JudySL Array Implementation

C/Makefile

@@ -1,6 +1,17 @@
 include ../include.mk
 binPath = ../bin
 libPath = ../lib
+#judySrc = impl/judy-1.0.5/src
+exOut = impl
+
+JUDY = ./impl/judy-1.0.5
+JUDY_INCDIR = 	$(JUDY)/src
+JUDY_LIBDIR = 	$(JUDY)/lib
+JUDY_HEADER = 	$(JUDY_INCDIR)/Judy.h
+JUDY_LIBBASE = 	Judy
+JUDY_LIB = 	$(JUDY_LIBDIR)/lib$(JUDY_LIBBASE).a
+
+
 
 libSources = impl/*.c
 cppSources = impl/*.cpp
@@ -10,7 +21,7 @@ libTests = tests/sonLib*.c tests/st*
 quickTreeObjects = ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o
 quickTreeLibPath = ../externalTools/quicktree_1.1/include/
 
-testProgs = ${binPath}/sonLibTests ${binPath}/sonLib_kvDatabaseTest ${binPath}/sonLib_cigarTest ${binPath}/sonLib_fastaCTest
+testProgs = ${binPath}/sonLibTests ${binPath}/sonLib_kvDatabaseTest ${binPath}/sonLib_cigarTest ${binPath}/sonLib_fastaCTest ${binPath}/hashBenchmark
 
 cflags += ${tokyoCabinetIncl} ${kyotoTycoonIncl} ${tokyoTyrantIncl} ${mysqlIncl} ${pgsqlIncl} -I${quickTreeLibPath}
 cppflags += ${kyotoTycoonIncl}
@@ -50,6 +61,22 @@ ${libPath}/%.h: inc/%.h
 	cp $< $@.tmp
 	mv $@.tmp $@
 
+${binPath}/hashBenchmark: tests/hashBenchmark.c ${libPath}/sonLib.a
+	${cxx} ${cflags} -I inc -I ${libPath} -o $@.tmp tests/hashBenchmark.c ${libPath}/sonLib.a -lm
+	mv $@.tmp $@
+
+#judySandbox: impl/judySandbox.c 
+#	#${cxx} ${flags} -I ${judySrc} -o judySandbox impl/judySandbox.c
+#	$(CC) -lJudy -o $@ $^ $(judySrc)
+
+#judySandbox: impl/judySandbox.c $(JUDY_HEADER) $(JUDY_LIB)
+#	$(CC) $(CFLAGS) -I $(JUDY_INCDIR) $(@F).c -L$(JUDY_LIBDIR) -l$(JUDY_LIBBASE) -o $@
+
+myJudyTest: #impl/myJudyTest.c
+	gcc -o myJudyTest impl/myJudyTest.c -lJudy
+	./myJudyTest
+	rm myJudyTest
+
 ${libPath}/sonLib.a : ${libSources} ${cppSources} $(foreach l, ${libHeaders}, ${libPath}/$(notdir $l)) ${libInternalHeaders}
 	@mkdir -p $(dir $@)
 	${cxx} ${cflags} -I inc -I ${libPath}/  -c ${libSources}

