<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "GitLab Mono"), JetBrains Mono, Menlo, DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=US-ASCII" http-equiv="Content-Type">
<title>
GitLab
</title>

<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>


<style>img {
max-width: 100%; height: auto;
}
body {
font-size: .875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px;
}
body {
font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px; font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">
Pierre Gruet pushed to branch upstream at <a href="https://salsa.debian.org/java-team/jalview">Debian Java Maintainers / jalview</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/java-team/jalview/-/commit/ea14fe6f7f1161ec0d5c6d40fe35d9a98d08b670">ea14fe6f</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2025-02-16T11:24:29+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.11.4.1+dfsg</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
1376 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#28e4a2e57ea1412e35cd955351520c20c1e52c43">
.settings/org.eclipse.jdt.core.prefs
</a>
</li>
<li class="file-stats">
<a href="#f73b278fdabab028fe5f65c62197e4b5634529e5">
RELEASE
</a>
</li>
<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
</a>
</li>
<li class="file-stats">
<a href="#1a8a89bb95ebca5f0f6e687ea3d1f744eb9eb046">
build_properties
</a>
</li>
<li class="file-stats">
<a href="#1ad41a3da9db5824e26a9bf4852a3b4b748defa9">
doc/AddingGroovySupport.html
</a>
</li>
<li class="file-stats">
<a href="#3d3a9779a404cdc30f87a6f27787f9e91e0a228d">
doc/JalviewRNASupport.html
</a>
</li>
<li class="file-stats">
<a href="#c4ef4636b11f572503dbde6bcdd8fabeb692400f">
doc/UnitTesting.html
</a>
</li>
<li class="file-stats">
<a href="#2731ee363d50c420e9d8c7115f64bd226248f9f7">
doc/biojsmsa-templates.html
</a>
</li>
<li class="file-stats">
<a href="#e9f34c6fe5c28caa59f872cb2f54d4a3bbdd7dcf">
doc/developing.html
</a>
</li>
<li class="file-stats">
<a href="#baf1bee556816a2aa75a3d12f225fb373fbcf0f7">
doc/i18n.html
</a>
</li>
<li class="file-stats">
<a href="#54b5e214b447551b0e0c8c11a04a296ef88222e4">
doc/index.html
</a>
</li>
<li class="file-stats">
<a href="#502e0a54560c0fc33c5d96a9bc24c142459cc3ca">
doc/newdmobj.html
</a>
</li>
<li class="file-stats">
<a href="#f4a18af286bdd45cb104d0f8df37581c785edff5">
examples/appletDeployment.html
</a>
</li>
<li class="file-stats">
<a href="#738f9a2ebc7d08ed5ab3cdfd30f811a8d37755bd">
examples/appletParameters.html
</a>
</li>
<li class="file-stats">
<a href="#2535a1ab9e69135853a1bf0603891983d144473f">
examples/applets.html
</a>
</li>
<li class="file-stats">
<a href="#8386d4066d7a6a6f3299ca96ef8416c95487fa41">
examples/embedded.html
</a>
</li>
<li class="file-stats">
<a href="#44ae1eaf2b2644d4aa343f0e7867204f6ca4ecca">
examples/formComplete.html
</a>
</li>
<li class="file-stats">
<a href="#703fa7c842e4af0891e0cff495e03bb9dfcc09ef">
examples/groovy/JvLoadTestHarness.groovy
</a>
</li>
<li class="file-stats">
<a href="#c880cc7ffb34a2b2fbeaa59d7f9b5d593e6ff0d2">
examples/groovy/JvLoadTester.groovy
</a>
</li>
<li class="file-stats">
<a href="#6cf7672a0ec3536e107c9a3d2674b3dac35e2e97">
examples/groovy/PIDmatrix.groovy
</a>
</li>
<li class="file-stats">
<a href="#66e8f93c4f4d209ab7c8c441e5ca78064de4526d">
examples/groovy/alignLoadedFile.groovy
</a>
</li>
<li class="file-stats">
<a href="#649935e72a42be5f9bdced29aee455ec26e92daf">
examples/groovy/annotationForSelectedSequence.groovy
</a>
</li>
<li class="file-stats">
<a href="#78516ac3cfba0f0a798f289fb83f5858f245d744">
examples/groovy/annotationsascsv.groovy
</a>
</li>
<li class="file-stats">
<a href="#677a22e456bde47899a2e8d4fbc3c75d9d1aa327">
examples/groovy/closures.groovy
</a>
</li>
<li class="file-stats">
<a href="#f07ef9032792a0bd11672b2f1a144feaea94117e">
examples/groovy/colourConserved.groovy
</a>
</li>
<li class="file-stats">
<a href="#5f6a8d4abdcee10f00ce28873a202c31bc4a0407">
examples/groovy/colourUnconserved.groovy
</a>
</li>
<li class="file-stats">
<a href="#b977db958b3a65c905b5c66c15c4515b00fdea7f">
examples/groovy/exportconsensus.groovy
</a>
</li>
<li class="file-stats">
<a href="#02872dc928654865f09f8849ba86e0b8255ad951">
examples/groovy/featuresCounter.groovy
</a>
</li>
<li class="file-stats">
<a href="#f1130dae7b5486e7fe6fa335208b876c11ae31e5">
examples/groovy/iterateOverAlignments.groovy
</a>
</li>
<li class="file-stats">
<a href="#050fb512f8f98fddd5a8d9a8ab925701df2965fa">
examples/groovy/parseproperties.groovy
</a>
</li>
<li class="file-stats">
<a href="#e3a4d33534c2308d4dd3c06a686ff6dd086daf56">
examples/groovy/printtitle.groovy
</a>
</li>
<li class="file-stats">
<a href="#cbef1ae08710300b26342de87c47c8b12b0483eb">
examples/groovy/removeFeaturesByGroup.groovy
</a>
</li>
<li class="file-stats">
<a href="#90aa76e75427bd4561acad6800275213fc0d4c33">
examples/groovy/selectColumnsByFeatureAndGroup.groovy
</a>
</li>
<li class="file-stats">
<a href="#cf8a16d9dfccce709112ae35f2b6c33cc3ab47b5">
examples/groovy/sitesForSelectedColumns.groovy
</a>
</li>
<li class="file-stats">
<a href="#4d891e7c85109866d2c003ec97cd309b8feb363e">
examples/groovy/stripUniprotPrefixes.groovy
</a>
</li>
<li class="file-stats">
<a href="#2045bc8dd003552abdd4b6034036258701a75d6d">
examples/groovy/visibleFeaturesCounter.groovy
</a>
</li>
<li class="file-stats">
<a href="#1ab8ec956fbe088e5afb6b394f5d36b4c5691a3b">
examples/includes/footer_jv.html
</a>
</li>
<li class="file-stats">
<a href="#5c16cf80dd30582152fc20f6b08c523b0012cab3">
examples/includes/header_jv.html
</a>
</li>
<li class="file-stats">
<a href="#13306c7a003ceb70ccb0ea3e7681d9920d5adaf4">
examples/includes/nav_jv.html
</a>
</li>
<li class="file-stats">
<a href="#0b044f1f3a433bf44b604424756173a457fa9c21">
examples/jalviewLiteJs.html
</a>
</li>
<li class="file-stats">
<a href="#0cf29ab112ad15226d1e7eba4f8337cce137f28e">
examples/javascriptLaunch.html
</a>
</li>
<li class="file-stats">
<a href="#0e1229047e7c51f290331589143264b8116df6d2">
examples/linkedapplets_ng.html
</a>
</li>
<li class="file-stats">
<a href="#bf9afc176268964e2a3618cc6bd7cc19fbfb5a50">
examples/testdata/test.html
</a>
</li>
<li class="file-stats">
<a href="#a6b9c2d09c1695d497db69df441056e6a4fdab1e">
help/help/helpTOC.xml
</a>
</li>
<li class="file-stats">
<a href="#58783cf125caa09cca9d824ea8dfff8af5246bef">
help/help/html/calculations/calculations.html
</a>
</li>
<li class="file-stats">
<a href="#2997a27a6ce165046b6b7d5105d22efdf9f1e2d3">
help/help/html/calculations/consensus.html
</a>
</li>
<li class="file-stats">
<a href="#f05025bda84357ab37f36fa30c98b28c4e13ebe2">
help/help/html/calculations/conservation.html
</a>
</li>
<li class="file-stats">
<a href="#c4f0516f4ab676f5d5a0018bf1f02727ed99a67f">
help/help/html/calculations/pairwise.html
</a>
</li>
<li class="file-stats">
<a href="#a1d12d82cd2311fa532c72f3bc7bea1d9980188a">
help/help/html/calculations/pasimap.html
</a>
</li>
<li class="file-stats">
<a href="#a3797627875f6057b6cb36977f296b99d3554f33">
help/help/html/calculations/pca.html
</a>
</li>
<li class="file-stats">
<a href="#ebcf59ccf6edeaba025723529084f01df887bea9">
help/help/html/calculations/protssconsensus.html
</a>
</li>
<li class="file-stats">
<a href="#3b574b4fe912319154acdbc1193857b12e90f989">
help/help/html/calculations/quality.html
</a>
</li>
<li class="file-stats">
<a href="#f30d7e287eb6a730f325441f9f555d374441b76a">
help/help/html/calculations/recoverInputdata.html
</a>
</li>
<li class="file-stats">
<a href="#b636399e435b0f19b92028e097ea749a84defa51">
help/help/html/calculations/redundancy.html
</a>
</li>
<li class="file-stats">
<a href="#48f473484e98edd47b8b2d76067ee05191cfd539">
help/help/html/calculations/referenceseq.html
</a>
</li>
<li class="file-stats">
<a href="#61ec79bbf32e0aa71509bac87aa3680088b41efa">
help/help/html/calculations/scorematrices.html
</a>
</li>
<li class="file-stats">
<a href="#b1eb7d94bc9246ea176f38b278ffce5e47e3ba80">
help/help/html/calculations/sorting.html
</a>
</li>
<li class="file-stats">
<a href="#e0e73061d2c7446bb9398aff2242990b100c845d">
help/help/html/calculations/structureconsensus.html
</a>
</li>
<li class="file-stats">
<a href="#4d2bad8be35da7adf6a6edbc0f0bd648fd59aa67">
help/help/html/calculations/tree.html
</a>
</li>
<li class="file-stats">
<a href="#c80e5ff081888f52b443e64ef38d002ebf843a31">
help/help/html/calculations/treeviewer.html
</a>
</li>
<li class="file-stats">
<a href="#9a324c1803d25efa72635fef4b7c7cc6f8db2d36">
help/help/html/colourSchemes/abovePID.html
</a>
</li>
<li class="file-stats">
<a href="#91565156edab501d7e726d2b68e9d3d728c0d3a3">
help/help/html/colourSchemes/annotationColouring.html
</a>
</li>
<li class="file-stats">
<a href="#5d5bc6d722779b52c0bb29665cea90329514b7e1">
help/help/html/colourSchemes/blosum.html
</a>
</li>
<li class="file-stats">
<a href="#c905b1b98397dfc3cd4c3ced6baf95f840e8739e">
help/help/html/colourSchemes/buried.html
</a>
</li>
<li class="file-stats">
<a href="#b2c234c558f11c2f15a720a50dd8a95204794741">
help/help/html/colourSchemes/clustal.html
</a>
</li>
<li class="file-stats">
<a href="#f7b0c90badd62d33824df3931001cdc347836908">
help/help/html/colourSchemes/conservation.html
</a>
</li>
<li class="file-stats">
<a href="#e9ff6c89236dc21d6d1ace82e44cee47ada232dc">
help/help/html/colourSchemes/gecos-blossom.html
</a>
</li>
<li class="file-stats">
<a href="#f45e8771df99793541321cbafbc4ec84de24300b">
help/help/html/colourSchemes/gecos-flower.html
</a>
</li>
<li class="file-stats">
<a href="#916447817f204171910db57bf150cabd2dad596a">
help/help/html/colourSchemes/gecos-ocean.html
</a>
</li>
<li class="file-stats">
<a href="#0eb871c71469e90f853aff82e70e3f308fa8ed81">
help/help/html/colourSchemes/gecos-sunset.html
</a>
</li>
<li class="file-stats">
<a href="#de14390fd2682c6d8285e57240313ee37eaaa8eb">
help/help/html/colourSchemes/helix.html
</a>
</li>
<li class="file-stats">
<a href="#6330eec3ace9684a91a00b41a96cb5ebb3f5587b">
help/help/html/colourSchemes/hydrophobic.html
</a>
</li>
<li class="file-stats">
<a href="#db25c342dd99d27ccec4b084e4a2296c99731737">
help/help/html/colourSchemes/index.html
</a>
</li>
<li class="file-stats">
<a href="#e80ed6e5546bdfb2511ca51a642bfa914464f672">
help/help/html/colourSchemes/nucleotide.html
</a>
</li>
<li class="file-stats">
<a href="#917271afd57543b7a53c1266a1f9ce856369b624">
help/help/html/colourSchemes/nucleotideambiguity.html
</a>
</li>
<li class="file-stats">
<a href="#10f1c65d0aea1cc0a5d493dddc4be90449b75176">
help/help/html/colourSchemes/pid.html
</a>
</li>
<li class="file-stats">
<a href="#89e9d5296cac8326696880051eb5d8036496a34a">
help/help/html/colourSchemes/purinepyrimidine.html
</a>
</li>
<li class="file-stats">
<a href="#4c15322637622173bea288837550ec49fa8c1db9">
help/help/html/colourSchemes/rnahelicesColouring.html
</a>
</li>
<li class="file-stats">
<a href="#6588850dfa859fd89ecc5128db02c0900de63dea">
help/help/html/colourSchemes/strand.html
</a>
</li>
<li class="file-stats">
<a href="#703de15b7b2eb39738d7cb4c43d3a5e3fe23b705">
help/help/html/colourSchemes/taylor.html
</a>
</li>
<li class="file-stats">
<a href="#6e2f3b1bf457354c8d836275a0f36bd620cfe717">
help/help/html/colourSchemes/textcolour.html
</a>
</li>
<li class="file-stats">
<a href="#6359d21d94f085fa3d292b4f1e354e707fea0432">
help/help/html/colourSchemes/turn.html
</a>
</li>
<li class="file-stats">
<a href="#756ce7c99bc413f4179a7882ff16dbf876fd9f8f">
help/help/html/colourSchemes/user.html
</a>
</li>
<li class="file-stats">
<a href="#a6b0b4ea017978a98601c3988cd11ef92353431d">
help/help/html/colourSchemes/zappo.html
</a>
</li>
<li class="file-stats">
<a href="#afdf9c2ddeef349562d4cd9c11869fff3e85540d">
help/help/html/editing/index.html
</a>
</li>
<li class="file-stats">
<a href="#1ce019b35bffff2f9083066d5a052c19df050c70">
help/help/html/features/annotation.html
</a>
</li>
<li class="file-stats">
<a href="#35b5025f6b1c535332b490c0079439edfecee79d">
help/help/html/features/annotationsFormat.html
</a>
</li>
<li class="file-stats">
<a href="#70e937523fa6801181f096b61176d4a8c60d906c">
help/help/html/features/bioJsonFormat.html
</a>
</li>
<li class="file-stats">
<a href="#885c5eeace0db470a5419afe423399ecd48bd972">
help/help/html/features/biojsmsa.html
</a>
</li>
<li class="file-stats">
<a href="#cf65b8636aa2452cc9bb4aa176aa56e060442d3b">
help/help/html/features/chimera.html
</a>
</li>
<li class="file-stats">
<a href="#0695e3a0fe3c0420bb690363b3349f3d7fcf88b3">
help/help/html/features/clarguments-advanced.html
</a>
</li>
<li class="file-stats">
<a href="#5961fe51dc54e841264c2d1662c5a4134cd5abe7">
help/help/html/features/clarguments-argfiles.html
</a>
</li>
<li class="file-stats">
<a href="#cb959ae7fb2b9c521e298fc21f22bbca10be267b">
help/help/html/features/clarguments-basic.html
</a>
</li>
<li class="file-stats">
<a href="#4bcc9516973334b872db00c7448aa66ce3d265cb">
help/help/html/features/clarguments-old.html
</a>
</li>
<li class="file-stats">
<a href="#9028717a5976efa2f396125f16f666f2f28103dd">
help/help/html/features/codingfeatures.html
</a>
</li>
<li class="file-stats">
<a href="#49b6a171e8e3a93634b7383e7e39d290e65c3227">
help/help/html/features/columnFilterByAnnotation.html
</a>
</li>
<li class="file-stats">
<a href="#5c08d392317d9110231f2d45c9defc2c2f572eb9">
help/help/html/features/commandline.html
</a>
</li>
<li class="file-stats">
<a href="#066c09b33ef836fa43a5463b771bc54481228329">
help/help/html/features/creatinFeatures.html
</a>
</li>
<li class="file-stats">
<a href="#16cf486e10071b0ea33aa164bda5a3e3370f63a4">
help/help/html/features/cursorMode.html
</a>
</li>
<li class="file-stats">
<a href="#604b8629ce6414f3d942456fe4999bd1ad6f3fc1">
help/help/html/features/editingFeatures.html
</a>
</li>
<li class="file-stats">
<a href="#41e5116b489b2c0fa0fb899f984702172d5cd497">
help/help/html/features/ensemblsequencefetcher.html
</a>
</li>
<li class="file-stats">
<a href="#cc979e591501ce255afb19b8c738d9bdfe440d63">
help/help/html/features/featuresFormat.html
</a>
</li>
<li class="file-stats">
<a href="#a844a2808522befabead45af60bd7e6f89889649">
help/help/html/features/featureschemes.html
</a>
</li>
<li class="file-stats">
<a href="#8cbec196d22cd01e4d277e491ed9075af5f71193">
help/help/html/features/featuresettings.html
</a>
</li>
<li class="file-stats">
<a href="#d297dc3adca799cc0d22b098f4770f930e945c8b">
help/help/html/features/groovy.html
</a>
</li>
<li class="file-stats">
<a href="#0f9d888d2771ec643fbb7b8b7d90eedd68a1b95f">
help/help/html/features/hiddenRegions.html
</a>
</li>
<li class="file-stats">
<a href="#8bc326dfd41740a7eed4ad0166e6a05722040c80">
help/help/html/features/importvcf.html
</a>
</li>
<li class="file-stats">
<a href="#8bda43ddbe6c6fa53069ec0c1b02be73eef84fe7">
help/help/html/features/jalarchive.html
</a>
</li>
<li class="file-stats">
<a href="#80946bbee6c633630587bca0c4e6eed7fddc8b4b">
help/help/html/features/jmol.html
</a>
</li>
<li class="file-stats">
<a href="#c6f8d39b6d1dfa0e41db8c6fac4b24024270d295">
help/help/html/features/jvlfiles.html
</a>
</li>
<li class="file-stats">
<a href="#96eecc7b703cf6117afb9a8a80d3acb83a857432">
help/help/html/features/mmcif.html
</a>
</li>
<li class="file-stats">
<a href="#f0d27d7159103a714a6c2a1afb4f4ec3db64f5e8">
help/help/html/features/multipleViews.html
</a>
</li>
<li class="file-stats">
<a href="#1118840f9ac579f44373e4fd2da92d3be122dcfb">
help/help/html/features/newkeystrokes.html
</a>
</li>
<li class="file-stats">
<a href="#c9ce034b8d7217903a11734d2ca9614ba8ed2a4e">
help/help/html/features/overview.html
</a>
</li>
<li class="file-stats">
<a href="#89e729af016f047fb78b4c568ad78d4090f8f45c">
help/help/html/features/paematrices.html
</a>
</li>
<li class="file-stats">
<a href="#56af27fe149c9243fb1176e1e5ef8dab3549aadb">
help/help/html/features/pdbsequencefetcher.html
</a>
</li>
<li class="file-stats">
<a href="#82beb29dcb158f974a19657eb0b7fea00f27eda1">
help/help/html/features/pdbviewer.html
</a>
</li>
<li class="file-stats">
<a href="#76be27809c0b48af2528ad842ca8dc62f2cf48c3">
help/help/html/features/preferences.html
</a>
</li>
<li class="file-stats">
<a href="#96a52ec5eee127e6a184cf1f2f307a1c07cb90cb">
help/help/html/features/pymol.html
</a>
</li>
<li class="file-stats">
<a href="#3cda99269306e5e32d845fcb7c22bd1284de4475">
help/help/html/features/search.html
</a>
</li>
<li class="file-stats">
<a href="#ede21e455c6a845c7620790f6a9c5f5c92bfaf15">
help/help/html/features/seqfeaturereport.html
</a>
</li>
<li class="file-stats">
<a href="#0be6301465c85ab46739c3af9cb13052443e5c93">
help/help/html/features/seqfeatures.html
</a>
</li>
<li class="file-stats">
<a href="#c0a0b057c4e99d44522c24ff10799d793a407c0e">
help/help/html/features/seqfetch.html
</a>
</li>
<li class="file-stats">
<a href="#5b67c009557bddb045c257c72493bd18ee05e7da">
help/help/html/features/seqmappings.html
</a>
</li>
<li class="file-stats">
<a href="#08c347b650d489668111089ce5658a2954a3b6fe">
help/help/html/features/siftsmapping.html
</a>
</li>
<li class="file-stats">
<a href="#dfe1837dd1d13ec6fa257c1a419a33621246a64f">
help/help/html/features/splitView.html
</a>
</li>
<li class="file-stats">
<a href="#dd1902d2d91decf2f1016e65c82499eb036b6dd8">
help/help/html/features/structurechooser.html
</a>
</li>
<li class="file-stats">
<a href="#8df1d46d257a162a97fe3fc819dbd64e2c8ba610">
help/help/html/features/uniprotqueryfields.html
</a>
</li>
<li class="file-stats">
<a href="#363714e2688507023b27ac8a50e5972541d928c5">
help/help/html/features/uniprotsequencefetcher.html
</a>
</li>
<li class="file-stats">
<a href="#bc0c8eb1f76ec4b2d310af77359305bf6abec93a">
help/help/html/features/varna.html
</a>
</li>
<li class="file-stats">
<a href="#880c4866f08e12b987493d8dced8175a6890af02">
help/help/html/features/viewingpdbs.html
</a>
</li>
<li class="file-stats">
<a href="#4d82276127357f1df7b11113dc1e3063cee1d141">
help/help/html/features/wrap.html
</a>
</li>
<li class="file-stats">
<a href="#ac21846c488ec4c00c2e6c928c9659876f09c80c">
help/help/html/features/xsspannotation.html
</a>
</li>
<li class="file-stats">
<a href="#b81a2154b696509ced6fd469141f9203403cb2c0">
help/help/html/groovy/featuresCounter.html
</a>
</li>
<li class="file-stats">
<a href="#1129ef44efa9d6ab9f426e69a8b48002bbe2da3f">
help/help/html/index.html
</a>
</li>
<li class="file-stats">
<a href="#8c2f2cdaa8d675793aa413a4bf7f0cc65f9a5513">
help/help/html/io/export.html
</a>
</li>
<li class="file-stats">
<a href="#87ebb532966622c9027d7e8918f4a5ec67f41698">
help/help/html/io/exportseqreport.html
</a>
</li>
<li class="file-stats">
<a href="#f08e1559e7b36d45c178ac882f78be5c54e4b00a">
help/help/html/io/fileformats.html
</a>
</li>
<li class="file-stats">
<a href="#4cfcccbf3d0855dedc180f1eafa3c932e3a81686">
help/help/html/io/index.html
</a>
</li>
<li class="file-stats">
<a href="#599fc0a1a91203be127a34078d24ff4f9ae2f2ed">
help/help/html/io/modellerpir.html
</a>
</li>
<li class="file-stats">
<a href="#6411a732a7783e1cc3c474e30a8ec73948a33822">
help/help/html/io/paematrixformat.html
</a>
</li>
<li class="file-stats">
<a href="#e83297020cbbcdaa010c25fe4f2e4d5e7d1a3f81">
help/help/html/io/tcoffeescores.html
</a>
</li>
<li class="file-stats">
<a href="#23605219eeef2953b98fa9a9d749a29a6a4890e3">
help/help/html/keys.html
</a>
</li>
<li class="file-stats">
<a href="#ba179223f7f2b7d90752f6888cc940166b4a54ad">
help/help/html/logging.html
</a>
</li>
<li class="file-stats">
<a href="#8218106ec9ad3dceddc01e3ec93004a84039a893">
help/help/html/memory.html
</a>
</li>
<li class="file-stats">
