ }
+
+}
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import jalview.bin.Cache;
+import jalview.ext.treeviewer.TreeControlsI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreePanelI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
+import jalview.ext.treeviewer.TreeViewerUtils;
+import jalview.gui.Desktop;
+import jalview.gui.EPSOptions;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Event;
+import java.awt.Font;
+import java.awt.Image;
+import java.awt.MenuComponent;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.FileOutputStream;
+
+import javax.accessibility.AccessibleContext;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JRootPane;
+import javax.swing.JSeparator;
+import javax.swing.event.InternalFrameListener;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.archaeopteryx.Configuration;
+import org.forester.archaeopteryx.MainFrame;
+import org.forester.phylogeny.Phylogeny;
+import org.jibble.epsgraphics.EpsGraphics2D;
+
+public class AptxFrame implements TreeFrameI
+{
+ private final MainFrame aptxFrame;
+
+ private TreeViewerBindingI viewBinding;
+
+ private TreePanelI aptxPanel;
+
+ private TreeControlsI aptxControls;
+
+
+ public AptxFrame(Phylogeny tree, Configuration aptxConfig,
+ String treeTitle)
+ {
+ this(Archaeopteryx.createApplication(tree,
+ aptxConfig,
+ treeTitle));
+
+ }
+
+
+ public AptxFrame(MainFrame aptx)
+ {
+
+ aptxFrame = aptx;
+ aptxPanel = new AptxTreePanel(
+ aptxFrame.getMainPanel().getCurrentTreePanel());
+ aptxControls = new AptxControlPanel(
+ aptxFrame.getMainPanel().getControlPanel());
+ adaptAptxGui(aptxFrame);
+
+ }
+
+ /**
+ * Hides certain redundant Archaeopteryx GUI elements such as the menu items
+ * for reading in trees and adds extra items related to Jalview such as the
+ * tree sorting menu item.
+ *
+ *
+ * @param aptxFrame
+ */
+ protected void adaptAptxGui(MainFrame aptxFrame)
+ {
+ JMenuBar frameBar = aptxFrame.getJMenuBar();
+ boolean epsAdded = false;
+ for (int i = 0; i < frameBar.getMenuCount();i++) {
+ JMenu menu = frameBar.getMenu(i);
+ int menuCount = menu.getMenuComponentCount();
+
+ if (menu.getText().contains("File"))
+ {
+ // hide all "Read from ..." and "New" menu items and any Separators that
+ // come directly after them
+ Component previousComp = null;
+ for (int x = 0; x < menuCount; x++)
+ {
+ Component menuItem = menu.getMenuComponent(x);
+ if (previousComp instanceof JMenuItem)
+ {
+ JMenuItem previousMenuItem = (JMenuItem) previousComp;
+ if (previousMenuItem.getText().startsWith("Read")
+ || previousMenuItem.getText()
+ .startsWith("New")
+ || previousMenuItem.getText()
+ .startsWith("Close Tab"))
+ {
+ previousComp.setVisible(false);
+
+ if (menuItem instanceof JSeparator)
+ {
+ menuItem.setVisible(false);
+ }
+
+ }
+
+ if ((!epsAdded) && previousMenuItem.getText()
+ .startsWith("Export to"))
+ {
+ JMenuItem exportEps = new JMenuItem("Export to EPS file...");
+ menu.add(exportEps, x);
+ exportEps.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ epsTree_actionPerformed(e);
+
+ }
+
+ });
+ epsAdded = true;
+
+ }
+ }
+ previousComp = menuItem;
+ }
+ }
+ else if (menu.getText().contains("Inference"))
+ {
+ menu.setVisible(false);
+ }
+ else if (menu.getText().contains("View"))
+ {
+ menu.addSeparator();
+ JMenuItem sortByTree = new JMenuItem("Sort alignment by tree");
+ JMenuItem refreshJalview = new JMenuItem(
+ "Filter alignment to show only currently visible sequences");
+
+ refreshJalview.setFont(menu.getFont());
+ refreshJalview.addActionListener(new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ TreeViewerBindingI bindingManager = TreeViewerUtils
+ .getActiveTreeViews().get(AptxFrame.this);
+ bindingManager.actionPerformed(e);
+ }
+ });
+
+ sortByTree.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ TreeViewerBindingI bindingManager = TreeViewerUtils
+ .getActiveTreeViews().get(AptxFrame.this);
+ bindingManager.sortByTree_actionPerformed();
+
+ }
+
+ });
+
+ menu.add(sortByTree);
+ menu.add(refreshJalview);
+
+ sortByTree.setFont(menu.getFont());
+
+
+
+ }
+
+ }
+ // aptxFrame.validate();
+ }
+
+ public void epsTree_actionPerformed(ActionEvent e)
+ {
+ boolean accurateText = true;
+
+ String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+ "Prompt each time");
+
+ // If we need to prompt, and if the GUI is visible then
+ // Prompt for EPS rendering style
+ if (renderStyle.equalsIgnoreCase("Prompt each time")
+ && !(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
+ {
+ EPSOptions eps = new EPSOptions();
+ renderStyle = eps.getValue();
+
+ if (renderStyle == null || eps.cancelled)
+ {
+ return;
+ }
+
+ }
+
+ if (renderStyle.equalsIgnoreCase("text"))
+ {
+ accurateText = false;
+ }
+
+ int width = getTreePanel().getWidth();
+ int height = getTreePanel().getHeight();
+
+ try
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(
+ MessageManager.getString("label.create_eps_from_tree"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(aptxFrame);
+
+ if (value != JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
+
+ Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
+
+ pg.setAccurateTextMode(accurateText);
+
+ getTreePanel().paintToFile(pg, width, height);
+
+ pg.flush();
+ pg.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ @Override
+ public TreePanelI getTreePanel()
+ {
+ return aptxPanel;
+ }
+
+ @Override
+ public TreeI getTree()
+ {
+ return aptxPanel.getTree();
+ }
+
+ @Override
+ public void checkMultipleTrees()
+ {
+ aptxFrame.activateSaveAllIfNeeded();
+
+ }
+
+ @Override
+ public int getNumberOfTrees()
+ {
+ return aptxFrame.getMainPanel().getTabbedPane().getTabCount();
+ }
+
+ @Override
+ public TreeControlsI getTreeControls()
+ {
+ return aptxControls;
+ }
+
+ @Override
+ public AccessibleContext getAccessibleContext()
+ {
+ return aptxFrame.getAccessibleContext();
+ }
+
+ @Override
+ public JRootPane getRootPane()
+ {
+ return aptxFrame.getRootPane();
+ }
+
+ @Override
+ public void setContentPane(Container contentPane)
+ {
+ aptxFrame.setContentPane(contentPane);
+
+ }
+
+ @Override
+ public Container getContentPane()
+ {
+ return aptxFrame.getContentPane();
+ }
+
+ @Override
+ public void setLayeredPane(JLayeredPane layeredPane)
+ {
+ aptxFrame.setLayeredPane(layeredPane);
+
+ }
+
+ @Override
+ public JLayeredPane getLayeredPane()
+ {
+ return aptxFrame.getLayeredPane();
+ }
+
+ @Override
+ public void setGlassPane(Component glassPane)
+ {
+ aptxFrame.setGlassPane(glassPane);
+
+ }
+
+ @Override
+ public Component getGlassPane()
+ {
+ return aptxFrame.getGlassPane();
+ }
+
+ @Override
+ public boolean imageUpdate(Image img, int infoflags, int x, int y,
+ int width, int height)
+ {
+ return aptxFrame.imageUpdate(img, infoflags, x, y, width, height);
+ }
+
+ @Override
+ public Font getFont()
+ {
+ return aptxFrame.getFont();
+ }
+
+ @Override
+ public void remove(MenuComponent comp)
+ {
+ aptxFrame.remove(comp);
+
+ }
+
+ @Deprecated
+ @Override
+ public boolean postEvent(Event evt)
+ {
+ return aptxFrame.postEvent(evt);
+ }
+
+ @Override
+ public void addFrameListener(InternalFrameListener listener)
+ {
+ aptxFrame.addInternalFrameListener(listener);
+
+ }
+
+ @Override
+ public void removeFrameListener(InternalFrameListener listener)
+ {
+ aptxFrame.removeInternalFrameListener(listener);
+
+ }
+
+ @Override
+ public InternalFrameListener[] getFrameListeners()
+ {
+ return aptxFrame.getInternalFrameListeners();
+
+ }
+
+ @Override
+ public void repaint()
+ {
+ aptxFrame.repaint();
+
+ }
+
+ @Override
+ public void setMinimumSize(Dimension dimension)
+ {
+ aptxFrame.setMinimumSize(dimension);
+
+ }
+
+ @Override
+ public boolean isShowing()
+ {
+ return aptxFrame.isShowing();
+ }
+
+ @Override
+ public Container getTopLevelAncestor()
+ {
+ return aptxFrame.getTopLevelAncestor();
+ }
+
+ @Override
+ public void addFrameToJalview(String title, boolean makeVisible,
+ int width, int height, boolean resizable, boolean ignoreMinSize)
+ {
+ Desktop.addInternalFrame(aptxFrame, title, makeVisible, width, height,
+ resizable, ignoreMinSize);
+
+ }
+
+ @Override
+ public TreeViewerBindingI getViewBinding()
+ {
+ return viewBinding;
+ }
+
+ @Override
+ public void setViewBinding(TreeViewerBindingI alignmentBinding)
+ {
+ viewBinding = alignmentBinding;
+ }
+
+
+ @Override
+ public void setMaximumSize(Dimension maximumSize)
+ {
+ aptxFrame.setMaximumSize(maximumSize);
+
+ }
+
+ @Override
+ public void setPreferredSize(Dimension preferredSize)
+ {
+ aptxFrame.setPreferredSize(preferredSize);
+
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import jalview.ext.forester.io.UtilityMethods;
+import jalview.ext.treeviewer.LoadedTreeAssociationI;
+import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeViewerUtils;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import org.forester.archaeopteryx.AptxUtil;
+import org.forester.archaeopteryx.Configuration;
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebserviceUtil;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.tol.TolParser;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.data.Identifier;
+import org.forester.util.ForesterUtil;
+
+/**
+ * Static class for creating Archaeopteryx tree viewer instances from calculated
+ * trees and letting them be bound to Jalview.
+ *
+ * @author kjvanderheide
+ *
+ */
+public final class AptxInit
+{
+ public final static InputStream CONFIG_LOC = AptxInit.class
+
+ .getResourceAsStream("/_aptx_jalview_configuration_file.txt");
+
+ public final static Configuration APTX_CONFIG = new Configuration(
+ CONFIG_LOC,
+ false, false);
+ // static
+ // {
+ // APTX_CONFIG.setBaseFontFamilyName(
+ // Desktop.instance.getFont().getFamily().replaceAll(" ", "_"));
+ // APTX_CONFIG.setBaseFontSize(Desktop.instance.getFont().getSize());
+ // }
+
+ private final static boolean VALIDATE_PHYLOXML_XSD = APTX_CONFIG
+ .isValidatePhyloXmlAgainstSchema();
+
+ private final static boolean REPLACE_NHX_UNDERSCORES = APTX_CONFIG
+ .isReplaceUnderscoresInNhParsing();
+
+ private final static boolean INTERNAL_NUMBERS_AS_CONFIDENCE = APTX_CONFIG
+ .isInternalNumberAreConfidenceForNhParsing();
+
+ private final static boolean MIDPOINT_REROOT = APTX_CONFIG
+ .isMidpointReroot();
+
+ private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
+ .getTaxonomyExtraction();
+
+
+ public static TreeFrameI createInstanceFromNhx(String treeTitle,
+ String nhxString, AlignmentViewport viewport)
+ throws IOException
+ {
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(treeTitle);
+ }
+
+ Phylogeny aptxPhylogeny = Phylogeny
+ .createInstanceFromNhxString(nhxString);
+ aptxPhylogeny.setName(treeTitle);
+
+ TreeFrameI aptxFrame = createAptxFrame(aptxPhylogeny, viewport,
+ treeTitle);
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
+ return aptxFrame;
+
+ }
+
+ /**
+ * Refactored from Archaeopteryx.main
+ *
+ * @param filePath
+ * @param viewport
+ * @return
+ * @throws IOException
+ * @throws FileNotFoundException
+ */
+ public static TreeFrameI[] createInstancesFromFile(File treeFile,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException
+ {
+ TreeFrameI[] aptxFrames = null;
+ if (UtilityMethods.canForesterReadFile(treeFile))
+ {
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(treeFile.getCanonicalPath());
+ }
+ boolean nhx_or_nexus = false;
+ final PhylogenyParser parser = ParserUtils
+ .createParserDependingOnFileType(treeFile,
+ VALIDATE_PHYLOXML_XSD);
+ if (parser instanceof NHXParser)
+ {
+ nhx_or_nexus = true;
+ final NHXParser nhx = (NHXParser) parser;
+ nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+ nhx.setIgnoreQuotes(false);
+ nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
+ }
+ else if (parser instanceof NexusPhylogeniesParser)
+ {
+ nhx_or_nexus = true;
+ final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) parser;
+ nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+ nex.setIgnoreQuotes(false);
+ }
+ else if (parser instanceof PhyloXmlParser)
+ {
+ if (VALIDATE_PHYLOXML_XSD == false)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("error.phyloxml_validation"),
+ MessageManager.getString("label.file_open_error"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+ Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser,
+ treeFile);
+ aptxFrames = new TreeFrameI[trees.length];
+
+ for (int i = 0; i < trees.length; i++)
+ {
+ Phylogeny aptxPhylogeny = trees[i];
+
+ if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
+ {
+ PhylogenyMethods
+ .transferInternalNodeNamesToConfidence(aptxPhylogeny, "");
+ }
+ String treeTitle = treeFile.getName() + "[" + i + "]";
+ aptxPhylogeny.setName(treeTitle);
+ aptxFrames[i] = createAptxFrame(aptxPhylogeny, viewport, treeTitle);
+
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+ }
+ return aptxFrames;
+ }
+
+
+ public static TreeFrameI[] createInstancesFromFile(
+ String filePath,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException
+ {
+ File treeFile = new File(filePath);
+ return createInstancesFromFile(treeFile, viewport);
+
+ }
+
+ public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
+ AlignmentViewport viewport)
+ throws FileNotFoundException, IOException, RuntimeException
+ {
+
+ String treeTitle = treeUrl.getFile();
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(treeTitle);
+ }
+ Phylogeny[] trees = AptxUtil.readPhylogeniesFromUrl(treeUrl,
+ VALIDATE_PHYLOXML_XSD,
+ REPLACE_NHX_UNDERSCORES, INTERNAL_NUMBERS_AS_CONFIDENCE,
+ TAXONOMY_EXTRACTION, MIDPOINT_REROOT);
+
+ TreeFrameI[] aptxFrames = new TreeFrameI[trees.length];
+ for (int i = 0; i < trees.length; i++)
+ {
+ Phylogeny aptxTree = trees[i];
+ aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
+ }
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
+ return aptxFrames;
+
+ }
+
+ /**
+ * Refactored from Forester's UrlTreeReader, this can be more efficient
+ *
+ * @param databaseIndex
+ * @param viewport
+ * @return
+ */
+ public static TreeFrameI[] createInstancesFromDb(
+ PhylogeniesWebserviceClient treeDbClient, String identifier,
+ AlignmentViewport viewport)
+ {
+
+ URL url = null;
+ Phylogeny[] trees = null;
+ TreeFrameI[] aptxFrames = null;
+
+ if ((identifier != null) && (identifier.trim().length() > 0))
+ {
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.startLoading(identifier);
+ }
+
+ identifier = identifier.trim();
+ if (treeDbClient.isQueryInteger())
+ {
+ identifier = identifier.replaceAll("^\\D+", "");
+
+ int id;
+ try
+ {
+ id = Integer.parseInt(identifier);
+ } catch (final NumberFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "error.database_id_has_letters", new String[]
+ { identifier }),
+ MessageManager.getString("label.invalid_url"),
+ JvOptionPane.ERROR_MESSAGE);
+ return new TreeFrameI[0];
+ }
+ identifier = id + "";
+ }
+ boolean exception = false;
+ try
+ {
+ String url_str = treeDbClient.getUrl();
+ url_str = url_str.replaceFirst(
+ PhylogeniesWebserviceClient.QUERY_PLACEHOLDER, identifier);
+ url = new URL(url_str);
+ PhylogenyParser parser = null;
+ switch (treeDbClient.getReturnFormat())
+ {
+ case TOL_XML_RESPONSE:
+ parser = new TolParser();
+ break;
+ case NEXUS:
+ parser = new NexusPhylogeniesParser();
+ ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+ break;
+ case TREEBASE_TREE:
+ parser = new NexusPhylogeniesParser();
+ ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+ ((NexusPhylogeniesParser) parser)
+ .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+ break;
+ case TREEBASE_STUDY:
+ parser = new NexusPhylogeniesParser();
+ ((NexusPhylogeniesParser) parser).setReplaceUnderscores(true);
+ ((NexusPhylogeniesParser) parser)
+ .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+ break;
+ case NH:
+ parser = new NHXParser();
+ ((NHXParser) parser)
+ .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+ ((NHXParser) parser).setReplaceUnderscores(true);
+ ((NHXParser) parser).setGuessRootedness(true);
+ break;
+ case NH_EXTRACT_TAXONOMY:
+ parser = new NHXParser();
+ ((NHXParser) parser).setTaxonomyExtraction(
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE);
+ ((NHXParser) parser).setReplaceUnderscores(false);
+ ((NHXParser) parser).setGuessRootedness(true);
+ break;
+ case PFAM:
+ parser = new NHXParser();
+ ((NHXParser) parser).setTaxonomyExtraction(
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT);
+ ((NHXParser) parser).setReplaceUnderscores(false);
+ ((NHXParser) parser).setGuessRootedness(true);
+ break;
+ case NHX:
+ parser = new NHXParser();
+ ((NHXParser) parser)
+ .setTaxonomyExtraction(NHXParser.TAXONOMY_EXTRACTION.NO);
+ ((NHXParser) parser).setReplaceUnderscores(false);
+ ((NHXParser) parser).setGuessRootedness(true);
+ break;
+ case PHYLOXML:
+ parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
+ break;
+ default:
+ throw new IllegalArgumentException(
+ "unknown format: " + treeDbClient.getReturnFormat());
+ }
+ //
+ // if (_main_frame.getMainPanel().getCurrentTreePanel() != null)
+ // {
+ // _main_frame.getMainPanel().getCurrentTreePanel().setWaitCursor();
+ // }
+ // else
+ // {
+ // _main_frame.getMainPanel().setWaitCursor();
+ // }
+ trees = ForesterUtil.readPhylogeniesFromUrl(url, parser);
+ aptxFrames = new TreeFrameI[trees.length];
+ } catch (final MalformedURLException e)
+ {
+ exception = true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "exception.unable_to_launch_url", new String[]
+ { url.toString() }),
+ MessageManager.getString("label.invalid_url"),
+ JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
+ } catch (final IOException e)
+ {
+ exception = true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Could not read from " + url + "\n"
+ + e.getLocalizedMessage(),
+ "Failed to read tree from " + treeDbClient.getName() + " for "
+ + identifier,
+ JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
+ } catch (final NumberFormatException e)
+ {
+ exception = true;
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Could not read from " + url + "\n"
+ + e.getLocalizedMessage(),
+ "Failed to read tree from " + treeDbClient.getName() + " for "
+ + identifier,
+ JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
+ } catch (final Exception e)
+ {
+ exception = true;
+ e.printStackTrace();
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ e.getLocalizedMessage(), "Unexpected Exception",
+ JvOptionPane.ERROR_MESSAGE);
+ System.err.println(e.getLocalizedMessage());
+ }
+ if ((trees != null) && (trees.length > 0))
+ {
+ int i = 0;
+ for (final Phylogeny aptxTree : trees)
+ {
+ if (!aptxTree.isEmpty())
+ {
+ if (treeDbClient.getName().equals(WebserviceUtil.TREE_FAM_NAME))
+ {
+ aptxTree.setRerootable(false);
+ aptxTree.setRooted(true);
+ }
+ if (treeDbClient.getProcessingInstructions() != null)
+ {
+ try
+ {
+ WebserviceUtil.processInstructions(treeDbClient,
+ aptxTree);
+ } catch (final PhyloXmlDataFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error:\n" + e.getLocalizedMessage(), "Error",
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ if (treeDbClient.getNodeField() != null)
+ {
+ try
+ {
+ PhylogenyMethods.transferNodeNameToField(aptxTree,
+ treeDbClient.getNodeField(), false);
+ } catch (final PhyloXmlDataFormatException e)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error:\n" + e.getLocalizedMessage(), "Error",
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ }
+ aptxTree.setIdentifier(
+ new Identifier(identifier, treeDbClient.getName()));
+ // _main_frame.getJMenuBar().remove(_main_frame.getHelpMenu());
+ // _main_frame.getMenuBarOfExternalTreeFrameI()
+ // .add(_main_frame.getHelpMenu());
+ // _main_frame.getMainPanel().addExternalTreeIInNewTab(ExternalTreeI,
+ // _main_frame.getConfiguration(),
+ // new File(url.getFile()).getName(), url.toString());
+
+
+ TreeFrameI aptxApp = createAptxFrame(aptxTree,
+ viewport,
+ url.getFile());
+ String my_name_for_file = "";
+ if (!ForesterUtil.isEmpty(aptxTree.getName()))
+ {
+ my_name_for_file = new String(aptxTree.getName())
+ .replaceAll(" ", "_");
+ }
+ else if (aptxTree.getIdentifier() != null)
+ {
+ final StringBuffer sb = new StringBuffer();
+ if (!ForesterUtil
+ .isEmpty(aptxTree.getIdentifier().getProvider()))
+ {
+ sb.append(aptxTree.getIdentifier().getProvider());
+ sb.append("_");
+ }
+ sb.append(aptxTree.getIdentifier().getValue());
+ my_name_for_file = new String(
+ sb.toString().replaceAll(" ", "_"));
+ }
+ aptxApp.getTreePanel()
+ .setTreeFile(new File(my_name_for_file));
+ // AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings(
+ // aptxTree, aptxApp.getMainPanel().getControlPanel(),
+ // APTX_CONFIG);
+ aptxApp.getTreeControls().displayEntireTree();
+
+ aptxApp.checkMultipleTrees();
+ aptxFrames[i++] = aptxApp;
+ }
+ }
+ }
+ else if (!exception) // ..what?