C/impl/.metadata/.log

@@ -0,0 +1,43 @@
+!SESSION 2017-05-23 13:14:11.297 -----------------------------------------------
+eclipse.buildId=4.5.0.I20150603-2000
+java.version=1.8.0_51
+java.vendor=Oracle Corporation
+BootLoader constants: OS=macosx, ARCH=x86_64, WS=cocoa, NL=en_US
+Framework arguments:  -product org.eclipse.epp.package.java.product -keyring /Users/alonpek/.eclipse_keyring -showlocation
+Command-line arguments:  -os macosx -ws cocoa -arch x86_64 -product org.eclipse.epp.package.java.product -keyring /Users/alonpek/.eclipse_keyring -showlocation
+
+!ENTRY org.eclipse.core.net 1 0 2017-05-23 13:14:51.292
+!MESSAGE System property http.nonProxyHosts has been set to local|*.local|169.254/16|*.169.254/16 by an external source. This value will be overwritten using the values from the preferences
+
+!ENTRY org.eclipse.cdt.launch 4 150 2017-05-23 13:17:08.273
+!MESSAGE Error starting process.
+!STACK 0
+java.io.IOException: Exec_tty error:Cannot run program "/Users/alonpek/Documents/workspace/sonLib/C/impl/judy-1.0.5/myJudyTest.c": Unknown reason
+	at org.eclipse.cdt.utils.spawner.Spawner.exec_pty(Spawner.java:387)
+	at org.eclipse.cdt.utils.spawner.Spawner.<init>(Spawner.java:99)
+	at org.eclipse.cdt.utils.spawner.ProcessFactory.exec(ProcessFactory.java:98)
+	at org.eclipse.cdt.launch.internal.LocalRunLaunchDelegate.exec(LocalRunLaunchDelegate.java:149)
+	at org.eclipse.cdt.launch.internal.LocalRunLaunchDelegate.runLocalApplication(LocalRunLaunchDelegate.java:94)
+	at org.eclipse.cdt.launch.internal.LocalRunLaunchDelegate.launch(LocalRunLaunchDelegate.java:63)
+	at org.eclipse.cdt.launch.internal.LocalCDILaunchDelegate.launch(LocalCDILaunchDelegate.java:73)
+	at org.eclipse.debug.internal.core.LaunchConfiguration.launch(LaunchConfiguration.java:885)
+	at org.eclipse.debug.internal.core.LaunchConfiguration.launch(LaunchConfiguration.java:739)
+	at org.eclipse.debug.internal.ui.DebugUIPlugin.buildAndLaunch(DebugUIPlugin.java:1039)
+	at org.eclipse.debug.internal.ui.DebugUIPlugin$8.run(DebugUIPlugin.java:1256)
+	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
+!SUBENTRY 1 org.eclipse.cdt.launch 4 150 2017-05-23 13:17:08.274
+!MESSAGE Exec_tty error:Cannot run program "/Users/alonpek/Documents/workspace/sonLib/C/impl/judy-1.0.5/myJudyTest.c": Unknown reason
+!STACK 0
+java.io.IOException: Exec_tty error:Cannot run program "/Users/alonpek/Documents/workspace/sonLib/C/impl/judy-1.0.5/myJudyTest.c": Unknown reason
+	at org.eclipse.cdt.utils.spawner.Spawner.exec_pty(Spawner.java:387)
+	at org.eclipse.cdt.utils.spawner.Spawner.<init>(Spawner.java:99)
+	at org.eclipse.cdt.utils.spawner.ProcessFactory.exec(ProcessFactory.java:98)
+	at org.eclipse.cdt.launch.internal.LocalRunLaunchDelegate.exec(LocalRunLaunchDelegate.java:149)
+	at org.eclipse.cdt.launch.internal.LocalRunLaunchDelegate.runLocalApplication(LocalRunLaunchDelegate.java:94)
+	at org.eclipse.cdt.launch.internal.LocalRunLaunchDelegate.launch(LocalRunLaunchDelegate.java:63)
+	at org.eclipse.cdt.launch.internal.LocalCDILaunchDelegate.launch(LocalCDILaunchDelegate.java:73)
+	at org.eclipse.debug.internal.core.LaunchConfiguration.launch(LaunchConfiguration.java:885)
+	at org.eclipse.debug.internal.core.LaunchConfiguration.launch(LaunchConfiguration.java:739)
+	at org.eclipse.debug.internal.ui.DebugUIPlugin.buildAndLaunch(DebugUIPlugin.java:1039)
+	at org.eclipse.debug.internal.ui.DebugUIPlugin$8.run(DebugUIPlugin.java:1256)
+	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)

C/impl/.metadata/.plugins/org.eclipse.cdt.core/.log

@@ -0,0 +1 @@
+*** SESSION May 23, 2017 13:14:59.64 -------------------------------------------

C/impl/.metadata/.plugins/org.eclipse.cdt.make.core/specs.c

@@ -0,0 +1 @@
+

C/impl/.metadata/.plugins/org.eclipse.cdt.make.core/specs.cpp

@@ -0,0 +1 @@
+

C/impl/.metadata/.plugins/org.eclipse.cdt.ui/dialog_settings.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+	<section name="org.eclipse.cdt.ui.text.hover.CMacroExpansionExploration">
+	</section>
+	<section name="completion_proposal_size">
+	</section>
+</section>