<a href="#747329240cdf4750c50d8e6f4c38c514c6714ec7">
help/help/html/menus/alignmentMenu.html
</a>
</li>
<li class="file-stats">
<a href="#67bf2e05483c701f59d97b0b9ad451475895b7de">
help/help/html/menus/alwannotation.html
</a>
</li>
<li class="file-stats">
<a href="#0251e99f8671a342db8cbaa7ef16075430117bc3">
help/help/html/menus/alwannotationpanel.html
</a>
</li>
<li class="file-stats">
<a href="#43a429263a097c6fd0b08000b9e50dd38e48601f">
help/help/html/menus/alwcalculate.html
</a>
</li>
<li class="file-stats">
<a href="#03fd33fbd616e46ad8b35c49651070643de426ea">
help/help/html/menus/alwcolour.html
</a>
</li>
<li class="file-stats">
<a href="#66c3c2b6565e6e77dd59acbd197a583a8fed1acd">
help/help/html/menus/alwedit.html
</a>
</li>
<li class="file-stats">
<a href="#f30f08713b531cbbdc98441ff3f221391adb197b">
help/help/html/menus/alwfile.html
</a>
</li>
<li class="file-stats">
<a href="#d88d65bd2c4860a0234c5f8cd1285462c923b29d">
help/help/html/menus/alwformat.html
</a>
</li>
<li class="file-stats">
<a href="#dfc4163f6a39892eda9c030892b6702bdd070614">
help/help/html/menus/alwselect.html
</a>
</li>
<li class="file-stats">
<a href="#b0a85f4aef72f1ec00b23585aba213a36e257960">
help/help/html/menus/alwview.html
</a>
</li>
<li class="file-stats">
<a href="#42393cd2f927dddb5a27f27d4ebe1c0d58acea99">
help/help/html/menus/desktopMenu.html
</a>
</li>
<li class="file-stats">
<a href="#1f582e3c00a8062ab39900a2c77b282dcbec122c">
help/help/html/menus/index.html
</a>
</li>
<li class="file-stats">
<a href="#bd946574daa81dff40970d6e0f93b301358d6561">
help/help/html/menus/popupMenu.html
</a>
</li>
<li class="file-stats">
<a href="#5b6aef365a058c996aa8adf78b9e5cebd478d17b">
help/help/html/menus/wsmenu.html
</a>
</li>
<li class="file-stats">
<a href="#97e9bb7b4e84ff34160e02aa863225128ba9ed44">
help/help/html/misc/aaproperties.html
</a>
</li>
<li class="file-stats">
<a href="#54c668375c26ccfd9c6384d6dcf655ad64bee554">
help/help/html/misc/aminoAcids.html
</a>
</li>
<li class="file-stats">
<a href="#f1aac4a89ea7b89fad159370714df1955634c0cd">
help/help/html/misc/geneticCode.html
</a>
</li>
<li class="file-stats">
<a href="#ac132525ddb85fdd9c12655b790f20067ad2ae1e">
help/help/html/na/index.html
</a>
</li>
<li class="file-stats">
<a href="#51928f95aad375f51fbe40dcda8d3c7c631d01db">
help/help/html/privacy.html
</a>
</li>
<li class="file-stats">
<a href="#6510ab8233d7248ad402aca54f03d97e40a3aad1">
help/help/html/webServices/AACon.html
</a>
</li>
<li class="file-stats">
<a href="#73f8295e91cdbab42b0bf275fbb15c3ec0d22804">
help/help/html/webServices/JABAWS.html
</a>
</li>
<li class="file-stats">
<a href="#97526d863cbf7da0231722f5c99f3257f48eb471">
help/help/html/webServices/RNAalifold.html
</a>
</li>
<li class="file-stats">
<a href="#c133bf7d7ba877a180bad132b4526d39ace9d11b">
help/help/html/webServices/dbreffetcher.html
</a>
</li>
<li class="file-stats">
<a href="#191de9026e5092235b4d2ff73fc54650bc21c0f2">
help/help/html/webServices/index.html
</a>
</li>
<li class="file-stats">
<a href="#b659fc66ffecdb1159080be3c8d62107b0b7167d">
help/help/html/webServices/jnet.html
</a>
</li>
<li class="file-stats">
<a href="#ad0989acb44c64ed7af211a171de8846dbc5ef25">
help/help/html/webServices/msaclient.html
</a>
</li>
<li class="file-stats">
<a href="#388127818e8918a3d7b9d5ffdf9f37693e4d5df7">
help/help/html/webServices/newsreader.html
</a>
</li>
<li class="file-stats">
<a href="#3c9f09b270aad52f2d7981a8568d226deddb0420">
help/help/html/webServices/proteinDisorder.html
</a>
</li>
<li class="file-stats">
<a href="#25cc455ca04005d21afc4adadd4998e313d91b2d">
help/help/html/webServices/shmr.html
</a>
</li>
<li class="file-stats">
<a href="#35c58d4207120a38e485eb07bc2eab3bae60abb7">
help/help/html/webServices/urllinks.html
</a>
</li>
<li class="file-stats">
<a href="#1563cb99752d7cd6e2c125613dee1cbfadc2307d">
help/help/html/webServices/webServicesParams.html
</a>
</li>
<li class="file-stats">
<a href="#3e6303be23fa24509ada00da4d680547c659246f">
help/help/html/webServices/webServicesPrefs.html
</a>
</li>
<li class="file-stats">
<a href="#b633497deb4eba941df2e3167aefdc8cce3dc029">
<span class="new-file">
+
help/markdown/releases/release-2_11_4_1.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#216629121f1d980a7d5d0cbf7ce7953402b46e95">
<span class="new-file">
+
help/markdown/whatsnew/whatsnew-2_11_4_1.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#355e1d0d8d7b1ffed2181d5599cbb7413a18c16d">
help/templates/releases.html
</a>
</li>
<li class="file-stats">
<a href="#4cc26ad3ed866b10a1263b26c85eac378bef1d01">
help/templates/whatsNew.html
</a>
</li>
<li class="file-stats">
<a href="#aa9a956ae93044ba06b7687c34d421fb5e37cdb2">
jalview-jalopy.xml
</a>
</li>
<li class="file-stats">
<a href="#564ad4f13250ab180174b4846504fd58cf6a1591">
nbbuild.xml
</a>
</li>
<li class="file-stats">
<a href="#80da317e63b4bda3df77cdf6f56dad6f1e658f84">
nbproject/project.xml
</a>
</li>
<li class="file-stats">
<a href="#2cceaa8d26d3c8c4ef8410981a325d1974611930">
schemas/jalview.nodesc.properties
</a>
</li>
<li class="file-stats">
<a href="#e251ea9ca3c783b7ec565d6b0afab8544c049518">
schemas/jalview.properties
</a>
</li>
<li class="file-stats">
<a href="#af8a6f43d7eac63e725810140249076144b72b19">
src/ext/vamsas/IRegistry.java
</a>
</li>
<li class="file-stats">
<a href="#d1dfd2c6d34d408cf53fb2e01fbb229571f22a01">
src/ext/vamsas/IRegistryService.java
</a>
</li>
<li class="file-stats">
<a href="#3fa45fdb8e753d7b052c0ec434404a13c75ebd88">
src/ext/vamsas/IRegistryServiceLocator.java
</a>
</li>
<li class="file-stats">
<a href="#b5a4f0640ac0dc0e5fc17506c1b796836db92699">
src/ext/vamsas/Jpred.java
</a>
</li>
<li class="file-stats">
<a href="#40ac23b0d5a21b12ac4f69a83190f60ed86e2d70">
src/ext/vamsas/JpredService.java
</a>
</li>
<li class="file-stats">
<a href="#332ef954e4544631a723f0183fa9b42c2fedfc7f">
src/ext/vamsas/JpredServiceLocator.java
</a>
</li>
<li class="file-stats">
<a href="#29abd5ffe43acadbcbb63800a07eaaf59246d192">
src/ext/vamsas/JpredSoapBindingStub.java
</a>
</li>
<li class="file-stats">
<a href="#2d83d5f4c638a18ea74be1c3229eeacfd3bcea7f">
src/ext/vamsas/MuscleWS.java
</a>
</li>
<li class="file-stats">
<a href="#e73b310ab23b3343cace068c2a67ea6fad704dde">
src/ext/vamsas/MuscleWSService.java
</a>
</li>
<li class="file-stats">
<a href="#5ed976e2afb9520c5696825e9f57dff78ef78c1f">
src/ext/vamsas/MuscleWSServiceLocator.java
</a>
</li>
<li class="file-stats">
<a href="#1d896f99d5c1e67a9607e8835c5877f5e585725f">
src/ext/vamsas/MuscleWSSoapBindingStub.java
</a>
</li>
<li class="file-stats">
<a href="#219ab41202659c93b234f8dbf937245470e9b0f8">
src/ext/vamsas/RegistryServiceSoapBindingStub.java
</a>
</li>
<li class="file-stats">
<a href="#7ad5a0d70f3bd48fd6d4e3f10da60dd72ceff46e">
src/ext/vamsas/SeqSearchI.java
</a>
</li>
<li class="file-stats">
<a href="#152a72e37dc004fabad487ab4e61c58f0bae18db">
src/ext/vamsas/SeqSearchServiceLocator.java
</a>
</li>
<li class="file-stats">
<a href="#edcfcf3b8d7f1ed712aa449d6b2543b9ad84c093">
src/ext/vamsas/SeqSearchServiceService.java
</a>
</li>
<li class="file-stats">
<a href="#3d73d3f9412e4c93d4dcbce301e596c5ed1797da">
src/ext/vamsas/SeqSearchServiceSoapBindingStub.java
</a>
</li>
<li class="file-stats">
<a href="#b23ad0f067b5d3409434f945bfbc8240fba24638">
src/ext/vamsas/ServiceHandle.java
</a>
</li>
<li class="file-stats">
<a href="#a2157eabf7c32a3d363b60189a366bc912c1687e">
src/ext/vamsas/ServiceHandles.java
</a>
</li>
<li class="file-stats">
<a href="#d28322e6a69f9951b5f0a17f5ab1da31cae8d267">
src/jalview/analysis/AAFrequency.java
</a>
</li>
<li class="file-stats">
<a href="#a683031e1b66bf2a4044b0d0f51272f41900a9c4">
src/jalview/analysis/AlignSeq.java
</a>
</li>
<li class="file-stats">
<a href="#c64c3be074aa2a09217fc6a21645fc643923d247">
src/jalview/analysis/AlignmentAnnotationUtils.java
</a>
</li>
<li class="file-stats">
<a href="#51312ebab86c575dd5a179f3feae86fa5391c94f">
src/jalview/analysis/AlignmentSorter.java
</a>
</li>
<li class="file-stats">
<a href="#ba997967e1d15d7e7956705f65fc780ae421c0cb">
src/jalview/analysis/AlignmentUtils.java
</a>
</li>
<li class="file-stats">
<a href="#a6c171a253bd146cbff916507664fb6da029a511">
src/jalview/analysis/AnnotationSorter.java
</a>
</li>
<li class="file-stats">
<a href="#5d21384d5c2dc72da12a4b4c0177b52e435b422b">
src/jalview/analysis/AverageDistanceEngine.java
</a>
</li>
<li class="file-stats">
<a href="#2b8b791f18813d33fcd3e3becde3761e15e5af2d">
src/jalview/analysis/AverageDistanceTree.java
</a>
</li>
<li class="file-stats">
<a href="#064b199d2c8889f06b8545d9bf6db8d6e5db466e">
src/jalview/analysis/CodingUtils.java
</a>
</li>
<li class="file-stats">
<a href="#a0e7b0fe03a175093fbf35430609e82c9d71a137">
src/jalview/analysis/CodonComparator.java
</a>
</li>
<li class="file-stats">
<a href="#d63e8170aa22dc888b4fd7475160a21ad1f62f3e">
src/jalview/analysis/Connectivity.java
</a>
</li>
<li class="file-stats">
<a href="#1196f2ab9bbb671e309a35636f2b2e51e14d3532">
src/jalview/analysis/ConnectivityException.java
</a>
</li>
<li class="file-stats">
<a href="#46c869d95ef99e1ccdd7ce0a5533b4825f730b90">
src/jalview/analysis/Conservation.java
</a>
</li>
<li class="file-stats">
<a href="#65737e5215dddc6056a4c61e6cce375e2fa13c09">
src/jalview/analysis/CrossRef.java
</a>
</li>
<li class="file-stats">
<a href="#18a6417b9ca30e57c5f8babb0ea871c9c36f417a">
src/jalview/analysis/Dna.java
</a>
</li>
<li class="file-stats">
<a href="#7dac259305be9565a1023a64dbd5f8e8bf27957d">
src/jalview/analysis/Finder.java
</a>
</li>
<li class="file-stats">
<a href="#570368777371b7bca03073b71ee7979ee602ac36">
src/jalview/analysis/GeneticCodeI.java
</a>
</li>
<li class="file-stats">
<a href="#1102cde05385eebbb9f85c69f3a8450ec9679abe">
src/jalview/analysis/GeneticCodes.java
</a>
</li>
<li class="file-stats">
<a href="#f4f8928720c3b80163504ffafcd686b6d32d785f">
src/jalview/analysis/Grouping.java
</a>
</li>
<li class="file-stats">
<a href="#3ed4304731c4c8b8385665061730063e68b0e617">
src/jalview/analysis/NJTree.java
</a>
</li>
<li class="file-stats">
<a href="#de5a25929548727de52ecb4e2b4fc548850ef37e">
src/jalview/analysis/PCA.java
</a>
</li>
<li class="file-stats">
<a href="#41a8858da577938e3bd32ec623cab49bab8cc20b">
src/jalview/analysis/PaSiMap.java
</a>
</li>
<li class="file-stats">
<a href="#3efa0a56836994929d3ccba10eb664d2d1e90419">
src/jalview/analysis/ParseProperties.java
</a>
</li>
<li class="file-stats">
<a href="#99d048fb2bfe69817b8a81947b7f2d16956ac841">
src/jalview/analysis/Rna.java
</a>
</li>
<li class="file-stats">
<a href="#c5a70b3f9a734c6549f3fe7a6bbaaa3792dd7114">
src/jalview/analysis/SecStrConsensus.java
</a>
</li>
<li class="file-stats">
<a href="#74b12ade2ed0915b5b1e69191aa98870ec1b8dc4">
src/jalview/analysis/SeqsetUtils.java
</a>
</li>
<li class="file-stats">
<a href="#bca524734b79eb0bd5bd1f26dcb2a969a09ac315">
src/jalview/analysis/SequenceIdMatcher.java
</a>
</li>
<li class="file-stats">
<a href="#c62eac4f83c2a234049be068b624864999c3d484">
src/jalview/analysis/StructureFrequency.java
</a>
</li>
<li class="file-stats">
<a href="#95e8d758294e0bc601af6fe9df039e643e4533b9">
src/jalview/analysis/TreeBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#b12c1bf35697a04a5d6d30ccfd60d1188952b3f3">
src/jalview/analysis/TreeEngine.java
</a>
</li>
<li class="file-stats">
<a href="#7dbc71e257002e7128dc493c6f6f11d43442e62d">
src/jalview/analysis/TreeModel.java
</a>
</li>
<li class="file-stats">
<a href="#38730d249c818d196ba73c2e8d78c2176ac4a4c8">
src/jalview/analysis/WUSSParseException.java
</a>
</li>
<li class="file-stats">
<a href="#b4fae33654c2d943ff87fc6760820616beacb0d3">
src/jalview/analysis/ccAnalysis.java
</a>
</li>
<li class="file-stats">
<a href="#dad547f6132b7793fc984bd455e98d58229b51e2">
src/jalview/analysis/scoremodels/DistanceScoreModel.java
</a>
</li>
<li class="file-stats">
<a href="#00471c93f6df258a9b0ca1ca968594c3f73023e9">
src/jalview/analysis/scoremodels/FeatureDistanceModel.java
</a>
</li>
<li class="file-stats">
<a href="#0c03745965edf4ae196f0170c4be8540ad70a7d4">
src/jalview/analysis/scoremodels/PIDModel.java
</a>
</li>
<li class="file-stats">
<a href="#8cb022d53c4718fa37a1e8ab5803915b5b10a523">
src/jalview/analysis/scoremodels/ScoreMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#1c28cb4aa9324570874130baf7265a5bf3c4b81d">
src/jalview/analysis/scoremodels/ScoreModels.java
</a>
</li>
<li class="file-stats">
<a href="#98cbe2a291307c213594eb0aad470230a020c2c5">
src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
</a>
</li>
<li class="file-stats">
<a href="#d5f291e46c4e6372b4bde95c7801d8fa8f282327">
src/jalview/analysis/scoremodels/SimilarityParams.java
</a>
</li>
<li class="file-stats">
<a href="#a6367e4f022fd3da3a8e4ea458dc409c6861c1f0">
src/jalview/analysis/scoremodels/SimilarityScoreModel.java
</a>
</li>
<li class="file-stats">
<a href="#841b01878ac348d78de1441b67d943cef115b72e">
src/jalview/analysis/scoremodels/SmithWatermanModel.java
</a>
</li>
<li class="file-stats">
<a href="#464262940f981f34ba7a3db41c99ac3565072536">
src/jalview/analytics/Plausible.java
</a>
</li>
<li class="file-stats">
<a href="#e1a92ae9ca2159272fd4fb630d5219406f1eaa22">
src/jalview/api/AlignCalcManagerI.java
</a>
</li>
<li class="file-stats">
<a href="#82a1c8e8000ff748cbc6999765501723c4936bbe">
src/jalview/api/AlignCalcWorkerI.java
</a>
</li>
<li class="file-stats">
<a href="#e186721cfc529fa38b11db4a6f040663a4533fb2">
src/jalview/api/AlignExportSettingsI.java
</a>
</li>
<li class="file-stats">
<a href="#7ba6c56221d73765e93cc709efbd589232f84037">
src/jalview/api/AlignViewControllerGuiI.java
</a>
</li>
<li class="file-stats">
<a href="#426e94ca00cbd19e2240bf409835198501617ae3">
src/jalview/api/AlignViewControllerI.java
</a>
</li>
<li class="file-stats">
<a href="#50955889c295dfaf973eac7d685d2eb01df8b98e">
src/jalview/api/AlignViewportI.java
</a>
</li>
<li class="file-stats">
<a href="#7f648c201ba1c49b55e82b5efe243d9e08d66e04">
src/jalview/api/AlignmentColsCollectionI.java
</a>
</li>
<li class="file-stats">
<a href="#337a934bf984bf1275d7fa7a054248b0887c83fd">
src/jalview/api/AlignmentRowsCollectionI.java
</a>
</li>
<li class="file-stats">
<a href="#035e5a6d9f1a62f0740ce173a812ce7a401a9e63">
src/jalview/api/AlignmentViewPanel.java
</a>
</li>
<li class="file-stats">
<a href="#f1ba45d6b73c7baffbff4440355ec9ed59476ec1">
src/jalview/api/BuildDetailsI.java
</a>
</li>
<li class="file-stats">
<a href="#f05ce4ac43dcf9254a6a1365ea8b776c7aeae2a4">
src/jalview/api/ComplexAlignFile.java
</a>
</li>
<li class="file-stats">
<a href="#66942772cfdf9fa12a7c6adfd429e5d079604018">
src/jalview/api/DBRefEntryI.java
</a>
</li>
<li class="file-stats">
<a href="#6be90392990aea8d91af39351c590281f08ed5a8">
src/jalview/api/FeatureColourI.java
</a>
</li>
<li class="file-stats">
<a href="#5a64a036aecba8af55c69ad7f010ff0f805d6286">
src/jalview/api/FeatureRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#c59fb5bc23750b2de7c75c53102fcb1dcc168f1e">
src/jalview/api/FeatureSettingsControllerI.java
</a>
</li>
<li class="file-stats">
<a href="#3e07f33c53a5277809fdc98e9bccdd8f97e4e52a">
src/jalview/api/FeatureSettingsModelI.java
</a>
</li>
<li class="file-stats">
<a href="#92efbe7b004fc90e4731973a1051b4f9779ffb81">
src/jalview/api/FeaturesDisplayedI.java
</a>
</li>
<li class="file-stats">
<a href="#65691f32e11d2d8d568470302b7314bc5e16be79">
src/jalview/api/FeaturesSourceI.java
</a>
</li>
<li class="file-stats">
<a href="#d146b26d880b446beb8bc530454d60c68ee05c0d">
src/jalview/api/FinderI.java
</a>
</li>
<li class="file-stats">
<a href="#4b68ae8ff7a7934c7652abc2853f82524aaebd71">
src/jalview/api/OOMHandlerI.java
</a>
</li>
<li class="file-stats">
<a href="#2fab50497c134cb5533d2f1c53cb95b9eb8216d1">
src/jalview/api/RendererListenerI.java
</a>
</li>
<li class="file-stats">
<a href="#21ccd37019b48bbfd0be377a467e83f1d69e5bc0">
src/jalview/api/RotatableCanvasI.java
</a>
</li>
<li class="file-stats">
<a href="#7d842427f3a43c12f5775a4ae01a58496ce4f029">
src/jalview/api/SequenceRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#000496bbe384da6d8b48c615f296462ec9323fac">
src/jalview/api/SequenceStructureBinding.java
</a>
</li>
<li class="file-stats">
<a href="#ff4ae1948bbc9810b4bc62d1ecdbee2119c6d6f7">
src/jalview/api/SiftsClientI.java
</a>
</li>
<li class="file-stats">
<a href="#5b950361e5fedef4d72b303e5b8d9e4e206c2321">
src/jalview/api/SplitContainerI.java
</a>
</li>
<li class="file-stats">
<a href="#05c302bb795b1562085078fbb3b4e8424cd3898b">
src/jalview/api/StructureSelectionManagerProvider.java
</a>
</li>
<li class="file-stats">
<a href="#d20bc4b6af50594bfd4c1a2c282591e59c2baff2">
src/jalview/api/ViewStyleI.java
</a>
</li>
<li class="file-stats">
<a href="#dc937e5d5cfd3ff311eb3c35cb32a3dd59c7137c">
src/jalview/api/analysis/PairwiseScoreModelI.java
</a>
</li>
<li class="file-stats">
<a href="#04dca6b734f38432e25eaee88df0e55f6c5530ee">
src/jalview/api/analysis/ScoreModelI.java
</a>
</li>
<li class="file-stats">
<a href="#1e3cad25471f923207f7d996dc28497fbff33915">
src/jalview/api/analysis/SimilarityParamsI.java
</a>
</li>
<li class="file-stats">
<a href="#a6e66e255fb0591041b3be4dc97ed34ef7121083">
src/jalview/api/structures/JalviewStructureDisplayI.java
</a>
</li>
<li class="file-stats">
<a href="#8307549ba868cf43a93b4f7142ce0a232c01174b">
src/jalview/appletgui/APopupMenu.java
</a>
</li>
<li class="file-stats">
<a href="#6c86e3c618f69a600803b204266bbc222d221225">
src/jalview/appletgui/AlignFrame.java
</a>
</li>
<li class="file-stats">
<a href="#6068518710d423fefaaa0f94b939b8ba5cacc5a5">
src/jalview/appletgui/AlignViewport.java
</a>
</li>
<li class="file-stats">
<a href="#8b0a2bc0f38000a0db0ef51473c8ce760ad1ceae">
src/jalview/appletgui/AlignmentPanel.java
</a>
</li>
<li class="file-stats">
<a href="#bea5a55c6d36b5906cdf383639109903e24c16cd">
src/jalview/appletgui/AnnotationColourChooser.java
</a>
</li>
<li class="file-stats">
<a href="#ed17f28761c612c2e94b43a08772577aa95769de">
src/jalview/appletgui/AnnotationColumnChooser.java
</a>
</li>
<li class="file-stats">
<a href="#68c5bbbfc5d1bfd18a998d713cfd3acd917c3927">
src/jalview/appletgui/AnnotationLabels.java
</a>
</li>
<li class="file-stats">
<a href="#dce148f98e301ab4d2ab15ad7f09c468b43ed2d1">
src/jalview/appletgui/AnnotationPanel.java
</a>
</li>
<li class="file-stats">
<a href="#b6cfb315e026207faa4a285c5327b24b24f17e1d">
src/jalview/appletgui/AnnotationRowFilter.java
</a>
</li>
<li class="file-stats">
<a href="#319cadddefb81bb794147d1d45168a62af9eb5b7">
src/jalview/appletgui/AppletJmol.java
</a>
</li>
<li class="file-stats">
<a href="#79207cf6b2115826d899e6d7f002210ccc7280c4">
src/jalview/appletgui/AppletJmolBinding.java
</a>
</li>
<li class="file-stats">
<a href="#74af91e9e107d756fa8b7108d3548ec12edca133">
src/jalview/appletgui/CutAndPasteTransfer.java
</a>
</li>
<li class="file-stats">
<a href="#9390acdeb977a53918ec8e7dffb5a93748e7e2d9">
src/jalview/appletgui/EditNameDialog.java
</a>
</li>
<li class="file-stats">
<a href="#20b6999977fe22d6cf19983123930355abc5d498">
src/jalview/appletgui/EmbmenuFrame.java
</a>
</li>
<li class="file-stats">
<a href="#e8b4a8e35e9b113468da4d71c42776ccf6f95d3e">
src/jalview/appletgui/ExtJmol.java
</a>
</li>
<li class="file-stats">
<a href="#5fae41da775ea43fae369e3235defc7c466026eb">
src/jalview/appletgui/FeatureColourChooser.java
</a>
</li>
<li class="file-stats">
<a href="#1ca431784dd31b2f0f3851e56e971992327f574e">
src/jalview/appletgui/FeatureRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#bab33cf876195e904860aad827f2342e917455c3">