+ {
+ JvOptionPane.showMessageDialog(null,
+ ForesterUtil.wordWrap(
+ "Failed to read in tree(s) from [" + url + "]", 80),
+ "Error", JvOptionPane.ERROR_MESSAGE);
+ }
+ if ((trees != null) && (trees.length > 0))
+ {
+ try
+ {
+ JvOptionPane.showMessageDialog(null,
+ ForesterUtil.wordWrap("Successfully read in "
+ + trees.length + " tree(s) from [" + url + "]",
+ 80),
+ "Success", JvOptionPane.INFORMATION_MESSAGE);
+ } catch (final Exception e)
+ {
+ // Not important if this fails, do nothing.
+ }
+ }
+ }
+
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+ return aptxFrames;
+
+
+ }
+
+
+
+ public static TreeFrameI createAptxFrame(TreeI aptxTree,
+ AlignmentViewport jalviewAlignport, String treeTitle)
+ {
+ validateConfig(APTX_CONFIG);
+ TreeFrameI aptxApp = aptxTree
+ .createTreeViewerFromTree(treeTitle);
+ TreeI jalviewTree = aptxApp.getTree();
+ LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(),
+ jalviewTree);
+ bindAptxNodes.associateLeavesToSequences();
+
+ TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
+ bindAptxNodes.getAlignmentWithNodes(),
+ bindAptxNodes.getNodesWithAlignment());
+ TreeViewerUtils.addTreeViewFrameToJalview(aptxApp);
+
+ // adaptAptxGui(aptxApp); //moved to AptxFrame
+ return aptxApp;
+ }
+
+
+ protected static TreeFrameI createAptxFrame(
+ final Phylogeny aptxTree,
+ final AlignmentViewport jalviewAlignport, String treeTitle)
+ {
+ validateConfig(APTX_CONFIG);
+ TreeFrameI aptxApp = new AptxFrame(aptxTree, APTX_CONFIG,
+ treeTitle);
+ TreeI jalviewTree = aptxApp.getTree();
+ LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+ jalviewAlignport.getAlignment().getSequencesArray(),
+ jalviewTree);
+ bindAptxNodes.associateLeavesToSequences();
+
+ TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
+ bindAptxNodes.getAlignmentWithNodes(),
+ bindAptxNodes.getNodesWithAlignment());
+ TreeViewerUtils.addTreeViewFrameToJalview(aptxApp);
+
+ // adaptAptxGui(aptxApp); //moved to AptxFrame
+ return aptxApp;
+ }
+
+
+ private static boolean validateConfig(Configuration aptxConfig)
+ {
+ if (aptxConfig == null || aptxConfig.isCouldReadConfigFile() == false)
+ {
+ int keepGoing = JvOptionPane.showConfirmDialog(Desktop.desktop,
+ MessageManager.getString("label.aptx_config_not_found"),
+ MessageManager.formatMessage("label.couldnt_locate",
+ new String[]
+ { "_aptx_jalview_configuration_file" }),
+ JvOptionPane.YES_NO_CANCEL_OPTION);
+
+ if (keepGoing == JvOptionPane.CANCEL_OPTION
+ || keepGoing == JvOptionPane.CLOSED_OPTION
+ || keepGoing == JvOptionPane.NO_OPTION)
+ {
+ return false;
+ }
+
+ }
+ return true;
+ }
+
+
+}
--- /dev/null
+// package jalview.ext.archaeopteryx;
+//
+// import jalview.analysis.TreeBuilder;
+// import jalview.datamodel.SequenceI;
+// import jalview.ext.forester.ForesterMatrix;
+// import jalview.ext.treeviewer.TreeBuilderI;
+// import jalview.ext.treeviewer.TreeI;
+// import jalview.ext.treeviewer.TreeNodeI;
+// import jalview.util.MappingUtils;
+// import jalview.util.MessageManager;
+//
+// import java.util.HashMap;
+// import java.util.Map;
+//
+// import org.forester.evoinference.matrix.distance.DistanceMatrix;
+// import org.forester.phylogeny.Phylogeny;
+// import org.forester.phylogeny.PhylogenyNode;
+//
+/// **
+// * Class for converting trees made in Jalview (through TreeBuilder) to trees
+// * compatible with Forester (Phylogeny objects).
+// *
+// * Note that this currently demands a 1:1 relationship between tree nodes and
+// * the sequences used for generating them.
+// *
+// * @author kjvanderheide
+// *
+// */
+// public class AptxTreeBuilder
+// implements TreeBuilderI
+// {
+// protected final SequenceI[] sequences;
+//
+// protected final DistanceMatrix distances;
+//
+// protected final TreeBuilder jalviewTree;
+//
+// public String treeTitle;
+//
+// private final TreeI aptxTree;
+//
+// private TreeNodeI rootNode;
+//
+// private final Map<SequenceI, TreeNodeI> alignmentWithNodes;
+//
+// private final Map<TreeNodeI, SequenceI> nodesWithAlignment;
+//
+// public AptxTreeBuilder(final TreeBuilder calculatedTree)
+// {
+// jalviewTree = calculatedTree;
+// sequences = jalviewTree.getSequences();
+// distances = ForesterMatrix.convertJalviewToForester(
+// jalviewTree.getDistances(), sequences);
+//
+// aptxTree = new Tree(new Phylogeny());
+// rootNode = TreeNode.getUniqueWrapper(new PhylogenyNode());
+//
+// int amountOfSequences = distances.getSize();
+// alignmentWithNodes = new HashMap<>(amountOfSequences);
+// nodesWithAlignment = new HashMap<>(amountOfSequences);
+//
+//
+// }
+//
+// @Override
+// public TreeI buildTree(final TreeNodeI treeRoot)
+// {
+//
+// if (treeRoot != null)
+// {
+// rootNode = treeRoot;
+// }
+//
+// buildTree();
+//
+// return aptxTree;
+//
+// }
+//
+//
+// @Override
+// public TreeI buildTree()
+// {
+//
+// for (SequenceI sequence : sequences)
+// {
+//
+// TreeNodeI sequenceNode = TreeNode
+// .getUniqueWrapper(
+// new PhylogenyNode(sequence.getName()));
+//
+// sequenceNode.setSequence(sequence);
+//
+// MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
+// sequenceNode, sequence);
+// MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
+// sequence, sequenceNode);
+// rootNode.addAsChild(sequenceNode);
+// }
+//
+//
+// aptxTree.setRoot(rootNode);
+//
+// treeTitle = generateTreeName();
+// aptxTree.setTreeName(treeTitle);
+//
+// return aptxTree;
+//
+// }
+//
+// @Override
+// public Map<SequenceI, TreeNodeI> getAlignmentBoundNodes()
+// {
+// return alignmentWithNodes;
+// }
+//
+// @Override
+// public Map<TreeNodeI, SequenceI> getNodesBoundAlignment()
+// {
+// return nodesWithAlignment;
+// }
+//
+//
+// /**
+// * Formats a localised title for the tree panel, like
+// * <p>
+// * Neighbour Joining Using BLOSUM62
+// * <p>
+// * For a tree loaded from file, just uses the file name
+// *
+// * @return
+// */
+// @Override
+// public String generateTreeName() // Move this and add selection region to the
+// // title when applicable
+// {
+// if (treeTitle != null) // will currently never happen, loaded tree file will
+// // take a different path
+// {
+// return treeTitle;
+// }
+// else
+// {
+// /*
+// * i18n description of Neighbour Joining or Average Distance method
+// */
+// String treecalcnm = MessageManager
+// .getString("label.tree_calc_" + jalviewTree.getClass()
+// .getSimpleName().substring(0, 2).toLowerCase());
+// /*
+// * short score model name (long description can be too long)
+// */
+// String smn = jalviewTree.getScoreModel().getName();
+//
+// /*
+// * put them together as <method> Using <model>
+// */
+// final String ttl = MessageManager
+// .formatMessage("label.treecalc_title", treecalcnm, smn);
+// return ttl;
+// }
+// }
+//
+//
+//
+//
+// }
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
+import jalview.ext.treeviewer.TreePanelI;
+import jalview.gui.PaintRefresher;
+
+import java.awt.Dimension;
+import java.awt.Event;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.MenuComponent;
+import java.awt.Rectangle;
+import java.awt.event.MouseListener;
+import java.io.File;
+import java.util.Set;
+
+import javax.accessibility.AccessibleContext;
+
+public class AptxTreePanel implements TreePanelI
+{
+ private final org.forester.archaeopteryx.TreePanel treeView;
+
+ private final TreeI tree;
+
+ private String sequenceSetId;
+
+ protected AptxTreePanel(
+ org.forester.archaeopteryx.TreePanel aptxTreePanel)
+ {
+ treeView = aptxTreePanel;
+ tree = new Tree(treeView.getPhylogeny());
+ }
+
+ protected AptxTreePanel(
+ org.forester.archaeopteryx.TreePanel aptxTreePanel,
+ TreeI aptxTree)
+ {
+ treeView = aptxTreePanel;
+ tree = aptxTree;
+
+ }
+
+ @Override
+ public void setTreeFile(File file)
+ {
+ treeView.setTreeFile(file);
+ }
+
+ @Override
+ public TreeI getTree()
+ {
+ return tree;
+ }
+
+ @Override
+ public File getTreeFile()
+ {
+ return treeView.getTreeFile();
+ }
+
+ @Override
+ public TreeNodeI findNode(int x, int y)
+ {
+ return TreeNode.getUniqueWrapper(treeView.findNode(x, y));
+ }
+
+ @Override
+ public void setMatchingNodes(Set<Long> hashSet)
+ {
+ treeView.setFoundNodes0(hashSet);
+
+ }
+
+ @Override
+ public Set<Long> getMatchingNodes()
+ {
+ return treeView.getFoundNodes0();
+ }
+
+ @Override
+ public AccessibleContext getAccessibleContext()
+ {
+ return treeView.getAccessibleContext();
+ }
+
+ @Override
+ public Font getFont()
+ {
+ return treeView.getFont();
+ }
+
+ @Override
+ public void remove(MenuComponent comp)
+ {
+ treeView.remove(comp);
+
+ }
+
+ @Deprecated
+ @Override
+ public boolean postEvent(Event evt)
+ {
+ return treeView.postEvent(evt);
+ }
+
+ @Override
+ public void addMouseListener(MouseListener listener)
+ {
+ treeView.addMouseListener(listener);
+ }
+
+ @Override
+ public void removeMouseListener(MouseListener listener)
+ {
+ treeView.removeMouseListener(listener);
+
+ }
+
+ @Override
+ public MouseListener[] getMouseListeners()
+ {
+ return treeView.getMouseListeners();
+ }
+
+ @Override
+ public void repaint()
+ {
+ treeView.repaint();
+
+ }
+
+ @Override
+ public void registerWithPaintRefresher(String sequenceSetIdentifier)
+ {
+ sequenceSetId = sequenceSetIdentifier;
+ PaintRefresher.Register(treeView, sequenceSetIdentifier);
+
+ }
+
+ @Override
+ public void notifyPaintRefresher(String sequenceSetIdentifier,
+ boolean alignmentChanged, boolean validateSequences)
+ {
+ PaintRefresher.Refresh(treeView, sequenceSetIdentifier,
+ alignmentChanged, validateSequences);
+
+ }
+
+ @Override
+ public void notifyPaintRefresher(boolean alignmentChanged,
+ boolean validateSequences)
+ {
+ if (sequenceSetId != null)
+ {
+ PaintRefresher.Refresh(treeView, sequenceSetId, alignmentChanged,
+ validateSequences);
+ }
+ else
+ {
+ // throw some kind of exception
+ }
+
+ }
+
+ @Override
+ public int getWidth()
+ {
+ return treeView.getWidth();
+ }
+
+ @Override
+ public int getHeight()
+ {
+ return treeView.getHeight();
+ }
+
+ @Override
+ public void paintToFile(Graphics2D pg, int width, int height)
+ {
+ treeView.paintFile(pg, false, width, height, 0, 0);
+
+ }
+
+ @Override
+ public boolean showingSubTree()
+ {
+ return treeView.isCurrentTreeIsSubtree();
+ }
+
+ @Override
+ public Rectangle getVisibleArea()
+ {
+ return treeView.getVisibleRect();
+ }
+
+ @Override
+ public float getPartitionThreshold()
+ {
+ return treeView.getThreshold();
+ }
+
+ @Override
+ public void setMinimumSize(Dimension minimumSize)
+ {
+ treeView.setMinimumSize(minimumSize);
+
+ }
+
+ @Override
+ public void setMaximumSize(Dimension maximumSize)
+ {
+ treeView.setMaximumSize(maximumSize);
+
+ }
+
+ @Override
+ public void setPreferredSize(Dimension preferredSize)
+ {
+ treeView.setPreferredSize(preferredSize);
+
+ }
+}
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
+import jalview.commands.CommandI;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
+import jalview.ext.treeviewer.TreePanelI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
+import jalview.ext.treeviewer.TreeViewerUtils;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.PaintRefresher;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.SwingUtilities;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+/**
+ * Class for binding the Archaeopteryx tree viewer to the Jalview alignment that
+ * it originates from, meaning that selecting sequences in the tree viewer also
+ * selects them in the alignment view and vice versa.
+ *
+ * @author kjvanderheide
+ *
+ */
+public final class JalviewBinding
+ implements TreeViewerBindingI
+{
+ private final TreeFrameI aptxFrame;
+
+ private TreePanelI treeView;
+
+ private AlignmentViewport parentAvport;
+
+ private final StructureSelectionManager ssm;
+
+ private Map<SequenceI, TreeNodeI> sequencesBoundToNodes;
+
+ private Map<TreeNodeI, SequenceI> nodesBoundToSequences;
+
+ private float rootX;
+
+ private float furthestNodeX;
+
+ private int nrTreeGroups = 0;
+
+ private boolean applyToAllViews = false;
+
+ /**
+ *
+ * @param archaeopteryx
+ *
+ * @param jalviewAlignmentViewport
+ * alignment viewport from which the tree was calculated.
+ *
+ * @param alignMappedToNodes
+ * map with sequences used to calculate the tree and matching tree
+ * nodes as key, value pair respectively.
+ *
+ * @param nodesMappedToAlign
+ * map with tree nodes and matching sequences used to calculate the
+ * tree as key, value pair respectively.
+ */
+ public JalviewBinding(final TreeFrameI archaeopteryx,
+ final AlignmentViewport jalviewAlignmentViewport,
+ final Map<SequenceI, TreeNodeI> alignMappedToNodes,
+ final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
+ {
+
+ if (archaeopteryx.getNumberOfTrees() > 1)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.tabs_detected_archaeopteryx"),
+ MessageManager.getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+
+ // deal with/prohibit null values here as that will cause problems
+ aptxFrame = archaeopteryx;
+ parentAvport = jalviewAlignmentViewport;
+ sequencesBoundToNodes = alignMappedToNodes;
+ nodesBoundToSequences = nodesMappedToAlign;
+
+ treeView = archaeopteryx.getTreePanel();
+ ssm = parentAvport.getStructureSelectionManager();
+
+ aptxFrame.setViewBinding(this);
+ ssm.addSelectionListener(this);
+ treeView.addMouseListener(this);
+ treeView.registerWithPaintRefresher(
+ parentAvport.getSequenceSetId());
+
+ aptxFrame.addFrameListener(new InternalFrameAdapter()
+ {
+
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ TreeViewerUtils.getActiveTreeViews().remove(aptxFrame);
+ ssm.removeSelectionListener(JalviewBinding.this);
+ }
+
+ });
+
+ // treeTabs.addChangeListener(new ChangeListener()
+ // {
+ //
+ // @Override
+ // public void stateChanged(ChangeEvent e)
+ // {
+ //
+ // SwingUtilities.invokeLater(new Runnable()
+ // {
+ //
+ // @Override
+ // /**
+ // * Resend the selection to the tree view when tabs get switched, this
+ // * has to be buried in invokeLater as Forester first resets the tree
+ // * view on switching tabs, without invokeLater this would get called
+ // * before Forester resets which would nullify the selection.