C/impl/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/history.version

@@ -0,0 +1 @@
+

C/impl/.metadata/.plugins/org.eclipse.core.resources/.root/.indexes/properties.version

@@ -0,0 +1 @@
+

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.cdt.debug.core.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.cdt.debug.core.cDebug.default_source_containers=<?xml version\="1.0" encoding\="UTF-8" standalone\="no"?>\n<sourceLookupDirector>\n<sourceContainers duplicates\="false">\n<container memento\="AbsolutePath" typeId\="org.eclipse.cdt.debug.core.containerType.absolutePath"/>\n<container memento\="programRelativePath" typeId\="org.eclipse.cdt.debug.core.containerType.programRelativePath"/>\n<container memento\="&lt;?xml version\=&quot;1.0&quot; encoding\=&quot;UTF-8&quot; standalone\=&quot;no&quot;?&gt;&\#10;&lt;project referencedProjects\=&quot;true&quot;/&gt;&\#10;" typeId\="org.eclipse.cdt.debug.core.containerType.project"/>\n</sourceContainers>\n</sourceLookupDirector>\n

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.cdt.ui.prefs

@@ -0,0 +1,4 @@
+eclipse.preferences.version=1
+spelling_locale_initialized=true
+useAnnotationsPrefPage=true
+useQuickDiffPrefPage=true

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+version=1

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.debug.core.prefs

@@ -0,0 +1,4 @@
+//org.eclipse.debug.core.PREFERRED_DELEGATES/org.eclipse.cdt.launch.applicationLaunchType=org.eclipse.cdt.dsf.gdb.launch.localCLaunch,debug,;org.eclipse.cdt.cdi.launch.localCLaunch,run,;
+//org.eclipse.debug.core.PREFERRED_DELEGATES/org.eclipse.cdt.launch.attachLaunchType=org.eclipse.cdt.dsf.gdb.launch.attachCLaunch,debug,;
+//org.eclipse.debug.core.PREFERRED_DELEGATES/org.eclipse.cdt.launch.postmortemLaunchType=org.eclipse.cdt.dsf.gdb.launch.coreCLaunch,debug,;
+eclipse.preferences.version=1

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.debug.ui.prefs

@@ -0,0 +1,3 @@
+eclipse.preferences.version=1
+org.eclipse.debug.ui.PREF_LAUNCH_PERSPECTIVES=<?xml version\="1.0" encoding\="UTF-8" standalone\="no"?>\n<launchPerspectives/>\n
+preferredTargets=org.eclipse.cdt.debug.ui.toggleCBreakpointTarget,org.eclipse.cdt.debug.ui.toggleCDynamicPrintfTarget\:org.eclipse.cdt.debug.ui.toggleCBreakpointTarget|

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.epp.logging.aeri.ui.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+problemsZipEtag="e51d52-55011bc65af40"

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.jdt.ui.prefs

@@ -0,0 +1,14 @@
+content_assist_proposals_background=255,255,255
+content_assist_proposals_foreground=0,0,0
+eclipse.preferences.version=1
+fontPropagated=true
+org.eclipse.jdt.internal.ui.navigator.layout=2
+org.eclipse.jdt.ui.editor.tab.width=
+org.eclipse.jdt.ui.formatterprofiles.version=12
+org.eclipse.jdt.ui.javadoclocations.migrated=true
+org.eclipse.jface.textfont=1|Monaco|11.0|0|COCOA|1|;
+proposalOrderMigrated=true
+spelling_locale_initialized=true
+tabWidthPropagated=true
+useAnnotationsPrefPage=true
+useQuickDiffPrefPage=true

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.m2e.discovery.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.m2e.discovery.pref.projects=

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.context.core.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+mylyn.attention.migrated=true

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.monitor.ui.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.mylyn.monitor.activity.tracking.enabled.checked=true

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.mylyn.tasks.ui.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+migrated.task.repositories.secure.store=true
+org.eclipse.mylyn.tasks.ui.filters.nonmatching=true
+org.eclipse.mylyn.tasks.ui.filters.nonmatching.encouraged=true
+org.eclipse.mylyn.tasks.ui.welcome.message=true