src/jalview/appletgui/FeatureSettings.java
</a>
</li>
<li class="file-stats">
<a href="#6b1b1dac12b57ca16b716e5a88a833bbc436bad5">
src/jalview/appletgui/Finder.java
</a>
</li>
<li class="file-stats">
<a href="#98161fdb73655594d140a5c9efc8f3ee51fc96b2">
src/jalview/appletgui/FontChooser.java
</a>
</li>
<li class="file-stats">
<a href="#a8e88749941e70a75fc9677bd1b5ebe3109ab682">
src/jalview/appletgui/IdCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#699a57cb0fbaba7924e63ef2e561ffc8d3dc5998">
src/jalview/appletgui/IdPanel.java
</a>
</li>
<li class="file-stats">
<a href="#2c9362fa02c99df9f99577738df2ba315845a3fa">
src/jalview/appletgui/IdwidthAdjuster.java
</a>
</li>
<li class="file-stats">
<a href="#de77e0de4481b2dd702374d369c815b8d26b1051">
src/jalview/appletgui/JVDialog.java
</a>
</li>
<li class="file-stats">
<a href="#c88798bd1efbe04526fe31176ec5d8e79294a264">
src/jalview/appletgui/OverviewCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#35376951684370966888cda17017a3737cb256ba">
src/jalview/appletgui/OverviewPanel.java
</a>
</li>
<li class="file-stats">
<a href="#90433a27c6222194691cbfbf40f825fee850b256">
src/jalview/appletgui/PCAPanel.java
</a>
</li>
<li class="file-stats">
<a href="#011af0a689b181478474a6976217d2fe71239da6">
src/jalview/appletgui/PaintRefresher.java
</a>
</li>
<li class="file-stats">
<a href="#8da127e1ebfca4ea597279c39ceb8f89305de214">
src/jalview/appletgui/PairwiseAlignPanel.java
</a>
</li>
<li class="file-stats">
<a href="#244263f5602fc69fffa3afe43ef114435b3c37c7">
src/jalview/appletgui/RedundancyPanel.java
</a>
</li>
<li class="file-stats">
<a href="#61596b98bde1125f105179c81d2e2f5a16fa1442">
src/jalview/appletgui/RotatableCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#f666946016bc5274c1a7f01779f78eb1b3429048">
src/jalview/appletgui/ScalePanel.java
</a>
</li>
<li class="file-stats">
<a href="#fcf23fcfeb0c750cf11f662ad948ed00d2de739f">
src/jalview/appletgui/SeqCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#d6c18b7deedc28811725046d5577e2b2e7e692c3">
src/jalview/appletgui/SeqPanel.java
</a>
</li>
<li class="file-stats">
<a href="#6fb659e747dae25e003fcb6a109d2fc24d50acde">
src/jalview/appletgui/SequenceRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#7f36122080896384cb902a3ef8191711c2adf4d2">
src/jalview/appletgui/SliderPanel.java
</a>
</li>
<li class="file-stats">
<a href="#36b06e7bd424c33b328036965d2bf3d45b74311b">
src/jalview/appletgui/SplitFrame.java
</a>
</li>
<li class="file-stats">
<a href="#cbd22ae0aed5bd660b9721256a63401cbd3a661f">
src/jalview/appletgui/TitledPanel.java
</a>
</li>
<li class="file-stats">
<a href="#48e69cea88cc838627306481297fd496f2802aed">
src/jalview/appletgui/Tooltip.java
</a>
</li>
<li class="file-stats">
<a href="#a12fa1a558309514315400fb7a4138db217da9f8">
src/jalview/appletgui/TreeCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#4cc7450ff21bfb624c2dc6e5a76eda0ab068ff15">
src/jalview/appletgui/TreePanel.java
</a>
</li>
<li class="file-stats">
<a href="#4bdc3da1320c6fe085bffd1b697b686de72a63ad">
src/jalview/appletgui/UserDefinedColours.java
</a>
</li>
<li class="file-stats">
<a href="#33d185529f1ebf6e43960e12cfcd0ec5481880e0">
src/jalview/bin/ArgsParser.java
</a>
</li>
<li class="file-stats">
<a href="#5426b6b1752fda89e92ccf2fc5a604b788a2e957">
src/jalview/bin/BuildDetails.java
</a>
</li>
<li class="file-stats">
<a href="#95e4d7dc8273296fd4d942c517f8232ffd1ba221">
src/jalview/bin/Cache.java
</a>
</li>
<li class="file-stats">
<a href="#1e386042bef8f3fc5bbe58da74336dedef02a01a">
src/jalview/bin/Commands.java
</a>
</li>
<li class="file-stats">
<a href="#4bd9be30f3353ad7cd6c804b95b960aca6428bc0">
src/jalview/bin/Console.java
</a>
</li>
<li class="file-stats">
<a href="#9ecbf90442f7e704f78c97df479fbe207e816c4d">
src/jalview/bin/GetMemory.java
</a>
</li>
<li class="file-stats">
<a href="#55f9c84c28f32242f6f0662b09c6b2ff9c7396af">
src/jalview/bin/GetdownLauncherUpdate.java
</a>
</li>
<li class="file-stats">
<a href="#c7f9bbca54ab2355d3d55f1a7d36d2fc7908e9e2">
src/jalview/bin/HiDPISetting.java
</a>
</li>
<li class="file-stats">
<a href="#a0def663ffa806208a3952eb79e8f002327163ba">
src/jalview/bin/Jalview.java
</a>
</li>
<li class="file-stats">
<a href="#66ff7030520326549520f0358cd5de66d2a236ee">
src/jalview/bin/JalviewJS2.java
</a>
</li>
<li class="file-stats">
<a href="#efbdaf3ba668699da004f13e23661fbe10bd66de">
src/jalview/bin/JalviewLite.java
</a>
</li>
<li class="file-stats">
<a href="#7afa79ef02007bc9160643ed3119ef814f4666c5">
src/jalview/bin/JalviewLiteURLRetrieve.java
</a>
</li>
<li class="file-stats">
<a href="#66b7be47971896011f6eddf17f8c29c0756c2580">
src/jalview/bin/JalviewTaskbar.java
</a>
</li>
<li class="file-stats">
<a href="#0dac37c97149db2e95116c082aff2c3db7a47c45">
src/jalview/bin/Launcher.java
</a>
</li>
<li class="file-stats">
<a href="#424b4caeddafbf7760a8f4d5bd175294a5d565cc">
src/jalview/bin/MemorySetting.java
</a>
</li>
<li class="file-stats">
<a href="#5ac66da25cecf6d6221b1f5089dedb4c431021c6">
src/jalview/bin/ScreenInfo.java
</a>
</li>
<li class="file-stats">
<a href="#7a0f4f38866a76341a5755c6ed7c681957a172b1">
src/jalview/bin/argparser/Arg.java
</a>
</li>
<li class="file-stats">
<a href="#13f5dfbf8e49bc6d18d551ca2ec10939f8da8753">
src/jalview/bin/argparser/ArgParser.java
</a>
</li>
<li class="file-stats">
<a href="#34347f0e6ef128787f17136af10895df69b296b8">
src/jalview/bin/argparser/ArgValue.java
</a>
</li>
<li class="file-stats">
<a href="#df28ed8ef13f813fe69e2fea5e3521303507402f">
src/jalview/bin/argparser/ArgValues.java
</a>
</li>
<li class="file-stats">
<a href="#649c50110583f441fa7c1b13418e88832c4b2121">
src/jalview/bin/argparser/ArgValuesMap.java
</a>
</li>
<li class="file-stats">
<a href="#22152eb5cbe8288d039bb0058283270fb96d1c4a">
src/jalview/bin/argparser/BootstrapArgs.java
</a>
</li>
<li class="file-stats">
<a href="#e43baaac4e625f5337c04d73c95a5b293b323e1e">
src/jalview/bin/argparser/SubVals.java
</a>
</li>
<li class="file-stats">
<a href="#232d7d535bb311dbe75ee9a137413cd1481667b8">
src/jalview/bin/groovy/JalviewObject.java
</a>
</li>
<li class="file-stats">
<a href="#dc38e5bc04b083b0abfefb066273405f7cd45127">
src/jalview/bin/groovy/JalviewObjectI.java
</a>
</li>
<li class="file-stats">
<a href="#2e139cc9d7da5bfa4a89d30e26019b9d8867a62c">
src/jalview/commands/ChangeCaseCommand.java
</a>
</li>
<li class="file-stats">
<a href="#c1a14f57372a37d0dbd125d5e3ec7c7dfdc47d8e">
src/jalview/commands/CommandI.java
</a>
</li>
<li class="file-stats">
<a href="#5bcb71d389aadd3e12db34a09b4f10f3b05e6be1">
src/jalview/commands/EditCommand.java
</a>
</li>
<li class="file-stats">
<a href="#a2f6ae00e1e5169d970481147bcdccbba50070bc">
src/jalview/commands/JustifyLeftOrRightCommand.java
</a>
</li>
<li class="file-stats">
<a href="#ec248cbc4dcdece77cd70206d53905f8c99790ae">
src/jalview/commands/OrderCommand.java
</a>
</li>
<li class="file-stats">
<a href="#5df9a0ea501f5cb6604702ab425442722674964b">
src/jalview/commands/RemoveGapColCommand.java
</a>
</li>
<li class="file-stats">
<a href="#1a5affe1f49f46f4e9f1699c286e76a6a1f9f958">
src/jalview/commands/RemoveGapsCommand.java
</a>
</li>
<li class="file-stats">
<a href="#1b624aeb229ec841af787888fbf526b16b920656">
src/jalview/commands/SlideSequencesCommand.java
</a>
</li>
<li class="file-stats">
<a href="#d285e60ff0e262fcce58e5b29e25a35cbefcf4f3">
src/jalview/commands/TrimRegionCommand.java
</a>
</li>
<li class="file-stats">
<a href="#5c98ee217d58705be35f9cf80a484a6a26539284">
src/jalview/controller/AlignViewController.java
</a>
</li>
<li class="file-stats">
<a href="#e73f8a542157d4ad2f30929f69d1d541a4b3bf93">
src/jalview/controller/FeatureSettingsController.java
</a>
</li>
<li class="file-stats">
<a href="#990db4116d80d8e9278f57611f8854a70d409a50">
src/jalview/controller/FeatureSettingsControllerGuiI.java
</a>
</li>
<li class="file-stats">
<a href="#5309e1bf60c0f6365ee18f79ed1f41f76dc300cc">
src/jalview/datamodel/ASequence.java
</a>
</li>
<li class="file-stats">
<a href="#35c3ee5c5fa12aeacb6ecbf1072bdeecaedfde98">
src/jalview/datamodel/ASequenceI.java
</a>
</li>
<li class="file-stats">
<a href="#4ac6a84e43d19db3eae542155f7d7280aa4ecbbf">
src/jalview/datamodel/AlignExportSettingsAdapter.java
</a>
</li>
<li class="file-stats">
<a href="#7208b24cad52f3b65aa6308b272e18ac10c899b4">
src/jalview/datamodel/AlignedCodon.java
</a>
</li>
<li class="file-stats">
<a href="#dab153a1b4fac9ea19a41c0b799ab9813f3b3c1f">
src/jalview/datamodel/AlignedCodonFrame.java
</a>
</li>
<li class="file-stats">
<a href="#d8932fa77478827cd30ca5a0fccf1cc970675ba3">
src/jalview/datamodel/Alignment.java
</a>
</li>
<li class="file-stats">
<a href="#62eee43c74cfbb5a93663a4622e108b32411ecf5">
src/jalview/datamodel/AlignmentAnnotation.java
</a>
</li>
<li class="file-stats">
<a href="#f1ab4715b9219adf6400b4aa3166c04b55204376">
src/jalview/datamodel/AlignmentExportData.java
</a>
</li>
<li class="file-stats">
<a href="#280e92807fc0c8374e7a6ef1fe6be6344b38594b">
src/jalview/datamodel/AlignmentI.java
</a>
</li>
<li class="file-stats">
<a href="#60a4c677526a800acab812fef716bb4b5d9b4a13">
src/jalview/datamodel/AlignmentOrder.java
</a>
</li>
<li class="file-stats">
<a href="#5c076dfa878099791ebf73625ced937d02b7aa3e">
src/jalview/datamodel/AlignmentView.java
</a>
</li>
<li class="file-stats">
<a href="#0fe07ef9ec3f9b1bac5390827df1b49c85b9ccf9">
src/jalview/datamodel/AllColsCollection.java
</a>
</li>
<li class="file-stats">
<a href="#d965951e8508a5d00f105d5e8ca2a1c1252e7cfe">
src/jalview/datamodel/AllColsIterator.java
</a>
</li>
<li class="file-stats">
<a href="#77d2c14e7691a23365b4d8019293a4f9fa9bbe63">
src/jalview/datamodel/AllRowsCollection.java
</a>
</li>
<li class="file-stats">
<a href="#ba765d30d3a528bff017d0bf15cd85e0ad2b6250">
src/jalview/datamodel/AllRowsIterator.java
</a>
</li>
<li class="file-stats">
<a href="#4ef3be7cfe49ed92e53e8e491ec7c4e10f00b6a2">
src/jalview/datamodel/AnnotatedCollectionI.java
</a>
</li>
<li class="file-stats">
<a href="#fa713b34a09b8e7b1933c390e816c5e98413db45">
src/jalview/datamodel/Annotation.java
</a>
</li>
<li class="file-stats">
<a href="#f2baa38613da24b73471711778598b54e9907bf4">
src/jalview/datamodel/BinaryNode.java
</a>
</li>
<li class="file-stats">
<a href="#15a9f720508d31b2d969d8db75a18f7ed6338259">
src/jalview/datamodel/BinarySequence.java
</a>
</li>
<li class="file-stats">
<a href="#346d7d8820e64c6a436b9f188b96d258c2c62ff6">
src/jalview/datamodel/CigarArray.java
</a>
</li>
<li class="file-stats">
<a href="#7394e2f5420d6f68f4e647aca5150631bced974a">
src/jalview/datamodel/CigarBase.java
</a>
</li>
<li class="file-stats">
<a href="#897cd81f18273bf121062b3818d7d1a6cadab718">
src/jalview/datamodel/CigarCigar.java
</a>
</li>
<li class="file-stats">
<a href="#8fad947df080dccbb78e3ba11ea731b352908981">
src/jalview/datamodel/CigarSimple.java
</a>
</li>
<li class="file-stats">
<a href="#62f7a63d2242959095d480d578b9fbd040745c68">
src/jalview/datamodel/ColumnSelection.java
</a>
</li>
<li class="file-stats">
<a href="#f0a9e7eec5b573d8f2035f64efc142ef1556a844">
src/jalview/datamodel/ContactListI.java
</a>
</li>
<li class="file-stats">
<a href="#f3344fec0bb2970cc4d521ecb606059f1e882671">
src/jalview/datamodel/ContactListImpl.java
</a>
</li>
<li class="file-stats">
<a href="#3cfde27e93b7ad8eaa250719a612f8ab06c4a91f">
src/jalview/datamodel/ContactListProviderI.java
</a>
</li>
<li class="file-stats">
<a href="#80e528c444663001d5c54ecf0a665f30098a61c2">
src/jalview/datamodel/ContactMapHolder.java
</a>
</li>
<li class="file-stats">
<a href="#45321502880b083c7b5df8ac763bfcb136e672ac">
src/jalview/datamodel/ContactMapHolderI.java
</a>
</li>
<li class="file-stats">
<a href="#2450a0a64c8dcbc1089dc4b4465d5d235b8fe141">
src/jalview/datamodel/ContactMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#7b96420abdfd5212ceaf53963b928138d45311e7">
src/jalview/datamodel/ContactMatrixI.java
</a>
</li>
<li class="file-stats">
<a href="#278ff6abed49bb8273232db0a01870aa1ca49e31">
src/jalview/datamodel/ContactRange.java
</a>
</li>
<li class="file-stats">
<a href="#2070621cdb25be2cc586fb2342560d6778640237">
src/jalview/datamodel/ContiguousI.java
</a>
</li>
<li class="file-stats">
<a href="#1bf99a8b1bb6d09271f4817da97a31fa7b72a2fb">
src/jalview/datamodel/DBRefEntry.java
</a>
</li>
<li class="file-stats">
<a href="#8b160ef2d7123609760254a65030039d24259a04">
src/jalview/datamodel/DBRefSource.java
</a>
</li>
<li class="file-stats">
<a href="#6aae3b999b0bba6b9cdc58c0942976a518e03f91">
src/jalview/datamodel/FeatureProperties.java
</a>
</li>
<li class="file-stats">
<a href="#f08b234ef7b64461d54b75fc0254245fe58bdcba">
src/jalview/datamodel/FloatContactMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#fa605f2c1fbcbd267cba2c3519c0fea8fd14321d">
src/jalview/datamodel/GeneLociI.java
</a>
</li>
<li class="file-stats">
<a href="#088d14ca21109cf4c63c934ad5c9d06dc80ec604">
src/jalview/datamodel/GeneLocus.java
</a>
</li>
<li class="file-stats">
<a href="#69e6607ada3010489eba25a456e9e9cc43b700d9">
src/jalview/datamodel/GraphLine.java
</a>
</li>
<li class="file-stats">
<a href="#1d9c2cb78802596dce102a4387f8b76612585458">
src/jalview/datamodel/GroupSet.java
</a>
</li>
<li class="file-stats">
<a href="#ae76697cf1d2c82c650cd322a9090195758f88b7">
src/jalview/datamodel/GroupSetHolder.java
</a>
</li>
<li class="file-stats">
<a href="#cb0a38984082c81b9a1b2d2c9082e980e8c6be8c">
src/jalview/datamodel/GroupSetI.java
</a>
</li>
<li class="file-stats">
<a href="#3e1a538ae4581952d5e5b5b9030edf13a083ed06">
src/jalview/datamodel/HiddenColumns.java
</a>
</li>
<li class="file-stats">
<a href="#92efa30f636975634512c2a7d72a076b3cadd9ec">
src/jalview/datamodel/HiddenColumnsCursor.java
</a>
</li>
<li class="file-stats">
<a href="#eb96691ae87bec5e980e94ae5866787a7ccd3aec">
src/jalview/datamodel/HiddenCursorPosition.java
</a>
</li>
<li class="file-stats">
<a href="#144709db302e398ecd9abdcaca72045cc06d4c88">
src/jalview/datamodel/HiddenSequences.java
</a>
</li>
<li class="file-stats">
<a href="#95b47b162667893a7a75f870935ea95895841c9f">
src/jalview/datamodel/IncompleteCodonException.java
</a>
</li>
<li class="file-stats">
<a href="#06dca239e7c7a20d89c98e505452267b373c48a0">
src/jalview/datamodel/MappedFeatures.java
</a>
</li>
<li class="file-stats">
<a href="#cf4d42e13b72f08994fe2e2d1aaf7c4c91715eea">
src/jalview/datamodel/Mapping.java
</a>
</li>
<li class="file-stats">
<a href="#ef95b8eaffc8a63cbe6dd80a096c33a6fea60bae">
src/jalview/datamodel/MappingType.java
</a>
</li>
<li class="file-stats">
<a href="#37476504f3c12d1a62cf205153546715227f83e6">
src/jalview/datamodel/NodeTransformI.java
</a>
</li>
<li class="file-stats">
<a href="#30c40153123ded9104e07d38be219f4cf602c8e0">
src/jalview/datamodel/PDBEntry.java
</a>
</li>
<li class="file-stats">
<a href="#a5e508e324ee9d5ebb1087a02914c0b03e801a74">
src/jalview/datamodel/Point.java
</a>
</li>
<li class="file-stats">
<a href="#6c4cff1b03ceaab68c6ece2ae4b6665b93131cd9">
src/jalview/datamodel/Profile.java
</a>
</li>
<li class="file-stats">
<a href="#dd3dbe13cb8bc03a3568a40b099cb61b60b77de5">
src/jalview/datamodel/ProfileI.java
</a>
</li>
<li class="file-stats">
<a href="#3832627928a4fa214763175ac3531e0dc8872161">
src/jalview/datamodel/Profiles.java
</a>
</li>
<li class="file-stats">
<a href="#3f37e86ee3796b5072a0514f8ff4fbf1d41b0773">
src/jalview/datamodel/ProfilesI.java
</a>
</li>
<li class="file-stats">
<a href="#0c9fce053e3fdd42a4c0c7a9a35a0c1f1c4d1a37">
src/jalview/datamodel/Provenance.java
</a>
</li>
<li class="file-stats">
<a href="#6cc1568cf9a1861acbb930377d414ddc0f5f711f">
src/jalview/datamodel/ProvenanceEntry.java
</a>
</li>
<li class="file-stats">
<a href="#38953ceafb18777b3abef638ad278bc79f05a900">
src/jalview/datamodel/Range.java
</a>
</li>
<li class="file-stats">
<a href="#49a9a6a759ddcdbe96ed15e9a09f6f37d35d2eee">
src/jalview/datamodel/RangeElementsIterator.java
</a>
</li>
<li class="file-stats">
<a href="#61898a924059ad0d459d37920c25106addb0bdb1">
src/jalview/datamodel/RangeIterator.java
</a>
</li>
<li class="file-stats">
<a href="#eddf104757a867ff159d6b56a327bd72237d01fe">
src/jalview/datamodel/ResidueCount.java
</a>
</li>
<li class="file-stats">
<a href="#cd946b3b78724d2d56c218363396bfa66f8c96a8">
src/jalview/datamodel/RnaViewerModel.java
</a>
</li>
<li class="file-stats">
<a href="#e474b11b2d3bf60a19754235e93532ecc2e548fa">
src/jalview/datamodel/SearchResultMatchI.java
</a>
</li>
<li class="file-stats">
<a href="#ca1bfa52a18c4f8038575cf12ca15e71415c95c1">
src/jalview/datamodel/SearchResults.java
</a>
</li>
<li class="file-stats">
<a href="#3f1aa8507f409f70215c7730dcaee17cd3198a09">
src/jalview/datamodel/SearchResultsI.java
</a>
</li>
<li class="file-stats">
<a href="#8dcbed961ce6f13da8c122ebeb6114cb84fbec2c">
src/jalview/datamodel/SecondaryStructureAnnotation.java
</a>
</li>
<li class="file-stats">
<a href="#55ebfbf1806eedbf6740e54b97afdd516c676106">
src/jalview/datamodel/SecondaryStructureCount.java
</a>
</li>
<li class="file-stats">
<a href="#72a352d068e3a8122c8ff50d6637b522f24e53cb">
src/jalview/datamodel/SeqCigar.java
</a>
</li>
<li class="file-stats">
<a href="#868c06a54d17586ff183ad34f2eda393fb84358b">
src/jalview/datamodel/SeqDistanceContactMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#f1f4acbab734a8f7bcb6d1a5d8c9d08d71985292">
src/jalview/datamodel/Sequence.java
</a>
</li>
<li class="file-stats">
<a href="#f6ebbfeefeec8e16b2dc49aaa9f3d6482aeb2ad9">
src/jalview/datamodel/SequenceCollectionI.java
</a>
</li>
<li class="file-stats">
<a href="#a033b922eba74237cf8354301b484be003115ac9">
src/jalview/datamodel/SequenceCursor.java
</a>
</li>
<li class="file-stats">
<a href="#8f868b99b1efec0b50649d0bec518dab44fd56c5">
src/jalview/datamodel/SequenceDummy.java
</a>
</li>
<li class="file-stats">
<a href="#2756dfa41719ff80970142945ac984f43581bc16">
src/jalview/datamodel/SequenceFeature.java
</a>
</li>
<li class="file-stats">
<a href="#ee6d77ad381f0335cd8576124011ce734d64eb85">
src/jalview/datamodel/SequenceGroup.java
</a>
</li>
<li class="file-stats">
<a href="#df619d1f22fadbeab67c68f35b3cccb83ee15ba5">
src/jalview/datamodel/SequenceI.java
</a>
</li>
<li class="file-stats">
<a href="#70eb78c52108e8743cc7ebe655457d07a5402897">
src/jalview/datamodel/SequenceNode.java
</a>
</li>
<li class="file-stats">
<a href="#b4f7a2d3e77ea74abca9621da4f11ee30120f41f">
src/jalview/datamodel/SequencePoint.java
</a>
</li>
<li class="file-stats">
<a href="#33865ad5b4121f813d8a40215b834478a60ea16f">
src/jalview/datamodel/StartRegionIterator.java
</a>
</li>
<li class="file-stats">
<a href="#8ef41433acbecb04241238b147a2bf182a64650a">
src/jalview/datamodel/StructureViewerModel.java
</a>
</li>
<li class="file-stats">
<a href="#b4a10dad1ca5334e1b5a7b7bba654e5e5e3e5635">
src/jalview/datamodel/VisibleColsCollection.java
</a>
</li>
<li class="file-stats">
<a href="#9b655363f6a99e494c0ff171d49935da1d875ec7">
src/jalview/datamodel/VisibleContigsIterator.java
</a>
</li>
<li class="file-stats">
<a href="#6cb56c81baa432469b7669beca8a4f786e5c17f7">
src/jalview/datamodel/VisibleRowsCollection.java
</a>
</li>
<li class="file-stats">
<a href="#3634cca2e301fc919cb3c490bb3c07115a4195aa">
src/jalview/datamodel/VisibleRowsIterator.java
</a>
</li>
<li class="file-stats">
<a href="#78d44c1db8d6bbfb1b6edd6f3968eab32c132260">
src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#50a364ece62cd23b7e7e03eb85105da45af72806">
src/jalview/datamodel/annotations/AnnotationRowBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#078ef88ac83b39482130874fc6cca2dfd17c81de">