+ // */
+ // public void run()
+ // {
+ // treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
+ // parentAvport.sendSelection();
+ // // PaintRefresher.Refresh(treeView,
+ // // parentAvport.getSequenceSetId());
+ //
+ // }
+ // });
+ //
+ // }
+ //
+ // });
+
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // reset hidden sequences first
+ parentAvport.showAllHiddenSeqs();
+
+ if (treeView.showingSubTree())
+ {
+ LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation(
+ parentAvport.getAlignment().getSequencesArray(),
+ treeView.getTree());
+ bindAptxNodes.associateLeavesToSequences();
+ sequencesBoundToNodes = bindAptxNodes.getAlignmentWithNodes();
+ nodesBoundToSequences = bindAptxNodes.getNodesWithAlignment();
+ TreeViewerUtils.associateNodesWithJalviewSequences(aptxFrame,
+ parentAvport, sequencesBoundToNodes, nodesBoundToSequences);
+
+ for (SequenceI seq : parentAvport.getAlignment().getSequencesArray())
+ {
+ if (!sequencesBoundToNodes.containsKey(seq))
+ {
+ parentAvport.hideSequence(new SequenceI[] { seq });
+ }
+ }
+ }
+
+ else
+ {
+
+ Rectangle visibleView = treeView.getVisibleArea();
+
+ for (TreeNodeI node : treeView.getTree().getRoot()
+ .getAllDescendants())
+ {
+ if (!(node.getXcoord() > visibleView.getMinX()
+ && node.getXcoord() < visibleView.getMaxX()
+ && node.getYcoord() > visibleView.getMinY()
+ && node.getYcoord() < visibleView.getMaxY()))
+ {
+ parentAvport
+ .hideSequence(new SequenceI[]
+ { nodesBoundToSequences.get(node) });
+ }
+ }
+
+ }
+
+
+
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ SwingUtilities.invokeLater(new Runnable() {
+
+ @Override
+ /**
+ * invokeLater so that this always runs after Forester's mouseClicked
+ */
+ public void run()
+ {
+ final TreeNodeI node = treeView.findNode(e.getX(),
+ e.getY());
+ if (node != null)
+ {
+ if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
+ // selection if shift
+ // IS NOT pressed
+ {
+ parentAvport.setSelectionGroup(null);
+
+ }
+ showNodeSelectionOnAlign(node);
+ }
+ else
+ {
+
+ partitionTree(e.getX());
+ }
+ treeView.notifyPaintRefresher(parentAvport.getSequenceSetId(),
+ false, false);
+ treeView.repaint();
+
+
+
+ }
+ });
+
+
+ }
+
+ @Override
+ public void mousePressed(final MouseEvent e)
+ {
+
+ }
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ }
+
+
+ @Override
+ public void selection(final SequenceGroup seqsel,
+ final ColumnSelection colsel, final HiddenColumns hidden,
+ final SelectionSource source)
+ {
+ if (source == parentAvport) // check if source is alignment from where the
+ // tree originates
+ {
+ treeView.setMatchingNodes(
+ new HashSet<Long>(seqsel.getSequences().size()));
+
+
+ for (SequenceI selectedSequence : seqsel.getSequences())
+ {
+ TreeNodeI matchingNode = sequencesBoundToNodes
+ .get(selectedSequence);
+ if (matchingNode != null)
+ {
+ treeView.getMatchingNodes().add(matchingNode.getId());
+
+
+ // if (!matchingNode.getBranchData().isHasBranchColor())
+ // {
+ // // Color foundNodesColour = treeView.getTreeColorSet()
+ // // .getFoundColor0();
+ // // matchingNode.getBranchData()
+ // // .setBranchColor(new BranchColor(foundNodesColour));
+ //
+ // }
+
+ }
+
+ }
+
+ treeView.repaint();
+ }
+
+
+ }
+
+ /**
+ * Partially refactored from TreeCanvas
+ */
+ public void partitionTree(final int x)
+ {
+ TreeI tree = treeView.getTree();
+
+ if (!tree.isEmpty())
+ {
+ // should be calculated on each partition as the tree can theoretically
+ // change in the meantime
+ TreeNodeI furthestNode = tree.getFurthestNode();
+ furthestNodeX = furthestNode.getXcoord();
+ rootX = tree.getRoot().getXcoord();
+
+ // don't bother if 0 distance tree or clicked x lies outside of tree
+ if (furthestNodeX != rootX && !(x > furthestNodeX))
+ {
+ float threshold = (x - rootX) / (furthestNodeX - rootX);
+ List<TreeNodeI> foundNodes = getNodesAboveThreshold(
+ threshold,
+ tree.getRoot());
+
+ }
+ else
+ {
+ // clear previous colours?
+ }
+ }
+
+
+ }
+
+ public List<TreeNodeI> getNodesAboveThreshold(float threshold,
+ TreeNodeI node)
+ {
+
+ List<TreeNodeI> nodesAboveThreshold = new ArrayList<>();
+
+ parentAvport.setSelectionGroup(null);
+ parentAvport.getAlignment().deleteAllGroups();
+ parentAvport.clearSequenceColours();
+ if (parentAvport.getCodingComplement() != null)
+ {
+ parentAvport.getCodingComplement().setSelectionGroup(null);
+ parentAvport.getCodingComplement().getAlignment().deleteAllGroups();
+ parentAvport.getCodingComplement().clearSequenceColours();
+ }
+
+
+ colourNodesAboveThreshold(nodesAboveThreshold, threshold,
+ node);
+ return nodesAboveThreshold;
+
+ }
+
+ /**
+ * Partially refactored from TreeCanvas colourGroups (can be made nicer).
+ *
+ * @param nodeList
+ * @param threshold
+ * @param treeLength
+ * @param node
+ * @return
+ */
+ private List<TreeNodeI> colourNodesAboveThreshold(
+ List<TreeNodeI> nodeList, float threshold,
+ TreeNodeI node)
+ {
+
+ for (TreeNodeI childNode : node.getDirectChildren())
+ {
+ childNode.setBranchColor(Color.black);
+ float nodeCutoff = (childNode.getXcoord() - rootX)
+ / (furthestNodeX - rootX);
+
+ if (nodeCutoff > threshold)
+ {
+ nodeList.add(childNode);
+
+ Color randomColour = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ childNode.setBranchColor(randomColour);
+
+ List<SequenceI> groupSeqs = new ArrayList<>();
+ SequenceI seq = nodesBoundToSequences.get(childNode);
+ if (seq != null)
+ {
+ groupSeqs.add(seq);
+ parentAvport.setSequenceColour(seq, randomColour);
+ }
+
+ List<TreeNodeI> descendantNodes = childNode
+ .getAllDescendants();
+ // .forEach instead?
+ for (TreeNodeI descNode : descendantNodes)
+ {
+ seq = nodesBoundToSequences.get(descNode);
+ if (seq != null)
+ {
+ groupSeqs.add(seq);
+ parentAvport.setSequenceColour(seq, randomColour);
+ }
+
+ descNode.setBranchColor(randomColour);
+ }
+
+ if (groupSeqs != null)
+ {
+ nrTreeGroups++;
+ groupThresholdSequences(groupSeqs, randomColour);
+ }}
+
+ else
+ {
+ colourNodesAboveThreshold(nodeList, threshold, childNode);
+ }
+ }
+
+ for (AlignmentPanel associatedPanel : getAssociatedPanels())
+ {
+
+ associatedPanel.updateAnnotation();
+
+ final AlignViewportI codingComplement = associatedPanel.getAlignViewport()
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ // GROSS
+ ((AlignViewport) codingComplement).getAlignPanel()
+ .updateAnnotation();
+ }
+ }
+
+
+ return nodeList;
+ }
+
+ public void groupThresholdSequences(List<SequenceI> groupedSeqs,
+ Color groupColour)
+ {
+ SequenceGroup treeGroup = new SequenceGroup(groupedSeqs, null, null,
+ true, true, false, 0,
+ parentAvport.getAlignment().getWidth() - 1);
+
+ ColourSchemeI cs = null;
+ if (parentAvport.getGlobalColourScheme() != null)
+ {
+ if (parentAvport.getGlobalColourScheme() instanceof UserColourScheme)
+ {
+ cs = new UserColourScheme(
+ ((UserColourScheme) parentAvport.getGlobalColourScheme())
+ .getColours());
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColourScheme(treeGroup,
+ ColourSchemeProperty.getColourName(
+ parentAvport.getGlobalColourScheme()));
+ }
+
+ }
+ treeGroup.setColourScheme(cs);
+ treeGroup.getGroupColourScheme().setThreshold(
+ parentAvport.getResidueShading().getThreshold(),
+ parentAvport.isIgnoreGapsConsensus());
+
+ treeGroup.setName("Tree Group " + nrTreeGroups);
+ treeGroup.setIdColour(groupColour);
+
+ for (AlignmentPanel associatedPanel : getAssociatedPanels())
+ {
+ AlignViewportI altViewport = associatedPanel
+ .getAlignViewport();
+
+ if (altViewport.getGlobalColourScheme() != null
+ && altViewport.getResidueShading()
+ .conservationApplied())
+ {
+ Conservation conserv = new Conservation(treeGroup.getName(),
+ treeGroup.getSequences(null), treeGroup.getStartRes(),
+ treeGroup.getEndRes());
+ conserv.calculate();
+ conserv.verdict(false, altViewport.getConsPercGaps());
+ treeGroup.getGroupColourScheme().setConservation(conserv);
+ }
+
+ altViewport.getAlignment().addGroup(treeGroup);
+ // TODO can we push all of the below into AlignViewportI?
+ final AlignViewportI codingComplement = altViewport
+ .getCodingComplement();
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(treeGroup,
+ parentAvport, codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq, groupColour.brighter());
+ }
+ }
+ }
+
+ }
+
+ }
+
+ /**
+ * may or may not need an extra repaint on the alignment view (check what kira
+ * does)
+ */
+ @Override
+ public void showNodeSelectionOnAlign(final TreeNodeI node)
+ {
+
+ if (node.isInternal())
+ {
+ showMatchingChildSequences(node);
+ }
+
+ else
+ {
+ showMatchingSequence(node);
+ }
+
+
+ }
+
+
+
+
+
+ @Override
+ public void showMatchingSequence(final TreeNodeI nodeToMatch)
+ {
+ SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
+ if (matchingSequence != null)
+ {
+ long nodeId = nodeToMatch.getId();
+ addOrRemoveInSet(treeView.getMatchingNodes(), nodeId);
+ treeSelectionChanged(matchingSequence);
+ parentAvport.sendSelection();
+
+ }
+ }
+
+ @Override
+ public void showMatchingChildSequences(final TreeNodeI parentNode)
+ {
+ // redundancy here, Forester already iterates through tree to get all
+ // descendants
+ List<TreeNodeI> childNodes = parentNode.getAllDescendants();
+
+
+ for (TreeNodeI childNode : childNodes)
+ {
+ // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE));
+
+ SequenceI matchingSequence = nodesBoundToSequences.get(childNode);
+ if (matchingSequence != null)
+ {
+ long nodeId = childNode.getId();
+ addOrRemoveInSet(treeView.getMatchingNodes(), nodeId);
+
+ treeSelectionChanged(matchingSequence);
+
+ }
+
+ }
+ parentAvport.sendSelection();
+
+
+ }
+
+ /**
+ * Refactored from TreeCanvas.
+ *
+ * @param sequence
+ * of the node selected in the tree viewer.
+ */
+ @Override
+ public void treeSelectionChanged(final SequenceI sequence)
+ {
+ if (!parentAvport.isClosed()) // alignment view could be closed
+ {
+ SequenceGroup selected = parentAvport.getSelectionGroup();
+
+ if (selected == null)
+ {
+ selected = new SequenceGroup();
+ parentAvport.setSelectionGroup(selected);
+ }
+
+ selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
+ selected.addOrRemove(sequence, true);
+ }
+
+ }
+
+ @Override
+ public void sortByTree_actionPerformed()
+ {
+
+ // if (applyToAllViews)
+
+ final ArrayList<CommandI> commands = new ArrayList<>();
+ for (AlignmentPanel ap : PaintRefresher
+ .getAssociatedPanels(parentAvport.getSequenceSetId()))
+ {
+ commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+ ap.alignFrame.addHistoryItem(new CommandI()
+ {
+
+ @Override
+ public void undoCommand(AlignmentI[] views)
+ {
+ for (CommandI tsort : commands)
+ {
+ tsort.undoCommand(views);
+ }
+ }
+
+ @Override
+ public int getSize()
+ {
+ return commands.size();
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return "Tree Sort (many views)";
+ }
+
+ @Override
+ public void doCommand(AlignmentI[] views)
+ {
+
+ for (CommandI tsort : commands)
+ {
+ tsort.doCommand(views);
+ }
+ }
+ });
+
+ ap.alignFrame.updateEditMenuBar();
+ }
+ }
+ // else
+ // {
+ // alignPanel.alignFrame.addHistoryItem(sortAlignmentIn(alignPanel));
+ // }
+
+
+
+ @Override
+ public CommandI sortAlignmentIn(AlignmentPanel ap)
+ {
+ AlignmentViewport viewport = ap.av;
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ try
+ {
+ AlignmentSorter.sortByTree(viewport.getAlignment(),
+ nodesBoundToSequences,
+ treeView.getTree());
+ CommandI undo;
+ undo = new OrderCommand("Tree Sort", oldOrder,
+ viewport.getAlignment());
+
+ ap.paintAlignment(true, false);
+ return undo;
+
+ } catch (Exception e)
+ {
+ System.err.println(e.getMessage());
+ }
+ return null;
+
+ }
+
+
+
+ /**
+ * TO BE MOVED
+ *
+ * @param set
+ * @param objectToCheck
+ */
+ public static <E> void addOrRemoveInSet(Set<E> set, E objectToCheck)
+ {
+ if (set.contains(objectToCheck))
+ {
+ set.remove(objectToCheck);
+ }
+ else
+ {
+ set.add(objectToCheck);
+ }
+
+ }
+
+ public AlignmentViewport getParentAvport()
+ {
+ return parentAvport;
+ }
+
+ public void setParentAvport(final AlignmentViewport parentAvport)
+ {
+ this.parentAvport = parentAvport;
+ }
+
+ public AlignmentPanel[] getAssociatedPanels()
+ {
+ return PaintRefresher
+ .getAssociatedPanels(parentAvport.getSequenceSetId());
+ }
+
+
+
+}
+
+
+
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+
+public class Tree implements TreeI
+{
+ private final Phylogeny tree;
+
+ // alternative to static maps in TreeNode
+ // private Map<PhylogenyNode, TreeNodeI> originalNodes = new HashMap<>(500);
+ // private Map<TreeNodeI, PhylogenyNode> wrappedNodes = new HashMap<>(500);
+
+ public Tree()
+ {
+ tree = new Phylogeny();
+ }
+
+ public Tree(Phylogeny aptxTree)
+ {
+ tree = aptxTree;
+ wrapAllTreeNodes();
+
+ }
+
+ private void wrapAllTreeNodes()
+ {
+ for (Iterator<PhylogenyNode> iterator = tree
+ .iteratorPostorder(); iterator.hasNext();)
+ {
+ PhylogenyNode foresterNode = iterator.next();
+ TreeNodeI treeNode = TreeNode
+ .getUniqueWrapper(foresterNode);
+
+ }
+ }
+
+ @Override
+ public TreeNodeI getRoot()
+ {
+ TreeNodeI root = TreeNode.getUniqueWrapper(tree.getRoot());
+ return root;
+ }
+
+ @Override
+ public void setTreeName(String name)
+ {
+ tree.setName(name);
+
+ }
+
+ @Override
+ public TreeNodeI getNodeWithName(String name)
+ {
+ return TreeNode.getUniqueWrapper(tree.getNode(name));
+
+ }
+
+ @Override
+ public String[] getAllLeafNames()
+ {
+ return tree.getAllExternalNodeNames();
+ }
+
+ @Override
+ public void setRerootable(boolean b)
+ {
+ tree.setRerootable(b);
+
+ }
+
+ @Override
+ public void setRooted(boolean b)
+ {
+ tree.setRooted(b);
+
+ }
+
+ @Override
+ public boolean isEmpty()
+ {
+ return tree.isEmpty();
+ }
+
+ @Override
+ public String getTreeName()
+ {
+ return tree.getName();
+ }
+
+ @Override
+ public void setRoot(TreeNodeI rootNode)
+ {
+ PhylogenyNode treeRoot = TreeNode.unwrapNode(rootNode);
+ tree.setRoot(treeRoot);
+ wrapAllTreeNodes();
+
+ }
+
+ @Override
+ public double getHeight(boolean adjustForCollapsedSubtrees)
+ {
+ return tree.calculateHeight(adjustForCollapsedSubtrees);
+ }
+
+ @Override
+ public Iterator<TreeNodeI> iterateInPreOrder()
+ {
+ Iterator<TreeNodeI> iter = new TreeIterator(
+ tree.iteratorPreorder());
+ return iter;
+ }
+
+ @Override
+ public Iterator<TreeNodeI> iterateInLevelOrder()
+ {
+ Iterator<TreeNodeI> iter = new TreeIterator(
+ tree.iteratorLevelOrder());
+ return iter;
+ }
+
+ @Override
+ public Iterator<TreeNodeI> iterateInPostOrder()
+ {
+ Iterator<TreeNodeI> iter = new TreeIterator(
+ tree.iteratorPostorder());
+ return iter;
+ }
+
+ @Override
+ public TreeNodeI getFurthestNode()
+ {
+ PhylogenyNode furthestNode = PhylogenyMethods
+ .calculateNodeWithMaxDistanceToRoot(tree);
+ return TreeNode.getUniqueWrapper(furthestNode);
+ }
+
+ @Override
+ public TreeFrameI createTreeViewerFromTree(String instanceTitle)
+ {
+ return new AptxFrame(Archaeopteryx.createApplication(tree,
+ AptxInit.APTX_CONFIG,
+ instanceTitle));
+ }
+
+ @Override
+ public List<SequenceI> getNodeSequences()
+ {
+ List<SequenceI> treeSeqs = new ArrayList<>();
+ Iterator<TreeNodeI> iter = iterateInPreOrder();
+ while (iter.hasNext())
+ {
+
+ SequenceI nodeSeq = iter.next().getSequence();
+ if (nodeSeq != null)
+ {
+ treeSeqs.add(nodeSeq);
+ }
+ }
+ return treeSeqs;
+ }
+
+ @Override
+ public TreeNodeI[] getAllNodes()
+ {
+ TreeNodeI[] treeNodes = new TreeNodeI[tree.getNodeCount()];
+ Iterator<TreeNodeI> iter = iterateInPreOrder();
+ int i = 0;
+ while (iter.hasNext())
+ {
+ treeNodes[i++] = iter.next();
+ }
+ return treeNodes;
+ }
+
+ @Override
+ public void writeToXml(File outputFile) throws IOException
+ {
+ PhylogenyWriter treeWriter = new PhylogenyWriter();
+ treeWriter.toPhyloXML(tree, 0, outputFile);
+
+
+ }
+
+}
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import jalview.ext.treeviewer.TreeNodeI;
+
+import java.util.Iterator;
+
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+
+public class TreeIterator implements Iterator<TreeNodeI>
+{
+ private final PhylogenyNodeIterator iter;
+
+ public TreeIterator(PhylogenyNodeIterator aptxIterator)
+ {
+ iter = aptxIterator;
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return iter.hasNext();
+ }
+
+ @Override
+ public TreeNodeI next()
+ {
+ TreeNodeI node = TreeNode.getUniqueWrapper(iter.next());
+ return node;
+ }
+
+}
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import jalview.datamodel.SequenceI;
+import jalview.ext.forester.DataConversions;
+import jalview.ext.treeviewer.TreeNodeI;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+
+public class TreeNode implements TreeNodeI
+{
+ private final PhylogenyNode node;
+
+ private SequenceI nodeSeq;
+
+ private static Map<PhylogenyNode, TreeNodeI> originalNodes = new HashMap<>(
+ 500); // prolly make this size dynamic?
+
+ private static Map<TreeNodeI, PhylogenyNode> wrappedNodes = new HashMap<>(
+ 500);
+
+ /**
+ * Please don't use me directly.
