├── .DS_Store ├── ConnectTheDots └── target │ ├── classes │ ├── edu │ │ └── msViz │ │ │ └── connectTheDots │ │ │ ├── AssociationScorer.class │ │ │ ├── TestRun.class │ │ │ ├── TraceClusterer.class │ │ │ ├── Utility.class │ │ │ ├── dataTypes │ │ │ ├── IsotopeTrace$ScanData.class │ │ │ ├── IsotopeTrace.class │ │ │ ├── IsotopicEnvelope.class │ │ │ ├── ProbabilityBundle$1.class │ │ │ ├── ProbabilityBundle$Config.class │ │ │ ├── ProbabilityBundle$RV.class │ │ │ ├── ProbabilityBundle.class │ │ │ ├── TraceCluster.class │ │ │ ├── TraceGrid.class │ │ │ └── TracesBundle.class │ │ │ └── probability │ │ │ ├── BayesianProbability$SeparationDistribution.class │ │ │ ├── BayesianProbability.class │ │ │ ├── FrequentistProbability.class │ │ │ ├── HybridProbability.class │ │ │ ├── ProbabilityAggregator$1.class │ │ │ ├── ProbabilityAggregator$PROB_MODEL.class │ │ │ └── ProbabilityAggregator.class │ └── frequentist.json │ ├── connectTheDots-1.0.jar │ ├── maven-archiver │ └── pom.properties │ ├── maven-status │ └── maven-compiler-plugin │ │ ├── compile │ │ └── default-compile │ │ │ ├── createdFiles.lst │ │ │ └── inputFiles.lst │ │ └── testCompile │ │ └── default-testCompile │ │ ├── createdFiles.lst │ │ └── inputFiles.lst │ ├── surefire-reports │ ├── TEST-edu.msViz.connectTheDots.AssociationScorerTest.xml │ ├── TEST-edu.msViz.connectTheDots.ClusteringTest.xml │ ├── TEST-edu.msViz.connectTheDots.DeclusterTest.xml │ ├── TEST-edu.msViz.connectTheDots.IsotopeTraceTest.xml │ ├── TEST-edu.msViz.connectTheDots.IsotopicEnvelopeTest.xml │ ├── TEST-edu.msViz.connectTheDots.ProbabilityAggregatorTest.xml │ ├── TEST-edu.msViz.connectTheDots.RealWorldTest.xml │ ├── TEST-edu.msViz.connectTheDots.TraceGridTest.xml │ ├── edu.msViz.connectTheDots.AssociationScorerTest.txt │ ├── edu.msViz.connectTheDots.ClusteringTest.txt │ ├── edu.msViz.connectTheDots.DeclusterTest.txt │ ├── edu.msViz.connectTheDots.IsotopeTraceTest.txt │ ├── edu.msViz.connectTheDots.IsotopicEnvelopeTest.txt │ ├── edu.msViz.connectTheDots.ProbabilityAggregatorTest.txt │ ├── edu.msViz.connectTheDots.RealWorldTest.txt │ └── edu.msViz.connectTheDots.TraceGridTest.txt │ └── test-classes │ ├── 2_colliding_envs_4_result_envs.csv │ ├── 5_traces_5_envelopes.csv │ ├── edu │ └── msViz │ │ └── connectTheDots │ │ ├── AssociationScorerTest.class │ │ ├── ClusteringTest.class │ │ ├── DeclusterTest.class │ │ ├── IsotopeTraceTest.class │ │ ├── IsotopicEnvelopeTest.class │ │ ├── ProbabilityAggregatorTest.class │ │ ├── RealWorldTest.class │ │ └── TraceGridTest.class │ ├── good_example.csv │ ├── interleaved_slight_overlap.csv │ ├── misaligned_peaks.csv │ ├── non_descending.csv │ ├── single_split.csv │ ├── so_close.csv │ ├── two_nearby_inconsistent.csv │ ├── ultimate_test.csv │ └── unassigned_trace.csv ├── README.md ├── client_mockups ├── Illustrator Files │ ├── MsViz_Grid.ai │ ├── MsViz_Interface_Main.ai │ ├── MsViz_Interface_Main2.ai │ ├── MsViz_Interface_Minimal.ai │ ├── MsViz_Interface_Slices.ai │ ├── MsViz_Interface_Test.ai │ ├── MsViz_Interface_Text.ai │ └── MsViz_Interface_ToggleTest.ai ├── PNGs │ ├── MsViz_Interace_4.png │ ├── MsViz_Interface_1.png │ ├── MsViz_Interface_2.png │ ├── MsViz_Interface_3.png │ └── MsViz_Interface_5.png └── Slices │ ├── Cursor.png │ ├── Interface_FullView.png │ ├── Legend.png │ └── LogoScreen.ai ├── comparison ├── makemanypaths.sh ├── makepath.py ├── makerandom.py ├── makeslice.py ├── manypath.sh ├── mz5_convert.sh ├── mz5_convert_once.sh ├── queries │ ├── 18185_path │ │ ├── 01.csv │ │ ├── 02.csv │ │ ├── 03.csv │ │ ├── 04.csv │ │ ├── 05.csv │ │ ├── 06.csv │ │ ├── 07.csv │ │ ├── 08.csv │ │ ├── 09.csv │ │ ├── 10.csv │ │ ├── 11.csv │ │ ├── 12.csv │ │ ├── 13.csv │ │ ├── 14.csv │ │ ├── 15.csv │ │ ├── 16.csv │ │ ├── 17.csv │ │ ├── 18.csv │ │ ├── 19.csv │ │ └── 20.csv │ ├── 18185_random.csv │ ├── OEMMA_XIC_path │ │ ├── 0.csv │ │ ├── 1.csv │ │ ├── 10.csv │ │ ├── 100.csv │ │ ├── 11.csv │ │ ├── 12.csv │ │ ├── 13.csv │ │ ├── 14.csv │ │ ├── 15.csv │ │ ├── 16.csv │ │ ├── 17.csv │ │ ├── 18.csv │ │ ├── 19.csv │ │ ├── 2.csv │ │ ├── 20.csv │ │ ├── 21.csv │ │ ├── 22.csv │ │ ├── 23.csv │ │ ├── 24.csv │ │ ├── 25.csv │ │ ├── 26.csv │ │ ├── 27.csv │ │ ├── 28.csv │ │ ├── 29.csv │ │ ├── 3.csv │ │ ├── 30.csv │ │ ├── 31.csv │ │ ├── 32.csv │ │ ├── 33.csv │ │ ├── 34.csv │ │ ├── 35.csv │ │ ├── 36.csv │ │ ├── 37.csv │ │ ├── 38.csv │ │ ├── 39.csv │ │ ├── 4.csv │ │ ├── 40.csv │ │ ├── 41.csv │ │ ├── 42.csv │ │ ├── 43.csv │ │ ├── 44.csv │ │ ├── 45.csv │ │ ├── 46.csv │ │ ├── 47.csv │ │ ├── 48.csv │ │ ├── 49.csv │ │ ├── 5.csv │ │ ├── 50.csv │ │ ├── 51.csv │ │ ├── 52.csv │ │ ├── 53.csv │ │ ├── 54.csv │ │ ├── 55.csv │ │ ├── 56.csv │ │ ├── 57.csv │ │ ├── 58.csv │ │ ├── 59.csv │ │ ├── 6.csv │ │ ├── 60.csv │ │ ├── 61.csv │ │ ├── 62.csv │ │ ├── 63.csv │ │ ├── 64.csv │ │ ├── 65.csv │ │ ├── 66.csv │ │ ├── 67.csv │ │ ├── 68.csv │ │ ├── 69.csv │ │ ├── 7.csv │ │ ├── 70.csv │ │ ├── 71.csv │ │ ├── 72.csv │ │ ├── 73.csv │ │ ├── 74.csv │ │ ├── 75.csv │ │ ├── 76.csv │ │ ├── 77.csv │ │ ├── 78.csv │ │ ├── 79.csv │ │ ├── 8.csv │ │ ├── 80.csv │ │ ├── 81.csv │ │ ├── 82.csv │ │ ├── 83.csv │ │ ├── 84.csv │ │ ├── 85.csv │ │ ├── 86.csv │ │ ├── 87.csv │ │ ├── 88.csv │ │ ├── 89.csv │ │ ├── 9.csv │ │ ├── 90.csv │ │ ├── 91.csv │ │ ├── 92.csv │ │ ├── 93.csv │ │ ├── 94.csv │ │ ├── 95.csv │ │ ├── 96.csv │ │ ├── 97.csv │ │ ├── 98.csv │ │ └── 99.csv │ ├── OEMMA_XIC_random.csv │ ├── OEMMA_query_bundle.zip │ ├── OEMMA_random.csv │ ├── OEMMA_rtmajor_path │ │ ├── 0.csv │ │ ├── 1.csv │ │ ├── 10.csv │ │ ├── 100.csv │ │ ├── 11.csv │ │ ├── 12.csv │ │ ├── 13.csv │ │ ├── 14.csv │ │ ├── 15.csv │ │ ├── 16.csv │ │ ├── 17.csv │ │ ├── 18.csv │ │ ├── 19.csv │ │ ├── 2.csv │ │ ├── 20.csv │ │ ├── 21.csv │ │ ├── 22.csv │ │ ├── 23.csv │ │ ├── 24.csv │ │ ├── 25.csv │ │ ├── 26.csv │ │ ├── 27.csv │ │ ├── 28.csv │ │ ├── 29.csv │ │ ├── 3.csv │ │ ├── 30.csv │ │ ├── 31.csv │ │ ├── 32.csv │ │ ├── 33.csv │ │ ├── 34.csv │ │ ├── 35.csv │ │ ├── 36.csv │ │ ├── 37.csv │ │ ├── 38.csv │ │ ├── 39.csv │ │ ├── 4.csv │ │ ├── 40.csv │ │ ├── 41.csv │ │ ├── 42.csv │ │ ├── 43.csv │ │ ├── 44.csv │ │ ├── 45.csv │ │ ├── 46.csv │ │ ├── 47.csv │ │ ├── 48.csv │ │ ├── 49.csv │ │ ├── 5.csv │ │ ├── 50.csv │ │ ├── 51.csv │ │ ├── 52.csv │ │ ├── 53.csv │ │ ├── 54.csv │ │ ├── 55.csv │ │ ├── 56.csv │ │ ├── 57.csv │ │ ├── 58.csv │ │ ├── 59.csv │ │ ├── 6.csv │ │ ├── 60.csv │ │ ├── 61.csv │ │ ├── 62.csv │ │ ├── 63.csv │ │ ├── 64.csv │ │ ├── 65.csv │ │ ├── 66.csv │ │ ├── 67.csv │ │ ├── 68.csv │ │ ├── 69.csv │ │ ├── 7.csv │ │ ├── 70.csv │ │ ├── 71.csv │ │ ├── 72.csv │ │ ├── 73.csv │ │ ├── 74.csv │ │ ├── 75.csv │ │ ├── 76.csv │ │ ├── 77.csv │ │ ├── 78.csv │ │ ├── 79.csv │ │ ├── 8.csv │ │ ├── 80.csv │ │ ├── 81.csv │ │ ├── 82.csv │ │ ├── 83.csv │ │ ├── 84.csv │ │ ├── 85.csv │ │ ├── 86.csv │ │ ├── 87.csv │ │ ├── 88.csv │ │ ├── 89.csv │ │ ├── 9.csv │ │ ├── 90.csv │ │ ├── 91.csv │ │ ├── 92.csv │ │ ├── 93.csv │ │ ├── 94.csv │ │ ├── 95.csv │ │ ├── 96.csv │ │ ├── 97.csv │ │ ├── 98.csv │ │ └── 99.csv │ └── OEMMA_rtmajor_random.csv ├── query.py ├── query_mzTree.py ├── query_util.py ├── queryconf.py ├── results │ ├── .~lock.summ_save1.csv# │ ├── .~lock.summ_save1.ods# │ ├── .~lock.summ_save2.csv# │ ├── OEMMA_rtmajor_adjacent.ods │ ├── OEMMA_rtmajor_random.ods │ ├── OEMMA_xic_adjacent.ods │ ├── OEMMA_xic_random.ods │ ├── conversion_times_size_on_disk.ods │ ├── figures │ │ ├── pdf │ │ │ ├── OEMMA_rtmajor_adjacent.pdf │ │ │ ├── OEMMA_rtmajor_random.pdf │ │ │ ├── OEMMA_xic_adjacent.pdf │ │ │ ├── OEMMA_xic_random.pdf │ │ │ ├── conversion_time.pdf │ │ │ ├── size_on_disk.pdf │ │ │ └── summarization_savings.pdf │ │ ├── pdf_bundle.zip │ │ └── svg │ │ │ ├── OEMMA_rtmajor_adjacent.svg │ │ │ ├── OEMMA_rtmajor_random.svg │ │ │ ├── OEMMA_xic_adjacent.svg │ │ │ ├── OEMMA_xic_random.svg │ │ │ ├── conversion_time.svg │ │ │ ├── size_on_disk.svg │ │ │ └── summarization_savings.svg │ ├── pre_disk_arrangement │ │ ├── 18185 │ │ │ ├── 18185_path.ods │ │ │ ├── 18185_rand.ods │ │ │ └── random_query_times_18185.png │ │ ├── OEMMA │ │ │ ├── OEMMA_mzTree_only_comparisons.ods │ │ │ ├── OEMMA_path.ods │ │ │ ├── OEMMA_random_bf=4.ods │ │ │ └── random_query_times_OEMMA.png │ │ └── sample2 │ │ │ ├── sample2_path.ods │ │ │ └── sample2_rand.ods │ ├── pre_node_point │ │ ├── OEMMA_path_queries.ods │ │ ├── OEMMA_random_queries.ods │ │ ├── OEMMA_wide_random.csv │ │ ├── conversion_results.txt │ │ ├── conversion_results_pt1.txt │ │ ├── conversion_times_size_on_disk.ods │ │ ├── mz5_conversion.txt │ │ └── raw_to_mzDB_results.txt │ ├── results_records.zip │ └── summ_savings.ods ├── summ.csv └── summarization_savings.py ├── documentation ├── benchmarks.xlsx ├── error_logging.txt ├── maven_tips.txt ├── partitioned_load_overview.odt ├── point_groups.txt ├── server_api.md ├── summ_strat_profiling.docx ├── summarization_screenshots │ ├── intensity_cutoff │ │ ├── intensity_cutoff_lvl0.PNG │ │ ├── intensity_cutoff_lvl0_2D.PNG │ │ └── intensity_cutoff_lvl1.PNG │ ├── uniform_sampling │ │ ├── uniform_sampling_lvl0.PNG │ │ ├── uniform_sampling_lvl0_2D.PNG │ │ └── uniform_sampling_lvl1.PNG │ ├── uniform_striding │ │ ├── uniform_striding_lvl0.PNG │ │ ├── uniform_striding_lvl0_2D.PNG │ │ └── uniform_striding_lvl1.PNG │ ├── weighted_sampling │ │ ├── weighted_sampling_lvl0.PNG │ │ ├── weighted_sampling_lvl0_2D.PNG │ │ └── weighted_sampling_lvl1.PNG │ ├── weighted_striding_no_sorting │ │ ├── weighted_striding_lvl0.PNG │ │ ├── weighted_striding_lvl0_2D.PNG │ │ └── weighted_striding_lvl1.PNG │ └── weighted_striding_sorting │ │ ├── weighted_striding_sorting_lvl0.PNG │ │ ├── weighted_striding_sorting_lvl0_2D.PNG │ │ └── weighted_striding_sorting_lvl1.PNG └── useful_tutorials.txt ├── jsms ├── 3rdparty.txt ├── css │ ├── graphview.css │ └── instructions.css ├── favicon.ico ├── images │ ├── buttons │ │ ├── _3d.svg │ │ ├── _3d_toggle.svg │ │ ├── add.svg │ │ ├── bk_add.svg │ │ ├── bk_cancel.svg │ │ ├── bk_delete.svg │ │ ├── bk_edit.svg │ │ ├── bk_ok.svg │ │ ├── bk_selectcurrent.svg │ │ ├── bkexport.svg │ │ ├── bkimport.svg │ │ ├── bkpair.svg │ │ ├── bkpair_toggle.svg │ │ ├── bkreport.svg │ │ ├── bookmark.svg │ │ ├── bookmark_toggle.svg │ │ ├── brush.svg │ │ ├── brush_toggle.svg │ │ ├── color_selection.txt │ │ ├── colorblind.svg │ │ ├── colorblind_toggle.svg │ │ ├── data.svg │ │ ├── detail.svg │ │ ├── detail_toggle.svg │ │ ├── envelope.svg │ │ ├── envelope_toggle.svg │ │ ├── help.svg │ │ ├── help_toggle.svg │ │ ├── hover.svg │ │ ├── hover_toggle.svg │ │ ├── jump.svg │ │ ├── jumpOptions.svg │ │ ├── jumpOptions_toggle.svg │ │ ├── jump_back.svg │ │ ├── noise.svg │ │ ├── noise_enabled.svg │ │ ├── refresh.svg │ │ ├── select.svg │ │ ├── totalion.svg │ │ ├── trace.svg │ │ └── trace_toggle.svg │ └── favicon.svg ├── index.html ├── instruction.html └── js │ ├── bookmarks.js │ ├── components │ ├── bookmarkSidebar.js │ └── toolbarButtons.js │ ├── dataBridge.js │ ├── dataControls.js │ ├── graph.js │ ├── graphRender.js │ ├── legend.js │ ├── libs │ ├── FileSaver.min.js │ ├── OrbitControls.js │ ├── jquery-3.3.1.min.js │ ├── three.min.js │ └── vue.min.js │ ├── segmentColors.js │ ├── segmentEditor.js │ ├── segmentTracker.js │ └── toolbars.js ├── msDataServer ├── pom.xml ├── src │ └── main │ │ └── java │ │ └── edu │ │ └── msViz │ │ ├── UI │ │ ├── ClusterPanel.java │ │ ├── ExportPanel.java │ │ ├── FilePanel.java │ │ ├── ServerPanel.java │ │ └── StartFrame.java │ │ ├── msHttpApi │ │ ├── CommandStack.java │ │ ├── HeadlessServer.java │ │ ├── MsDataServer.java │ │ └── MzTreePointDatabaseConnection.java │ │ └── mzTree │ │ ├── IO │ │ ├── CsvExporter.java │ │ ├── Decoder.java │ │ ├── LabelledMsDataRange.java │ │ ├── MsDataRange.java │ │ └── MzmlParser.java │ │ ├── ImportState.java │ │ ├── MsDataPoint.java │ │ ├── MzTree.java │ │ ├── MzTreeNode.java │ │ ├── MzTreeTest.java │ │ ├── PointCache.java │ │ ├── harnesses │ │ ├── ConversionResults.java │ │ ├── MzTreeAccess.java │ │ ├── MzTreeConversion.java │ │ ├── MzmlPointCounter.java │ │ └── Segmentation.java │ │ ├── storage │ │ ├── HybridStorage.java │ │ ├── IntensityTracker.java │ │ ├── StorageFacade.java │ │ └── StorageFacadeFactory.java │ │ └── summarization │ │ ├── IntensityCutoffStrategy.java │ │ ├── SummarizationStrategy.java │ │ ├── SummarizationStrategyFactory.java │ │ ├── UniformSamplingStrategy.java │ │ ├── UniformStridingStrategy.java │ │ ├── WeightedReservoirSampling.java │ │ ├── WeightedSamplingStrategy.java │ │ └── WeightedStridingStrategy.java └── target │ └── msDataServer-1.0.jar ├── pom.xml ├── tracesegmentation ├── README.md ├── pom.xml └── src │ └── main │ └── java │ └── edu │ └── umt │ └── ms │ └── traceSeg │ ├── .DS_Store │ ├── HttpPointDatabaseConnection.java │ ├── Point.java │ ├── PointDatabaseConnection.java │ ├── TraceSegmentation.java │ └── TraceSegmenter.java ├── xnet.tar.gz └── xnet ├── README.txt ├── output.csv ├── pom.xml ├── src ├── main │ ├── java │ │ └── edu │ │ │ └── msViz │ │ │ └── xnet │ │ │ ├── AssociationScorer.java │ │ │ ├── TestRun.java │ │ │ ├── TraceClusterer.java │ │ │ ├── Utility.java │ │ │ ├── dataTypes │ │ │ ├── IsotopeTrace.java │ │ │ ├── IsotopicEnvelope.java │ │ │ ├── ProbabilityBundle.java │ │ │ ├── TraceCluster.java │ │ │ ├── TraceGrid.java │ │ │ └── TracesBundle.java │ │ │ └── probability │ │ │ ├── BayesianProbability.java │ │ │ ├── FrequentistProbability.java │ │ │ ├── HybridProbability.java │ │ │ └── ProbabilityAggregator.java │ └── resources │ │ ├── frequentist.json │ │ └── good_example.csv └── test │ ├── java │ └── edu │ │ └── msViz │ │ └── xnet │ │ ├── AssociationScorerTest.java │ │ ├── ClusteringTest.java │ │ ├── DeclusterTest.java │ │ ├── IsotopeTraceTest.java │ │ ├── IsotopicEnvelopeTest.java │ │ ├── ProbabilityAggregatorTest.java │ │ ├── RealWorldTest.java │ │ └── TraceGridTest.java │ └── resources │ ├── 2_colliding_envs_4_result_envs.csv │ ├── 5_traces_5_envelopes.csv │ ├── good_example.csv │ ├── interleaved_slight_overlap.csv │ ├── misaligned_peaks.csv │ ├── non_descending.csv │ ├── single_split.csv │ ├── so_close.csv │ ├── two_nearby_inconsistent.csv │ ├── 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