src/jalview/datamodel/features/FeatureAttributeType.java
</a>
</li>
<li class="file-stats">
<a href="#32334b14e9f6de22a6a803a9fd28e9cabb5f78b2">
src/jalview/datamodel/features/FeatureAttributes.java
</a>
</li>
<li class="file-stats">
<a href="#b61e0235e5b88e2f1a32be9582614e8b4446f37c">
src/jalview/datamodel/features/FeatureLocationI.java
</a>
</li>
<li class="file-stats">
<a href="#078eac15cc4d7d3c0b6b66611116cb2791dbfe87">
src/jalview/datamodel/features/FeatureMatcher.java
</a>
</li>
<li class="file-stats">
<a href="#5fe42d8468f7668aebabb4f88429b475037a3a68">
src/jalview/datamodel/features/FeatureMatcherI.java
</a>
</li>
<li class="file-stats">
<a href="#60e3f84b6bb486902fffc5ddbb88ac690840e92e">
src/jalview/datamodel/features/FeatureMatcherSet.java
</a>
</li>
<li class="file-stats">
<a href="#0283f6865bcca9787eeb513542796597b4b06ea3">
src/jalview/datamodel/features/FeatureMatcherSetI.java
</a>
</li>
<li class="file-stats">
<a href="#a1f16b033c7d8366e5e139e1a161242eaacddf39">
src/jalview/datamodel/features/FeatureSource.java
</a>
</li>
<li class="file-stats">
<a href="#ab9e2c2ed8aa5feefe1b2ac5bf9abb7544818dac">
src/jalview/datamodel/features/FeatureSourceI.java
</a>
</li>
<li class="file-stats">
<a href="#ae77d384b73cde75844c0060663429ae683346f0">
src/jalview/datamodel/features/FeatureSources.java
</a>
</li>
<li class="file-stats">
<a href="#f875aa965c2faf8ce9613e3c11fa0f8ae55f0237">
src/jalview/datamodel/features/FeatureStore.java
</a>
</li>
<li class="file-stats">
<a href="#0f76fd81f69fac2c88de7e52287359137940641e">
src/jalview/datamodel/features/SequenceFeatures.java
</a>
</li>
<li class="file-stats">
<a href="#53a8bfb92aaf4913a5bf188bcce3d94a1652896d">
src/jalview/datamodel/features/SequenceFeaturesI.java
</a>
</li>
<li class="file-stats">
<a href="#28f2a9accf7772708202294561883169cc8fba7a">
src/jalview/exceptions/JalviewException.java
</a>
</li>
<li class="file-stats">
<a href="#1b1c7e7f331225fac81c41be6042bc1e79c90828">
src/jalview/ext/android/ContainerHelpers.java
</a>
</li>
<li class="file-stats">
<a href="#0b9157c5a8ffb2cd3c67dd03a70d021fed690645">
src/jalview/ext/android/SparseDoubleArray.java
</a>
</li>
<li class="file-stats">
<a href="#cab1470537bafe03f9a738763b5a752493fac4c3">
src/jalview/ext/android/SparseIntArray.java
</a>
</li>
<li class="file-stats">
<a href="#f78ed6c1dc2a8896171b0b11e52c4d27337a9b6a">
src/jalview/ext/android/SparseShortArray.java
</a>
</li>
<li class="file-stats">
<a href="#38036a829e83a5a996c6231e8d7ea49a5f24ec37">
src/jalview/ext/ensembl/EnsemblCdna.java
</a>
</li>
<li class="file-stats">
<a href="#fc3fc0b0def8be9da89d6205be8b1eeaad0fe248">
src/jalview/ext/ensembl/EnsemblCds.java
</a>
</li>
<li class="file-stats">
<a href="#27708e2854600a2713306a07f3165a231ed5b2a7">
src/jalview/ext/ensembl/EnsemblData.java
</a>
</li>
<li class="file-stats">
<a href="#f1b8ff142877e2b76cbee41434032d5ccb97ae72">
src/jalview/ext/ensembl/EnsemblFeatures.java
</a>
</li>
<li class="file-stats">
<a href="#f9b0d1ee0dd2584f264a732e90e3981e0ef4a3d4">
src/jalview/ext/ensembl/EnsemblGene.java
</a>
</li>
<li class="file-stats">
<a href="#6aa1f9dd771376ecc090dbcafa4e306da4c50332">
src/jalview/ext/ensembl/EnsemblGenome.java
</a>
</li>
<li class="file-stats">
<a href="#24e8e0a0b5fd6c6781b2d4b4d44a58ce3462e301">
src/jalview/ext/ensembl/EnsemblGenomes.java
</a>
</li>
<li class="file-stats">
<a href="#d1989b496f87da2896617c5287b2c0a629740f81">
src/jalview/ext/ensembl/EnsemblInfo.java
</a>
</li>
<li class="file-stats">
<a href="#c7e813a6607e71296aca31baec0669daf3cc49cb">
src/jalview/ext/ensembl/EnsemblLookup.java
</a>
</li>
<li class="file-stats">
<a href="#0e71c2e61f59892114d302051d573184250709f6">
src/jalview/ext/ensembl/EnsemblMap.java
</a>
</li>
<li class="file-stats">
<a href="#c3b8f3dc47c5ace0b2680f41ebc3a89ea23c8286">
src/jalview/ext/ensembl/EnsemblProtein.java
</a>
</li>
<li class="file-stats">
<a href="#901180b5bf71338f0031be4853a622ff808928c9">
src/jalview/ext/ensembl/EnsemblRestClient.java
</a>
</li>
<li class="file-stats">
<a href="#848c86b97b7a1153daceeee2b961b41b3ff16907">
src/jalview/ext/ensembl/EnsemblSeqProxy.java
</a>
</li>
<li class="file-stats">
<a href="#81970b8a2d453d4379465a4900051e964034ea31">
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
</a>
</li>
<li class="file-stats">
<a href="#b241e9ea53a047313e7aa2e8012a80187e97b1be">
src/jalview/ext/ensembl/EnsemblSymbol.java
</a>
</li>
<li class="file-stats">
<a href="#ce786376edf3bf0abf5d8468af5a30d40472b424">
src/jalview/ext/ensembl/EnsemblXref.java
</a>
</li>
<li class="file-stats">
<a href="#9866c165c14ed0695be33525404d053d2b9f8216">
src/jalview/ext/ensembl/Species.java
</a>
</li>
<li class="file-stats">
<a href="#a9f5e3aee0f3aaf2b7dddd196cdad7065abf4477">
src/jalview/ext/htsjdk/HtsContigDb.java
</a>
</li>
<li class="file-stats">
<a href="#3f9c58518559e4172d8ccdd31928983e2663e829">
src/jalview/ext/htsjdk/VCFReader.java
</a>
</li>
<li class="file-stats">
<a href="#72abdead7a2126154206c75319b364964ced7420">
src/jalview/ext/jmol/JalviewJmolBinding.java
</a>
</li>
<li class="file-stats">
<a href="#4b8e65c66ec7999287d97fbe9e8fabe77d872f4f">
src/jalview/ext/jmol/JmolCommands.java
</a>
</li>
<li class="file-stats">
<a href="#69b03e3988beaa75190ee4a3ab722823c755f436">
src/jalview/ext/jmol/JmolParser.java
</a>
</li>
<li class="file-stats">
<a href="#1adb9b6943ec1c757fa0da2ef3e582f5c448e81f">
src/jalview/ext/paradise/Annotate3D.java
</a>
</li>
<li class="file-stats">
<a href="#971b7101fd20747d71402fc570d1a69b0d8b4469">
src/jalview/ext/pymol/PymolCommands.java
</a>
</li>
<li class="file-stats">
<a href="#768492d435d5011d1606a0d348037a4c9ed09b02">
src/jalview/ext/pymol/PymolManager.java
</a>
</li>
<li class="file-stats">
<a href="#68ad7ca0b41139b20cb3c3bc687346cd619cf690">
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
</a>
</li>
<li class="file-stats">
<a href="#37e5f112bfcbee294cb35e859aa7de0c6d1c2340">
src/jalview/ext/rbvi/chimera/ChimeraListener.java
</a>
</li>
<li class="file-stats">
<a href="#886282cd358c091d1facc1a90f68814e4c3632a0">
src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
</a>
</li>
<li class="file-stats">
<a href="#5185bc93f2570d5b6968e32aa4ddb18ca0c233e6">
src/jalview/ext/rbvi/chimera/ChimeraXManager.java
</a>
</li>
<li class="file-stats">
<a href="#ea548f3a3cacc37c497a81bc15752622c0193867">
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
</a>
</li>
<li class="file-stats">
<a href="#e097ffd169cdbb665a0c1a82746e94683ee1adc3">
src/jalview/ext/so/SequenceOntology.java
</a>
</li>
<li class="file-stats">
<a href="#23b2242ee8269457a0cf5ef0f1c5fa5e8e89ea18">
src/jalview/ext/varna/JalviewVarnaBinding.java
</a>
</li>
<li class="file-stats">
<a href="#4122a913b770f6c87aa7dbd7feb1cf6061865776">
src/jalview/ext/varna/RnaModel.java
</a>
</li>
<li class="file-stats">
<a href="#2d298a3b2529491f8c4350e3b4acb3a19626a373">
src/jalview/ext/varna/VarnaCommands.java
</a>
</li>
<li class="file-stats">
<a href="#9553cf854b6973eeb32178ddac58bf6add17244d">
src/jalview/fts/api/FTSData.java
</a>
</li>
<li class="file-stats">
<a href="#0d87838d11c1962cb874c390ebb47dad254e9449">
src/jalview/fts/api/FTSDataColumnI.java
</a>
</li>
<li class="file-stats">
<a href="#2d38ba355f8b740f8f1890a02184590413d9b0ca">
src/jalview/fts/api/FTSRestClientI.java
</a>
</li>
<li class="file-stats">
<a href="#fbcf7b621773942ddd6e298c67d42da2b6b8089a">
src/jalview/fts/api/GFTSPanelI.java
</a>
</li>
<li class="file-stats">
<a href="#0f2aa1a1e7add784948c68a932abb24541586079">
src/jalview/fts/api/StructureFTSRestClientI.java
</a>
</li>
<li class="file-stats">
<a href="#b320d466616792f53c1662d7ab0ace4026597205">
src/jalview/fts/core/DecimalFormatTableCellRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#3ab5c46e3249076e2bf9f0d6490294975c551865">
src/jalview/fts/core/FTSDataColumnPreferences.java
</a>
</li>
<li class="file-stats">
<a href="#51a0e283fe9911acdb3442b628855eb0cdabc5d4">
src/jalview/fts/core/FTSRestClient.java
</a>
</li>
<li class="file-stats">
<a href="#3b9441ab69743b607855ea2258529013f55fc19b">
src/jalview/fts/core/FTSRestRequest.java
</a>
</li>
<li class="file-stats">
<a href="#fff998922521ac040f0ab239230a57a18333e6dc">
src/jalview/fts/core/FTSRestResponse.java
</a>
</li>
<li class="file-stats">
<a href="#0c65b5bf0da983a6a47cf682b84cfa67fbe37fff">
src/jalview/fts/core/GFTSPanel.java
</a>
</li>
<li class="file-stats">
<a href="#49d2d31aebccc7f01764d19260a4ba393d7719e7">
src/jalview/fts/service/alphafold/AlphafoldRestClient.java
</a>
</li>
<li class="file-stats">
<a href="#fa83c1ed5d4fdc66b6ccf7284fe7d86c3635c782">
src/jalview/fts/service/pdb/PDBFTSPanel.java
</a>
</li>
<li class="file-stats">
<a href="#aff35a0d979bb027cf8d20fd5a2cc178c588d1fa">
src/jalview/fts/service/pdb/PDBFTSRestClient.java
</a>
</li>
<li class="file-stats">
<a href="#06880bdba6b797c8d7838129a14a508ca4531da5">
src/jalview/fts/service/threedbeacons/TDB_FTSData.java
</a>
</li>
<li class="file-stats">
<a href="#8c8e39c894487c212bca52131886f38c37cfde82">
src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
</a>
</li>
<li class="file-stats">
<a href="#63ec3254554183b0fd4e38141778624e4d08f53d">
src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
</a>
</li>
<li class="file-stats">
<a href="#a5ce91878596f858a7a625e0260e6f2cab436e08">
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
</a>
</li>
<li class="file-stats">
<a href="#3dfe6d360553e78f65457517bbd6bc8a93783da7">
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
</a>
</li>
<li class="file-stats">
<a href="#e99218260dc2790933dfb9c6671a9c7ad31ed89b">
src/jalview/gui/APQHandlers.java
</a>
</li>
<li class="file-stats">
<a href="#ce83e17e97494fc9a2d12be7014811e2d73863c4">
src/jalview/gui/AlignExportOptions.java
</a>
</li>
<li class="file-stats">
<a href="#e6e4f2800076c86fb126064ba96b12a715eff8ba">
src/jalview/gui/AlignFrame.java
</a>
</li>
<li class="file-stats">
<a href="#f4208d748e5f09b36f52e7c7c6b640a1354a0187">
src/jalview/gui/AlignViewport.java
</a>
</li>
<li class="file-stats">
<a href="#6f97762bd188e4bf1285cb053ab236135661a9a3">
src/jalview/gui/AlignmentPanel.java
</a>
</li>
<li class="file-stats">
<a href="#602d65224558e2f26a4a93c750dc1611e65b9d0b">
src/jalview/gui/AnnotationChooser.java
</a>
</li>
<li class="file-stats">
<a href="#a555aef4f422a6185a6d9cb765fb0f6ae86cd1ff">
src/jalview/gui/AnnotationColourChooser.java
</a>
</li>
<li class="file-stats">
<a href="#ab5b9bb806cb333928ecc70698c3185098c19b1c">
src/jalview/gui/AnnotationColumnChooser.java
</a>
</li>
<li class="file-stats">
<a href="#73dc61bdd11ffce0617ef298195ac78677de47b0">
src/jalview/gui/AnnotationExporter.java
</a>
</li>
<li class="file-stats">
<a href="#dca95343a5f6d356cadd29fa70c3f2c5718ccd26">
src/jalview/gui/AnnotationLabels.java
</a>
</li>
<li class="file-stats">
<a href="#257fc811c632262c64e092e2e54eee2f1b81c08a">
src/jalview/gui/AnnotationPanel.java
</a>
</li>
<li class="file-stats">
<a href="#54e35d0dd973a724cad30e47a600b6da11284bc3">
src/jalview/gui/AnnotationRowFilter.java
</a>
</li>
<li class="file-stats">
<a href="#bba86e47b33d8cb184f745a986c8a0bb22b10835">
src/jalview/gui/AppJmol.java
</a>
</li>
<li class="file-stats">
<a href="#e0c6d1ed4e13e4054903ec246482039a58c96418">
src/jalview/gui/AppJmolBinding.java
</a>
</li>
<li class="file-stats">
<a href="#8259c19e5bcc7d3dae642f4b080dd4d4fe00acef">
src/jalview/gui/AppVarna.java
</a>
</li>
<li class="file-stats">
<a href="#1231ad4c210db482692bf41ff0c940dd9026b52b">
src/jalview/gui/AppVarnaBinding.java
</a>
</li>
<li class="file-stats">
<a href="#8029f953d1efc13a4aa628bb05940a8e6fc8fd18">
src/jalview/gui/AssociatePdbFileWithSeq.java
</a>
</li>
<li class="file-stats">
<a href="#adbef46382018535c80ca6c83e9b5c31d9ab2079">
src/jalview/gui/BlogReader.java
</a>
</li>
<li class="file-stats">
<a href="#be8cc8160e86c0616e1d0a97d21cf814fee27bfe">
src/jalview/gui/CalculationChooser.java
</a>
</li>
<li class="file-stats">
<a href="#df7f56ebfd12bbf99bccf29e466c730557c57a6d">
src/jalview/gui/ChimeraViewFrame.java
</a>
</li>
<li class="file-stats">
<a href="#ebaeaa9761fb3e47dcdff680c5a305df30e4e28f">
src/jalview/gui/ChimeraXViewFrame.java
</a>
</li>
<li class="file-stats">
<a href="#75d31485d086d3b8c210c7587794741d0523c88f">
src/jalview/gui/ColourMenuHelper.java
</a>
</li>
<li class="file-stats">
<a href="#1a860df86b1819f653860ec1f80fb983e3e7ff1f">
src/jalview/gui/ComboBoxTooltipRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#b82f926e544ce66a08fd96980a4e83722fed9bd8">
src/jalview/gui/Console.java
</a>
</li>
<li class="file-stats">
<a href="#1c9880514247c5af488fd19dc2f184af7cfd1092">
src/jalview/gui/CrossRefAction.java
</a>
</li>
<li class="file-stats">
<a href="#d9559ba41d3b41be9ef6d30bd61289c27b635a11">
src/jalview/gui/CutAndPasteHtmlTransfer.java
</a>
</li>
<li class="file-stats">
<a href="#f3fefce128af502a7193b8624776f5ddf8f4bdd0">
src/jalview/gui/CutAndPasteTransfer.java
</a>
</li>
<li class="file-stats">
<a href="#8d87249cc8ccf992d4d818b651c7cc866f69f68e">
src/jalview/gui/Desktop.java
</a>
</li>
<li class="file-stats">
<a href="#117f84d3a00359b13331bb9ec9b1abfd7234c00b">
src/jalview/gui/EditNameDialog.java
</a>
</li>
<li class="file-stats">
<a href="#ed0efe68c4233176013e393ededc5810a13de3ea">
src/jalview/gui/FeatureEditor.java
</a>
</li>
<li class="file-stats">
<a href="#8f6a4cd95cc5ec9b431f35205921fd2a32455267">
src/jalview/gui/FeatureRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#2a8ffddd6c3b044faf8aa21d885eea7d80f08b77">
src/jalview/gui/FeatureSettings.java
</a>
</li>
<li class="file-stats">
<a href="#6ad6f09f320bc6a5c12b52741fe4a6cd6f5ebf72">
src/jalview/gui/FeatureTypeSettings.java
</a>
</li>
<li class="file-stats">
<a href="#8335537932fe2d5744381d841c59bd7f81ca08e5">
src/jalview/gui/Finder.java
</a>
</li>
<li class="file-stats">
<a href="#089e034213483ce300d34c9e6f60dc0c7f6b0fa5">
src/jalview/gui/FontChooser.java
</a>
</li>
<li class="file-stats">
<a href="#3b9d979f46494d444ce4f707ef5b098bd286e9a2">
src/jalview/gui/Help.java
</a>
</li>
<li class="file-stats">
<a href="#00b403c42753c137fdc7d388205c14b440fe0f6d">
src/jalview/gui/IProgressIndicator.java
</a>
</li>
<li class="file-stats">
<a href="#d8bc9707c5bff651bacb51fb0e24a154f7c27855">
src/jalview/gui/IProgressIndicatorHandler.java
</a>
</li>
<li class="file-stats">
<a href="#92b01fa5fb50e0bcbbe7f66886240a04aed8bcff">
src/jalview/gui/IdCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#0084a96d9003cdb377be43c18ccd5b94fc03280e">
src/jalview/gui/IdPanel.java
</a>
</li>
<li class="file-stats">
<a href="#9d2b1f0c7ed142078f93bf8a65cd8c0acc5b882c">
src/jalview/gui/IdwidthAdjuster.java
</a>
</li>
<li class="file-stats">
<a href="#131bc791b2cebf3505f7a978449edb85a7b11f2b">
src/jalview/gui/ImageExporter.java
</a>
</li>
<li class="file-stats">
<a href="#4a5863235fc4d5db1aa9eece0f07ae4e2e34f8f5">
src/jalview/gui/JDatabaseTree.java
</a>
</li>
<li class="file-stats">
<a href="#93c73d0892798018bc41fb25ecf1d910c14ac670">
src/jalview/gui/JalviewBooleanRadioButtons.java
</a>
</li>
<li class="file-stats">
<a href="#fe6c51e781f8d12e7572ee4a73805a3f7705379a">
src/jalview/gui/JalviewChangeSupport.java
</a>
</li>
<li class="file-stats">
<a href="#887717c7cda311b73d26ca83b64f2f703403b5af">
src/jalview/gui/JalviewChimeraBindingModel.java
</a>
</li>
<li class="file-stats">
<a href="#60b308e4439d103e716c8979293839bd347c2e97">
src/jalview/gui/JalviewChimeraXBindingModel.java
</a>
</li>
<li class="file-stats">
<a href="#e797dd994cd8b0c0b884e5a3718f5d990982ac8b">
src/jalview/gui/JalviewColourChooser.java
</a>
</li>
<li class="file-stats">
<a href="#7b0529a31e651cc3b7473294f0c692f31d8be421">
src/jalview/gui/JalviewDialog.java
</a>
</li>
<li class="file-stats">
<a href="#7ef886b6b669914f529102c9af2aed69dfa84a7e">
src/jalview/gui/JvOptionPane.java
</a>
</li>
<li class="file-stats">
<a href="#af3efbee1f5d2e833bcee83751deca36b4f772d8">
src/jalview/gui/JvSwingUtils.java
</a>
</li>
<li class="file-stats">
<a href="#29167f532c9623afa749634297b1b75cdd5fe686">
src/jalview/gui/LineartOptions.java
</a>
</li>
<li class="file-stats">
<a href="#64c2af415917d8271df65ed2f7a716c8a020e07f">
src/jalview/gui/MenuChooser.java
</a>
</li>
<li class="file-stats">
<a href="#4799279541707c284bf97c5d965fa7505cce30bc">
src/jalview/gui/OOMWarning.java
</a>
</li>
<li class="file-stats">
<a href="#1812df9f93f86a50775680d83263b307cbaed43f">
src/jalview/gui/OptsAndParamsPage.java
</a>
</li>
<li class="file-stats">
<a href="#ae721b1c3e4e97968a027ce7631aff59d4e69755">
src/jalview/gui/OptsParametersContainerI.java
</a>
</li>
<li class="file-stats">
<a href="#aba45e786d1ea2ffa691ca63529b0e7293bb070d">
src/jalview/gui/OverviewCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#626156b72dbf25ba24f4e8ff2d839c676f78cab9">
src/jalview/gui/OverviewPanel.java
</a>
</li>
<li class="file-stats">
<a href="#a3fd3b7c571bca5b8b191710d3ae7045b693b218">
src/jalview/gui/PCAPanel.java
</a>
</li>
<li class="file-stats">
<a href="#54c67657f65a1c9ad87a4dcd2649738ccf424e1f">
src/jalview/gui/PaSiMapPanel.java
</a>
</li>
<li class="file-stats">
<a href="#8c16641d62dd3d99ebe75a509a4551add5271d3f">
src/jalview/gui/PaintRefresher.java
</a>
</li>
<li class="file-stats">
<a href="#b3f6b2a8ce6daec624d54346e39cbdb1e82e5589">
src/jalview/gui/PairwiseAlignPanel.java
</a>
</li>
<li class="file-stats">
<a href="#4005f127c4e2ff346fc0c88702fc5c7081c1160c">
src/jalview/gui/PopupMenu.java
</a>
</li>
<li class="file-stats">
<a href="#0c21d07a52cf8aef88366906de9f1891411eb4ff">
src/jalview/gui/Preferences.java
</a>
</li>
<li class="file-stats">
<a href="#151388485f75bbbbbd08bb8888c68e3f5233e7a2">
src/jalview/gui/ProgressBar.java
</a>
</li>
<li class="file-stats">
<a href="#c2fa9d6f5000b69834599f3d797bde8344f69d89">
src/jalview/gui/ProgressPanel.java
</a>
</li>
<li class="file-stats">
<a href="#9a0446840c9b2614f9f13e6b4548c8dbc9e170f0">
src/jalview/gui/PromptUserConfig.java
</a>
</li>
<li class="file-stats">
<a href="#7e52f1e6e1fbb5b1448e4480415c8afd8a3ab26e">
src/jalview/gui/PymolBindingModel.java
</a>
</li>
<li class="file-stats">
<a href="#17b77d91e7cdf9f54ebb08da0cfa837fcabf4c2c">
src/jalview/gui/PymolViewer.java
</a>
</li>
<li class="file-stats">
<a href="#67d6614e98bbb3120bfe6878a062363ae85c1f32">
src/jalview/gui/QuitHandler.java
</a>
</li>
<li class="file-stats">
<a href="#75ee872255b9cfc1bae159312997f968355c52c3">
src/jalview/gui/RedundancyPanel.java
</a>
</li>
<li class="file-stats">
<a href="#7f2399edaf90e53a079a6f024102749621e14f93">
src/jalview/gui/RestInputParamEditDialog.java
</a>
</li>
<li class="file-stats">
<a href="#9e90e187feed7bbc2cc514ad5dfa6b5a9f6c6aa6">
src/jalview/gui/RestServiceEditorPane.java
</a>
</li>
<li class="file-stats">
<a href="#c46153d60234a83c2ede3ef420aa82927b0e5277">
src/jalview/gui/RotatableCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#4c3d58de7b98ff2c23aaf8303268334484b20f63">
src/jalview/gui/ScalePanel.java
</a>
</li>
<li class="file-stats">
<a href="#9f74abc25d1b9c2072968ca1d86a4e5e6f3b7e8e">
src/jalview/gui/SeqCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#83457d071ace610469ff8fbd15ad6829892c61f1">
src/jalview/gui/SeqPanel.java
</a>
</li>
<li class="file-stats">
<a href="#664ec07f02cf8004a44ad47de7cc3d02ee772255">
src/jalview/gui/SequenceFetcher.java
</a>
</li>
<li class="file-stats">
<a href="#3a89117d2777d5456c5a603fa1c9d29fe9033fe3">
src/jalview/gui/SequenceRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#0b7579f5e8b4bd9a7e972df42e95049d8f4cae8e">
src/jalview/gui/Slider.java