+ *
+ * @param aptxNode
+ */
+ private TreeNode(PhylogenyNode aptxNode)
+ {
+ node = aptxNode;
+ if (aptxNode.getNodeData().getSequence() != null)
+ {
+ nodeSeq = DataConversions
+ .createJalviewSequence(aptxNode);
+ }
+ originalNodes.put(aptxNode, this);
+ wrappedNodes.put(this, aptxNode);
+
+ }
+
+
+ @Override
+ public String getNodeName()
+ {
+ return node.getName();
+ }
+
+
+ @Override
+ public List<TreeNodeI> getAllDescendants()
+ {
+
+ List<PhylogenyNode> descNodes = PhylogenyMethods
+ .getAllDescendants(node);
+ return getUniqueWrappers(descNodes);
+
+
+ }
+
+ @Override
+ public List<TreeNodeI> getExternalDescendants()
+ {
+ List<PhylogenyNode> extDescNodes = node.getAllExternalDescendants();
+ return getUniqueWrappers(extDescNodes);
+ }
+
+
+ @Override
+ public List<TreeNodeI> getDirectChildren()
+ {
+ List<PhylogenyNode> childNodes = node.getDescendants();
+ return getUniqueWrappers(childNodes);
+
+
+ }
+
+
+
+ @Override
+ public void setSequence(SequenceI seq)
+ {
+ nodeSeq = seq;
+ org.forester.phylogeny.data.Sequence foresterFormatSeq = DataConversions
+ .createForesterSequence(seq, true);
+ node.getNodeData().setSequence(foresterFormatSeq);
+
+ }
+
+ @Override
+ public SequenceI getSequence()
+ {
+ return nodeSeq;
+ }
+
+ @Override
+ public void addAsChild(TreeNodeI childNode)
+ {
+ PhylogenyNode aptxNode = unwrapNode(childNode);
+
+ node.addAsChild(aptxNode);
+
+ }
+
+ @Override
+ public long getId()
+ {
+ return node.getId();
+ }
+
+ @Override
+ public float getXcoord()
+ {
+ return node.getXcoord();
+ }
+
+ @Override
+ public void setBranchColor(Color branchColor)
+ {
+ PhylogenyMethods.setBranchColorValue(node, branchColor);
+
+ }
+
+ @Override
+ public boolean isInternal()
+ {
+ return node.isInternal();
+ }
+
+ public static List<TreeNodeI> getUniqueWrappers(
+ List<PhylogenyNode> aptxNodes)
+ {
+ List<TreeNodeI> wrappedNodes = new ArrayList<>(
+ aptxNodes.size());
+
+ for (PhylogenyNode aptxNode : aptxNodes)
+ {
+ wrappedNodes.add(getUniqueWrapper(aptxNode));
+ }
+ return wrappedNodes;
+ }
+
+ /**
+ * This method should be used to create new wrappers as there is a possibility
+ * the Archaeopteryx node was already introduced to Jalview previously so this
+ * avoids giving one node duplicate wrappers
+ *
+ * @param aptxNode
+ * @return
+ */
+ public static TreeNodeI getUniqueWrapper(
+ PhylogenyNode aptxNode)
+ {
+ if (aptxNode == null)
+ {
+ return null;
+ }
+ TreeNodeI wrappedNode = originalNodes.get(aptxNode);
+ if (wrappedNode == null)
+ {
+ wrappedNode = new TreeNode(aptxNode);
+ }
+ return wrappedNode;
+ }
+
+ /**
+ * Attempts to unwrap the given node, if the unwrapped node already exists it
+ * is simply returned as is. If it is not however, the wrapper will be used to
+ * create a new Archaeopteryx node. This way it becomes possible to construct
+ * new Archaeopteryx nodes from different tree viewers, as long as they
+ * implement the interface.
+ *
+ * @param wrappedNode
+ * @return
+ */
+ protected static PhylogenyNode unwrapNode(TreeNodeI wrappedNode)
+ {
+ if (wrappedNode == null)
+ {
+ return null;
+ }
+ PhylogenyNode aptxNode = wrappedNodes.get(wrappedNode);
+ if (aptxNode == null)
+ {
+ // expand this
+ aptxNode = new PhylogenyNode(wrappedNode.getNodeName());
+
+ }
+ return aptxNode;
+
+ }
+
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = (int) (prime * result
+ + ((node == null) ? 0 : (node.hashCode() * getId())));
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ TreeNode other = (TreeNode) obj;
+ if (node == null)
+ {
+ if (other.node != null)
+ {
+ return false;
+ }
+ }
+ if (getId() != other.getId())
+ {
+ return false;
+ }
+
+ if (!node.equals(other.node))
+ {
+ return false;
+ }
+ return true;
+ }
+
+
+ @Override
+ public float getYcoord()
+ {
+ return node.getYcoord();
+ }
+
+}
--- /dev/null
+package jalview.ext.forester;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.math.MatrixI;
+
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.phylogeny.PhylogenyNode;
+
+public final class DataConversions
+{
+ public static org.forester.phylogeny.data.Sequence createForesterSequence(
+ final SequenceI jalviewSequence, final boolean sequenceIsAligned)
+ {
+ org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
+
+ if (jalviewSequence.getDescription() != null)
+ {
+ foresterSeq.setName(jalviewSequence.getDescription());
+ }
+
+ // all tree sequences should be aligned already
+ foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
+
+ foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
+
+ // add checks for DNA or RNA (infer from forester itself?)
+ if (jalviewSequence.isProtein())
+ {
+ try
+ {
+ foresterSeq.setType("protein");
+ } catch (final PhyloXmlDataFormatException ignore)
+ {
+ // do nothing
+ }
+
+ }
+
+ return foresterSeq;
+
+ }
+
+ public static SequenceI createJalviewSequence(
+ PhylogenyNode foresterNode)
+ {
+ String seq = foresterNode.getNodeData().getSequence()
+ .getMolecularSequence();
+ String seqName = foresterNode.getName();
+
+ SequenceI jalviewSeq = new Sequence(seqName, seq, 1,
+ seq.length() + 1);
+ return jalviewSeq.deriveSequence();
+
+
+ }
+
+
+ // public static org.forester.phylogeny.data.Accession
+ // createForesterAccession(
+ // SequenceI jalviewSequence)
+ // {
+ //
+ //
+ // org.forester.phylogeny.data.Accession foresterAcs = new
+ // org.forester.phylogeny.data.Accession();
+ //
+ // return foresterAcs;
+ // }
+
+ public static DistanceMatrix createForesterDistanceMatrix(
+ final MatrixI jalviewInputMatrix,
+ final String[] matrixIdentifiers)
+ {
+
+ DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
+ matrixIdentifiers);
+ return foresterMatrix;
+
+ }
+
+ public static DistanceMatrix createForesterDistanceMatrix(
+ final MatrixI jalviewInputMatrix,
+ final SequenceI[] matrixSequences)
+ {
+ DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
+ matrixSequences);
+ return foresterMatrix;
+
+ }
+
+
+}
--- /dev/null
+package jalview.ext.forester;
+
+import jalview.datamodel.SequenceI;
+import jalview.math.MatrixI;
+import jalview.util.MessageManager;
+
+import java.io.IOException;
+import java.io.Writer;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.NoSuchElementException;
+import java.util.stream.IntStream;
+
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.util.ForesterUtil;
+import org.forester.util.IllegalFormatUseException;
+
+public class ForesterMatrix implements DistanceMatrix
+{
+ private final static NumberFormat PHYLIP_FORMATTER = new DecimalFormat(
+ "0.000000"); // straight from forester
+
+ private final MatrixI jalviewMatrix;
+
+ private final String[] identifiers;
+
+ public ForesterMatrix(final MatrixI jalviewInputMatrix,
+ final SequenceI[] matrixSequences)
+ {
+ this.jalviewMatrix = jalviewInputMatrix;
+ this.identifiers = new String[matrixSequences.length];
+
+ int i = 0;
+ for (SequenceI sequence : matrixSequences)
+ {
+ identifiers[i] = sequence.getName();
+ i++;
+ }
+
+ }
+
+ public ForesterMatrix(final MatrixI jalviewInputMatrix,
+ final String[] matrixIdentifiers)
+ {
+ this.jalviewMatrix = jalviewInputMatrix;
+ this.identifiers = matrixIdentifiers;
+
+ }
+
+ @Override
+ public String getIdentifier(final int i)
+ {
+ return identifiers[i]; // add handling if index is out of bounds
+ }
+
+
+ @Override
+ public int getIndex(final String identifier)
+ {
+ try {
+ return IntStream.range(0, identifiers.length)
+ .filter(x -> identifier.equals(identifiers[x])).findAny()
+ .getAsInt(); // stream to bypass otherwise having to duplicate the
+ // list
+ // with Arrays.aslist
+ }
+ catch (NoSuchElementException ex) {
+ throw new Error(MessageManager.formatMessage(
+ "exception.invalid_matrix_identifier", new String[]
+ { identifier }));
+ }
+ }
+
+ /**
+ * Returns the length of whichever is longest, columns or rows
+ */
+ @Override
+ public int getSize()
+ {
+ return jalviewMatrix.getValues().length;
+ }
+
+ /**
+ * See {@link MatrixI#getValue(int,int)} except that the order of column, row
+ * in the parameters is inverted here (as that is how forester demands it)
+ */
+ @Override
+ public double getValue(final int col, final int row)
+ {
+ return jalviewMatrix.getValue(row, col);
+ }
+
+ @Override
+ public void setIdentifier(final int i, final String identifier)
+ {
+ identifiers[i] = identifier;
+
+ }
+
+ /**
+ * See {@link MatrixI#setValue()} except that the order of column, row in the
+ * parameters is inverted here (as that is how forester demands it)
+ */
+ @Override
+ public void setValue(final int col, final int row, final double distance)
+ {
+ jalviewMatrix.setValue(row, col, distance);
+
+ }
+
+ @Override
+ public StringBuffer toStringBuffer(Format format)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * See {@link MatrixI#getValues()}
+ */
+ @Override
+ public double[][] getValues()
+ {
+ return jalviewMatrix.getValues();
+ }
+
+ @Override
+ public void write(final Writer w) throws IOException // directly copied from
+ // forester
+ {
+ w.write(" ");
+ w.write(getSize() + "");
+ w.write(ForesterUtil.LINE_SEPARATOR);
+ for (int row = 0; row < getSize(); ++row)
+ {
+ if (!ForesterUtil.isEmpty(getIdentifier(row)))
+ {
+ w.write(ForesterUtil.pad(getIdentifier(row), 10, ' ', false)
+ .toString());
+ w.write(' ');
+ w.write(' ');
+ }
+ else
+ {
+ throw new IllegalFormatUseException(
+ "Phylip format does not allow empty identifiers");
+ }
+ for (int col = 0; col < getSize(); ++col)
+ {
+ w.write(PHYLIP_FORMATTER.format(getValue(col, row)));
+ if (col < (getSize() - 1))
+ {
+ w.write(' ');
+ w.write(' ');
+ }
+ }
+ if (row < (getSize() - 1))
+ {
+ w.write(ForesterUtil.LINE_SEPARATOR);
+ }
+ }
+
+ }
+
+ public static DistanceMatrix convertJalviewToForester(
+ final MatrixI jalviewInputMatrix,
+ final SequenceI[] matrixSequences)
+ {
+ return DataConversions.createForesterDistanceMatrix(
+ jalviewInputMatrix, matrixSequences);
+
+ }
+
+ public static DistanceMatrix convertJalviewToForester(
+ final MatrixI jalviewInputMatrix,
+ final String[] matrixIdentifiers)
+ {
+ return DataConversions.createForesterDistanceMatrix(
+ jalviewInputMatrix, matrixIdentifiers);
+
+ }
+
+
+}
\ No newline at end of file
--- /dev/null
+package jalview.ext.forester.io;
+
+import jalview.ext.archaeopteryx.AptxInit;
+import jalview.ext.archaeopteryx.Tree;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeParserI;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.util.PhylogenyParserException;
+import org.forester.phylogeny.Phylogeny;
+
+public class ForesterParser
+ implements TreeParserI
+{
+ private final PhylogenyParser parser;
+
+ private TreeI[] parsedTrees;
+
+ protected ForesterParser(PhylogenyParser foresterParser, File file)
+ throws PhylogenyParserException, IOException
+ {
+ parser = foresterParser;
+ parser.setSource(file);
+ }
+
+ public static ForesterParser createNexusParser(File file)
+ throws PhylogenyParserException, IOException
+ {
+ NexusPhylogeniesParser nxParser = new NexusPhylogeniesParser();
+ nxParser.setReplaceUnderscores(
+ AptxInit.APTX_CONFIG.isReplaceUnderscoresInNhParsing());
+ nxParser.setIgnoreQuotes(false);
+ return new ForesterParser(nxParser, file);
+ }
+
+ public static ForesterParser createPhyloXmlParser(File file)
+ throws PhylogenyParserException, IOException
+ {
+ if (AptxInit.APTX_CONFIG.isValidatePhyloXmlAgainstSchema())
+ {
+ return new ForesterParser(
+ PhyloXmlParser.createPhyloXmlParserXsdValidating(), file);
+ }
+ else
+ {
+ return new ForesterParser(PhyloXmlParser.createPhyloXmlParser(),
+ file);
+ }
+ }
+
+ // ParserBasedPhylogenyFactory.getInstance().create(foresterParser, source)
+ @Override
+ public TreeI[] parse() throws IOException
+ {
+ Phylogeny[] foresterTrees = parser.parse();
+ parsedTrees = new TreeI[foresterTrees.length];
+
+ for (int i = 0; i < foresterTrees.length; i++)
+ {
+ parsedTrees[i] = new Tree(foresterTrees[i]);
+ }
+ return parsedTrees;
+
+ }
+
+ @Override
+ public void setSource(Object source) throws IOException
+ {
+ parser.setSource(source);
+
+ }
+
+ @Override
+ public String getName()
+ {
+ return parser.getName();
+ }
+
+
+ @Override
+ public TreeI[] getParsedTrees()
+ {
+ return parsedTrees;
+ }
+}
\ No newline at end of file
--- /dev/null
+package jalview.ext.forester.io;
+
+import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeParserI;
+import jalview.io.AlignFile;
+import jalview.io.FileParse;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+public class NexusFile extends AlignFile
+{
+
+ public NexusFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * This does not properly work for Nexus yet as Forester's parser doesn't
+ * parse the actual sequences to the tree.
+ */
+ @Override
+ public void parse() throws IOException
+ {
+ TreeParserI parser = ForesterParser
+ .createNexusParser(new File(getDataName()));
+ TreeI[] trees = parser.parse();
+ List<SequenceI> treeSeqs = trees[0].getNodeSequences();
+ for (SequenceI seq : treeSeqs)
+ {
+ seqs.add(seq);
+ }
+ }
+
+ }
+
+
--- /dev/null
+package jalview.ext.forester.io;
+
+import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeParserI;
+import jalview.io.AlignFile;
+import jalview.io.FileParse;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+public class PhyloXmlFile extends AlignFile
+{
+
+ public PhyloXmlFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public void parse() throws IOException
+ {
+ TreeParserI parser = ForesterParser
+ .createPhyloXmlParser(new File(getDataName()));
+ TreeI[] trees = parser.parse();
+ List<SequenceI> treeSeqs = trees[0].getNodeSequences();
+ for (SequenceI seq : treeSeqs)
+ {
+ seqs.add(seq);
+ }
+
+ }
+
+}
--- /dev/null
+package jalview.ext.forester.io;
+
+
+import javax.swing.filechooser.FileFilter;
+
+import org.forester.archaeopteryx.MainFrame;
+
+
+public enum SupportedTreeFileFilter
+{
+ NHFILTER(MainFrame.nhfilter), NHXFILTER(MainFrame.nhxfilter),
+ XMLFILTER(MainFrame.xmlfilter), TOLFILTER(MainFrame.tolfilter),
+ NEXUSFILTER(MainFrame.nexusfilter),
+ DEFAULTFILTER(MainFrame.defaultfilter);
+
+ private final FileFilter treeFilter;
+
+ SupportedTreeFileFilter(final FileFilter treeFilter)
+ {
+ this.treeFilter = treeFilter;
+
+ }
+
+ public void printSupportedFormats()
+ {
+ for (SupportedTreeFileFilter format : SupportedTreeFileFilter.values())
+ {
+ System.out.println(format.getTreeFilter().getDescription());
+ }
+ }
+
+ public FileFilter getTreeFilter()
+ {
+ return treeFilter;
+ }
+
+}
--- /dev/null
+package jalview.ext.forester.io;
+
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebservicesManager;
+
+public class TreeDatabaseMenuBuilder
+{
+ final WebservicesManager webservicesManager;
+
+
+ public TreeDatabaseMenuBuilder()
+
+ {
+ webservicesManager = WebservicesManager
+ .getInstance();
+
+ }
+
+ public JMenu createDbMenu()
+ {
+ JMenu treeDbMenu = new JMenu();
+ JMenuItem[] treeDatabaseMenuItems = new JMenuItem[webservicesManager
+ .getAvailablePhylogeniesWebserviceClients().size()];
+
+ for (int i = 0; i < treeDatabaseMenuItems.length; ++i)
+ {
+ final PhylogeniesWebserviceClient client = webservicesManager
+ .getAvailablePhylogeniesWebserviceClient(i);
+ treeDatabaseMenuItems[i] = new JMenuItem(
+ client.getMenuName());
+ treeDbMenu.add(treeDatabaseMenuItems[i]);
+
+ }
+ return treeDbMenu;
+
+ }
+
+ public List<PhylogeniesWebserviceClient> getTreeDatabases()
+ {
+ return webservicesManager.getAvailablePhylogeniesWebserviceClients();
+ }
+
+}
--- /dev/null
+package jalview.ext.forester.io;
+
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+
+import java.io.File;
+
+import org.forester.util.ForesterUtil;
+
+public class UtilityMethods
+{
+ public static boolean canForesterReadFile(File treeFile)
+ {
+ final String err = ForesterUtil.isReadableFile(treeFile);
+ if (!ForesterUtil.isEmpty(err))
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, err,
+ MessageManager.getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ return false;
+ }
+ return true;
+ }
+}
private static final String ALPHACARBON = "CA";
- private List<String> chainNames = new ArrayList<String>();
+ private List<String> chainNames = new ArrayList<>();
- private Hashtable<String, String> chainFile = new Hashtable<String, String>();
+ private Hashtable<String, String> chainFile = new Hashtable<>();
/*
* Object through which we talk to Chimera
/*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
- private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
+ private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
String lastHighlightCommand;
String file = pe.getFile();
try
{
- List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
+ List<ChimeraModel> modelsToMap = new ArrayList<>();
List<ChimeraModel> oldList = viewer.getModelList();
boolean alreadyOpen = false;
// exit thread if Chimera Viewer is closed in Jalview
}
}
- });
+ }, "ChimeraMonitor");
chimeraMonitor.start();
}
protected List<AtomSpec> convertStructureResiduesToAlignment(
List<String> structureSelection)
{
- List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
+ List<AtomSpec> atomSpecs = new ArrayList<>();
for (String atomSpec : structureSelection)
{
try
--- /dev/null
+package jalview.ext.treeviewer;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
+
+/**
+ * Interface for associating the leaves of a loaded in (not calculated) tree to
+ * the alignment sequences in Jalview.
+ *
+ * @author kjvanderheide
+ *
+ *
+ */
+public interface LoadedTreeAssociationI
+{
+ public void associateLeavesToSequences();
+
+ public Map<SequenceI, TreeNodeI> getAlignmentWithNodes();
+
+ public Map<TreeNodeI, SequenceI> getNodesWithAlignment();
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.SequenceI;
+import jalview.util.MappingUtils;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+
+public class LoadedTreeSequenceAssociation
+ implements LoadedTreeAssociationI
+{
+ SequenceI[] alignSequences;
+
+ TreeI tree;
+
+ Map<SequenceI, TreeNodeI> alignmentWithNodes;
+
+ Map<TreeNodeI, SequenceI> nodesWithAlignment;
+
+ public LoadedTreeSequenceAssociation(SequenceI[] alignmentSequences,
+ TreeI extTree)
+ {
+ alignSequences = alignmentSequences;
+ tree = extTree;
+ alignmentWithNodes = new HashMap<>(alignSequences.length);
+ nodesWithAlignment = new HashMap<>(alignSequences.length);
+
+ }
+
+ /**
+ * Tries to match sequences from Jalview with tree nodes in Archaeopteryx and
+ * fills in the tree node with sequence data if a match is found.
+ *
+ * Partially refactored from the old Jalview TreeModel
+ * associateLeavesToSequences method.
+ *
+ * @param seqs
+ * @param aptxTree
+ */
+ @Override
+ public void associateLeavesToSequences()
+
+ {
+ SequenceIdMatcher algnIds = new SequenceIdMatcher(alignSequences);
+ SequenceI nodeSequence;
+ String nodeSequenceName;
+
+ if (!tree.isEmpty())
+ {
+ for (final Iterator<TreeNodeI> iter = tree
+ .iterateInPreOrder(); iter
+ .hasNext();)
+ {
+ TreeNodeI treeNode = iter.next();
+ nodeSequenceName = treeNode.getNodeName();
+
+ nodeSequence = algnIds.findIdMatch(nodeSequenceName);
+ if (nodeSequence != null)
+ {
+ // is there already a sequence present for the node?
+ // If so, does it actually match Jalview's sequence?
+ if (treeNode.getSequence() != null)
+ {
+ if (!(treeNode.getSequence().getSequenceAsString()
+ .equals(nodeSequence.getSequenceAsString())))
+ {
+ System.err.println(
+ "Sequence detected in tree node that does not match corresponding Jalview sequence:"
+ + nodeSequenceName);
+ // which sequence gets precedence?