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.team.ui.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+org.eclipse.team.ui.first_time=false

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.editors.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+overviewRuler_migration=migrated_3.1

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.ide.prefs

@@ -0,0 +1,5 @@
+PROBLEMS_FILTERS_MIGRATE=true
+eclipse.preferences.version=1
+platformState=1439332745814
+quickStart=false
+tipsAndTricks=true

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+showIntro=false

C/impl/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs

@@ -0,0 +1,3 @@
+//org.eclipse.ui.commands/state/org.eclipse.ui.navigator.resources.nested.changeProjectPresentation/org.eclipse.ui.commands.radioState=false
+PLUGINS_NOT_ACTIVATED_ON_STARTUP=org.eclipse.m2e.discovery;
+eclipse.preferences.version=1

C/impl/.metadata/.plugins/org.eclipse.debug.core/.launches/New_configuration.launch

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.cdt.launch.applicationLaunchType">
+<intAttribute key="org.eclipse.cdt.launch.ATTR_BUILD_BEFORE_LAUNCH_ATTR" value="1"/>
+<stringAttribute key="org.eclipse.cdt.launch.COREFILE_PATH" value=""/>
+<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_NAME" value="/Users/alonpek/Documents/workspace/sonLib/C/impl/judy-1.0.5/myJudyTest.c"/>
+<stringAttribute key="org.eclipse.cdt.launch.PROJECT_ATTR" value=""/>
+<booleanAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_AUTO_ATTR" value="false"/>
+<stringAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_ID_ATTR" value=""/>
+</launchConfiguration>

C/impl/.metadata/.plugins/org.eclipse.debug.ui/dialog_settings.xml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<section name="Workbench">
+	<section name="org.eclipse.debug.ui.STRING_VARIABLE_SELECTION_DIALOG_SECTION">
+		<item value="382" key="DIALOG_WIDTH"/>
+		<item value="1|.SF NS Text|11.0|0|COCOA|1|.SFNSText" key="DIALOG_FONT_NAME"/>
+		<item value="538" key="DIALOG_HEIGHT"/>
+		<item value="-7" key="DIALOG_X_ORIGIN"/>
+		<item value="-224" key="DIALOG_Y_ORIGIN"/>
+	</section>
+	<section name="org.eclipse.debug.ui.LAUNCH_CONFIGURATIONS_DIALOG_SECTION">
+		<item value="800" key="DIALOG_WIDTH"/>
+		<item value="1|.SF NS Text|11.0|0|COCOA|1|.SFNSText" key="DIALOG_FONT_NAME"/>
+		<item value=", org.eclipse.cdt.launch.applicationLaunchType, " key="org.eclipse.debug.ui.EXPANDED_NODES"/>
+		<item value="762" key="org.eclipse.debug.ui.DIALOG_SASH_WEIGHTS_2"/>
+		<item value="640" key="DIALOG_HEIGHT"/>
+		<item value="237" key="org.eclipse.debug.ui.DIALOG_SASH_WEIGHTS_1"/>
+	</section>
+</section>

C/impl/.metadata/.plugins/org.eclipse.debug.ui/launchConfigurationHistory.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchHistory>
+<launchGroup id="org.eclipse.debug.ui.launchGroup.debug">
+<mruHistory>
+<launch memento="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#10;&lt;launchConfiguration local=&quot;true&quot; path=&quot;New_configuration&quot;/&gt;&#10;"/>
+</mruHistory>
+<favorites/>
+</launchGroup>
+<launchGroup id="org.eclipse.debug.ui.launchGroup.profile">
+<mruHistory/>
+<favorites/>
+</launchGroup>
+<launchGroup id="org.eclipse.ui.externaltools.launchGroup">
+<mruHistory/>
+<favorites/>
+</launchGroup>
+<launchGroup id="org.eclipse.debug.ui.launchGroup.run">
+<mruHistory>
+<launch memento="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#10;&lt;launchConfiguration local=&quot;true&quot; path=&quot;New_configuration&quot;/&gt;&#10;"/>
+</mruHistory>
+<favorites/>
+</launchGroup>
+</launchHistory>