</a>
</li>
<li class="file-stats">
<a href="#e57a5ee43ccd04977463b7bcc1da6a1c9d36c968">
src/jalview/gui/SliderPanel.java
</a>
</li>
<li class="file-stats">
<a href="#dad294ea1ee9799ec29e881b0232b3a0d1c7c86d">
src/jalview/gui/SplashScreen.java
</a>
</li>
<li class="file-stats">
<a href="#277a78a1606448454d8ace88683bf0f16cd5513d">
src/jalview/gui/SplitFrame.java
</a>
</li>
<li class="file-stats">
<a href="#5a8d8961db066deecbaee267b5d982329698c0c6">
src/jalview/gui/StructureChooser.java
</a>
</li>
<li class="file-stats">
<a href="#f3f7c479760b5e78fa2811dbe8b5c826a5012237">
src/jalview/gui/StructureViewer.java
</a>
</li>
<li class="file-stats">
<a href="#7b3a76ef5278ee3ca2b34553ec0d8d8969398b65">
src/jalview/gui/StructureViewerBase.java
</a>
</li>
<li class="file-stats">
<a href="#f67ee73b8c109051a71ccc17bf706b1b2891167a">
src/jalview/gui/TextColourChooser.java
</a>
</li>
<li class="file-stats">
<a href="#434ed88356083dd8b80cd54542745aceb64b4782">
src/jalview/gui/TreeCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#205ae64b43527e5e077ede627723e0ac3eed6e75">
src/jalview/gui/TreePanel.java
</a>
</li>
<li class="file-stats">
<a href="#3dd7b980edc9ad3b1bdda6a18778c35b874ed6a3">
src/jalview/gui/UserDefinedColours.java
</a>
</li>
<li class="file-stats">
<a href="#f909d013fc413436297bb048098968d4b3d0b471">
src/jalview/gui/UserQuestionnaireCheck.java
</a>
</li>
<li class="file-stats">
<a href="#300631b673c205d7ab53aec5f39ba47d5d0ef5ab">
src/jalview/gui/VamsasApplication.java
</a>
</li>
<li class="file-stats">
<a href="#50b16fd83f8b7f00ed26dd65d96664e45ddd2d5b">
src/jalview/gui/ViewSelectionMenu.java
</a>
</li>
<li class="file-stats">
<a href="#dbfa0444242701b0a5212936fc642a0e3b7a8173">
src/jalview/gui/WebserviceInfo.java
</a>
</li>
<li class="file-stats">
<a href="#cadb085b203c8cb3e7f7ef5da3080463d9248dbf">
src/jalview/gui/WsJobParameters.java
</a>
</li>
<li class="file-stats">
<a href="#ade26df0955504a2b6eea5c6e2a4032640e4a95e">
src/jalview/gui/WsParamSetManager.java
</a>
</li>
<li class="file-stats">
<a href="#d3723ba977b9926a7515b95cb8df0c1ce4841838">
src/jalview/gui/WsPreferences.java
</a>
</li>
<li class="file-stats">
<a href="#53d60284af59f3fb18f921b69e808bf548a7a6f9">
src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
</a>
</li>
<li class="file-stats">
<a href="#f9209f22d41a662b958c9ccc1293535ca5a4f1ca">
src/jalview/gui/structurechooser/StructureChooserQuerySource.java
</a>
</li>
<li class="file-stats">
<a href="#b86b2fdfd44418bae0a185224d32cdbcf9d4140d">
src/jalview/gui/structurechooser/TDBResultAnalyser.java
</a>
</li>
<li class="file-stats">
<a href="#f749c65054612671c61412b5e2eeba2189379848">
src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
</a>
</li>
<li class="file-stats">
<a href="#6e15b5f46a1ce83b5982f52e55a1a99401541aea">
src/jalview/httpserver/AbstractRequestHandler.java
</a>
</li>
<li class="file-stats">
<a href="#c7679010f1a80b985b0b2be23f063ff74737da23">
src/jalview/httpserver/HttpServer.java
</a>
</li>
<li class="file-stats">
<a href="#69a9abb4caf703b0ba1e7d6837c6695ed7cb5790">
src/jalview/io/AMSAFile.java
</a>
</li>
<li class="file-stats">
<a href="#56091bf903f5712c312dd85a8a19c70f5d8cd78c">
src/jalview/io/AlignFile.java
</a>
</li>
<li class="file-stats">
<a href="#834d569ff6ccbb73a4bd4f9995c1eaf775a6d042">
src/jalview/io/AlignmentFileReaderI.java
</a>
</li>
<li class="file-stats">
<a href="#a16fdfeeff9da72cda155ea2e883699c296c0870">
src/jalview/io/AlignmentFileWriterI.java
</a>
</li>
<li class="file-stats">
<a href="#30d9b4644f5d61fe0b057773c945d030536d8a1e">
src/jalview/io/AlignmentProperties.java
</a>
</li>
<li class="file-stats">
<a href="#2cde94b622284e5523ab83e6e67b6c6583c582e6">
src/jalview/io/AnnotationFile.java
</a>
</li>
<li class="file-stats">
<a href="#df4ebb1eed0fa432b2044b6fe3d7dc62fb6e6d72">
src/jalview/io/AppletFormatAdapter.java
</a>
</li>
<li class="file-stats">
<a href="#70ef7eb96cd3827bbc200b39f7a798e23579eba3">
src/jalview/io/BLCFile.java
</a>
</li>
<li class="file-stats">
<a href="#382ab9677102a9ef79fc4c28fe277177ae5aab9b">
src/jalview/io/BackupFilenameFilter.java
</a>
</li>
<li class="file-stats">
<a href="#c5418901d0d44b96d60fa69e948e0631c45012ae">
src/jalview/io/BackupFilenameParts.java
</a>
</li>
<li class="file-stats">
<a href="#58d5d913ad78478ca67c3d483ab90f9a5fa827d2">
src/jalview/io/BackupFiles.java
</a>
</li>
<li class="file-stats">
<a href="#95bec1be35df083a3e5cf1599e9cb772fe3d966f">
src/jalview/io/BackupFilesPresetEntry.java
</a>
</li>
<li class="file-stats">
<a href="#d8bfd257609ef7e47d25790343d1660468a45d4d">
src/jalview/io/BioJsHTMLOutput.java
</a>
</li>
<li class="file-stats">
<a href="#9b100e0ee7136b121deaa8981dc1f34142dcdf13">
src/jalview/io/ClustalFile.java
</a>
</li>
<li class="file-stats">
<a href="#8c113d7afc79bf10fe0cb26ea8d28ce82a2c94d4">
src/jalview/io/DBRefFile.java
</a>
</li>
<li class="file-stats">
<a href="#f4599d01971dd59b95a3266b91a361edbbc321e9">
src/jalview/io/DataSourceType.java
</a>
</li>
<li class="file-stats">
<a href="#587b3ef729e1a4577827e264f5d5373c62721d41">
src/jalview/io/EMBLLikeFlatFile.java
</a>
</li>
<li class="file-stats">
<a href="#d24096fd92e4d609548e32cca5ac3e6c0fd5a4eb">
src/jalview/io/EmblFlatFile.java
</a>
</li>
<li class="file-stats">
<a href="#641d17738010dd1e5c6f37406e20238b0c6dd145">
src/jalview/io/FastaFile.java
</a>
</li>
<li class="file-stats">
<a href="#3d9c391de91928a49d2d86abadf56199df8e3615">
src/jalview/io/FeaturesFile.java
</a>
</li>
<li class="file-stats">
<a href="#ea7bedce52d10f0a78bc65dd1be6be74ee3915f6">
src/jalview/io/FileFormat.java
</a>
</li>
<li class="file-stats">
<a href="#27e74c16f689503c26da3c0eb470008b9cbc0cac">
src/jalview/io/FileFormatException.java
</a>
</li>
<li class="file-stats">
<a href="#ae9715f099a26afa4f5a1b36006f6324e7a67730">
src/jalview/io/FileFormatI.java
</a>
</li>
<li class="file-stats">
<a href="#ca0bb88764fc11df21edfa96622534011f00da4e">
src/jalview/io/FileFormats.java
</a>
</li>
<li class="file-stats">
<a href="#3181d034c0d71a3fb7579b4c46233c32fd8c8122">
src/jalview/io/FileLoader.java
</a>
</li>
<li class="file-stats">
<a href="#9422c684ced4b150712bee1d4aeccefaf65a582e">
src/jalview/io/FileParse.java
</a>
</li>
<li class="file-stats">
<a href="#dfdb1d1ec9cd4734bd801cc88283c681109a82e7">
src/jalview/io/FormatAdapter.java
</a>
</li>
<li class="file-stats">
<a href="#884b5f2ae29dcc44ec7f0fb20774964a0f6cf65d">
src/jalview/io/GenBankFile.java
</a>
</li>
<li class="file-stats">
<a href="#1b70674d2e231b7043973cdc48864ecd1b591dac">
src/jalview/io/HTMLOutput.java
</a>
</li>
<li class="file-stats">
<a href="#49e056d0067b92252520cc8f6c31282be7abf21a">
src/jalview/io/HtmlFile.java
</a>
</li>
<li class="file-stats">
<a href="#c4da5fd63b088cc07c7abb91e41127432ad2cc56">
src/jalview/io/HtmlSvgOutput.java
</a>
</li>
<li class="file-stats">
<a href="#844c5c3279ecd07ad3655ccd35e0ce269498dd05">
src/jalview/io/IdentifyFile.java
</a>
</li>
<li class="file-stats">
<a href="#ebcbcac3be431f10b414f4c361f35bdfbf5a608a">
src/jalview/io/InputStreamParser.java
</a>
</li>
<li class="file-stats">
<a href="#bda2c2240a3c62e929f4ec949b02233b7cc31ceb">
src/jalview/io/IntKeyStringValueEntry.java
</a>
</li>
<li class="file-stats">
<a href="#2222397f7855f6b8076b5b12635e908ef325cdce">
src/jalview/io/JPredFile.java
</a>
</li>
<li class="file-stats">
<a href="#fc1a2cf6b5520187457a67d56c1a247bad67c926">
src/jalview/io/JSONFile.java
</a>
</li>
<li class="file-stats">
<a href="#9696f92f723bbdb51c1cdcd5e3309242c18b1ddb">
src/jalview/io/JalviewFileChooser.java
</a>
</li>
<li class="file-stats">
<a href="#b4250fc16af941699e216c0b40d08dc5027ad492">
src/jalview/io/JalviewFileFilter.java
</a>
</li>
<li class="file-stats">
<a href="#1859ccfd2c23bde492d747a4b1b6a2cfbdf706e2">
src/jalview/io/JalviewFileView.java
</a>
</li>
<li class="file-stats">
<a href="#5a942ecc3f3fc0972d45e8494ad90dddf591785a">
src/jalview/io/JnetAnnotationMaker.java
</a>
</li>
<li class="file-stats">
<a href="#2186574338b7378566d7a3969cd6149f8a9f80ef">
src/jalview/io/MSFfile.java
</a>
</li>
<li class="file-stats">
<a href="#fdf0f335a0d936924cb34be245317f5956581731">
src/jalview/io/ModellerDescription.java
</a>
</li>
<li class="file-stats">
<a href="#4a7603529131cb77f0db925d64718e01f802bf74">
src/jalview/io/NewickFile.java
</a>
</li>
<li class="file-stats">
<a href="#ee633cec1493a71729ad8fd0b6dfba2fa36574d2">
src/jalview/io/PContactPredictionFile.java
</a>
</li>
<li class="file-stats">
<a href="#93995695194d99b71fbc122ad2aa1e27b30b62f9">
src/jalview/io/PDBFeatureSettings.java
</a>
</li>
<li class="file-stats">
<a href="#8b5d2755e25e850df086fb7c218c0b581909e2e4">
src/jalview/io/PIRFile.java
</a>
</li>
<li class="file-stats">
<a href="#9e42012f5b0572b9f804a5713e84f007e2519444">
src/jalview/io/PfamFile.java
</a>
</li>
<li class="file-stats">
<a href="#c523e8ab733d168d08780ebfc31dbcbe88109c4a">
src/jalview/io/PhylipFile.java
</a>
</li>
<li class="file-stats">
<a href="#ad9b54c516d73550847eb0ec7919b9f6ff62a2b8">
src/jalview/io/PileUpfile.java
</a>
</li>
<li class="file-stats">
<a href="#4d3344f5c3481cc66a203256b69a407dd132811e">
src/jalview/io/RnamlFile.java
</a>
</li>
<li class="file-stats">
<a href="#721b22a6091d44194ddee6d52b1fa594897976f9">
src/jalview/io/ScoreMatrixFile.java
</a>
</li>
<li class="file-stats">
<a href="#205a307b19dca03141338d4a30c49d5be8be1bc2">
src/jalview/io/SequenceAnnotationReport.java
</a>
</li>
<li class="file-stats">
<a href="#b7530f75d8a84a4aca84a3bff71a94eedb73fff3">
src/jalview/io/SimpleBlastFile.java
</a>
</li>
<li class="file-stats">
<a href="#65cd97172b903cdab19f964be818877d06a12a6d">
src/jalview/io/StockholmFile.java
</a>
</li>
<li class="file-stats">
<a href="#178ecb0b4d55f9384c5c942d80d729556c843869">
src/jalview/io/StructureFile.java
</a>
</li>
<li class="file-stats">
<a href="#d6507458717750735260ac7f5f95e497d29cc217">
src/jalview/io/TCoffeeScoreFile.java
</a>
</li>
<li class="file-stats">
<a href="#d2958dad3b5c1c04e73d22c3bef34162b2636c96">
src/jalview/io/VamsasAppDatastore.java
</a>
</li>
<li class="file-stats">
<a href="#333b05186999e884462bb0b40607fbf4aca944b9">
src/jalview/io/WSWUBlastClient.java
</a>
</li>
<li class="file-stats">
<a href="#00b090138aa967824c5949697150ea793cc19e38">
src/jalview/io/cache/AppCache.java
</a>
</li>
<li class="file-stats">
<a href="#b1398cb006c23b791d951ae88d70ac6d6fe60202">
src/jalview/io/cache/JvCacheableInputBox.java
</a>
</li>
<li class="file-stats">
<a href="#e16f344a62d28401ff40d3c05675edac34a025b0">
src/jalview/io/exceptions/ImageOutputException.java
</a>
</li>
<li class="file-stats">
<a href="#2a1732c255d6e33e48e897e4e08c62a9569a4df0">
src/jalview/io/gff/ExonerateHelper.java
</a>
</li>
<li class="file-stats">
<a href="#5d4578a76da985b4ce39b1768a161ec2f4101caf">
src/jalview/io/gff/Gff2Helper.java
</a>
</li>
<li class="file-stats">
<a href="#3aa2daf2f6c5051b42a2d05ff10ae63e5d67044b">
src/jalview/io/gff/Gff3Helper.java
</a>
</li>
<li class="file-stats">
<a href="#42ad8bd10743076281039641905a010f7538159c">
src/jalview/io/gff/GffConstants.java
</a>
</li>
<li class="file-stats">
<a href="#698b087d2c5f9dd6e37f2f54811360bf5a823a63">
src/jalview/io/gff/GffHelperBase.java
</a>
</li>
<li class="file-stats">
<a href="#8c1d621480a445e329926dd43efbe7aa3a2de052">
src/jalview/io/gff/GffHelperFactory.java
</a>
</li>
<li class="file-stats">
<a href="#32dac64c3023b9c9a573c3f1712495980ded5272">
src/jalview/io/gff/GffHelperI.java
</a>
</li>
<li class="file-stats">
<a href="#0d50b5d94da6f5b6c640e89a1854894190c9fe62">
src/jalview/io/gff/InterProScanHelper.java
</a>
</li>
<li class="file-stats">
<a href="#14b6638a75cc219912144d642f362b33dde53f1e">
src/jalview/io/gff/SequenceOntologyFactory.java
</a>
</li>
<li class="file-stats">
<a href="#37afce4ba571005bd331e98d6894b64164274e90">
src/jalview/io/gff/SequenceOntologyI.java
</a>
</li>
<li class="file-stats">
<a href="#f4e3b254e6be7119dd21956013387ed14b296e7b">
src/jalview/io/gff/SequenceOntologyLite.java
</a>
</li>
<li class="file-stats">
<a href="#a83527f592e2012370d79ca5138c3fd8f6a996fd">
src/jalview/io/packed/DataProvider.java
</a>
</li>
<li class="file-stats">
<a href="#2057c2b4adfc8c16a517452cb5fd3f55083c04b1">
src/jalview/io/packed/JalviewDataset.java
</a>
</li>
<li class="file-stats">
<a href="#7ae1b70ae77c0afd6b06d9cd9edbb9b5a8f6396b">
src/jalview/io/packed/ParsePackedSet.java
</a>
</li>
<li class="file-stats">
<a href="#375e242cc1c858cd07ed9bc1de6a7851424a280b">
src/jalview/io/packed/SimpleDataProvider.java
</a>
</li>
<li class="file-stats">
<a href="#fc0c3265e81ddc57ba6bb6210451eb806f224ffd">
src/jalview/io/vamsas/Datasetsequence.java
</a>
</li>
<li class="file-stats">
<a href="#7049465596f101b367365d1ec481f5398b18fa44">
src/jalview/io/vamsas/DatastoreItem.java
</a>
</li>
<li class="file-stats">
<a href="#293ddcaa92220aa65654ee4409f698a63cee2933">
src/jalview/io/vamsas/DatastoreRegistry.java
</a>
</li>
<li class="file-stats">
<a href="#739a7ffe5f9dbde7134dc01ca4ffb7688711fb09">
src/jalview/io/vamsas/Dbref.java
</a>
</li>
<li class="file-stats">
<a href="#b577edceb2a749ee1a81c21976cc1db9374c1954">
src/jalview/io/vamsas/LocalDocSyncObject.java
</a>
</li>
<li class="file-stats">
<a href="#114802336b36d7c6c2f239a352e327fb52e4a8ce">
src/jalview/io/vamsas/Rangetype.java
</a>
</li>
<li class="file-stats">
<a href="#48d3f2b3038efe1986dee480b347be8ff91b1e9e">
src/jalview/io/vamsas/Sequencefeature.java
</a>
</li>
<li class="file-stats">
<a href="#894e378a69d8ce424843b180f5d2f6c9091100b4">
src/jalview/io/vamsas/Sequencemapping.java
</a>
</li>
<li class="file-stats">
<a href="#1ebebaa3ae53b5435b9348c8c4fc290afd02c055">
src/jalview/io/vamsas/Tree.java
</a>
</li>
<li class="file-stats">
<a href="#a2955052b9661c5bb98d97bf553372ebf1bef10a">
src/jalview/io/vcf/VCFLoader.java
</a>
</li>
<li class="file-stats">
<a href="#d633400dffeed4b01d07a31352cd52b4e8a7f484">
src/jalview/javascript/JSFunctionExec.java
</a>
</li>
<li class="file-stats">
<a href="#fb3d92e2b2aceb7687272bc5bb4ec0f27017c739">
src/jalview/javascript/JalviewLiteJsApi.java
</a>
</li>
<li class="file-stats">
<a href="#a2f64ef82729a17066634b641bf01b366e394f14">
src/jalview/javascript/JsCallBack.java
</a>
</li>
<li class="file-stats">
<a href="#610f00c36977e6f8755c4f4dae5c0526de2b6122">
src/jalview/javascript/JsSelectionSender.java
</a>
</li>
<li class="file-stats">
<a href="#077dd9af8dcc11d8bd5a2eaa02d68463827e6014">
src/jalview/javascript/MouseOverListener.java
</a>
</li>
<li class="file-stats">
<a href="#13f37b9776db660d3f430d0f67c2c437a8748024">
src/jalview/javascript/MouseOverStructureListener.java
</a>
</li>
<li class="file-stats">
<a href="#e7730660744d1eff1cb53c875e66fe3b9a7486cd">
src/jalview/javascript/json/JSON.java
</a>
</li>
<li class="file-stats">
<a href="#747ddf1c616f5cd96f66b55e3375849981d37b63">
src/jalview/javascript/web/Client.java
</a>
</li>
<li class="file-stats">
<a href="#2f2f71cf8507b13ccfbb5b8166e6c70de60ee377">
src/jalview/javascript/web/ClientResponse.java
</a>
</li>
<li class="file-stats">
<a href="#7d787f3f485213bad782cb9ba41a8616eff5a944">
src/jalview/javascript/web/WebResource.java
</a>
</li>
<li class="file-stats">
<a href="#47080afd16cfd8c81ede059ca6eba1b465aaff60">
src/jalview/jbgui/FilterOption.java
</a>
</li>
<li class="file-stats">
<a href="#172533a4e0ef5396914c9eb1113e84600270ec92">
src/jalview/jbgui/GAlignFrame.java
</a>
</li>
<li class="file-stats">
<a href="#159fee133d65b0f776ec26cc3f34b547a41c66a6">
src/jalview/jbgui/GAlignmentPanel.java
</a>
</li>
<li class="file-stats">
<a href="#067f6e36de578dbb31790b0a41c8cd0162138ab3">
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
</a>
</li>
<li class="file-stats">
<a href="#49afd0bfcd681e8af250ffb124271965cd59feb5">
src/jalview/jbgui/GCutAndPasteTransfer.java
</a>
</li>
<li class="file-stats">
<a href="#ef64c35b49e2035c6f4e14a2536b73367d7601cf">
src/jalview/jbgui/GDesktop.java
</a>
</li>
<li class="file-stats">
<a href="#7a8edb085ac49309c15186e52645a2ae1842ed49">
src/jalview/jbgui/GFinder.java
</a>
</li>
<li class="file-stats">
<a href="#9cc4c2bd3ef576433a2a0325e7be3d7354ceeb2f">
src/jalview/jbgui/GFontChooser.java
</a>
</li>
<li class="file-stats">
<a href="#da17dc8b96b8ae6ed5a43f1eb8dbc77a29e9e663">
src/jalview/jbgui/GPCAPanel.java
</a>
</li>
<li class="file-stats">
<a href="#ffb05822ed4500d1b671c578e1874a169de3ca78">
src/jalview/jbgui/GPaSiMapPanel.java
</a>
</li>
<li class="file-stats">
<a href="#9df4acbddc7c8e20fb5b6a174f5a24fea7333808">
src/jalview/jbgui/GPairwiseAlignPanel.java
</a>
</li>
<li class="file-stats">
<a href="#785bc3ae69b381ba78de57aec44159840b334ac3">
src/jalview/jbgui/GPreferences.java
</a>
</li>
<li class="file-stats">
<a href="#68787e72e74f54f0a298c7157d79c7df29c0a70a">
src/jalview/jbgui/GRestInputParamEditDialog.java
</a>
</li>
<li class="file-stats">
<a href="#562ccdfbf393a1ade203c9c6cdd27fffe9054164">
src/jalview/jbgui/GRestServiceEditorPane.java
</a>
</li>
<li class="file-stats">
<a href="#8c8aedb6646125766c84aacbd5e8168f33b417bb">
src/jalview/jbgui/GRnaStructureViewer.java
</a>
</li>
<li class="file-stats">
<a href="#348b961f85fa617416612104c38aeac06995bd51">
src/jalview/jbgui/GSequenceLink.java
</a>
</li>
<li class="file-stats">
<a href="#9f2923b119bf78c852c7de514460798707924261">
src/jalview/jbgui/GSliderPanel.java
</a>
</li>
<li class="file-stats">
<a href="#56dbb17bf6b322f9ecdf64d8671a2703d5c461df">
src/jalview/jbgui/GSplitFrame.java
</a>
</li>
<li class="file-stats">
<a href="#0bd151ca349d1043b62dda323279ab00faf7e8ae">
src/jalview/jbgui/GStructureChooser.java
</a>
</li>
<li class="file-stats">
<a href="#b108b4fa737dc42cf05854e88768f33783ce5c13">
src/jalview/jbgui/GStructureViewer.java
</a>
</li>
<li class="file-stats">
<a href="#25340f9854cba52024c7ceb61613119e48fa93a6">
src/jalview/jbgui/GTreePanel.java
</a>
</li>
<li class="file-stats">
<a href="#c1f356b663cfb60813923a7bdf1802f21cb4cc34">
src/jalview/jbgui/GUserDefinedColours.java
</a>
</li>
<li class="file-stats">
<a href="#8b6301915993be33d5d79c278f911b13e12f1a93">
src/jalview/jbgui/GWebserviceInfo.java
</a>
</li>
<li class="file-stats">
<a href="#766b1f33f042f433aeb733dee0abeb579115bc0d">
src/jalview/jbgui/GWsPreferences.java
</a>
</li>
<li class="file-stats">
<a href="#81574af42c88cf521cb48381d5ccbb7b34f0d1bb">
src/jalview/json/binding/biojs/BioJSReleasePojo.java
</a>
</li>
<li class="file-stats">
<a href="#1a0003ae757c0bbc4e8dfc81a74cff024a68958b">
src/jalview/json/binding/biojs/BioJSRepositoryPojo.java
</a>
</li>
<li class="file-stats">
<a href="#9ab080cdb559ec34f1f3cf3b7f769120c0d20a41">
src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
</a>
</li>
<li class="file-stats">
<a href="#d8848471884845cf69af7d11b9fa33aea485542f">
src/jalview/json/binding/biojson/v1/AlignmentPojo.java
</a>
</li>
<li class="file-stats">
<a href="#e9a791f26439271ec41b01ea938464ddb4200ca8">
src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java
</a>
</li>
<li class="file-stats">
<a href="#b0814150d2805cff6cc86e5b3cb92a6e5430d815">
src/jalview/json/binding/biojson/v1/AnnotationPojo.java
</a>
</li>
<li class="file-stats">
<a href="#89b5c357545ffa1a192392f7a750b7e96436ad0d">
src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
</a>
</li>
<li class="file-stats">
<a href="#44b4bccf0d5e0e0bf54fc9017ee4e5fc1557db33">
src/jalview/json/binding/biojson/v1/SequenceFeaturesPojo.java
</a>
</li>
<li class="file-stats">
<a href="#0164cd1a1ff0b61876f73cfbdf127ec46b078604">
src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
</a>
</li>
<li class="file-stats">