+
+ }
+
+ }
+ else
+ {
+ treeNode.setSequence(nodeSequence);
+ }
+ MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
+ nodeSequence, treeNode);
+ MappingUtils.putWithDuplicationCheck(nodesWithAlignment, treeNode,
+ nodeSequence);
+
+
+ }
+
+ }
+
+ }
+ }
+
+
+
+ @Override
+ public Map<SequenceI, TreeNodeI> getAlignmentWithNodes()
+ {
+ return alignmentWithNodes;
+ }
+
+ @Override
+ public Map<TreeNodeI, SequenceI> getNodesWithAlignment()
+ {
+ return nodesWithAlignment;
+ }
+
+
+}
+
+
+
+
+
+
--- /dev/null
+package jalview.ext.treeviewer;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
+
+/**
+ * @author kjvanderheide
+ *
+ */
+public interface TreeBuilderI
+{
+ public TreeI buildTree(TreeNodeI treeRoot);
+
+ public TreeI buildTree();
+
+ public Map<SequenceI, TreeNodeI> getAlignmentBoundNodes();
+
+ public Map<TreeNodeI, SequenceI> getNodesBoundAlignment();
+
+ public String generateTreeName();
+
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+public interface TreeControlsI
+{
+ public void defaultSettings();
+
+ public void displayEntireTree();
+
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.MenuContainer;
+import java.awt.image.ImageObserver;
+
+import javax.accessibility.Accessible;
+import javax.swing.RootPaneContainer;
+import javax.swing.WindowConstants;
+import javax.swing.event.InternalFrameListener;
+
+public interface TreeFrameI
+ extends Accessible, WindowConstants, RootPaneContainer,
+ ImageObserver, MenuContainer
+{
+ public abstract TreePanelI getTreePanel();
+
+ public abstract TreeI getTree();
+
+ public abstract void checkMultipleTrees();
+
+ public abstract int getNumberOfTrees();
+
+ public TreeControlsI getTreeControls();
+
+ public void addFrameListener(InternalFrameListener listener);
+
+ public void removeFrameListener(InternalFrameListener listener);
+
+ public InternalFrameListener[] getFrameListeners();
+
+ public void repaint();
+
+ public boolean isShowing();
+
+ public Container getTopLevelAncestor();
+
+ public void addFrameToJalview(String title, boolean makeVisible,
+ int width, int height, boolean resizable, boolean ignoreMinSize);
+
+ public TreeViewerBindingI getViewBinding();
+
+ public void setViewBinding(TreeViewerBindingI alignmentBinding);
+
+ public void setMinimumSize(Dimension minimumSize);
+
+ public void setMaximumSize(Dimension maximumSize);
+
+ public void setPreferredSize(Dimension preferredSize);
+
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+import jalview.datamodel.SequenceI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.List;
+
+public interface TreeI
+{
+ public TreeNodeI getRoot();
+
+ public TreeNodeI getNodeWithName(String name);
+
+ public TreeNodeI getFurthestNode();
+
+ public TreeNodeI[] getAllNodes();
+
+ public String[] getAllLeafNames();
+
+ public List<SequenceI> getNodeSequences();
+
+ public void setTreeName(String treeTitle);
+
+ public void setRerootable(boolean b);
+
+ public void setRooted(boolean b);
+
+ public boolean isEmpty();
+
+ public String getTreeName();
+
+ public void setRoot(TreeNodeI rootNode);
+
+ public double getHeight(boolean adjustForCollapsedSubtrees);
+
+ public Iterator<TreeNodeI> iterateInPreOrder();
+
+ public Iterator<TreeNodeI> iterateInLevelOrder();
+
+ public Iterator<TreeNodeI> iterateInPostOrder();
+
+ TreeFrameI createTreeViewerFromTree(String instanceTitle);
+
+ public void writeToXml(File outputFile) throws IOException;
+
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.List;
+
+public interface TreeNodeI
+{
+
+ public String getNodeName();
+
+ public List<TreeNodeI> getAllDescendants();
+
+ public List<TreeNodeI> getExternalDescendants();
+
+ public List<TreeNodeI> getDirectChildren();
+
+ public void setSequence(SequenceI seq);
+
+ public SequenceI getSequence();
+
+ public void addAsChild(TreeNodeI childNode);
+
+ public long getId();
+
+ public float getXcoord();
+
+ public float getYcoord();
+
+ public void setBranchColor(Color branchColor);
+
+ public boolean isInternal();
+
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+import java.awt.Dimension;
+import java.awt.Graphics2D;
+import java.awt.MenuContainer;
+import java.awt.Rectangle;
+import java.awt.event.MouseListener;
+import java.io.File;
+import java.util.Set;
+
+import javax.accessibility.Accessible;
+
+public interface TreePanelI extends Accessible, MenuContainer
+{
+
+
+ public abstract void setTreeFile(File file);
+
+ public abstract File getTreeFile();
+
+ public abstract TreeI getTree();
+
+ public abstract TreeNodeI findNode(int x, int y);
+
+ public abstract void setMatchingNodes(Set<Long> matchingNodes);
+
+ public abstract Set<Long> getMatchingNodes();
+
+ public void addMouseListener(MouseListener listener);
+
+ public void removeMouseListener(MouseListener listener);
+
+ public MouseListener[] getMouseListeners();
+
+ public void repaint();
+
+ public void registerWithPaintRefresher(String sequenceSetIdentifier);
+
+ public void notifyPaintRefresher(boolean alignmentChanged,
+ boolean validateSequences);
+
+ public void notifyPaintRefresher(String newSeqSetIdentifier,
+ boolean alignmentChanged, boolean validateSequences);
+
+ public int getWidth();
+
+ public int getHeight();
+
+ public abstract void paintToFile(Graphics2D pg, int width, int height);
+
+ public boolean showingSubTree();
+
+ public float getPartitionThreshold();
+
+ public abstract Rectangle getVisibleArea();
+
+ public void setMinimumSize(Dimension minimumSize);
+
+ public void setMaximumSize(Dimension maximumSize);
+
+ public void setPreferredSize(Dimension preferredSize);
+
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+import java.io.IOException;
+
+public interface TreeParserI
+ {
+ public TreeI[] parse() throws IOException;
+
+ public void setSource(Object source) throws IOException;
+
+ public String getName();
+
+ public TreeI[] getParsedTrees();
+
+ }
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.treeviewer;
+
+import jalview.commands.CommandI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+
+import java.awt.event.ActionListener;
+import java.awt.event.MouseListener;
+
+/**
+ *
+ * Interface for binding a tree viewer to Jalview alignments. Assumes a tree
+ * viewer will both want to receive and send selection events.
+ *
+ * @author kjvanderheide
+ *
+ *
+ */
+public interface TreeViewerBindingI
+ extends ActionListener, MouseListener, SelectionListener,
+ SelectionSource
+{
+ /**
+ * If a node is selected in the tree panel this method highlights the
+ * corresponding sequence in the Jalview alignment view. If an internal node
+ * is selected all child sequences get highlighted as well.
+ */
+ public void showNodeSelectionOnAlign(TreeNodeI node);
+
+ public void treeSelectionChanged(SequenceI sequence);
+
+ public void showMatchingSequence(TreeNodeI nodeToMatch);
+
+ public void showMatchingChildSequences(TreeNodeI parentNode);
+
+ public void sortByTree_actionPerformed();
+
+ public CommandI sortAlignmentIn(AlignmentPanel alignPanel);
+
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+public interface TreeViewerConfigI
+{
+
+}
--- /dev/null
+package jalview.ext.treeviewer;
+
+import jalview.datamodel.SequenceI;
+import jalview.ext.archaeopteryx.JalviewBinding;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Dimension;
+import java.io.File;
+import java.util.HashMap;
+import java.util.Map;
+
+public final class TreeViewerUtils
+{
+ private static Map<TreeFrameI, TreeViewerBindingI> activeViews = new HashMap<>();
+
+ public static TreeViewerBindingI associateNodesWithJalviewSequences(
+ final TreeFrameI treeFrame,
+ final AlignmentViewport jalviewAlignViewport,
+ final Map<SequenceI, TreeNodeI> alignMappedToNodes,
+ final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
+ {
+ TreeViewerBindingI treeBinding = new JalviewBinding(treeFrame,
+ jalviewAlignViewport,
+ alignMappedToNodes, nodesMappedToAlign);
+ jalviewAlignViewport.setCurrentExtTree(treeFrame.getTree());
+ activeViews.put(treeFrame, treeFrame.getViewBinding());
+
+ return treeBinding;
+ }
+
+ public static TreeFrameI addTreeViewFrameToJalview(
+ final TreeFrameI treeFrame)
+ {
+ int width = 400;
+ int height = 550;
+ treeFrame.setMinimumSize(new Dimension(width, height));
+ // aptxApp.setFont(Desktop.instance.getFont());
+ // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());
+ String frameTitle = MessageManager.getString("label.aptx_title");
+ File treeFile = treeFrame.getTreePanel().getTreeFile();
+ if (treeFile != null)
+ {
+ frameTitle += MessageManager.formatMessage("label.aptx_title_append",
+ new String[]
+ { treeFile.getAbsolutePath() });
+ }
+ // Usually redundant as this is done when associating nodes as well but that
+ // step could be bypassed
+ activeViews.put(treeFrame, treeFrame.getViewBinding());
+
+ treeFrame.addFrameToJalview(frameTitle, true, width, height, true,
+ false);
+ return treeFrame;
+
+ }
+
+ public static Map<TreeFrameI, TreeViewerBindingI> getActiveTreeViews()
+ {
+ return activeViews;
+ }
+
+}
public void transferToSequenceFetcher(String ids)
{
seqFetcher.getTextArea().setText(ids);
- Thread worker = new Thread(seqFetcher);
+ Thread worker = new Thread(seqFetcher, "GFTSSeqFetcher");
worker.start();
}
private static String defaultFTSFrameTitle = MessageManager
.getString("label.pdb_sequence_fetcher");
- private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+ private static Map<String, Integer> tempUserPrefs = new HashMap<>();
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
// mainFrame.dispose();
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<String>();
+ HashSet<String> selectedIdsSet = new HashSet<>();
int primaryKeyColIndex = 0;
try
{
String ids = selectedIds.toString();
// System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
seqFetcher.getTextArea().setText(ids);
- Thread worker = new Thread(seqFetcher);
+ Thread worker = new Thread(seqFetcher, "PDBFTSSeqFetcher");
worker.start();
delayAndEnableActionButtons();
}
import jalview.analysis.Dna;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
-import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.ext.archaeopteryx.AptxInit;
+import jalview.ext.forester.io.SupportedTreeFileFilter;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeViewerBindingI;
+import jalview.ext.treeviewer.TreeViewerUtils;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridLayout;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.beans.PropertyChangeEvent;
import java.io.File;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComboBox;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebservicesManager;
+
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*/
- void updateEditMenuBar()
+ public void updateEditMenuBar()
{
if (viewport.getHistoryList().size() > 0)
/**
* Constructs a tree panel and adds it to the desktop
*
- * @param type
- * tree type (NJ or AV)
- * @param modelName
- * name of score model used to compute the tree
- * @param options
- * parameters for the distance or similarity calculation
+ * @param params
+ * @param treeAlgo
+ *
+ * @param tree
+ *
+ *
*/
- void newTreePanel(String type, String modelName,
- SimilarityParamsI options)
+ void newTreePanel(TreeModel tree, String treeAlgo,
+ String substitutionMatrix)
{
String frameTitle = "";
TreePanel tp;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- for (SequenceI _s : sg.getSequences())
+ for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
{
if (_s.getLength() < sg.getEndRes())
{
}
}
- tp = new TreePanel(alignPanel, type, modelName, options);
+ tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
frameTitle += " from ";
}
}
+
/**
* Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
* TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
List<Component> comps = PaintRefresher.components
.get(viewport.getSequenceSetId());
List<TreePanel> treePanels = new ArrayList<>();
+
+ Map<TreeFrameI, TreeViewerBindingI> aptxFrames = TreeViewerUtils
+ .getActiveTreeViews();
+
for (Component comp : comps)
{
+ // old treepanels
if (comp instanceof TreePanel)
{
treePanels.add((TreePanel) comp);
}
+
}
- if (treePanels.size() < 1)
+ if (treePanels.isEmpty() && aptxFrames.isEmpty())
{
sortByTreeMenu.setVisible(false);
return;
sortByTreeMenu.setVisible(true);
+ for (Entry<TreeFrameI, TreeViewerBindingI> aptxFrameWithBinding : aptxFrames
+ .entrySet())
+ {
+ TreeFrameI aptxFrame = aptxFrameWithBinding.getKey();
+ TreeViewerBindingI binding = aptxFrameWithBinding.getValue();
+
+ // future support for multiple tabs
+ // for (org.forester.archaeopteryx.TreePanel aptxTree : aptxFrame
+ // .getMainPanel().getTreePanels())
+ {
+ final JMenuItem item = new JMenuItem(
+ aptxFrame.getTree().getTreeName());
+
+ item.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ binding.sortByTree_actionPerformed(); // redundant here??
+ addHistoryItem(binding.sortAlignmentIn(alignPanel));
+ }
+
+ });
+ sortByTreeMenu.add(item);
+ }
+
+
+
+ }
+
+
+
+
+
+ // old treepanels
for (final TreePanel tp : treePanels)
{
final JMenuItem item = new JMenuItem(tp.getTitle());
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
+ chooseTreeFile();
+ }
+
+ @Override
+ protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
+ {
+ chooseTreeUrl();
+ }
+
+ @Override
+ protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb(0, null);
+
+ }
+
+ @Override
+ protected void loadTreeBase_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb(1, null);
+
+ }
+ @Override
+ protected void loadTreePfam_actionPerformed(ActionEvent e)
+ {
+
+ // only DBRefs of first sequence are checked for matching DB for now,
+ // iterating through them all seems excessive
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+ String dbId = null;
+ for (DBRefEntry pfamRef : DBRefUtils
+ .searchRefsForSource(seq.getDBRefs(), "pfam"))
+ {
+ if (pfamRef.getAccessionId().startsWith("PF"))
+ {
+ dbId = pfamRef.getAccessionId().replaceAll("[A-Za-z]", "");
+ }
+
+ }
+ chooseTreeDb(2, dbId);
+
+ }
+ @Override
+ protected void loadTreeFam_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb(3, null);
+
+ }
+
+ @Override
+ protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+ {
+ chooseTreeDb(4, null);
+
+ }
+
+
+
+
+
+ public void chooseTreeFile()
+ {
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
- MessageManager.getString("label.select_newick_like_tree_file"));
+ MessageManager.getString("label.select_tree_file")); // modify
chooser.setToolTipText(
- MessageManager.getString("label.load_tree_file"));
+ MessageManager.getString("label.load_tree_for_sequence_set"));
+ for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
+ .values())
+ {
+ chooser.setFileFilter(treeFormat.getTreeFilter());
+ }
int value = chooser.showOpenDialog(null);
{
String filePath = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
+
+
+ NewickFile fin = null; // old tree
try
{
- fin = new NewickFile(filePath, DataSourceType.FILE);
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
+ AptxInit.createInstancesFromFile(filePath, viewport);
+
+ // fin = new NewickFile(filePath, DataSourceType.FILE);
+ // viewport.setCurrentTree(viewport.getAlignPanel().alignFrame
+ // .showNewickTree(fin, filePath).getTree());
+
} catch (Exception ex)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ JvOptionPane.showMessageDialog(this, ex.getMessage(),
MessageManager.getString("label.problem_reading_tree_file"),
JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
- if (fin != null && fin.hasWarningMessage())
+
+ }
+ }
+
+ /**
+ * Break up and move to TreeParser?
+ */
+ public void chooseTreeUrl()
+ {
+
+ JLabel label = new JLabel(
+ MessageManager.getString("label.tree_url_example"));
+ // add "example" button
+ final JComboBox<String> history = new JComboBox<>();
+
+ JPanel panel = new JPanel(new GridLayout(2, 1));
+ panel.add(label);
+ panel.add(history);
+ history.setPreferredSize(new Dimension(400, 20));
+ history.setEditable(true);
+ history.addItem("http://www.");
+
+ String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+ StringTokenizer st;
+
+ if (historyItems != null)
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager
- .getString("label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
+ st = new StringTokenizer(historyItems, "\t");
+
+ while (st.hasMoreTokens())
+ {
+ history.addItem(st.nextToken());
+ }
+ }
+
+ int reply = JvOptionPane.showInternalConfirmDialog(this, panel,
+ MessageManager.getString("label.load_tree_url"),
+ JvOptionPane.OK_CANCEL_OPTION);
+
+ if (reply == JvOptionPane.OK_OPTION)
+ {
+
+ String urlString = history.getSelectedItem().toString();
+ URL treeUrl;
+
+ try
+ {
+ FileFormatI format = null;
+
+ format = new IdentifyFile().identify(urlString, DataSourceType.URL);
+ // add actual use for the format identification (jalview .jar files)
+ treeUrl = new URL(urlString);
+ AptxInit.createInstancesFromUrl(treeUrl, viewport);
+
+ } catch (IOException | RuntimeException e)
+ {
+ JvOptionPane.showMessageDialog(this, MessageManager.formatMessage(
+ "exception.failed_to_read_data_from_source", new String[]
+ { urlString }),
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.ERROR_MESSAGE);
+ e.printStackTrace();
}
}
+ else
+ {
+
+ }
+ }
+
+ /**
+ * Disgustingly hardcoded atm.
+ *
+ * @param databaseIndex
+ */
+ public void chooseTreeDb(int databaseIndex, String defaultIdentifier)
+ {
+ final WebservicesManager webservices_manager = WebservicesManager
+ .getInstance();
+ final PhylogeniesWebserviceClient client = webservices_manager
+ .getAvailablePhylogeniesWebserviceClient(databaseIndex);
+ String identifier = JvOptionPane
+ .showInternalInputDialog(Desktop.desktop,
+ client.getInstructions() + "\n(Reference: "
+ + client.getReference() + ")",
+ client.getDescription(), JvOptionPane.QUESTION_MESSAGE,
+ null, null, defaultIdentifier)
+ .toString();
+
+ AptxInit.createInstancesFromDb(client, identifier, viewport);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
private boolean buildingMenu = false;
+ public void BuildTreeDbMenu()
+ {
+
+ }
/**
* Generates menu items and listener event actions for web service clients
*
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
+ final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
+
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
+ wsmenu.add(phylogenmenu);
// No search services yet
// wsmenu.add(seqsrchmenu);
}
buildingMenu = false;
}
- }).start();
+ }, "BuildWebService").start();
}
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
- new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
+ "CrossReferences")
.start();
}
ex.printStackTrace();
}
}
- }).start();
+ }, "DropFile").start();
}
}
});
dbRefFetcher.fetchDBRefs(false);
}
- }).start();
+ }, "BuildFetchDBMenu").start();
}
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
-import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
-import java.util.Vector;
import javax.swing.JInternalFrame;
* return the alignPanel containing the given viewport. Use this to get the
* components currently handling the given viewport.