<a href="#ad7d983f8b9b3d16245d0b409bacf48e818a4d6d">
src/jalview/json/binding/biojson/v1/SequencePojo.java
</a>
</li>
<li class="file-stats">
<a href="#a0c58296697e49bb1e136fc91a540c80ceb3fe40">
src/jalview/log/JLogger.java
</a>
</li>
<li class="file-stats">
<a href="#497c83db04cbcb2fdc814e3e86a0015c01ae20a7">
src/jalview/log/JLoggerI.java
</a>
</li>
<li class="file-stats">
<a href="#c5f1e32249f9b2cb41c6ed834c5bf99f385310fa">
src/jalview/log/JLoggerLog4j.java
</a>
</li>
<li class="file-stats">
<a href="#fe0fb181cd4ab5256ef6af76aa76114f524ecada">
src/jalview/log/JalviewAppender.java
</a>
</li>
<li class="file-stats">
<a href="#f97c63243b07d814be4e314c789648334f30e25b">
src/jalview/math/AlignmentDimension.java
</a>
</li>
<li class="file-stats">
<a href="#4f6f8aff4f090c74780372e9935c9804c39a62fe">
src/jalview/math/Matrix.java
</a>
</li>
<li class="file-stats">
<a href="#3229e42f51b19cd5bad0b66b47da0c0c269f1b40">
src/jalview/math/MatrixI.java
</a>
</li>
<li class="file-stats">
<a href="#6131c387805c8ed3c35e58277c0ed3f809d3f5cb">
src/jalview/math/MiscMath.java
</a>
</li>
<li class="file-stats">
<a href="#a7631b80c6416bbfac5c22061861c8c910dac3c2">
src/jalview/math/RotatableMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#d7ac998a8747e09f345fe22f7c2899fa241d95bb">
src/jalview/math/SameLengthException.java
</a>
</li>
<li class="file-stats">
<a href="#04b71c3c74d1a83f03b4db582d9cbe12452ef04a">
src/jalview/math/SparseMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#fc77a6068956e926c6a32ac3a3961a02a324f1d9">
src/jalview/project/Jalview2XML.java
</a>
</li>
<li class="file-stats">
<a href="#1247751133939984692ffaa438b4d33e3871e3b9">
src/jalview/renderer/AnnotationRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#56183e6e03e5798fd0c31a569f19bbfd82a25e9b">
src/jalview/renderer/AnnotationRendererFactory.java
</a>
</li>
<li class="file-stats">
<a href="#4c0d7238167dd9bf31f205f5389bdc5f78cb75f6">
src/jalview/renderer/AwtRenderPanelI.java
</a>
</li>
<li class="file-stats">
<a href="#f6000a90c06daa5d8d4303fdae1b220394f07296">
src/jalview/renderer/ContactGeometry.java
</a>
</li>
<li class="file-stats">
<a href="#4f9804b78223b3fc3718b20ed61ad7f349393b97">
src/jalview/renderer/ContactMapRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#33195f80987d96702e9eb7933517d5942cfdcb86">
src/jalview/renderer/OverviewRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#40dc82bde0a26f07c33066f5900444f6f0b8fdba">
src/jalview/renderer/OverviewResColourFinder.java
</a>
</li>
<li class="file-stats">
<a href="#6ccb8a0617696ccaf15d0d960e0de2d5b6971380">
src/jalview/renderer/ResidueColourFinder.java
</a>
</li>
<li class="file-stats">
<a href="#65eff97a4db1f1871ca4972fdf1f5ac01c55963d">
src/jalview/renderer/ResidueShader.java
</a>
</li>
<li class="file-stats">
<a href="#49ab3ecd674768896418311f11511b920a1db051">
src/jalview/renderer/ResidueShaderI.java
</a>
</li>
<li class="file-stats">
<a href="#d29ec9517520b3061e8993a25fbeb3d217c899dc">
src/jalview/renderer/ScaleRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#5cef729db8c1d12884137f3da3bf5559f3b4ebf2">
src/jalview/renderer/api/AnnotationRendererFactoryI.java
</a>
</li>
<li class="file-stats">
<a href="#1d4f66e098c5bf29d758f454ebd819992731bee8">
src/jalview/renderer/api/AnnotationRowRendererI.java
</a>
</li>
<li class="file-stats">
<a href="#c8e4c0fd0bf9815d44ea64161f89fcfa868394b2">
src/jalview/renderer/seqfeatures/FeatureColourFinder.java
</a>
</li>
<li class="file-stats">
<a href="#5dc5e4e8453dcfc0094eb9b3bad6b2a52a4e1e8c">
src/jalview/renderer/seqfeatures/FeatureRenderer.java
</a>
</li>
<li class="file-stats">
<a href="#5d43a0a488d7a47716447632061b43851765ea1c">
src/jalview/rest/RestHandler.java
</a>
</li>
<li class="file-stats">
<a href="#283c276a522dd0432a0f800c6824689af8a33f65">
src/jalview/schemes/AnnotationColourGradient.java
</a>
</li>
<li class="file-stats">
<a href="#d0e34af6ce307598780be9fcf1651b511b1c2364">
src/jalview/schemes/BlossomColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#840f41ab591f7d6b7af9c984e8a1c032201d8e51">
src/jalview/schemes/Blosum62ColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#0a3e18b0b8655caa6aa51fb570be40feab4483e5">
src/jalview/schemes/BuriedColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#6741ae92489885794000d53c281c0aabdb4c5cbb">
src/jalview/schemes/ClustalxColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#6b1368278c8aebae43364d097c953e39175479bd">
src/jalview/schemes/ColourSchemeI.java
</a>
</li>
<li class="file-stats">
<a href="#137ef90eeb154932bc3840b0d347a11d2894d361">
src/jalview/schemes/ColourSchemeLoader.java
</a>
</li>
<li class="file-stats">
<a href="#4bc02bce00866904c76d981bcbd92bd3d905c9c8">
src/jalview/schemes/ColourSchemeProperty.java
</a>
</li>
<li class="file-stats">
<a href="#e97f83cb0f42f0277723f02e378132f5237b30bd">
src/jalview/schemes/ColourSchemes.java
</a>
</li>
<li class="file-stats">
<a href="#96b6e41bf4dd7bf7e0499e413f19d54c05f6bde1">
src/jalview/schemes/Consensus.java
</a>
</li>
<li class="file-stats">
<a href="#f47ac316a1c89de852c8c9eca7cbc6ab58316684">
src/jalview/schemes/CovariationColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#93e322a012231f2f68155de8508bf4db719e0248">
src/jalview/schemes/FeatureColour.java
</a>
</li>
<li class="file-stats">
<a href="#566604a2b6a2a58a3f6b6a3292a775af737959f2">
src/jalview/schemes/FeatureSettingsAdapter.java
</a>
</li>
<li class="file-stats">
<a href="#9653aaad51d3d46c0bba93758070a35f6def6174">
src/jalview/schemes/FlowerColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#9035fda7706b836679ff8c7dab5bb35ac8edae0c">
src/jalview/schemes/FollowerColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#823ba7419068f3d3b96e4a3ab4794fa9718b8a89">
src/jalview/schemes/HelixColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#a02426a67bc346b9532f6760b87d78e6e236950c">
src/jalview/schemes/HydrophobicColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#7b62f68b64af0452c66a96e0dd5186be4cb3ed01">
src/jalview/schemes/IdColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#a04909311d0ba40a7ecf33532483e399bf4ffe87">
src/jalview/schemes/JalviewColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#f4fd2d115ac6efd284af99f2e5e109dc114746bc">
src/jalview/schemes/NucleotideAmbiguityColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#3028011a2d81ebb46e3fb9d9838fcd3f7693abc4">
src/jalview/schemes/NucleotideColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#2db3ed189d4e781719e9050d0103c925777040f7">
src/jalview/schemes/OceanColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#2459ba9b039f3c3633ebb6563f2bc545889db40c">
src/jalview/schemes/PIDColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#42757a97ca52fb28c55252852eb743d6e910fefc">
src/jalview/schemes/PurinePyrimidineColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#3275dd80ae495e5788077e71332e0b6e443c78f6">
src/jalview/schemes/RNAHelicesColour.java
</a>
</li>
<li class="file-stats">
<a href="#dbbf046376e5fdfdcff474d5b44c8cf438caa9cb">
src/jalview/schemes/RNAHelicesColourChooser.java
</a>
</li>
<li class="file-stats">
<a href="#6b8960590865165163cda661a31e8b887ba62f09">
src/jalview/schemes/RNAInteractionColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#44d940a52783daf9d4ef7cb053aa27e18c5c15f7">
src/jalview/schemes/ResidueColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#ae8b1993a60aa39278f4a12c9707ff40de706b30">
src/jalview/schemes/ResidueProperties.java
</a>
</li>
<li class="file-stats">
<a href="#fd80c504cf32cc306e489417cfe83d0758aefa25">
src/jalview/schemes/ScoreColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#0d699b506db35397e40d38232ec84cf32489b846">
src/jalview/schemes/StrandColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#e02e3cc0134a6b41626cd785f3430b271c2bd732">
src/jalview/schemes/SunsetColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#8f5fff6fb837511ac1a717262dc19c368d8cff88">
src/jalview/schemes/TCoffeeColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#843dc065337d61923da0a3312f706f59ef3b6e66">
src/jalview/schemes/TaylorColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#0c39910884619914bbbb5f75935d0b1ee17859d7">
src/jalview/schemes/TurnColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#5a1c7e67abc8f2a18342f4c1f1a63450a04fac8c">
src/jalview/schemes/UserColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#3daf231c1be9550f5b9dccacedd112d265ce9803">
src/jalview/schemes/ZappoColourScheme.java
</a>
</li>
<li class="file-stats">
<a href="#57f610523935b0a7aad745be520e383ff6140ed8">
src/jalview/structure/AlignmentViewPanelListener.java
</a>
</li>
<li class="file-stats">
<a href="#14447b8a58c44a1fe0801f5acfdd24bc7979607d">
src/jalview/structure/AtomSpec.java
</a>
</li>
<li class="file-stats">
<a href="#0cd43bcdccd467ce134aad8b431187f59b775c0d">
src/jalview/structure/AtomSpecModel.java
</a>
</li>
<li class="file-stats">
<a href="#1f70a98ea455cbafc24ff622fc2769ea07508fde">
src/jalview/structure/CommandListener.java
</a>
</li>
<li class="file-stats">
<a href="#e36b1358a6ce0897349026c2a0cccdb30443f083">
src/jalview/structure/SecondaryStructureListener.java
</a>
</li>
<li class="file-stats">
<a href="#c156077757de5c34e2d35fb3528ff2fdcdb8f170">
src/jalview/structure/SelectionListener.java
</a>
</li>
<li class="file-stats">
<a href="#c2526f23a423dda0dcb507e2625c5b72f737c927">
src/jalview/structure/SelectionSource.java
</a>
</li>
<li class="file-stats">
<a href="#1b3cd33119e17c9e33c7bfcb02e463cbe4559b7e">
src/jalview/structure/SequenceListener.java
</a>
</li>
<li class="file-stats">
<a href="#4ff78f4b77e5738aca8d8cb202a2a6cc67af4b23">
src/jalview/structure/StructureCommand.java
</a>
</li>
<li class="file-stats">
<a href="#e71a057e18e872f94c68fcca7fd22411c72611e9">
src/jalview/structure/StructureCommandI.java
</a>
</li>
<li class="file-stats">
<a href="#03ab85ae7fbe3ee26e7e33551a39dbeed44173fb">
src/jalview/structure/StructureCommandsBase.java
</a>
</li>
<li class="file-stats">
<a href="#23a94511a8af05af016f34a4e41481972c84f1a8">
src/jalview/structure/StructureCommandsI.java
</a>
</li>
<li class="file-stats">
<a href="#397747e38edddc58fe1d27a99cfc42fb929ed284">
src/jalview/structure/StructureImportSettings.java
</a>
</li>
<li class="file-stats">
<a href="#31d7eac432e4615a08c1dd2497613af71de5f62a">
src/jalview/structure/StructureListener.java
</a>
</li>
<li class="file-stats">
<a href="#456943cc8b61d82e69dbfd6186ac99eb2a8e8167">
src/jalview/structure/StructureMapping.java
</a>
</li>
<li class="file-stats">
<a href="#567f07c81f54c78448f4bd0995cc63589163afb2">
src/jalview/structure/StructureMappingcommandSet.java
</a>
</li>
<li class="file-stats">
<a href="#75add0438c0a2bdca09d35d2482ec8d5770dddb1">
src/jalview/structure/StructureSelectionManager.java
</a>
</li>
<li class="file-stats">
<a href="#197ada5bc552ae28e662e04ba2625df5340e64c4">
src/jalview/structure/VamsasListener.java
</a>
</li>
<li class="file-stats">
<a href="#4e5deb96516d8fcaa82d4150be559e713d72d3ee">
src/jalview/structure/VamsasSource.java
</a>
</li>
<li class="file-stats">
<a href="#af04a37beb599d5a536383201c24efbda409fa97">
src/jalview/structures/models/AAStructureBindingModel.java
</a>
</li>
<li class="file-stats">
<a href="#fd8b56ecfda9b90a6d9e6210bdd0263d6e43fdd8">
src/jalview/structures/models/SequenceStructureBindingModel.java
</a>
</li>
<li class="file-stats">
<a href="#d514d3aa5504fa725848a9c29aea664c5fd43779">
src/jalview/urls/CustomUrlProvider.java
</a>
</li>
<li class="file-stats">
<a href="#ca2e4a98c17600e0dc36362ef9ddda3d908ab1e4">
src/jalview/urls/IdOrgSettings.java
</a>
</li>
<li class="file-stats">
<a href="#1b94b11ea308a7b56988d7b6684cfb4ae160c1b0">
src/jalview/urls/IdentifiersUrlProvider.java
</a>
</li>
<li class="file-stats">
<a href="#9bea85d00132893becb69adb090257a87b3bb31c">
src/jalview/urls/UrlLinkDisplay.java
</a>
</li>
<li class="file-stats">
<a href="#62490fefc0709619d342ad679b57827a254d10de">
src/jalview/urls/UrlLinkTableModel.java
</a>
</li>
<li class="file-stats">
<a href="#caa6436775aca831b2fd4da985179088abab50bb">
src/jalview/urls/UrlProvider.java
</a>
</li>
<li class="file-stats">
<a href="#9dbc047d963e9badda9300908be8f1cbaee9be3b">
src/jalview/urls/UrlProviderImpl.java
</a>
</li>
<li class="file-stats">
<a href="#c873f194e39be50139725e827008189819c631bc">
src/jalview/urls/api/UrlProviderFactoryI.java
</a>
</li>
<li class="file-stats">
<a href="#9a43bddc8c3b43c539630930ef0b466d992026a6">
src/jalview/urls/api/UrlProviderI.java
</a>
</li>
<li class="file-stats">
<a href="#8ddb504a1f95d3a4f81a4832d5c342d15c7c12b9">
src/jalview/urls/applet/AppletUrlProviderFactory.java
</a>
</li>
<li class="file-stats">
<a href="#3189476d5185c24b682ff667bdc45924a3ddea03">
src/jalview/urls/desktop/DesktopUrlProviderFactory.java
</a>
</li>
<li class="file-stats">
<a href="#79d16d010e10420decc6b39c8ccad4241c719b05">
src/jalview/util/AWTConsole.java
</a>
</li>
<li class="file-stats">
<a href="#53e953aee576b1c5d8e2a6284ef7cfb973e19431">
src/jalview/util/ArgParserUtils.java
</a>
</li>
<li class="file-stats">
<a href="#6cf3baf55031e14e14380ec9a75698ab5d2fde89">
src/jalview/util/ArrayUtils.java
</a>
</li>
<li class="file-stats">
<a href="#9a8336da4b46129aa2abbe91783c5a5509781861">
src/jalview/util/BrowserLauncher.java
</a>
</li>
<li class="file-stats">
<a href="#da88f0fb0e0c580b45ae9fdaab4d123c3394a482">
src/jalview/util/CaseInsensitiveString.java
</a>
</li>
<li class="file-stats">
<a href="#240af85e0e9733e0d604356fa6172cc1e96a0f37">
src/jalview/util/ChannelProperties.java
</a>
</li>
<li class="file-stats">
<a href="#c863f083860dd092f8928586a041cdec9b5431ce">
src/jalview/util/ColorUtils.java
</a>
</li>
<li class="file-stats">
<a href="#974d3bf2f437f7bc25c9db9bd9a3fd940c9203c8">
src/jalview/util/Comparison.java
</a>
</li>
<li class="file-stats">
<a href="#90fdb35ffe56cf6baf3a26decaf09afaf83a8022">
src/jalview/util/Constants.java
</a>
</li>
<li class="file-stats">
<a href="#8af77d2a9081cfd3e25dd5a9746a127f5bf0a615">
src/jalview/util/DBRefUtils.java
</a>
</li>
<li class="file-stats">
<a href="#5b4ae67b25630e2c1c72c7dc11486bbddba8efb7">
src/jalview/util/DnaUtils.java
</a>
</li>
<li class="file-stats">
<a href="#b4cbe82607567e8e13c15173f3230efb53a36fdc">
src/jalview/util/ErrorLog.java
</a>
</li>
<li class="file-stats">
<a href="#d873f2e0fd7c14c11471071915b24f62ed10cbee">
src/jalview/util/FileUtils.java
</a>
</li>
<li class="file-stats">
<a href="#fed44ea8fc6772f7a05fe58d27d7d4460ac6d58f">
src/jalview/util/Format.java
</a>
</li>
<li class="file-stats">
<a href="#9673fbd17dea1bd0b79791c4224ccf176c8dc55a">
src/jalview/util/GroupUrlLink.java
</a>
</li>
<li class="file-stats">
<a href="#e8eb1130209b509089c6964bb5cc0cbdf0207c04">
src/jalview/util/HttpUtils.java
</a>
</li>
<li class="file-stats">
<a href="#94c5df1dce6a1ca779fe581f8c2879a84cc8faf4">
src/jalview/util/ImageMaker.java
</a>
</li>
<li class="file-stats">
<a href="#678917fcf6a359115401177e293f00f70c8e4caf">
src/jalview/util/IntRangeComparator.java
</a>
</li>
<li class="file-stats">
<a href="#81e6f6884338937d82e459e9085a99ae7377f5ea">
src/jalview/util/JSONUtils.java
</a>
</li>
<li class="file-stats">
<a href="#38e9a521f525243dfd529ebaa2e628be2fa638e4">
src/jalview/util/LaunchUtils.java
</a>
</li>
<li class="file-stats">
<a href="#3793b8967970926287d01a90a5698b1b4537b415">
src/jalview/util/LinkedIdentityHashSet.java
</a>
</li>
<li class="file-stats">
<a href="#bd9c536cbedaf399b5a424e3490f825ee44c12e6">
src/jalview/util/Log4j.java
</a>
</li>
<li class="file-stats">
<a href="#7ca9f6df49aa6e144d191f94ea65db6c56f995a7">
src/jalview/util/MapList.java
</a>
</li>
<li class="file-stats">
<a href="#7e38f028b13c12feb6b8228a1653ca01d3b07e2a">
src/jalview/util/MapUtils.java
</a>
</li>
<li class="file-stats">
<a href="#910110a2090dedb850a49887de18a41abe0cc432">
src/jalview/util/MappingUtils.java
</a>
</li>
<li class="file-stats">
<a href="#8f4f50c4000a9c9f421ab2307180c42879b37df2">
src/jalview/util/MathUtils.java
</a>
</li>
<li class="file-stats">
<a href="#1c9be06cab8aec9fc90ff393b1db065e045439eb">
src/jalview/util/MessageManager.java
</a>
</li>
<li class="file-stats">
<a href="#c69fcf5826c39a47702d432faed5547a911d06e5">
src/jalview/util/ParseHtmlBodyAndLinks.java
</a>
</li>
<li class="file-stats">
<a href="#162f9a6207c91b211882c499abfc16a0d23497ed">
src/jalview/util/Platform.java
</a>
</li>
<li class="file-stats">
<a href="#5fc1fcd600a54f3c40e9980c5f275d469ee78196">
src/jalview/util/QuickSort.java
</a>
</li>
<li class="file-stats">
<a href="#2377a7f8171114f9aac22cdca38e4b8b436e5997">
src/jalview/util/ReverseListIterator.java
</a>
</li>
<li class="file-stats">
<a href="#eb2e1a0c7acd8e4a517545ad5f744e50c11c65bd">
src/jalview/util/SetUtils.java
</a>
</li>
<li class="file-stats">
<a href="#c61f6c3dd4130fc72d3f245414bc40528a4b081c">
src/jalview/util/ShiftList.java
</a>
</li>
<li class="file-stats">
<a href="#1f61cbcf88be059b37e203ce6de92a53962b7108">
src/jalview/util/ShortcutKeyMaskExWrapper.java
</a>
</li>
<li class="file-stats">
<a href="#f22cf5270b81a4ab035ea36eeebc68f0e99df2b0">
src/jalview/util/ShortcutKeyMaskExWrapper11.java
</a>
</li>
<li class="file-stats">
<a href="#1c705ad99b61b925f1295858c501e1ccfd47f1e7">
src/jalview/util/ShortcutKeyMaskExWrapper8.java
</a>
</li>
<li class="file-stats">
<a href="#622b956a281a8bd20586a3e21c1ba094bbb90769">
src/jalview/util/ShortcutKeyMaskExWrapperI.java
</a>
</li>
<li class="file-stats">
<a href="#7bbabccf7ac700bf8203acc35955a68966a6275b">
src/jalview/util/SparseCount.java
</a>
</li>
<li class="file-stats">
<a href="#67da514e9e94c1f3068cc26e5615dff40166a3ea">
src/jalview/util/StringUtils.java
</a>
</li>
<li class="file-stats">
<a href="#e5e89f6eb8c5c0cef4ca6dee99690e106e4b941b">
src/jalview/util/TableSorter.java
</a>
</li>
<li class="file-stats">
<a href="#ab071ea7b10def8c07f1b1225ab0d8d13dad4c08">
src/jalview/util/UrlConstants.java
</a>
</li>
<li class="file-stats">
<a href="#5a427acf1fbcd50645da2c1e31880a9ada57d383">
src/jalview/util/UrlLink.java
</a>
</li>
<li class="file-stats">
<a href="#91bf60ab81cf7e41038c021c24712dde6dc9636c">
src/jalview/util/UserAgent.java
</a>
</li>
<li class="file-stats">
<a href="#e601e7c97f1090aaf586ee6bff5a95cc2cbb4d04">
src/jalview/util/dialogrunner/DialogRunnerI.java
</a>
</li>
<li class="file-stats">
<a href="#c1136dcd25e1d090105853e529b22cfb301d6a02">
src/jalview/util/imagemaker/BitmapImageSizing.java
</a>
</li>
<li class="file-stats">
<a href="#c1cd2d91568645fea3e900aa670a7b4127899e78">
src/jalview/util/jarInputStreamProvider.java
</a>
</li>
<li class="file-stats">
<a href="#e60627f7101ae32caa2bf66e5beb6c135c4cea7e">
src/jalview/util/matcher/Condition.java
</a>
</li>
<li class="file-stats">
<a href="#1aebd6d9ec9ffa76835067b3c9f865890e90f55f">
src/jalview/util/matcher/Matcher.java
</a>
</li>
<li class="file-stats">
<a href="#3b9f76e115b6e65a9f3a774cf63725577665dbb0">
src/jalview/util/matcher/MatcherI.java
</a>
</li>
<li class="file-stats">
<a href="#3c4a1cf808aebef2359617607774136afc614057">
src/jalview/viewmodel/AlignmentViewport.java
</a>
</li>
<li class="file-stats">
<a href="#360974d91342fbd44769248dc36223d10f6e0be8">
src/jalview/viewmodel/OverviewDimensions.java
</a>
</li>
<li class="file-stats">
<a href="#35d4856c616af0ae383a14e8c658ddbef35c8e54">
src/jalview/viewmodel/OverviewDimensionsHideHidden.java
</a>
</li>
<li class="file-stats">
<a href="#da69f1cc5d26d7e59257fd42384d19059cf0e264">
src/jalview/viewmodel/OverviewDimensionsShowHidden.java
</a>
</li>
<li class="file-stats">
<a href="#3ffa13ab5dd522fce8d99c11dc68f1adf5d3169c">
src/jalview/viewmodel/PCAModel.java
</a>
</li>
<li class="file-stats">
<a href="#ea628578f1269091c16cb8f77701c4352c1b8495">
src/jalview/viewmodel/PaSiMapModel.java
</a>
</li>
<li class="file-stats">
<a href="#3c870f2117933cfb27ecce7efcb066be06199908">
src/jalview/viewmodel/ViewportListenerI.java
</a>
</li>
<li class="file-stats">
<a href="#3405345812bfa7c7be3ce90d36008389ba44eda5">
src/jalview/viewmodel/ViewportProperties.java
</a>
</li>
<li class="file-stats">
<a href="#205adddb2f9ae2f13b1846880493128485c4ffda">
src/jalview/viewmodel/ViewportRanges.java
</a>
</li>
<li class="file-stats">
<a href="#20c1315a04968872cdb90c26dc26c1c581d3b282">
src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java
</a>
</li>
<li class="file-stats">
<a href="#b1abde65e4359e3825004dc9b22c6ef7c370dcb6">
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
</a>
</li>
<li class="file-stats">
<a href="#821fe5096b1fc80669be13c77d62973432c20e04">
src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
</a>
</li>
<li class="file-stats">
<a href="#f665385524503dd450fbd42525ee89d113b09bee">
src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java
</a>
</li>
<li class="file-stats">
<a href="#86d715ed233d23b9c16d5f37d93aa1e364124b8a">
src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
</a>
</li>
<li class="file-stats">
<a href="#0939acb0bf35493405eb78dc72a480059984913f">
src/jalview/viewmodel/styles/ViewStyle.java
</a>
</li>
<li class="file-stats">
<a href="#c72c284b3dc950992dfb32f8caed32f2bd2e3fe9">
src/jalview/workers/AlignCalcManager.java
</a>
</li>
<li class="file-stats">
<a href="#1f984ebba2b102ce8a3854b7ffbc259fe4e09d1d">
src/jalview/workers/AlignCalcWorker.java
</a>
</li>
<li class="file-stats">
<a href="#7f0f3745dc56f8eb88e773b9babf12be4e73a813">
src/jalview/workers/AlignmentAnnotationFactory.java
</a>
</li>
<li class="file-stats">
<a href="#0533d85d6abc13c563cb8b52b9913e45af2a9f6d">
src/jalview/workers/AnnotationProviderI.java
</a>
</li>
<li class="file-stats">
<a href="#3522136b0e161060fe3b80d071e2bd86121a7af3">
src/jalview/workers/AnnotationWorker.java
</a>
</li>
<li class="file-stats">
<a href="#c5fa386ec7cf8e3b1209b52179e2005ffd2dd0df">
src/jalview/workers/ColumnCounterSetWorker.java
</a>
</li>
<li class="file-stats">
<a href="#8a89f03e42ef58bd6da1e9db3458b34bfbf2ae89">
src/jalview/workers/ComplementConsensusThread.java
</a>
</li>
<li class="file-stats">
<a href="#646b086810af8e7fdeefeb6b1e72221173c37ec2">
src/jalview/workers/ConsensusThread.java
</a>
</li>
<li class="file-stats">
<a href="#04994035468df24407ae7635eb2caa04201664d0">
src/jalview/workers/ConservationThread.java
</a>
</li>
<li class="file-stats">
<a href="#270e1e435e6c12b9021da1f6ee72e1c95ab7fd69">
src/jalview/workers/FeatureSetCounterI.java
</a>
</li>
<li class="file-stats">
<a href="#a3779f9304c5fe2dc3378557fef7160d279694bd">
src/jalview/workers/SecondaryStructureConsensusThread.java
</a>
</li>
<li class="file-stats">
<a href="#7e58d1bd115211e3cad287908c8f19f7d4f18053">
src/jalview/workers/StrucConsensusThread.java
</a>
</li>
<li class="file-stats">
<a href="#5db074b80ac812120257366fd7c9db9aaeebac83">
src/jalview/ws/AWSThread.java
</a>
</li>
<li class="file-stats">
<a href="#7b3b242307f017fe7045fcb8677c4746af51fd23">
src/jalview/ws/AWsJob.java
</a>
</li>
<li class="file-stats">
<a href="#ab4e61fc81d60274d10f5a7a7b913e26edccf0c1">
src/jalview/ws/DBRefFetcher.java
</a>
</li>
<li class="file-stats">
<a href="#4043319b20ca7aeff50bbcaaeedeef3911d6c4c0">
src/jalview/ws/HttpClientUtils.java
</a>
</li>
<li class="file-stats">
<a href="#69765ad125f791f1b08bcc5b1ab7a1582721e8d0">
src/jalview/ws/JobStateSummary.java
</a>
</li>
<li class="file-stats">
<a href="#14a855f77c655f69853c48b55fd293a0b75c66a8">
src/jalview/ws/SequenceFetcher.java
</a>
</li>
<li class="file-stats">
<a href="#8ddd6e2724ae1834277b777b59109561574c85a4">
src/jalview/ws/SequenceFetcherFactory.java
</a>
</li>
<li class="file-stats">
<a href="#e3b75676c3f9318fd60fe9eb4c090f787b2ea577">
src/jalview/ws/WSClient.java
</a>
</li>
<li class="file-stats">
<a href="#dd02e666563c0083e59cd8bf65422f248f2644e3">
src/jalview/ws/WSClientI.java
</a>
</li>
<li class="file-stats">
<a href="#679b20363d1b6a368297c13dfd591178f33134bc">
src/jalview/ws/WSMenuEntryProviderI.java
</a>
</li>
<li class="file-stats">
<a href="#a2351e1de8c6857ff91486981866187b14e40321">
src/jalview/ws/datamodel/MappableContactMatrixI.java
</a>
</li>
<li class="file-stats">
<a href="#575c3ba705ae892bdbf71797f0a8f1a8d4680e0e">
src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#087d8cfc548e936bf83de20e6104a55b063c50aa">
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#eb5b9a6267978ae940c926a9c89bfa10595afb99">
src/jalview/ws/dbsources/EBIAlfaFold.java
</a>
</li>
<li class="file-stats">
<a href="#67c924491b22833bb38a51095447a99734a088b9">
src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
</a>
</li>
<li class="file-stats">
<a href="#165b4a61a4ca4c6c74e5e159d369fcb0c10417f1">
src/jalview/ws/dbsources/EmblCdsSource.java
</a>
</li>
<li class="file-stats">
<a href="#ad01d8fee742093779a43ca63f9be8475fe657f0">
src/jalview/ws/dbsources/EmblFlatfileSource.java
</a>
</li>
<li class="file-stats">
<a href="#7aea2eac9701f9339aa43d0d4d3ac14cb558c5ec">
src/jalview/ws/dbsources/EmblSource.java
</a>
</li>
<li class="file-stats">
<a href="#ebea50ce44192f19794c3dcc5a0578ed4a2aee97">
src/jalview/ws/dbsources/EmblXmlSource.java
</a>
</li>
<li class="file-stats">
<a href="#87037e0eb78d8078c2b58ddea4153648458549b0">
src/jalview/ws/dbsources/GeneDbSource.java
</a>
</li>
<li class="file-stats">
<a href="#605274a341c20c9c52e8de5cb7019366317f537e">
src/jalview/ws/dbsources/Pdb.java
</a>
</li>
<li class="file-stats">
<a href="#489b71a9218be31473f90b58a06ef2906a0d7373">
src/jalview/ws/dbsources/Pfam.java
</a>
</li>
<li class="file-stats">
<a href="#f6bd15653e39c300dcfdbc3a21f180714c794dad">
src/jalview/ws/dbsources/PfamFull.java
</a>
</li>
<li class="file-stats">
<a href="#f23660905b0e64b10f599d806a19e48111f0e2f9">
src/jalview/ws/dbsources/PfamSeed.java
</a>
</li>
<li class="file-stats">
<a href="#81fe715646af2a700876c4927eac079b14d6d7f1">
src/jalview/ws/dbsources/Rfam.java
</a>
</li>
<li class="file-stats">
<a href="#eb41b31c9e76232dd17212b28364ec660605fa66">
src/jalview/ws/dbsources/RfamFull.java
</a>
</li>
<li class="file-stats">
<a href="#57f61d708c16968b2d69737c8538dd64a2f87b95">
src/jalview/ws/dbsources/RfamSeed.java
</a>
</li>
<li class="file-stats">
<a href="#6d3e845d84bb4a3fc1438994059850276c086e81">
src/jalview/ws/dbsources/TDBeacons.java
</a>
</li>
<li class="file-stats">
<a href="#6cd82e9fcb178678bd1d970677a4ee547ca1782b">
src/jalview/ws/dbsources/Uniprot.java
</a>
</li>
<li class="file-stats">
<a href="#fda4a8e79b5dc4b582e8061a0feaa7fdbbf0f549">
src/jalview/ws/dbsources/UniprotName.java
</a>
</li>
<li class="file-stats">
<a href="#c341c3c7742e991de234b6bdeab1753db5f3a47b">
src/jalview/ws/dbsources/Xfam.java
</a>
</li>
<li class="file-stats">
<a href="#a2f5e371b50a26e066c6f30b639aeded63ba0856">
src/jalview/ws/ebi/EBIFetchClient.java
</a>
</li>
<li class="file-stats">
<a href="#3b20249210a7ea2160666957786d83ae485f8d62">
src/jalview/ws/io/mime/HttpContentHandler.java
</a>
</li>
<li class="file-stats">
<a href="#739fe415a68eb46d15f9135eeb054e1682402227">
src/jalview/ws/io/mime/JalviewMimeContentHandler.java
</a>
</li>
<li class="file-stats">
<a href="#f5e1a2915cd78223a6db64b7e7c39941219fd143">
src/jalview/ws/io/mime/MimeTypes.java
</a>
</li>
<li class="file-stats">
<a href="#f73492c885337b9b06c047d36590ab9f49cbacab">
src/jalview/ws/jws1/Annotate3D.java
</a>
</li>
<li class="file-stats">
<a href="#1c7d3af6d94db8e70ccc979f26862625ce4c0212">
src/jalview/ws/jws1/Discoverer.java
</a>
</li>
<li class="file-stats">
<a href="#1b3175e6c9c403c776d5720d0bd74fbcad7e0d08">
src/jalview/ws/jws1/JPredClient.java
</a>
</li>
<li class="file-stats">
<a href="#ac32a56b3b26e2e2019b47c866f0c45b4b954509">
src/jalview/ws/jws1/JPredThread.java
</a>
</li>
<li class="file-stats">
<a href="#c37fed71b5628286814892f3411009e7dfd71e9f">
src/jalview/ws/jws1/JWS1Thread.java
</a>
</li>
<li class="file-stats">
<a href="#ac561ffdd64d3206b0163fe5394a11f9ace05cf7">
src/jalview/ws/jws1/MsaWSClient.java
</a>
</li>
<li class="file-stats">
<a href="#07dead2a14aa74471813a95cd50c3cd022bd7f71">
src/jalview/ws/jws1/MsaWSThread.java
</a>
</li>
<li class="file-stats">
<a href="#ba82fb0f4f3944f774a7b5533d8aeff7edc8cb72">
src/jalview/ws/jws1/SeqSearchWSClient.java
</a>
</li>
<li class="file-stats">
<a href="#2cd6f41c08a7d1b0763271c058f576b469a8a009">
src/jalview/ws/jws1/SeqSearchWSThread.java
</a>
</li>
<li class="file-stats">
<a href="#5b9bf00c35dbbc6401db6e610535b6653a128586">
src/jalview/ws/jws1/WS1Client.java
</a>
</li>
<li class="file-stats">
<a href="#144bc736c19b4bfe9267267b5e61a47a381bf651">
src/jalview/ws/jws1/WSJob.java
</a>
</li>
<li class="file-stats">
<a href="#e4d17608b7024b645ab87b205481f21456df49f6">
src/jalview/ws/jws2/AAConClient.java
</a>
</li>
<li class="file-stats">
<a href="#8bd04470701a63206f987e9602008caa45d14d99">
src/jalview/ws/jws2/AADisorderClient.java
</a>
</li>
<li class="file-stats">
<a href="#97410a6399e94422f4449b8813f43653b1f5d7cb">
src/jalview/ws/jws2/AWS2Thread.java
</a>
</li>
<li class="file-stats">
<a href="#44ed59806b6b39db7e64499a8089b72b4511707e">
src/jalview/ws/jws2/AbstractJabaCalcWorker.java
</a>
</li>
<li class="file-stats">
<a href="#ab8d09ea287b9126df13fb0c668371d8f9763708">
src/jalview/ws/jws2/JWs2Job.java
</a>
</li>
<li class="file-stats">
<a href="#206579e24a4f61c4bb368e553d7024d851519870">
src/jalview/ws/jws2/JabaParamStore.java
</a>
</li>
<li class="file-stats">
<a href="#e682fee34240a51e9d03430fb258e70795429265">
src/jalview/ws/jws2/JabaPreset.java
</a>
</li>
<li class="file-stats">
<a href="#8f1bf1b99927c3ad6b39ea86624cbf63cefad813">
src/jalview/ws/jws2/JabaWsServerQuery.java
</a>
</li>
<li class="file-stats">
<a href="#2bc80eb2c2253e809a021ed14c7da9f3c057bbc2">
src/jalview/ws/jws2/JabawsCalcWorker.java
</a>
</li>
<li class="file-stats">
<a href="#837b1859bf7d77e20165e98b3c0475f7d95d6b74">
src/jalview/ws/jws2/JabawsMsaInterfaceAlignCalcWorker.java
</a>
</li>
<li class="file-stats">
<a href="#73fb52bac5bbe41cb404caa020119752fbf5002d">
src/jalview/ws/jws2/Jws2Client.java
</a>
</li>
<li class="file-stats">
<a href="#d56b81a41ad6b3d0ba3ec250e0155ff093d0f5fd">
src/jalview/ws/jws2/Jws2Discoverer.java
</a>
</li>
<li class="file-stats">
<a href="#4c23a68c0f31009aa16265f5e5a7a8b992262bf1">
src/jalview/ws/jws2/MsaWSClient.java
</a>
</li>
<li class="file-stats">
<a href="#5e823ac5fbca6f2604dcd72e1f8b28ecff9b7b8e">
src/jalview/ws/jws2/MsaWSThread.java
</a>
</li>
<li class="file-stats">
<a href="#96704ab21ead72bed2aa5f3a4470fcad3dc7d301">
src/jalview/ws/jws2/ParameterUtils.java
</a>
</li>
<li class="file-stats">
<a href="#40d6df30f4ac40c52fb95a05bd0eea33bbb4b3e9">
src/jalview/ws/jws2/RNAalifoldClient.java
</a>
</li>
<li class="file-stats">
<a href="#7f553a0e1e9b7221f1dc3b84b22481b155baaf78">
src/jalview/ws/jws2/SequenceAnnotationWSClient.java
</a>
</li>
<li class="file-stats">
<a href="#e203355d73654fe2f5be3b586edc453ccd8793da">
src/jalview/ws/jws2/dm/AAConSettings.java
</a>
</li>
<li class="file-stats">
<a href="#9d48db17a032d243f295a8ca603d371146c3a155">
src/jalview/ws/jws2/dm/JabaOption.java
</a>
</li>
<li class="file-stats">
<a href="#95f70138484582c86544520df7b8bacf027d8ff9">
src/jalview/ws/jws2/dm/JabaParameter.java
</a>
</li>
<li class="file-stats">
<a href="#9dd0cb5dee9f9120fbadace52491f866e773dd79">
src/jalview/ws/jws2/dm/JabaValueConstrain.java
</a>
</li>
<li class="file-stats">
<a href="#abb98804fab0bd89b96d3811f01bea385e4f293e">
src/jalview/ws/jws2/dm/JabaWsParamSet.java
</a>
</li>
<li class="file-stats">
<a href="#6980bae280fd4b8647a2ed6f95d0af5ee7b295aa">
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
</a>
</li>
<li class="file-stats">
<a href="#f20e510eefd161ef4c90e7bab429005071abc361">
src/jalview/ws/jws2/jabaws2/Jws2InstanceFactory.java
</a>
</li>
<li class="file-stats">
<a href="#5996995a38c1d7b69ad7312dad590c4b90f13096">
src/jalview/ws/params/ArgumentI.java
</a>
</li>
<li class="file-stats">
<a href="#9b43e960ac76705feb9c8911cf3d661d6b7e5ff7">
src/jalview/ws/params/AutoCalcSetting.java
</a>
</li>
<li class="file-stats">
<a href="#1bfc5fb7226cf7f8ae162698baf48fc3fee13fd2">
src/jalview/ws/params/InvalidArgumentException.java
</a>
</li>
<li class="file-stats">
<a href="#380203de4ac1b6397f622291734b7816d45fc782">
src/jalview/ws/params/OptionI.java
</a>
</li>
<li class="file-stats">
<a href="#9260c10d2cba2fadec5301b6bd80beacb56c5b4d">
src/jalview/ws/params/ParamDatastoreI.java
</a>
</li>
<li class="file-stats">
<a href="#2a232cf4ce250468604c4d6c871d960eb9854fe3">
src/jalview/ws/params/ParamManager.java
</a>
</li>
<li class="file-stats">
<a href="#33dddb4054ed61cac579f04631053b233c7bd48a">
src/jalview/ws/params/ParameterI.java
</a>
</li>
<li class="file-stats">
<a href="#a59e9aaf804d0c69f4ffa4232f938eaf0aca8951">
src/jalview/ws/params/ValueConstrainI.java
</a>
</li>
<li class="file-stats">
<a href="#5022d8710448ac39426eb99ad33de7ddd457fc7a">
src/jalview/ws/params/WsParamSetI.java
</a>
</li>
<li class="file-stats">
<a href="#fad8c92c6b33d03faf1458dc6136b79576ca6cc8">
src/jalview/ws/params/simple/BooleanOption.java
</a>
</li>
<li class="file-stats">
<a href="#892a68cc93eea6faebbd07f8976ef923a4ff3541">
src/jalview/ws/params/simple/IntegerParameter.java
</a>
</li>
<li class="file-stats">
<a href="#dc05522024ea10459460bf8c2a1ea310843fdd0f">
src/jalview/ws/params/simple/Option.java
</a>
</li>
<li class="file-stats">
<a href="#517e9137d6fec25170e156298eaea1f442695872">
src/jalview/ws/params/simple/Parameter.java
</a>
</li>
<li class="file-stats">
<a href="#e74835fd684cc3209b72670443b0e80a365e09d9">
src/jalview/ws/params/simple/StringChoiceParameter.java
</a>
</li>
<li class="file-stats">
<a href="#ffce37e13183141f1652ce5674dd25c04ad7d51f">
src/jalview/ws/rest/AlignmentProcessor.java
</a>
</li>
<li class="file-stats">
<a href="#c537c3c4e03e86ff283d436cd39458037e87d934">
src/jalview/ws/rest/HttpResultSet.java
</a>
</li>
<li class="file-stats">
<a href="#68d07d047d831bdefd74bcb8ebe632722a697d35">
src/jalview/ws/rest/InputType.java
</a>
</li>
<li class="file-stats">
<a href="#edf9648b70654010840afb601fa9f428d79aa210">
src/jalview/ws/rest/NoValidInputDataException.java
</a>
</li>
<li class="file-stats">
<a href="#2dbc3ae78fc56fce58ff379c29234ccbbc7ec674">
src/jalview/ws/rest/RestClient.java
</a>
</li>
<li class="file-stats">
<a href="#8a311f5edceed6cb25c3cb712dd0ab799dccf29c">
src/jalview/ws/rest/RestJob.java
</a>
</li>
<li class="file-stats">
<a href="#803a8b79c7f2e1046c03ddf47b9a1dd32cb7620f">
src/jalview/ws/rest/RestJobThread.java
</a>
</li>
<li class="file-stats">
<a href="#54ca83314ca739dda00ecf8a1fe19b6e5167c63c">
src/jalview/ws/rest/RestServiceDescription.java
</a>
</li>
<li class="file-stats">
<a href="#13db37f056e7442bb45baf11e765cbf694cf4e75">
src/jalview/ws/rest/params/Alignment.java
</a>
</li>
<li class="file-stats">
<a href="#cb083bde68efbd24c9173102349bdf5fb8c5a5e2">
src/jalview/ws/rest/params/AnnotationFile.java
</a>
</li>
<li class="file-stats">
<a href="#a258026871ac518fbacedd0fb7b968bc9244c6aa">
src/jalview/ws/rest/params/JobConstant.java
</a>
</li>
<li class="file-stats">
<a href="#2e4fbfd50725c2af49085bb798aee24a608728ab">
src/jalview/ws/rest/params/SeqGroupIndexVector.java
</a>
</li>
<li class="file-stats">
<a href="#d219466bed4e63cbea79d9aefd7f1288837a7e40">
src/jalview/ws/rest/params/SeqIdVector.java
</a>
</li>
<li class="file-stats">
<a href="#1af87e90539b62bcca2d1c34e6fc2da1562904eb">
src/jalview/ws/rest/params/SeqVector.java
</a>
</li>
<li class="file-stats">
<a href="#9e1f54a2e67b6b03198f0c74a53e8b24cc5c1ac8">
src/jalview/ws/rest/params/Tree.java
</a>
</li>
<li class="file-stats">
<a href="#0f59651f53db5d82e447fd50daa8fae35536d99a">
src/jalview/ws/seqfetcher/ASequenceFetcher.java
</a>
</li>
<li class="file-stats">
<a href="#6dd0a2aa5aa4abff89f1848fe9983ff53992a292">
src/jalview/ws/seqfetcher/DbSourceProxy.java
</a>
</li>
<li class="file-stats">
<a href="#65178e28bd6fcb32ec1fde94085657673fff5e19">
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
</a>
</li>
<li class="file-stats">
<a href="#ee6ace4261ecdc700a988a82c181358eadbc105e">
src/jalview/ws/sifts/MappingOutputPojo.java
</a>
</li>
<li class="file-stats">
<a href="#16af56d42876833fc264478ce4d1a9e1962cb0a8">
src/jalview/ws/sifts/SiftsClient.java
</a>
</li>
<li class="file-stats">
<a href="#190abfaaeb62bae4e2d3b81c7fcf91ad4a9e649a">
src/jalview/ws/sifts/SiftsException.java
</a>
</li>
<li class="file-stats">
<a href="#2e13be94a6eb1779d9544ae56f805843a3b82000">
src/jalview/ws/sifts/SiftsSettings.java
</a>
</li>
<li class="file-stats">
<a href="#ab646d67b1dbaca798450e28ed2f0031de415763">
src/jalview/ws/uimodel/AlignAnalysisUIText.java
</a>
</li>
<li class="file-stats">
<a href="#7963eb69968da0f1a665c812cad471bf68f158e7">
src/jalview/ws/utils/UrlDownloadClient.java
</a>
</li>
<li class="file-stats">
<a href="#f85e75a060a0ce60ac5f392e7008aecbbc69071b">
src/mc_view/AppletPDBCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#aaeccee34d268b6202b313d87287769ed1286915">
src/mc_view/AppletPDBViewer.java
</a>
</li>
<li class="file-stats">
<a href="#a26995ff92f7ef18f2fa8c2366c56819d3f04f19">
src/mc_view/Atom.java
</a>
</li>
<li class="file-stats">
<a href="#77e13e2d5dd8890717cc91180e2daafa1e503284">
src/mc_view/Bond.java
</a>
</li>
<li class="file-stats">
<a href="#9a7f2c3f052b5e7fb493c273666da98fcb2b6a30">
src/mc_view/MCMatrix.java
</a>
</li>
<li class="file-stats">
<a href="#0f178682f4c6a76fa9f477a4fd8fe205b33cd644">
src/mc_view/PDBCanvas.java
</a>
</li>
<li class="file-stats">
<a href="#f823e8a9bd7d63818bc2c7d0cddd2402c9a3c6d9">
src/mc_view/PDBChain.java
</a>
</li>
<li class="file-stats">
<a href="#0aa1c2d48cd7efc694fd5e42505a1079671ee2ae">
src/mc_view/PDBfile.java
</a>
</li>
<li class="file-stats">
<a href="#c24a6bc6c948b0b6edd28f03b2f199e9555423f5">
src/mc_view/Residue.java
</a>
</li>
<li class="file-stats">
<a href="#a6b54c86dfcf458a157a6174d85f0b753fb48aff">
src/mc_view/Zsort.java
</a>
</li>
<li class="file-stats">
<a href="#14d470835051785c24556bdacb9c90976a759a3b">
src/org/jibble/epsgraphics/EpsDocument.java
</a>
</li>
<li class="file-stats">
<a href="#38ec1c055fcb92ae10a1f169100e79ff336fdb59">
src/org/jibble/epsgraphics/EpsException.java
</a>
</li>
<li class="file-stats">
<a href="#2f9bee697b525db676233ed2fd11a6ae91b2ea26">
src/org/jibble/epsgraphics/EpsGraphics2D.java
</a>
</li>
<li class="file-stats">
<a href="#edeab877a61378f677369b362e167cf601326cb7">
src/uk/ac/ebi/picr/model/CrossReference.java
</a>
</li>
<li class="file-stats">
<a href="#e544ad35dd9b504d9d88caca51ba11d237a93f43">
src/uk/ac/ebi/picr/model/CrossReference_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#a475aa5a5d4a373526224b30b1d74fd23f6ff90a">
src/uk/ac/ebi/picr/model/UPEntry.java
</a>
</li>
<li class="file-stats">
<a href="#12e68cbae9aa6e6595f465f955ffe5e378ac6a3f">
src/uk/ac/ebi/picr/model/UPEntry_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#bcb8a58c644aebb71a3e2b817e421fe25c8fe304">
src/uk/ac/ebi/www/Data.java
</a>
</li>
<li class="file-stats">
<a href="#72cd8c9fdcc7d570e28e6a50aa448a7598980269">
src/uk/ac/ebi/www/InputParams.java
</a>
</li>
<li class="file-stats">
<a href="#98ae625c59a8b3869743a1b7c43c8d60baa2c8a1">