*
- * @param av
* @return null or an alignPanel guaranteed to have non-null alignFrame
* reference
*/
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
addingStructures = false;
- worker = new Thread(this);
+ worker = new Thread(this, "OpenJmol");
worker.start();
this.addInternalFrameListener(new InternalFrameAdapter()
package jalview.gui;
import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeCalculator;
+import jalview.analysis.TreeModel;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.SequenceGroup;
+import jalview.ext.archaeopteryx.AptxInit;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyVetoException;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
- List<String> tips = new ArrayList<String>();
+ List<String> tips = new ArrayList<>();
/*
* the most recently opened PCA results panel
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+ final JComboBox<String> scoreModelsCombo = new JComboBox<>();
scoreModelsCombo.setRenderer(renderer);
/*
{
Object curSel = comboBox.getSelectedItem();
toolTips.clear();
- DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+ DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
/*
* now we can actually add entries to the combobox,
/**
* Open and calculate the selected tree or PCA on 'OK'
+ *
+ * @throws IOException
*/
protected void calculate_actionPerformed()
{
boolean doPCA = pca.isSelected();
- String modelName = modelNames.getSelectedItem().toString();
+ String substitutionMatrix = modelNames.getSelectedItem().toString();
SimilarityParamsI params = getSimilarityParameters(doPCA);
if (doPCA)
{
- openPcaPanel(modelName, params);
+ openPcaPanel(substitutionMatrix, params);
}
else
{
- openTreePanel(modelName, params);
+ try
+ {
+ createTree(substitutionMatrix, params);
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+
+
+
+
+
}
// closeFrame();
}
- /**
- * Open a new Tree panel on the desktop
- *
- * @param modelName
- * @param params
- */
- protected void openTreePanel(String modelName, SimilarityParamsI params)
+ protected void createTree(String substitutionMatrix,
+ SimilarityParamsI params) throws IOException
+ {
+ String treeAlgo = determineTreeAlgo();
+ TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
+ substitutionMatrix, params);
+ TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport());
+
+ // AptxInit.createInstanceFromCalculation(calculatedTree);
+
+ TreeModel tree = new TreeModel(calculatedTree);
+ jalview.io.NewickFile newick = new jalview.io.NewickFile(
+ tree.getTopNode());
+ String output = newick.print(tree.hasBootstrap(), tree.hasDistances(),
+ tree.hasRootDistance());
+ AptxInit.createInstanceFromNhx(af.getTitle(), output,
+ af.getViewport());
+ // openTreePanel(tree, treeAlgo, substitutionMatrix);
+ }
+
+
+ protected String determineTreeAlgo() // to be modified & expanded
+ {
+ String treeAlgorithm = neighbourJoining.isSelected()
+ ? TreeBuilder.NEIGHBOUR_JOINING
+ : TreeBuilder.AVERAGE_DISTANCE;
+
+ return treeAlgorithm;
+
+ }
+
+ protected void checkEnoughSequences(AlignViewport viewport)
{
- /*
- * gui validation shouldn't allow insufficient sequences here, but leave
- * this check in in case this method gets exposed programmatically in future
- */
- AlignViewport viewport = af.getViewport();
SequenceGroup sg = viewport.getSelectionGroup();
if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
{
JvOptionPane.WARNING_MESSAGE);
return;
}
+ }
- String treeType = neighbourJoining.isSelected()
- ? TreeBuilder.NEIGHBOUR_JOINING
- : TreeBuilder.AVERAGE_DISTANCE;
- af.newTreePanel(treeType, modelName, params);
+ /**
+ * Open a new Tree panel on the desktop
+ *
+ * @param tree
+ * @param params
+ * @param treeAlgo
+ */
+ protected void openTreePanel(TreeModel tree, String treeAlgo,
+ String substitutionMatrix)
+ {
+ /*
+ * gui validation shouldn't allow insufficient sequences here, but leave
+ * this check in in case this method gets exposed programmatically in future
+ */
+ checkEnoughSequences(af.getViewport());
+
+ af.newTreePanel(tree, treeAlgo, substitutionMatrix);
}
/**
initMenus();
addingStructures = false;
- worker = new Thread(this);
+ worker = new Thread(this, "OpenChimera");
worker.start();
this.addInternalFrameListener(new InternalFrameAdapter()
// Starting two seperate threads to read from the PipedInputStreams
//
- reader = new Thread(this);
+ reader = new Thread(this, "ConsoleReader1");
reader.setDaemon(true);
reader.start();
//
- reader2 = new Thread(this);
+ reader2 = new Thread(this, "ConsoleReader2");
reader2.setDaemon(true);
reader2.start();
// and a thread to append text to the textarea
- textAppender = new Thread(this);
+ textAppender = new Thread(this, "ConsoleTextAppend");
textAppender.setDaemon(true);
textAppender.start();
}
// We do it with a seperate Thread becasue we don't wan't to break a Thread
// used by the Console.
System.out.println("\nLets throw an error on this console");
- errorThrower = new Thread(this);
+ errorThrower = new Thread(this, "ConsoleErrorLog");
errorThrower.setDaemon(true);
errorThrower.start();
}
import javax.swing.JCheckBox;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
{
if (sourceRegistry == null)
{
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "PaintDas");
worker.start();
}
}
}
}
- Vector<jalviewSourceI> selected = new Vector<jalviewSourceI>();
+ Vector<jalviewSourceI> selected = new Vector<>();
for (String source : selectedSources)
{
jalviewSourceI srce = sourceRegistry.getSource(source);
{
saveProperties(jalview.bin.Cache.applicationProperties);
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "RepaintDas");
worker.start();
}
private void setCapabilities(DasSourceRegistryI sourceRegistry2)
{
- Vector<String> authority = new Vector<String>();
- Vector<String> type = new Vector<String>();
- Vector<String> label = new Vector<String>();
- Vector<String> taxIds = new Vector<String>();
+ Vector<String> authority = new Vector<>();
+ Vector<String> type = new Vector<>();
+ Vector<String> label = new Vector<>();
+ Vector<String> taxIds = new Vector<>();
authority.add("Any");
type.add("Any");
label.add("Any");
fileFormat);
Cache.log.debug("Filechooser init thread finished.");
}
- }).start();
+ }, "InitFileChooser").start();
// Add the service change listener
changeSupport.addJalviewPropertyChangeListener("services",
new PropertyChangeListener()
Desktop.instance.setProgressBar(null, now);
jvnews.showNews();
}
- }).start();
+ }, "ShowNewsWindow").start();
}
}
}
if (format == null)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_locate",
- new Object[]
+ MessageManager.formatMessage(
+ "label.couldnt_locate",
+ new String[]
{ url }),
MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
{
new SplashScreen(true);
}
- }).start();
+ }, "ShowAboutMenu").start();
}
public StringBuffer getAboutMessage(boolean shortv)
}
setProgressBar(null, choice.hashCode());
}
- }).start();
+ }, "SaveJalviewProject").start();
}
}
}
setProgressBar(null, choice.hashCode());
}
- }).start();
+ }, "LoadJalviewProject").start();
}
}
dsktp.v_client.initial_update();
}
- });
+ }, "VamsasSession");
rthr.start();
}
};
{
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
// javax.swing.SwingUtilities.invokeLater(jvq);
- new Thread(jvq).start();
+ new Thread(jvq, "CheckQuestionnaire").start();
}
public void checkURLLinks()
this.showMemoryUsage = showMemory;
if (showMemory)
{
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "ShowMemoryUsage");
worker.start();
}
repaint();
}
// JAL-940 - disabled JWS1 service configuration - always start discoverer
// until we phase out completely
- (t0 = new Thread(discoverer)).start();
+ (t0 = new Thread(discoverer, "Discoverer")).start();
}
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
progress.setProgressBar(null, this.hashCode());
}
}
- }).start();
+ }, "OpenURL").start();
}
public static WsParamSetManager wsparamManager = null;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.ext.archaeopteryx.AptxInit;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeViewerUtils;
import jalview.ext.varna.RnaModel;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.io.NewickFile;
import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
jms.addTree(tree);
}
}
+
+ }
+ }
+ }
+ if (!storeDS && av.getCurrentExtTree() != null)
+ {
+ Set<TreeFrameI> externalTreeViews = TreeViewerUtils
+ .getActiveTreeViews()
+ .keySet();
+ for (TreeFrameI treeView : externalTreeViews)
+ {
+ TreeI tree = treeView.getTree();
+ try
+ {
+ tree.writeToXml(new File("word"));
+ copyFileToJar(jout, "word", "aptx-test");
+
+
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
}
+
}
+
}
+
+
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
String varnaStateFile = varna.getStateInfo(model.rna);
jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
- copyFileToJar(jout, varnaStateFile, jarEntryName);
+
rnaSessions.put(model, jarEntryName);
}
SecondaryStructure ss = new SecondaryStructure();
if (loadTreesAndStructures)
{
loadTrees(jms, view, af, av, ap);
+ loadExternalTrees(jprovider, jms, av);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
}
// and finally return.
return af;
}
+
+ private void loadExternalTrees(jarInputStreamProvider jprovider,
+ JalviewModelSequence jms, AlignViewport av)
+ {
+ String treeFile = copyJarEntry(jprovider, "aptx-test", "aptx", null);
+ if (treeFile != null)
+ {
+ try
+ {
+ AptxInit.createInstancesFromFile(treeFile, av);
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ }
+
+
/**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
{
Tree tree = jms.getTree(t);
+ NewickFile newick = new jalview.io.NewickFile(tree.getNewick());
+
+ TreeFrameI externalViewer = AptxInit.createInstanceFromNhx(
+ tree.getTitle(), tree.getNewick(),
+ av);
+
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{
+
+
tp = af.showNewickTree(
- new jalview.io.NewickFile(tree.getNewick()),
+ newick,
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());
if (tree.getId() != null)
if (this.frefedSequence == null)
{
- frefedSequence = new Vector<SeqFref>();
+ frefedSequence = new Vector<>();
}
viewportsAdded.clear();
frame.setVisible(true);
}
- }).start();
+ }, "UnblockedDialog").start();
}
else
{
return;
}
- Thread thread = new Thread(this);
+ Thread thread = new Thread(this, "UpdateOverview");
thread.start();
repaint();
*/
public class PaintRefresher
{
- static Map<String, List<Component>> components = new HashMap<String, List<Component>>();
+ static Map<String, List<Component>> components = new HashMap<>();
/**
* Add the given component to those registered under the given sequence set
}
else
{
- List<Component> vcoms = new ArrayList<Component>();
+ List<Component> vcoms = new ArrayList<>();
vcoms.add(comp);
components.put(seqSetId, vcoms);
}
}
}
- static AlignmentPanel[] getAssociatedPanels(String id)
+ public static AlignmentPanel[] getAssociatedPanels(String id)
{
List<Component> comps = components.get(id);
if (comps == null)
{
return new AlignmentPanel[0];
}
- List<AlignmentPanel> tmp = new ArrayList<AlignmentPanel>();
+ List<AlignmentPanel> tmp = new ArrayList<>();
for (Component comp : comps)
{
if (comp instanceof AlignmentPanel)
showLink(url);
}
- }).start();
+ }, "ShowURLMenu").start();
}
});
}
}
- }).start();
+ }, "ShowGroupURLMenu").start();
}
});
slider.setMaximum(100);
slider.setValue(100);
- Thread worker = new Thread(this);
+ Thread worker = new Thread(this, "CreateRedundancyPanel");
worker.start();
frame = new JInternalFrame();
{
this.interactiveDialog = interactive;
// show a splashscreen that will disapper
- Thread t = new Thread(this);
+ Thread t = new Thread(this, "ShowSplashScreen");
t.start();
}
MouseAdapter closer = new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
try
/**
* Create splash screen, display it and clear it off again.
*/
+ @Override
public void run()
{
initSplashScreenWindow();
return new Dimension(image.getWidth(this) + 8, image.getHeight(this));
}
+ @Override
public void paintComponent(Graphics g)
{
g.setColor(Color.white);
// and call ourselves again.
addStructure(pdbentry, seqs, chains, align, alignFrame);
}
- }).start();
+ }, "Adding3DStructureQueue").start();
return;
}
}
addingStructures = true;
_started = false;
alignAddedStructures = align;
- worker = new Thread(this);
+ worker = new Thread(this, "Adding3DStructure");
worker.start();
return;
}
*/
void startPrinting()
{
- Thread thread = new Thread(this);
+ Thread thread = new Thread(this, "PrintTreeCanvas");
thread.start();
}
Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
- Vector<SequenceI> sequences = new Vector<SequenceI>();
+ Vector<SequenceI> sequences = new Vector<>();
for (int j = 0; j < l.size(); j++)
{
package jalview.gui;
import jalview.analysis.AlignmentSorter;
-import jalview.analysis.AverageDistanceTree;
-import jalview.analysis.NJTree;
-import jalview.analysis.TreeBuilder;
import jalview.analysis.TreeModel;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import java.awt.event.ActionListener;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.List;
import javax.swing.ButtonGroup;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
import org.jibble.epsgraphics.EpsGraphics2D;
*/
public class TreePanel extends GTreePanel
{
- String treeType;
+ String substitutionMatrix;
- String scoreModelName; // if tree computed
+ String treeType;
String treeTitle; // if tree loaded
- SimilarityParamsI similarityParams;
-
TreeCanvas treeCanvas;
TreeModel tree;
* Creates a new TreePanel object.
*
* @param ap
- * @param type
- * @param modelName
- * @param options
+ * @param tree
+ * @param treeType
+ * @param substitutionMatrix
*/
- public TreePanel(AlignmentPanel ap, String type, String modelName,
- SimilarityParamsI options)
+ public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
+ String substitutionMatrix)
{
super();
- this.similarityParams = options;
- initTreePanel(ap, type, modelName, null, null);
+ this.treeType = treeType;
+ this.substitutionMatrix = substitutionMatrix;
+ this.tree = tree;
+ initTreePanel(ap, tree);
// We know this tree has distances. JBPNote TODO: prolly should add this as
// a userdefined default
// showDistances(true);
}
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param alignPanel
+ * @param newtree
+ * @param theTitle
+ * @param inputData
+ */
public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
String theTitle, AlignmentView inputData)
{
super();
this.treeTitle = theTitle;
- initTreePanel(alignPanel, null, null, newtree, inputData);
+ initTreePanel(alignPanel, newtree, inputData);
}
public AlignmentI getAlignment()
return treeCanvas.av;
}
- void initTreePanel(AlignmentPanel ap, String type, String modelName,
- NewickFile newTree, AlignmentView inputData)
+ /**
+ * Initialize a tree panel based on a calculated tree
+ *
+ * @param ap
+ * @param tree
+ */
+ void initTreePanel(AlignmentPanel ap, TreeModel tree)
{
+ buildTreeCanvas(ap);
- av = ap.av;
- this.treeType = type;
- this.scoreModelName = modelName;
+ TreeLoader tl = new TreeLoader(null, null);
+ tl.start();
- treeCanvas = new TreeCanvas(this, ap, scrollPane);
- scrollPane.setViewportView(treeCanvas);
+ }
- PaintRefresher.Register(this, ap.av.getSequenceSetId());
+ /**
+ * Initialize a tree panel based on a loaded in tree file.
+ *
+ * @param ap
+ * @param loadedTree
+ * @param inputData
+ */
+ void initTreePanel(AlignmentPanel ap,
+ NewickFile loadedTree, AlignmentView inputData)
+ {
+ buildTreeCanvas(ap);
- buildAssociatedViewMenu();
+ TreeLoader tl = new TreeLoader(loadedTree, inputData);
+ tl.start();
+ }
- final PropertyChangeListener listener = addAlignmentListener();
+public void buildTreeCanvas(AlignmentPanel ap) {
+ av = ap.av;
- /*
- * remove listener when window is closed, so that this
- * panel can be garbage collected
- */
- addInternalFrameListener(new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(InternalFrameEvent evt)
- {
- if (av != null)
- {
- av.removePropertyChangeListener(listener);
- }
- }
- });
+ treeCanvas = new TreeCanvas(this, ap, scrollPane);
+ scrollPane.setViewportView(treeCanvas);
- TreeLoader tl = new TreeLoader(newTree, inputData);
- tl.start();
- }
+ PaintRefresher.Register(this, ap.av.getSequenceSetId());
- /**
- * @return
- */
- protected PropertyChangeListener addAlignmentListener()
- {
- final PropertyChangeListener listener = new PropertyChangeListener()
+ buildAssociatedViewMenu();
+
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
@Override
public void propertyChange(PropertyChangeEvent evt)
repaint();
}
}
- };
- av.addPropertyChangeListener(listener);
- return listener;
+ });
+
+
+
+
}
@Override
class TreeLoader extends Thread
{
- private NewickFile newtree;
+ private NewickFile newTree;
private AlignmentView odata = null;
public TreeLoader(NewickFile newickFile, AlignmentView inputData)
{
- this.newtree = newickFile;
+ this.newTree = newickFile;
this.odata = inputData;
- if (newickFile != null)
+ if (newTree != null)
{
// Must be outside run(), as Jalview2XML tries to
// update distance/bootstrap visibility at the same time
- showBootstrap(newickFile.HasBootstrap());
- showDistances(newickFile.HasDistances());
+ showBootstrap(newTree.hasBootstrap());
+ showDistances(newTree.hasDistances());
+
}
+
}
@Override
public void run()
{
- if (newtree != null)
+ if (newTree != null)
{
tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
- newtree);
+ newTree);
if (tree.getOriginalData() == null)
{
originalSeqData.setVisible(false);
}
+
+
+
}
- else
- {
- ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName, treeCanvas.ap);
- TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
- ? new NJTree(av, sm, similarityParams)
- : new AverageDistanceTree(av, sm, similarityParams);
- tree = new TreeModel(njtree);
- showDistances(true);
- }
+ showTree(tree);
+ }
+
+ public void showTree(TreeModel tree)
+ {
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
treeCanvas.setTree(tree);
treeCanvas.repaint();
+
av.setCurrentTree(tree);
if (av.getSortByTree())
{
sortByTree_actionPerformed();
}
+
}
}
* @param e
*/
@Override
- public void sortByTree_actionPerformed()
+ public void sortByTree_actionPerformed()// modify for Aptx
{
if (treeCanvas.applyToAllViews)
*
* @return
*/
- public String getPanelTitle()
+ public String getPanelTitle() // to be moved/fixed
{
if (treeTitle != null)
{
return treeTitle;
}
-
- /*
- * i18n description of Neighbour Joining or Average Distance method
- */
- String treecalcnm = MessageManager
- .getString("label.tree_calc_" + treeType.toLowerCase());
-
- /*
- * short score model name (long description can be too long)
- */
- String smn = scoreModelName;
-
- /*
- * put them together as <method> Using <model>
- */
- final String ttl = MessageManager.formatMessage("label.treecalc_title",
- treecalcnm, smn);
- return ttl;
+ else
+ {
+ /*
+ * i18n description of Neighbour Joining or Average Distance method
+ */
+ String treecalcnm = MessageManager
+ .getString("label.tree_calc_" + treeType.toLowerCase());
+
+ /*
+ * short score model name (long description can be too long)
+ */
+ String smn = substitutionMatrix;
+
+ /*
+ * put them together as <method> Using <model>
+ */
+ final String ttl = MessageManager
+ .formatMessage("label.treecalc_title", treecalcnm, smn);
+ return ttl;
+ }
}
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($Version-Rel$)
+ * Copyright (C) $Year-Rel$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+/**
+ * @author kjvanderheide
+ *
+ */
+public class TreeParams implements OptsParametersContainerI
+{
+
+ @Override
+ public void refreshParamLayout()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void argSetModified(Object modifiedElement, boolean b)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+}
Cache.log.info("Jalview finished updating to the Vamsas Session.");
}
- });
+ }, "UpdateVamsas");
udthread.start();
}
import javax.swing.JComponent;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTabbedPane;
AnimatedPanel ap = new AnimatedPanel();
titlePanel.add(ap, BorderLayout.CENTER);
- Thread thread = new Thread(ap);
+ Thread thread = new Thread(ap, "AnimatedPanel");
thread.start();
final WebserviceInfo thisinfo = this;
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void cancel_actionPerformed(ActionEvent e)
{
if (!serviceIsCancellable)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
BufferedImage offscreen;
+ @Override
public void run()
{
startTime = System.currentTimeMillis();
}
}
+ @Override
public void paintComponent(Graphics g1)
{
drawPanel();
renderAsHtml = b;
}
+ @Override
public void hyperlinkUpdate(HyperlinkEvent e)
{
Desktop.hyperlinkUpdate(e);
import java.util.Vector;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTable;
import javax.swing.JTextField;
wsUrls = Jws2Discoverer.getDiscoverer().getServiceUrls();
if (!wsUrls.isEmpty())
{
- oldUrls = new Vector<String>(wsUrls);
+ oldUrls = new Vector<>(wsUrls);
}
else
{
oldUrls = null;
- wsUrls = new Vector<String>();
+ wsUrls = new Vector<>();
}
wsList.setDefaultRenderer(Integer.class, new JabaWSStatusRenderer());
wsList.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
rsbsUrls = jalview.ws.rest.RestClient.getRsbsDescriptions();
if (rsbsUrls != null)
{
- oldRsbsUrls = new Vector<String>(rsbsUrls);
+ oldRsbsUrls = new Vector<>(rsbsUrls);
}
else
{
oldRsbsUrls = null;
- rsbsUrls = new Vector<String>();
+ rsbsUrls = new Vector<>();
}
updateRsbsList();
enableEnfinServices.setSelected(
updateWsMenuConfig(false);
refreshWsMenu(true);
}
- }).start();
+ }, "RefreshWebServices").start();
}
progressBar.setVisible(false);
validate();
}
- }).start();
+ }, "RefreshWebServicesMenuProgressBar").start();
}
else
Desktop.instance.setProgressBar(null, ct);
}
- }).start();
+ }, "RefreshWebServicesMenu").start();
}
}
updateWsMenuConfig(false);
refreshWsMenu(showProgressInDialog);
}
- }).start();
+ }, "UpdateAndRefreshWebServicesMenu").start();
}
}
e.printStackTrace();
return;
}
- new Thread(this).start();
+ new Thread(this, "ExportBioJsHTML").start();
}
File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
Objects.requireNonNull(dirName, "dirName MUST not be null!");
Objects.requireNonNull(directory, "directory MUST not be null!");
- TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
+ TreeMap<String, File> versionFileMap = new TreeMap<>();
for (File file : directory.listFiles())
{
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
+import jalview.ext.forester.io.PhyloXmlFile;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
{
return false;
}
- };
+ },
+ // Nexus("Nexus", "nex,nexus,nx,tre", true, true)
+ // {
+ //
+ // @Override
+ // public AlignmentFileReaderI getReader(FileParse source)
+ // throws IOException
+ // {
+ // return new NexusFile(source);
+ // }
+ //
+ // @Override
+ // public AlignmentFileWriterI getWriter(AlignmentI al)
+ // {
+ // // handle within Aptx?
+ // return null;
+ // }
+ //
+ // @Override
+ // public boolean isTextFormat()
+ // {
+ // return true;
+ // }
+ //
+ // @Override
+ // public boolean isTreeFile()
+ // {
+ // return true;
+ // }
+ //
+ // },
+ PhyloXML("PhyloXML", "phyloxml,phylo.xml,pxml", true, true)
+ {
+
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new PhyloXmlFile(source);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ // handle within Aptx?
+ return null;
+ }
+
+ @Override
+ public boolean isTextFormat()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isTreeFile()
+ {
+ return true;
+ }
+ };
private boolean writable;
private boolean readable;
return false;
}
+ @Override
+ public boolean isTreeFile()
+ {
+ return false;
+ }
+
/**
* By default, answers true, indicating the format is one that can be
* identified by IdentifyFile. Formats that cannot be identified should
* @return
*/
boolean isStructureFile();
+
+ /**
+ * Answers true if the file format can contain a phylogenetic tree.
+ *
+ * @return
+ */
+ boolean isTreeFile();
}
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.archaeopteryx.AptxInit;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
this.protocol = protocol;
this.format = format;
- final Thread loader = new Thread(this);
+ final Thread loader = new Thread(this, "LoadFile");
SwingUtilities.invokeLater(new Runnable()
{
*/
protected AlignFrame _LoadFileWaitTillLoaded()
{
- Thread loader = new Thread(this);
+ Thread loader = new Thread(this, "LoadFileWithWaiting");
loader.start();
while (loader.isAlive())
return alignFrame;
}
+ // add support for recently opened Aptx trees
public void updateRecentlyOpened()
{
Vector recent = new Vector();
alignFrame.getViewport()
.applyFeaturesStyle(proxyColourScheme);
}
+ if (format.isTreeFile())
+ {
+ // make generic instead of Aptx specific?
+ AptxInit.createInstancesFromFile(file,
+ alignFrame.getViewport());
+
+ }
alignFrame.statusBar.setText(MessageManager.formatMessage(
"label.successfully_loaded_file", new String[]
{ title }));
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
+
try
{
alignFrame.setMaximum(jalview.bin.Cache
e.printStackTrace();
return;
}
- new Thread(this).start();
+ new Thread(this, "ExportSvgHTML").start();
}
public int printUnwrapped(int pwidth, int pheight, int pi,
reply = FileFormat.Phylip;
break;
}
- else
+ else if (!lineswereskipped && looksLikeJnetData(data))
{
- if (!lineswereskipped && looksLikeJnetData(data))
- {
reply = FileFormat.Jnet;
break;
- }
+
}
+ else // phylogenetic file
+ {
+ String identifier = data.toLowerCase();
+ String secondLine = source.nextLine().toLowerCase();
+ if (identifier.startsWith("<phyloxml")
+ || secondLine.startsWith("<phyloxml"))
+ {
+ reply = FileFormat.PhyloXML;
+ break;
+ }
+ // commented out, nexus parser is troublesome
+ // else if (((identifier.startsWith("nexus"))
+ // || (identifier.startsWith("#nexus"))
+ // || (identifier.startsWith("# nexus"))
+ // || (identifier.startsWith("begin"))))
+ // {
+ // reply = FileFormat.Nexus;
+ // break;
+ // }
+ }
lineswereskipped = true; // this means there was some junk before any
// key file signature
}
{
SequenceNode root;
- private boolean HasBootstrap = false;
+ private boolean hasBootstrap = false;
- private boolean HasDistances = false;
+ private boolean hasDistances = false;
- private boolean RootHasDistance = false;
+ private boolean rootHasDistance = false;
// File IO Flags
- boolean ReplaceUnderscores = false;
+ boolean replaceUnderscores = false;
boolean printRootInfo = true;
*/
public NewickFile(SequenceNode newtree, boolean bootstrap)
{
- HasBootstrap = bootstrap;
+ hasBootstrap = bootstrap;
root = newtree;
}
boolean distances)
{
root = newtree;
- HasBootstrap = bootstrap;
- HasDistances = distances;
+ hasBootstrap = bootstrap;
+ hasDistances = distances;
}
/**
boolean distances, boolean rootdistance)
{
root = newtree;
- HasBootstrap = bootstrap;
- HasDistances = distances;
- RootHasDistance = rootdistance;
+ hasBootstrap = bootstrap;
+ hasDistances = distances;
+ rootHasDistance = rootdistance;
}
/**
// @tree annotations
// These are set automatically by the reader
- public boolean HasBootstrap()
+ public boolean hasBootstrap()
{
- return HasBootstrap;
+ return hasBootstrap;
}
/**
*
* @return DOCUMENT ME!
*/
- public boolean HasDistances()
+ public boolean hasDistances()
{
- return HasDistances;
+ return hasDistances;
}
- public boolean HasRootDistance()
+ public boolean hasRootDistance()
{
- return RootHasDistance;
+ return rootHasDistance;
}
/**
{
if (nodename == null)
{
- if (ReplaceUnderscores)
+ if (replaceUnderscores)
{
nodename = uqnodename.stringMatched(1).replace('_', ' ');
}
{
bootstrap = (new Integer(nbootstrap.stringMatched(1)))
.intValue();
- HasBootstrap = true;
+ hasBootstrap = true;
} catch (Exception e)
{
Error = ErrorStringrange(Error, "Can't parse bootstrap value",
try
{
distance = (new Float(ndist.stringMatched(1))).floatValue();
- HasDistances = true;
+ hasDistances = true;
nodehasdistance = true;
} catch (Exception e)
{
// Write node info here
c.setName(nodename);
// Trees without distances still need a render distance
- c.dist = (HasDistances) ? distance : DefDistance;
+ c.dist = (hasDistances) ? distance : DefDistance;
// be consistent for internal bootstrap defaults too
- c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
+ c.setBootstrap((hasBootstrap) ? bootstrap : DefBootstrap);
if (c == realroot)
{
- RootHasDistance = nodehasdistance; // JBPNote This is really
+ rootHasDistance = nodehasdistance; // JBPNote This is really
// UGLY!!! Ensure root node gets
// its given distance
}
{
// Find a place to put the leaf
SequenceNode newnode = new SequenceNode(null, c, nodename,
- (HasDistances) ? distance : DefDistance,
- (HasBootstrap) ? bootstrap : DefBootstrap, false);
+ (hasDistances) ? distance : DefDistance,
+ (hasBootstrap) ? bootstrap : DefBootstrap, false);
parseNHXNodeProps(c, commentString2);
commentString2 = null;
// Insert a dummy node for polytomy
// dummy nodes have distances
SequenceNode newdummy = new SequenceNode(null, c, null,
- (HasDistances ? 0 : DefDistance), 0, true);
+ (hasDistances ? 0 : DefDistance), 0, true);
newdummy.SetChildren(c.left(), newnode);
c.setLeft(newdummy);
}
// (root.right()!=null && root.isDummy())
root = (SequenceNode) root.right().detach(); // remove the imaginary root.
- if (!RootHasDistance)
+ if (!rootHasDistance)
{
- root.dist = (HasDistances) ? 0 : DefDistance;
+ root.dist = (hasDistances) ? 0 : DefDistance;
}
}
v = iv.intValue(); // jalview only does integer bootstraps
// currently
c.setBootstrap(v);
- HasBootstrap = true;
+ hasBootstrap = true;
}
// more codes here.
} catch (Exception e)
{
synchronized (this)
{
- boolean boots = this.HasBootstrap;
- this.HasBootstrap = withbootstraps;
+ boolean boots = this.hasBootstrap;
+ this.hasBootstrap = withbootstraps;
String rv = print();
- this.HasBootstrap = boots;
+ this.hasBootstrap = boots;
return rv;
}
{
synchronized (this)
{
- boolean dists = this.HasDistances;
- this.HasDistances = withdists;
+ boolean dists = this.hasDistances;
+ this.hasDistances = withdists;
String rv = print(withbootstraps);
- this.HasDistances = dists;
+ this.hasDistances = dists;
return rv;
}
private String printNodeField(SequenceNode c)
{
return ((c.getName() == null) ? "" : nodeName(c.getName()))
- + ((HasBootstrap) ? ((c.getBootstrap() > -1)
+ + ((hasBootstrap) ? ((c.getBootstrap() > -1)
? ((c.getName() != null ? " " : "") + c.getBootstrap())
: "") : "")
- + ((HasDistances) ? (":" + c.dist) : "");
+ + ((hasDistances) ? (":" + c.dist) : "");
}
/**
{
return (printRootInfo)
? (((root.getName() == null) ? "" : nodeName(root.getName()))
- + ((HasBootstrap)
+ + ((hasBootstrap)
? ((root.getBootstrap() > -1)
? ((root.getName() != null ? " " : "")
+ +root.getBootstrap())
: "")
: "")
- + ((RootHasDistance) ? (":" + root.dist) : ""))
+ + ((rootHasDistance) ? (":" + root.dist) : ""))
: "";
}
{
if (executor == null)
{
- executor = new Thread(new JSFunctionExec(jvlite));
+ executor = new Thread(new JSFunctionExec(jvlite),
+ "JavaScript");
executor.start();
}
synchronized (jsExecQueue)
private boolean showAutoCalculatedAbove = false;
- private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
private SplitContainerI splitFrame;
}
});
- JMenuItem loadTreeMenuItem = new JMenuItem(
- MessageManager.getString("label.load_associated_tree"));
- loadTreeMenuItem.setActionCommand(
- MessageManager.getString("label.load_tree_for_sequence_set"));
- loadTreeMenuItem.addActionListener(new ActionListener()
+ JMenuItem loadTreeFile = new JMenuItem(
+ MessageManager.getString("label.from_file"));
+
+ loadTreeFile.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
+ JMenuItem loadTreeUrl = new JMenuItem(
+ MessageManager.getString("label.from_url"));
+ loadTreeUrl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreeUrlItem_actionPerformed(e);
+ }
+ });
+
+
+
+ JMenuItem loadTreeBaseStudy = new JMenuItem(
+ MessageManager.getString("label.treebase_study"));
+ loadTreeBaseStudy.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreeBaseStudy_actionPerformed(e);
+
+ } });
+
+
+
+ JMenuItem loadTreeBase = new JMenuItem(
+ MessageManager.getString("label.treebase"));
+ loadTreeBase.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreeBase_actionPerformed(e);
+
+ }
+
+
+ });
+ JMenuItem loadTreePfam = new JMenuItem(
+ MessageManager.getString("label.pfam"));
+ loadTreePfam.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreePfam_actionPerformed(e);
+
+ }
+
+ });
+ JMenuItem loadTreeFam = new JMenuItem(
+ MessageManager.getString("label.treefam"));
+ loadTreeFam.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreeFam_actionPerformed(e);
+
+ }
+
+ });
+
+ JMenuItem loadTreeOfLife = new JMenuItem(
+ MessageManager.getString("label.tree_of_life"));
+ loadTreeOfLife.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreeOfLife_actionPerformed(e);
+
+ }
+
+
+ });
+
scaleAbove.setVisible(false);
scaleAbove.setText(MessageManager.getString("action.scale_above"));
scaleAbove.addActionListener(new ActionListener()
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
+
+ JMenu loadTreeDb = new JMenu(
+ MessageManager.getString("label.from_database"));
+
+ JMenu loadTreeMenu = new JMenu(
+ MessageManager.getString("label.load_associated_tree"));
+ // loadTreeMenu.setToolTipText(
+ // MessageManager.getString("label.load_tree_for_sequence_set"));
+
JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
+
+ loadTreeDb.add(loadTreeBaseStudy);
+ loadTreeDb.add(loadTreeBase);
+ loadTreeDb.add(loadTreePfam);
+ loadTreeDb.add(loadTreeFam);
+ loadTreeDb.add(loadTreeOfLife);
+
+ loadTreeMenu.add(loadTreeFile);
+ loadTreeMenu.add(loadTreeUrl);
+ loadTreeMenu.add(loadTreeDb);
+
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(selectMenu);
fileMenu.add(exportImageMenu);
fileMenu.add(exportFeatures);
fileMenu.add(exportAnnotations);
- fileMenu.add(loadTreeMenuItem);
+ fileMenu.add(loadTreeMenu);
fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
// JAL-574
// selectMenu.addSeparator();
// selectMenu.add(listenToViewSelections);
+
+
+ }
+
+ protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeFam_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreePfam_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeBase_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
}
/**
}
+ protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+
+
/**
* Template method to handle the 'load T-Coffee scores' menu event.
* <p>
}
}
}
+
+
+ @Override
+ public double[][] getValues()
+ {
+ return value;
+ }
}
double getValue(int i, int j);
/**
- * Sets the value at row i, colum j
+ * Sets the value at row i, column j
*
* @param i
* @param j
*/
double[] getRow(int i);
+ /**
+ * Answers all values present in the Matrix ordered by row,column
+ *
+ * @return the double array containing the values ordered in {row values} per
+ * column
+ */
+ double[][] getValues();
+
+
MatrixI copy();
MatrixI transpose();
*/
private jalview.schemabinding.version2.FeatureSettings _featureSettings;
+ /**
+ * List of external trees
+ */
+ private java.util.Vector<jalview.ext.treeviewer.TreeFrameI> _extTreeList;
+
// ----------------/
// - Constructors -/
// ----------------/
this._viewportList = new java.util.Vector();
this._userColoursList = new java.util.Vector();
this._treeList = new java.util.Vector();
+ this._extTreeList = new java.util.Vector<>();
}
// -----------/
}
/**
+ * Unused.
+ *
+ * @param treeViewer
+ */
+ public void addExtTreeViewer(jalview.ext.treeviewer.TreeFrameI treeViewer)
+ {
+ this._extTreeList.add(treeViewer);
+ }
+
+ /**
+ * Unused.
+ *
+ * @param index
+ * @param treeViewer
+ */
+ public void addExtTreeViewer(final int index,
+ jalview.ext.treeviewer.TreeFrameI treeViewer)
+ {
+ this._extTreeList.add(index, treeViewer);
+ }
+ /**
*
*
* @param vUserColours
}
/**
+ * Unused.
+ *
+ * @param index
+ * @return
+ * @throws java.lang.IndexOutOfBoundsException
+ */
+ public jalview.ext.treeviewer.TreeFrameI getExtTreeViewer(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._extTreeList.size())
+ {
+ throw new IndexOutOfBoundsException("getExtTreeViewer: Index value '"
+ + index + "' not in range [0.."
+ + (this._extTreeList.size() - 1) + "]");
+ }
+
+ return _extTreeList.get(index);
+ }
+
+ /**
+ * Unused.
+ *
+ * @return
+ */
+ public jalview.ext.treeviewer.TreeFrameI[] getExtTreeViewer()
+ {
+ jalview.ext.treeviewer.TreeFrameI[] array = new jalview.ext.treeviewer.TreeFrameI[0];
+ return this._extTreeList.toArray(array);
+ }
+
+ /**
+ * Unused.
+ *
+ * @return
+ */
+ public int getExtTreeViewerCount()
+ {
+ return this._extTreeList.size();
+ }
+
+ /**
* Method getUserColours.
*
* @param index
// create all components and add them
frame = new Frame("Java Console");
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- Dimension frameSize = new Dimension((int) (screenSize.width / 2),
- (int) (screenSize.height / 2));
- int x = (int) (frameSize.width / 2);
- int y = (int) (frameSize.height / 2);
+ Dimension frameSize = new Dimension(screenSize.width / 2,
+ screenSize.height / 2);
+ int x = frameSize.width / 2;
+ int y = frameSize.height / 2;
frame.setBounds(x, y, frameSize.width, frameSize.height);
textArea = new TextArea();
// Starting two seperate threads to read from the PipedInputStreams
//
- reader = new Thread(this);
+ reader = new Thread(this, "AWTConsoleReader1");
reader.setDaemon(true);
reader.start();
//
- reader2 = new Thread(this);
+ reader2 = new Thread(this, "AWTConsoleReader2");
reader2.setDaemon(true);
reader2.start();
.getLocalGraphicsEnvironment();
String[] fontNames = ge.getAvailableFontFamilyNames();
for (int n = 0; n < fontNames.length; n++)
+ {
System.out.println(fontNames[n]);
+ }
// Testing part: simple an error thrown anywhere in this JVM will be printed
// on the Console
// We do it with a seperate Thread becasue we don't wan't to break a Thread
// used by the Console.
System.out.println("\nLets throw an error on this console");
- errorThrower = new Thread(this);
+ errorThrower = new Thread(this, "AWTConsoleErrorLog");
errorThrower.setDaemon(true);
errorThrower.start();
}
+ @Override
public synchronized void windowClosed(WindowEvent evt)
{
quit = true;
System.exit(0);
}
+ @Override
public synchronized void windowClosing(WindowEvent evt)
{
frame.setVisible(false); // default behaviour of JFrame
frame.dispose();
}
+ @Override
public synchronized void actionPerformed(ActionEvent evt)
{
textArea.setText("");
}
+ @Override
public synchronized void run()
{
try
textArea.append(input);
}
if (quit)
+ {
return;
+ }
}
while (Thread.currentThread() == reader2)
textArea.append(input);
}
if (quit)
+ {
return;
+ }
}
} catch (Exception e)
{
{
int available = in.available();
if (available == 0)
+ {
break;
+ }
byte b[] = new byte[available];
in.read(b);
input = input + new String(b, 0, b.length);
/*
* lookup from lower-case form of a name to its canonical (standardised) form
*/
- private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
+ private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
- private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<String, String>();
+ private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<>();
static
{
canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
+ canonicalSourceNameLookup.put("pfam", DBRefSource.PFAM);
+
// Make sure we have lowercase entries for all canonical string lookups
Set<String> keys = canonicalSourceNameLookup.keySet();
for (String k : keys)
{
return dbrefs;
}
- HashSet<String> srcs = new HashSet<String>();
+ HashSet<String> srcs = new HashSet<>();
for (String src : sources)
{
srcs.add(src.toUpperCase());
}
- List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> res = new ArrayList<>();
for (DBRefEntry dbr : dbrefs)
{
String source = getCanonicalName(dbr.getSource());
static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
DbRefComp comparator)
{
- List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> rfs = new ArrayList<>();
if (refs == null || entry == null)
{
return rfs;
public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
String source)
{
- List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> matches = new ArrayList<>();
if (dbRefs != null && source != null)
{
for (DBRefEntry dbref : dbRefs)
// nothing to do
return;
}
- List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> selfs = new ArrayList<>();
{
DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
sequence.getDBRefs());
selfs.remove(p);
}
}
- List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> toPromote = new ArrayList<>();
for (DBRefEntry p : pr)
{
- List<String> promType = new ArrayList<String>();
+ List<String> promType = new ArrayList<>();
if (sequence.isProtein())
{
switch (getCanonicalName(p.getSource()))
}
}
}
+
+
+ public static <K, V> Map<K, V> putWithDuplicationCheck(Map<K, V> map, K key,
+ V value)
+ {
+ if (!map.containsKey(key))
+ {
+ map.put(key, value);
+ }
+ else
+ {
+ jalview.bin.Cache.log.warn(
+ "Attempt to add duplicate entry detected for map with key: "
+ + key.toString() + " and value: " + value.toString());
+ }
+
+ return map;
+
+ }
}
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.ext.treeviewer.TreeI;
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
changeSupport = null;
ranges = null;
currentTree = null;
+ currentExtTree = null;
selectionGroup = null;
setAlignment(null);
}
protected TreeModel currentTree = null;
+ protected TreeI currentExtTree = null;
+
@Override
public boolean hasSearchResults()
{
}
@Override
- public void setCurrentTree(TreeModel tree)
+ public void setCurrentTree(TreeModel tree) // adapt to Aptx
{
currentTree = tree;
}
{
return currentTree;
}
+
+ public TreeI getCurrentExtTree()
+ {
+ return currentExtTree;
+ }
+
+ public void setCurrentExtTree(TreeI externalTree)
+ {
+ currentExtTree = externalTree;
+ }
+
}
DbSourceProxy[] sources, FeatureSettings featureSettings,
boolean isNucleotide)
{
- listeners = new ArrayList<FetchFinishedListenerI>();
+ listeners = new ArrayList<>();
this.progressWindow = progressIndicatorFrame;
alseqs = new SequenceI[seqs.length];
SequenceI[] ds = new SequenceI[seqs.length];
{
// af.featureSettings_actionPerformed(null);
String[] defdb = null;
- List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
+ List<DbSourceProxy> selsources = new ArrayList<>();
Vector<jalviewSourceI> dasselsrc = (featureSettings != null)
? featureSettings.getSelectedSources()
: new DasSourceBrowser().getSelectedSources();
{
defdb = DBRefSource.PROTEINDBS;
}
- List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ List<DbSourceProxy> srces = new ArrayList<>();
for (String ddb : defdb)
{
List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
// TODO can we not simply write
// if (waitTillFinished) { run(); } else { new Thread(this).start(); }
- Thread thread = new Thread(this);
+ Thread thread = new Thread(this, "FetchDBRef");
thread.start();
running = true;
}
else if (seqs == null)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
seqs.addElement(seq);
}
}
else
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
seqs.addElement(seq);
}
e.printStackTrace();
}
- Vector<SequenceI> sdataset = new Vector<SequenceI>(
+ Vector<SequenceI> sdataset = new Vector<>(
Arrays.asList(dataset));
- List<String> warningMessages = new ArrayList<String>();
+ List<String> warningMessages = new ArrayList<>();
int db = 0;
while (sdataset.size() > 0 && db < dbSources.length)
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
sdataset.copyInto(currSeqs);// seqs that are to be validated against
// dbSources[db]
- Vector<String> queries = new Vector<String>(); // generated queries curSeq
- seqRefs = new Hashtable<String, Vector<SequenceI>>();
+ Vector<String> queries = new Vector<>(); // generated queries curSeq
+ seqRefs = new Hashtable<>();
int seqIndex = 0;
{
// Work out which sequences this sequence matches,
// taking into account all accessionIds and names in the file
- Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
+ Vector<SequenceI> sequenceMatches = new Vector<>();
// look for corresponding accession ids
DBRefEntry[] entryRefs = DBRefUtils
.selectRefs(retrievedSeq.getDBRefs(), new String[]
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- Vector<SequenceI> nseq = new Vector<SequenceI>();
+ Vector<SequenceI> nseq = new Vector<>();
for (int i = 0; sequencesArray != null
&& i < sequencesArray.length; i++)
{
if (reply == JvOptionPane.YES_OPTION)
{
- Thread thread = new Thread(new FetchDBRefs());
+ Thread thread = new Thread(new FetchDBRefs(),
+ "FetchDBReferenceManager");
thread.start();
}
else
private void _startFetching()
{
running = true;
- new Thread(new FetchSeqFeatures()).start();
+ new Thread(new FetchSeqFeatures(), "FetchSeqFeatures").start();
}
class FetchSeqFeatures implements Runnable
public void run()
{
final Discoverer discoverer = this;
- Thread discoverThread = new Thread()
+ Thread discoverThread = new Thread() // no function?
{
@Override
public void run()
running = true;
// first set up exclusion list if needed
- final Set<String> ignoredServices = new HashSet<String>();
+ final Set<String> ignoredServices = new HashSet<>();
for (String ignored : Cache
.getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
{
{
validServiceUrls.removeAllElements();
}
- ArrayList<String> svctypes = new ArrayList<String>();
+ ArrayList<String> svctypes = new ArrayList<>();
- List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
+ List<JabaWsServerQuery> qrys = new ArrayList<>();
for (final String jwsserver : getServiceUrls())
{
JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
}
qrys.add(squery);
- new Thread(squery).start();
+ new Thread(squery, "JabaQuery").start();
}
boolean finished = true;
do
+ svctypes.indexOf(svc.serviceType);
}
jalview.util.QuickSort.sort(spos, svcs);
- services = new Vector<Jws2Instance>();
+ services = new Vector<>();
for (Jws2Instance svc : svcs)
{
if (!ignoredServices.contains(svc.serviceType))
{
if (services == null)
{
- services = new Vector<Jws2Instance>();
+ services = new Vector<>();
}
System.out.println(
"Discovered service: " + jwsservers + " " + service.toString());
service.hasParameters();
if (validServiceUrls == null)
{
- validServiceUrls = new Vector<String>();
+ validServiceUrls = new Vector<>();
}
validServiceUrls.add(jwsservers);
}
* for moment we keep them separate.
*/
JMenu atpoint;
- List<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+ List<Jws2Instance> enumerableServices = new ArrayList<>();
// jws2al.removeAll();
- Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
- Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+ Map<String, Jws2Instance> preferredHosts = new HashMap<>();
+ Map<String, List<Jws2Instance>> alternates = new HashMap<>();
for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
{
if (!isRecalculable(service.action))
{
if (ph == null)
{
- ph = new ArrayList<Jws2Instance>();
+ ph = new ArrayList<>();
}
ph.add(service);
alternates.put(service.serviceType, ph);
changeSupport.firePropertyChange("services",
new Vector<Jws2Instance>(), services);
};
- }).start();
+ }, "LoadPreferredService").start();
}
});
*/
JMenu atpoint;
- List<String> hostLabels = new ArrayList<String>();
- Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
- Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
- ArrayList<String> hostlist = new ArrayList<String>();
+ List<String> hostLabels = new ArrayList<>();
+ Hashtable<String, String> lasthostFor = new Hashtable<>();
+ Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
+ ArrayList<String> hostlist = new ArrayList<>();
for (Jws2Instance service : enumerableServices)
{
ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
if (hostservices == null)
{
hosts.put(service.getHost(),
- hostservices = new ArrayList<Jws2Instance>());
+ hostservices = new ArrayList<>());
hostlist.add(service.getHost());
}
hostservices.add(service);
{
if (args.length > 0)
{
- testUrls = new ArrayList<String>();
+ testUrls = new ArrayList<>();
for (String url : args)
{
testUrls.add(url);
// return test urls, if there are any, instead of touching cache
return testUrls;
}
- List<String> urls = new ArrayList<String>();
+ List<String> urls = new ArrayList<>();
if (this.preferredUrl != null)
{
public Vector<Jws2Instance> getServices()
{
return (services == null) ? new Vector<Jws2Instance>()
- : new Vector<Jws2Instance>(services);
+ : new Vector<>(services);
}
/**
{
if (urlsWithoutServices == null)
{
- urlsWithoutServices = new Vector<String>();
+ urlsWithoutServices = new Vector<>();
}
if ((invalidServiceUrls == null
{
if (invalidServiceUrls == null)
{
- invalidServiceUrls = new Vector<String>();
+ invalidServiceUrls = new Vector<>();
}
if (!invalidServiceUrls.contains(jwsservers))
{
*/
public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
{
- HashSet<String> urls = new HashSet<String>();
+ HashSet<String> urls = new HashSet<>();
urls.addAll(Arrays.asList(serviceURLs));
Jws2Instance match = null;
if (services != null)
return match;
}
- Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+ Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();;
/**
* get current preferred service of the given type, or global default
String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
if (preferredServiceMap == null)
{
- preferredServiceMap = new HashMap<String, Map<String, String>>();
+ preferredServiceMap = new HashMap<>();
}
Map<String, String> prefmap = preferredServiceMap.get(afid);
if (prefmap == null)
{
- prefmap = new HashMap<String, String>();
+ prefmap = new HashMap<>();
preferredServiceMap.put(afid, prefmap);
}
prefmap.put(serviceType, selectedServer.getHost());
--- /dev/null
+// package jalview.ext.archaeopteryx;
+//
+// import static org.testng.Assert.assertEquals;
+// import static org.testng.Assert.assertTrue;
+//
+// import jalview.analysis.NJTree;
+// import jalview.analysis.TreeBuilder;
+// import jalview.analysis.scoremodels.ScoreModels;
+// import jalview.analysis.scoremodels.SimilarityParams;
+// import jalview.api.analysis.ScoreModelI;
+// import jalview.api.analysis.SimilarityParamsI;
+// import jalview.bin.Jalview;
+// import jalview.datamodel.Alignment;
+// import jalview.datamodel.AlignmentI;
+// import jalview.datamodel.Sequence;
+// import jalview.datamodel.SequenceI;
+// import jalview.gui.AlignViewport;
+//
+// import org.forester.archaeopteryx.MainFrame;
+// import org.forester.archaeopteryx.TreePanel;
+// import org.forester.phylogeny.Phylogeny;
+// import org.testng.annotations.BeforeClass;
+// import org.testng.annotations.Test;
+//
+// public class AptxJalviewSequenceTreeTest extends TreeViewTest
+// {
+// TreeBuilder jalviewTree;
+//
+// TreePanel treePanel;
+//
+// Phylogeny tree;
+//
+// MainFrame aptx;
+//
+// Jalview jalview;
+//
+// @Override
+// @BeforeClass(alwaysRun = true)
+// public void setUpTree()
+// {
+// SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
+// SequenceI seq2 = new Sequence("Seq2", "ABCDEFTHIJ");
+// SequenceI seq3 = new Sequence("Seq3", "BCFWDHIJ");
+// SequenceI seq4 = new Sequence("Seq4", "WTHISTHIS");
+//
+// AlignmentI al = new Alignment(
+// new SequenceI[]
+// { seq1, seq2, seq3, seq4 });
+// AlignViewport alignViewport = new AlignViewport(al);
+//
+// ScoreModelI scoreModel = ScoreModels.getInstance().getBlosum62();
+// SimilarityParamsI similarityParams = new SimilarityParams(true, true,
+// true, false);
+//
+// jalviewTree = new NJTree(alignViewport, scoreModel,
+// similarityParams);
+// }
+//
+// @Override
+// @BeforeClass(dependsOnMethods = { "setUpTree" })
+// public void createTreeView()
+// {
+// treeView = AptxInit.createInstanceFromCalculation(jalviewTree);
+// aptx = (MainFrame) treeView; // still pretty ugly
+//
+// treePanel = aptx.getMainPanel().getCurrentTreePanel();
+// tree = treePanel.getPhylogeny();
+//
+// }
+//
+// @Override
+// public void testTreeLoaded()
+// {
+// assertTrue(tree != null);
+//
+// }
+//
+// @Override
+// public void testTreeTitle()
+// {
+// assertTrue(tree.getName().contains("Neighbour Joining Using BLOSUM62"));
+//
+// }
+//
+// @Override
+// public void testChildNodesCount()
+// {
+// assertEquals(
+// tree.getNode("Seq2").getParent().getNumberOfExternalNodes(), 2);
+//
+// }
+//
+// @Override
+// public void testExistingBranchName()
+// {
+// tree.getNode("Seq4");
+//
+// }
+//
+// @Override
+// public void testChildToParentBranchLength()
+// {
+// assertEquals(tree.getNode("Seq1").getDistanceToParent(), 5.25);
+//
+// }
+//
+// @Test(
+// groups = "Functional",
+// expectedExceptions = IllegalArgumentException.class)
+// public void testInvalidBranchName()
+// {
+// tree.getNode("I shouldn't exist");
+//
+// }
+//
+// @Override
+// public void testNodeToRootBranchLength()
+// {
+// assertEquals(tree.getNode("Seq3").calculateDistanceToRoot(), 19.13);
+//
+// }
+//
+// @Override
+// public void testDistantNodeToRootBranchLength()
+// {
+// assertEquals(tree.getNode("Seq2").calculateDistanceToRoot(),
+// 3.75 + 35.75 + 19.13);
+//
+// }
+//
+//
+//
+//
+// }
--- /dev/null
+// package jalview.ext.archaeopteryx;
+//
+// import static org.testng.Assert.assertEquals;
+// import static org.testng.Assert.assertTrue;
+//
+// import jalview.gui.Desktop;
+//
+// import org.forester.archaeopteryx.Archaeopteryx;
+// import org.forester.archaeopteryx.MainFrame;
+// import org.forester.archaeopteryx.TreePanel;
+// import org.forester.phylogeny.Phylogeny;
+// import org.forester.phylogeny.PhylogenyNode;
+// import org.testng.annotations.BeforeClass;
+// import org.testng.annotations.Test;
+//
+// public class AptxPhylogenyTreeTest extends TreeViewTest
+// {
+// final Phylogeny inputTree = new Phylogeny();
+//
+// final PhylogenyNode rootNode = new PhylogenyNode("root");
+//
+// final PhylogenyNode ancestor1Node = new PhylogenyNode("ancestor 1");
+//
+// final PhylogenyNode ancestor2Node = new PhylogenyNode("leaf 2");
+//
+// final PhylogenyNode leaf1aNode = new PhylogenyNode("leaf 1a");
+//
+// final PhylogenyNode leaf1bNode = new PhylogenyNode("leaf 1b");
+//
+// final PhylogenyNode leaf1cNode = new PhylogenyNode("leaf 1c");
+//
+// Phylogeny tree;
+//
+// TreePanel treePanel;
+//
+// MainFrame aptx;
+//
+//
+// @Override
+// @BeforeClass(alwaysRun = true)
+// public void setUpTree()
+// {
+// ancestor1Node.addAsChild(leaf1aNode);
+// ancestor1Node.addAsChild(leaf1bNode);
+// ancestor1Node.addAsChild(leaf1cNode);
+//
+// rootNode.addAsChild(ancestor1Node);
+// rootNode.addAsChild(ancestor2Node);
+//
+// leaf1aNode.setDistanceToParent(2);
+// leaf1bNode.setDistanceToParent(3);
+// leaf1cNode.setDistanceToParent(4);
+//
+// ancestor1Node.setDistanceToParent(36);
+// ancestor2Node.setDistanceToParent(42);
+//
+// inputTree.setName("test");
+// inputTree.setRoot(rootNode);
+// inputTree.setRooted(true);
+//
+// }
+//
+// @Override
+// @BeforeClass(dependsOnMethods = { "setUpJalview", "setUpTree" })
+// public void createTreeView()
+// {
+// treeView = Archaeopteryx.createApplication(inputTree);
+// aptx = (MainFrame) treeView; // pretty ugly
+// treePanel = aptx.getMainPanel().getCurrentTreePanel();
+// tree = treePanel.getPhylogeny();
+//
+// Desktop.addInternalFrame(aptx, "Archaeopteryx", 500, 500);
+//
+// }
+//
+//
+//
+// @Test(groups = "Functional")
+// public void testMainPanelExists()
+// {
+// assertTrue(aptx.getMainPanel() != null);
+// }
+//
+// @Test(groups = "Functional")
+// public void testTreePanelExists()
+// {
+// assertTrue(treePanel != null);
+// }
+//
+// @Override
+// public void testTreeTitle()
+// {
+// assertTrue(tree.getName().equals("test"));
+//
+// }
+//
+// @Test(
+// groups = "Functional",
+// expectedExceptions = IllegalArgumentException.class)
+// public void testInvalidBranchName()
+// {
+// tree.getNode("I shouldn't exist");
+//
+// }
+//
+// @Override
+// public void testExistingBranchName()
+// {
+// tree.getNode("leaf 2");
+//
+// }
+//
+// @Override
+// public void testTreeLoaded()
+// {
+// assertTrue(tree != null);
+// }
+//
+// @Override
+// public void testChildNodesCount()
+// {
+// assertEquals(tree.getNode("ancestor 1").getNumberOfExternalNodes(), 3);
+//
+// }
+//
+// @Override
+// public void testChildToParentBranchLength()
+// {
+// assertEquals(tree.getNode("leaf 1a").getDistanceToParent(), 2.0);
+//
+// }
+//
+// @Override
+// public void testNodeToRootBranchLength()
+// {
+// assertEquals(tree.getNode("leaf 2").getDistanceToParent(), 42.0);
+//
+// }
+//
+// @Override
+// public void testDistantNodeToRootBranchLength()
+// {
+// assertEquals(tree.getNode("leaf 1c").calculateDistanceToRoot(),
+// 4.0 + 36.0);
+//
+// }
+//
+//
+//
+//
+//
+//
+//
+// }
--- /dev/null
+package jalview.ext.archaeopteryx;
+
+import static org.testng.Assert.assertTrue;
+
+import jalview.bin.Jalview;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public abstract class TreeViewTest
+{
+ Jalview jalview;
+
+ TreeFrameI treeView;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ public abstract void setUpTree();
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJalview()
+ {
+ String[] args = new String[0];
+ Jalview.main(args);
+ }
+
+ public abstract void createTreeView();
+
+ @Test(groups = "Functional")
+ public void testTreeViewExists()
+ {
+ assertTrue(treeView != null);
+ }
+
+ @Test(groups = "Functional")
+ public void testTreeViewBoundToJalview()
+ {
+ assertTrue(treeView.getTopLevelAncestor() instanceof Desktop);
+ }
+
+ @Test(groups = "Functional")
+ public void testShowingTreeView()
+ {
+ assertTrue(treeView.isShowing());
+ }
+
+ @Test(groups = "Functional")
+ public abstract void testTreeLoaded();
+
+ @Test(groups = "Functional")
+ public abstract void testTreeTitle();
+
+ @Test(groups = "Functional")
+ public abstract void testExistingBranchName();
+
+ @Test(groups = "Functional")
+ public abstract void testChildNodesCount();
+
+ @Test(groups = "Functional")
+ public abstract void testChildToParentBranchLength();
+
+ @Test(groups = "Functional")
+ public abstract void testNodeToRootBranchLength();
+
+ @Test(groups = "Functional")
+ public abstract void testDistantNodeToRootBranchLength();
+}
af.openTreePcaDialog();
CalculationChooser dialog = af.alignPanel.getCalculationDialog();
dialog.openPcaPanel("BLOSUM62", dialog.getSimilarityParameters(true));
- dialog.openTreePanel("BLOSUM62", dialog.getSimilarityParameters(false));
+ try
+ {
+ dialog.createTree("BLOSUM62", dialog.getSimilarityParameters(false));
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
/*
* wait until Tree and PCA have been computed
SequenceNode tree = nf.getTree();
AssertJUnit.assertTrue(stage + "Null Tree", tree != null);
stage = "Creating newick file from testTree " + treename;
- String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
- nf.HasDistances());
+ String gentree = new NewickFile(tree).print(nf.hasBootstrap(),
+ nf.hasDistances());
AssertJUnit.assertTrue(stage + "Empty string generated",
gentree != null && gentree.trim().length() > 0);
stage = "Parsing regenerated testTree " + treename;
git://source.jalview.org / jalview.git / commitdiff