src/uk/ac/ebi/www/WSFile.java
</a>
</li>
<li class="file-stats">
<a href="#6c9507b7a9f8285d2bf44d6a9d16ee55864037d9">
src/uk/ac/ebi/www/WSWUBlast.java
</a>
</li>
<li class="file-stats">
<a href="#ae36a574f21c53c7405009ae0960f9ed9b8a5678">
src/uk/ac/ebi/www/WSWUBlastService.java
</a>
</li>
<li class="file-stats">
<a href="#05a495ace33311c7101b03991a0848f8bb84be3b">
src/uk/ac/ebi/www/WSWUBlastServiceLocator.java
</a>
</li>
<li class="file-stats">
<a href="#24f192de0a4058296ade39aaac8c5cb3d1f4f5f3">
src/uk/ac/ebi/www/WSWUBlastSoapBindingStub.java
</a>
</li>
<li class="file-stats">
<a href="#ea9d167c1fde90ced95112d68742972cfa668cab">
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
</a>
</li>
<li class="file-stats">
<a href="#57578bfd06d2d648bd8130d304320a8427856aa7">
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperInterface.java
</a>
</li>
<li class="file-stats">
<a href="#eb305568e29f10cff0fd5e7c26da105c4f9df442">
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperService.java
</a>
</li>
<li class="file-stats">
<a href="#9f7c406809243c1a2ebc03ca8e8ed9796665a6cc">
src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperServiceLocator.java
</a>
</li>
<li class="file-stats">
<a href="#dc8af9b70179c15422d9ad178c6d03683d5a4777">
src/vamsas/IMsaWS.java
</a>
</li>
<li class="file-stats">
<a href="#775021b592b5d6c366ec325053b4c733eb23a6f1">
src/vamsas/objects/simple/Alignment.java
</a>
</li>
<li class="file-stats">
<a href="#914e46cc093ae8208a5b56e9c0eea2b5bd4d4d74">
src/vamsas/objects/simple/Alignment_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#7a0f876a1e198ba63024c32420cb82676d8de4bf">
src/vamsas/objects/simple/JpredResult.java
</a>
</li>
<li class="file-stats">
<a href="#22dd75f6b4469d7f5dd55011318170d49a4832c7">
src/vamsas/objects/simple/JpredResult_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#bb53fe1491c6273a957ef3e6f31aa4da1f7faeb8">
src/vamsas/objects/simple/MsaResult.java
</a>
</li>
<li class="file-stats">
<a href="#96304297ef6f5c36d3d6d65909b4b928edef33f3">
src/vamsas/objects/simple/MsaResult_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#267b80baf1b4138e61efeb39787e29a6638b68dc">
src/vamsas/objects/simple/Msfalignment.java
</a>
</li>
<li class="file-stats">
<a href="#b742d1c1e26fba4d26909ea8769dd4d07b15db52">
src/vamsas/objects/simple/Msfalignment_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#166ce85c78d6ea65d26d925beb4c845f70d77fca">
src/vamsas/objects/simple/Object.java
</a>
</li>
<li class="file-stats">
<a href="#d6fea3460a168a51a0249c5e7bba6cecd63ab67f">
src/vamsas/objects/simple/Object_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#eb5ce3d37f157f4b0e7265c9d058eba6051cd8a5">
src/vamsas/objects/simple/Result.java
</a>
</li>
<li class="file-stats">
<a href="#231c1adbabc8ce3a6e9aa56d4ac0e52b5dd58f71">
src/vamsas/objects/simple/Result_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#0825b2a5c9b99e4292a2f9742f21a54d7a84ba38">
src/vamsas/objects/simple/Secstructpred.java
</a>
</li>
<li class="file-stats">
<a href="#544219f1d30891eeb2cf72fe04a2162539fffdfe">
src/vamsas/objects/simple/Secstructpred_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#3814ab7b0d56f79330253f2318f1b7dd4ee2323c">
src/vamsas/objects/simple/SeqSearchResult.java
</a>
</li>
<li class="file-stats">
<a href="#893cab361a2fbac5434580e0cacd80e015a1773c">
src/vamsas/objects/simple/SeqSearchResult_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#7a67146342a795b4331e5ca7bb5ec3b00b008f83">
src/vamsas/objects/simple/Sequence.java
</a>
</li>
<li class="file-stats">
<a href="#7af6603dadc855a7a164602c747b5676894d8e78">
src/vamsas/objects/simple/SequenceSet.java
</a>
</li>
<li class="file-stats">
<a href="#5c3a30f2efd462981fb8ae112b1120f3bc520bc3">
src/vamsas/objects/simple/SequenceSet_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#99edd333f54aa83cdd05c81b6f7becf7bc875aad">
src/vamsas/objects/simple/Sequence_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#9324990cf02b0cd9bca3bdb23e95605bedf6adf7">
src/vamsas/objects/simple/WsJobId.java
</a>
</li>
<li class="file-stats">
<a href="#7f0c0a28f53cef29491817fb9524fef00eca30a5">
src/vamsas/objects/simple/WsJobId_Helper.java
</a>
</li>
<li class="file-stats">
<a href="#a0ee5dbe0f78d73f23207b28700056f027673a53">
test/jalview/analysis/AAFrequencyTest.java
</a>
</li>
<li class="file-stats">
<a href="#39c35cb9546669a367c12faf3460d2406f71a0be">
test/jalview/analysis/AlignSeqTest.java
</a>
</li>
<li class="file-stats">
<a href="#f1b893f73f189c735a2598079e169caa6a4d9abe">
test/jalview/analysis/AlignmentAnnotationUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#d68148d1b2144093419a72c20cccc0d27e1ac7c0">
test/jalview/analysis/AlignmentGenerator.java
</a>
</li>
<li class="file-stats">
<a href="#1d405f43abf10e5aa27e2d7dfc23c9d54d0620f7">
test/jalview/analysis/AlignmentSorterTest.java
</a>
</li>
<li class="file-stats">
<a href="#3cf3ebddb8d5b04280dca77763ba7b696fbb2a21">
test/jalview/analysis/AlignmentUtilsTests.java
</a>
</li>
<li class="file-stats">
<a href="#4cdd5178292c21e53c1eedc2cd8e02302b1d77b9">
test/jalview/analysis/AnnotationSorterTest.java
</a>
</li>
<li class="file-stats">
<a href="#42fc37d21aab56e3d22cd22cc65977bd0f4f7b48">
test/jalview/analysis/AverageDistanceEngineTest.java
</a>
</li>
<li class="file-stats">
<a href="#f0de86c8812654ec05194097214e714bf2b80747">
test/jalview/analysis/CodingUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#4055ace8b2792555615c5c11b052d956afa5198f">
test/jalview/analysis/ConservationTest.java
</a>
</li>
<li class="file-stats">
<a href="#350c879309c770f1b5fc7bb05c557246f9729c33">
test/jalview/analysis/CrossRefTest.java
</a>
</li>
<li class="file-stats">
<a href="#b524b4ff592def9ca18b90f12bd905e2d493e9b7">
test/jalview/analysis/DnaTest.java
</a>
</li>
<li class="file-stats">
<a href="#2e86fcf7d74c0a039ebdb411260024c629037ac4">
test/jalview/analysis/FinderTest.java
</a>
</li>
<li class="file-stats">
<a href="#6865686716a200f3467c375368f4d7166a96c50f">
test/jalview/analysis/GeneticCodesTest.java
</a>
</li>
<li class="file-stats">
<a href="#85f87460f87fa8507d9e34b92257faaedc2deda8">
test/jalview/analysis/GroupingTest.java
</a>
</li>
<li class="file-stats">
<a href="#637df6dd186371faf65a349831aaa7ae8d860e07">
test/jalview/analysis/ParsePropertiesTest.java
</a>
</li>
<li class="file-stats">
<a href="#3443a2f0c0d99fa5ab34346960fc7534419d3dd3">
test/jalview/analysis/RnaTest.java
</a>
</li>
<li class="file-stats">
<a href="#e084111696d9b54282686d48d2dbee6771a71cc1">
test/jalview/analysis/SeqsetUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#10c2947628adae401633a3fbebb5f1882f3aaeb2">
test/jalview/analysis/SequenceIdMatcherTest.java
</a>
</li>
<li class="file-stats">
<a href="#1621d0b9f076e91aef66ca2b458a8a5870b3127a">
test/jalview/analysis/TestAlignSeq.java
</a>
</li>
<li class="file-stats">
<a href="#615040c34ff2e20d1ff672fd06bb1555fcf7e183">
test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
</a>
</li>
<li class="file-stats">
<a href="#d5e8e51fd7942c0d3361b3f2ea7b687537da76c1">
test/jalview/analysis/scoremodels/PIDModelTest.java
</a>
</li>
<li class="file-stats">
<a href="#b1241aed00fc4413320694f03e7d956ac27e693d">
test/jalview/analysis/scoremodels/ScoreMatrixTest.java
</a>
</li>
<li class="file-stats">
<a href="#cefc560e5aaee9082ca8f01352d3a7f386f79a6d">
test/jalview/analysis/scoremodels/ScoreModelsTest.java
</a>
</li>
<li class="file-stats">
<a href="#0e202dc4273baabcd7deee197401f530c410eaf1">
test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java
</a>
</li>
<li class="file-stats">
<a href="#658b8b7ff73fba9eb5211dd1aefc85489efdc056">
test/jalview/bin/ArgsParserTest.java
</a>
</li>
<li class="file-stats">
<a href="#d1fc58310629f204401b55b49225cc82497d39c4">
test/jalview/bin/CacheTest.java
</a>
</li>
<li class="file-stats">
<a href="#8630cb01f4bc46a8248251a9a9446546ef58409c">
test/jalview/bin/CommandLineOperations.java
</a>
</li>
<li class="file-stats">
<a href="#642dbdcacb0b12d2f27644161ea690d5892fdd28">
test/jalview/bin/CommandLineOperationsNG.java
</a>
</li>
<li class="file-stats">
<a href="#51413477a04f574e2aab1a68f2e57b5a7ea53de1">
test/jalview/bin/CommandsTest.java
</a>
</li>
<li class="file-stats">
<a href="#9275f2e7a6d00107a191a4db986ba06b1d547fc2">
test/jalview/bin/CommandsTest2.java
</a>
</li>
<li class="file-stats">
<a href="#2abc65993a26ea89cfe3cd853a995fb558cb55ac">
test/jalview/bin/HiDPISettingTest1.java
</a>
</li>
<li class="file-stats">
<a href="#38e6512b86187738a5f8bb5c3d2891cc6ef67613">
test/jalview/bin/HiDPISettingTest2.java
</a>
</li>
<li class="file-stats">
<a href="#822566d49068ee8586996b2370f129831cda6316">
test/jalview/bin/JalviewLiteTest.java
</a>
</li>
<li class="file-stats">
<a href="#037f629163cdecc893655183428a8cb8a48dba41">
test/jalview/bin/MemorySettingTest.java
</a>
</li>
<li class="file-stats">
<a href="#6fecd93ba2f2f317890d9e358e9b8c7c60445e11">
test/jalview/bin/argparser/ArgParserTest.java
</a>
</li>
<li class="file-stats">
<a href="#33f7fae72b63f922902b51839395d334211d4508">
test/jalview/commands/EditCommandTest.java
</a>
</li>
<li class="file-stats">
<a href="#d93942aa4f830a2728575f15f27b53dfb369c053">
test/jalview/commands/TrimRegionCommandTest.java
</a>
</li>
<li class="file-stats">
<a href="#bfafd0434baf73d8466627ef74836b9bdd9b6ec5">
test/jalview/controller/AlignViewControllerTest.java
</a>
</li>
<li class="file-stats">
<a href="#48eeac62b6fecb14ccf78b6aec85abe8a3871731">
test/jalview/datamodel/AlignedCodonFrameTest.java
</a>
</li>
<li class="file-stats">
<a href="#63152e894e1d469e79abf4d3e50dcc693b61e03d">
test/jalview/datamodel/AlignedCodonIteratorTest.java
</a>
</li>
<li class="file-stats">
<a href="#83bfcb6df642ba172a6f0d72204917e07c390b91">
test/jalview/datamodel/AlignedCodonTest.java
</a>
</li>
<li class="file-stats">
<a href="#59eeb5a87266499dc74db082983bed1fb019bdcf">
test/jalview/datamodel/AlignmentAnnotationTests.java
</a>
</li>
<li class="file-stats">
<a href="#818d4ec69df57c87c8faa8f4d46ea9bc3501429e">
test/jalview/datamodel/AlignmentTest.java
</a>
</li>
<li class="file-stats">
<a href="#5541949aa746b23c4313481cf870d5dfe3aeb263">
test/jalview/datamodel/AlignmentViewTest.java
</a>
</li>
<li class="file-stats">
<a href="#078fc9bf6454e301e86121a3ae1f717ccbd66d8a">
test/jalview/datamodel/AllColsIteratorTest.java
</a>
</li>
<li class="file-stats">
<a href="#9658943eaea6caa2f1c8b750bf16894f9b3268c6">
test/jalview/datamodel/AllRowsIteratorTest.java
</a>
</li>
<li class="file-stats">
<a href="#cdaaa7d5b2a3b13dc3113fb3e8ae815300ab17c2">
test/jalview/datamodel/CigarArrayTest.java
</a>
</li>
<li class="file-stats">
<a href="#b661ccd907936683e95caecd939be1e499960d47">
test/jalview/datamodel/ColumnSelectionTest.java
</a>
</li>
<li class="file-stats">
<a href="#fde449d10b6cdecebff29dd8a61abaaf1e4aa48d">
test/jalview/datamodel/ConcurrentModificationTest.java
</a>
</li>
<li class="file-stats">
<a href="#c780c70fff2884bbdf4ce8b7532a894142f2bf2d">
test/jalview/datamodel/ContactMatrixTest.java
</a>
</li>
<li class="file-stats">
<a href="#794543cebbe2a584cb2f03f46f745c9ee90fd17d">
test/jalview/datamodel/ContactRangeTest.java
</a>
</li>
<li class="file-stats">
<a href="#b884f2f064a360021565d2c2ea3d6f4cd8cd12fc">
test/jalview/datamodel/DBRefEntryTest.java
</a>
</li>
<li class="file-stats">
<a href="#01014ffdedece87afd206abc6946005e02537888">
test/jalview/datamodel/HiddenColumnsCursorTest.java
</a>
</li>
<li class="file-stats">
<a href="#f159bae7c2bed10831db7c82418e28f63d3798e7">
test/jalview/datamodel/HiddenColumnsTest.java
</a>
</li>
<li class="file-stats">
<a href="#e39f5c35621c1e20d4e7818068c37a6a02caca98">
test/jalview/datamodel/HiddenSequencesTest.java
</a>
</li>
<li class="file-stats">
<a href="#7363765579db546bfed481d2ee6d1d5dd21b9fbd">
test/jalview/datamodel/MappedFeaturesTest.java
</a>
</li>
<li class="file-stats">
<a href="#97dbf5892f938c6ca6c01ac83b199b64aeaeb1fa">
test/jalview/datamodel/MappingTest.java
</a>
</li>
<li class="file-stats">
<a href="#a66cd1fcf28c49f39c226fc16c6f0b1ace9d82b0">
test/jalview/datamodel/MappingTypeTest.java
</a>
</li>
<li class="file-stats">
<a href="#ade14df786d7c15d339b3795e94abf839e3e1ad7">
test/jalview/datamodel/MatchTest.java
</a>
</li>
<li class="file-stats">
<a href="#fda99441d2ce3b169c8559ab69af0d00bd5b6272">
test/jalview/datamodel/PAEContactMatrixTest.java
</a>
</li>
<li class="file-stats">
<a href="#1d3949011766b27e830a9935ecff8f50073328b7">
test/jalview/datamodel/PDBEntryTest.java
</a>
</li>
<li class="file-stats">
<a href="#79f2c98d8d50684ce306e86e8b801dc56cda9b3d">
test/jalview/datamodel/RangeElementsIteratorTest.java
</a>
</li>
<li class="file-stats">
<a href="#11155a4ba5e2c3e7bc74547149099e171ac86f4e">
test/jalview/datamodel/ResidueCountTest.java
</a>
</li>
<li class="file-stats">
<a href="#c2b62699313b53e6344518dac51702184d7b4339">
test/jalview/datamodel/SearchResultsTest.java
</a>
</li>
<li class="file-stats">
<a href="#8bc81e900a4c095d8c8162317a6c576534b7c88c">
test/jalview/datamodel/SeqCigarTest.java
</a>
</li>
<li class="file-stats">
<a href="#77c8b3d42b5b932ddfb205748475cf1a10d428ab">
test/jalview/datamodel/SequenceDummyTest.java
</a>
</li>
<li class="file-stats">
<a href="#4bb755207efa69ec06bdb6f769e7138e325ef09b">
test/jalview/datamodel/SequenceFeatureTest.java
</a>
</li>
<li class="file-stats">
<a href="#0c4f0c51950db7eb5421b2eeb0518371ce0fa23e">
test/jalview/datamodel/SequenceGroupTest.java
</a>
</li>
<li class="file-stats">
<a href="#43c83a2bec64163cb63805ce54ae0799a1b33607">
test/jalview/datamodel/SequenceTest.java
</a>
</li>
<li class="file-stats">
<a href="#fb2571ce6363561b647aee67f9f5fd2e2f24f1af">
test/jalview/datamodel/StartRegionIteratorTest.java
</a>
</li>
<li class="file-stats">
<a href="#c0d64e760e86a9951e88f6026c999c69a56ea995">
test/jalview/datamodel/VisibleContigsIteratorTest.java
</a>
</li>
<li class="file-stats">
<a href="#be10ca943a92fe73766c6fcc07ed1689898af8c2">
test/jalview/datamodel/VisibleRowsIteratorTest.java
</a>
</li>
<li class="file-stats">
<a href="#12b3c4ab5eae4107df38f7d971529d59af247c2c">
test/jalview/datamodel/features/FeatureAttributesTest.java
</a>
</li>
<li class="file-stats">
<a href="#db4a474c7eb629f0ccf2b705432315e05ab372e1">
test/jalview/datamodel/features/FeatureMatcherSetTest.java
</a>
</li>
<li class="file-stats">
<a href="#2d31de1b26be530f2ae8499d7bd9fda2c8017b9f">
test/jalview/datamodel/features/FeatureMatcherTest.java
</a>
</li>
<li class="file-stats">
<a href="#4b21b348d795de4fd6132ed1a87640e5dcf984b1">
test/jalview/datamodel/features/FeatureStoreTest.java
</a>
</li>
<li class="file-stats">
<a href="#96c23a7c6e1f1f3699ada4075367e86d9635ed0a">
test/jalview/datamodel/features/SequenceFeaturesTest.java
</a>
</li>
<li class="file-stats">
<a href="#1c990386111910261361df150cfa41ad66255433">
test/jalview/ext/android/SparseDoubleArrayTest.java
</a>
</li>
<li class="file-stats">
<a href="#c21e7b3c8aaa15352e9f6b045c8bef3a6a1efc42">
test/jalview/ext/android/SparseIntArrayTest.java
</a>
</li>
<li class="file-stats">
<a href="#debb73afdced7ba9ce6678464c5861f7317388f5">
test/jalview/ext/android/SparseShortArrayTest.java
</a>
</li>
<li class="file-stats">
<a href="#0d1aa81dc6f7e72b9eae48862655fc91c4704d5d">
test/jalview/ext/ensembl/EnsemblCdnaTest.java
</a>
</li>
<li class="file-stats">
<a href="#062af4b38a6ea7fec425b06a7bc36f142eb0aaa6">
test/jalview/ext/ensembl/EnsemblCdsTest.java
</a>
</li>
<li class="file-stats">
<a href="#c82dff61cf56af89024937c5578aab3acad03386">
test/jalview/ext/ensembl/EnsemblGeneTest.java
</a>
</li>
<li class="file-stats">
<a href="#9e505c6ac5e5e3a034d8bb8a299559728868f020">
test/jalview/ext/ensembl/EnsemblGenomeTest.java
</a>
</li>
<li class="file-stats">
<a href="#5894e8d03e38aa475d14ce320341fce5191bae7a">
test/jalview/ext/ensembl/EnsemblProteinTest.java
</a>
</li>
<li class="file-stats">
<a href="#1565d0f8b45134c37ecccb5ccf21c77aa34b1cb2">
test/jalview/ext/ensembl/EnsemblRestClientTest.java
</a>
</li>
<li class="file-stats">
<a href="#a45c39cbe58dbe1743b5ac268a4bf3f19592685f">
test/jalview/ext/ensembl/EnsemblSeqProxyAdapter.java
</a>
</li>
<li class="file-stats">
<a href="#fc68ea8340d19ad89b6dc8f81bf198b75cec9d92">
test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
</a>
</li>
<li class="file-stats">
<a href="#315842387d83d5b782af2ce4240017909ddddcdf">
test/jalview/ext/ensembl/EnsemblXrefTest.java
</a>
</li>
<li class="file-stats">
<a href="#e1960d38d322cb09e02e89b70c5a6933b86255e6">
test/jalview/ext/ensembl/SpeciesTest.java
</a>
</li>
<li class="file-stats">
<a href="#3bd3a13d5e6472a3a4c31f26e90714635c39a055">
test/jalview/ext/htsjdk/TestHtsContigDb.java
</a>
</li>
<li class="file-stats">
<a href="#b684d3bfc01e6033c59af65cb55ef536a3e2b798">
test/jalview/ext/htsjdk/VCFReaderTest.java
</a>
</li>
<li class="file-stats">
<a href="#16b5a338877d0ebcdd2fdb860e0602429d5b28e6">
test/jalview/ext/jmol/JmolCommandsTest.java
</a>
</li>
<li class="file-stats">
<a href="#5d6ea31519b29e45635941a87ed9d3414c22a8f7">
test/jalview/ext/jmol/JmolParserTest.java
</a>
</li>
<li class="file-stats">
<a href="#905118b8d5d8d740e7a86e452536dcdc125a804b">
test/jalview/ext/jmol/JmolViewerTest.java
</a>
</li>
<li class="file-stats">
<a href="#f408a72ad754e1928c88f75a1f098e0d5cf4a1b3">
test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
</a>
</li>
<li class="file-stats">
<a href="#08f7d88f0b92b65ba59d27f1007309a1021faf30">
test/jalview/ext/paradise/TestAnnotate3D.java
</a>
</li>
<li class="file-stats">
<a href="#dc3beb9c7694753e38b199f429256a97e84ee0ff">
test/jalview/ext/pymol/PymolCommandsTest.java
</a>
</li>
<li class="file-stats">
<a href="#35cd7a446a881e6ba75945fef841b390383f9dff">
test/jalview/ext/pymol/PymolManagerTest.java
</a>
</li>
<li class="file-stats">
<a href="#efc2109fe0e554150d3b426bf0433cce7aae12b1">
test/jalview/ext/rbvi/chimera/AllTests.java
</a>
</li>
<li class="file-stats">
<a href="#f4643e8a634b30ee745d4b3cfa2e28300c473204">
test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
</a>
</li>
<li class="file-stats">
<a href="#28b8d59593642cca2a06407fa0d7928706b7ed08">
test/jalview/ext/rbvi/chimera/ChimeraConnect.java
</a>
</li>
<li class="file-stats">
<a href="#44e2ac5edfd074b5c2cd6f30ac28477b7c926d4a">
test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java
</a>
</li>
<li class="file-stats">
<a href="#efe8e0cb5e73fceb1e7cc4f4d761f3d8460081c2">
test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
</a>
</li>
<li class="file-stats">
<a href="#b23c70f2677e3eb15a008fbdf1fac47b053908a9">
test/jalview/ext/so/SequenceOntologyTest.java
</a>
</li>
<li class="file-stats">
<a href="#4f8fcd7dc05de774d9dd20605c947652ecb8da8c">
test/jalview/fts/core/FTSRestClientTest.java
</a>
</li>
<li class="file-stats">
<a href="#0f71ef19bc36d1ca933c0b1724031f2a9d51ec80">
test/jalview/fts/service/pdb/PDBFTSPanelTest.java
</a>
</li>
<li class="file-stats">
<a href="#da8aa8db692537f3dc735aa237b779f2a3dd84e9">
test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
</a>
</li>
<li class="file-stats">
<a href="#8e730a1019c02c8f15b28f4eef3277b4c08f08c0">
test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java
</a>
</li>
<li class="file-stats">
<a href="#1e792e3d43271ed694cd7f1920c0e22a4f876f18">
test/jalview/fts/threedbeacons/TDBeaconsPanelTest.java
</a>
</li>
<li class="file-stats">
<a href="#bee3056e0a2dbc909989abf58b87ffc98e2246df">
test/jalview/gui/AlignFrameTest.java
</a>
</li>
<li class="file-stats">
<a href="#a8d086c51710dba9327cfeedf3f6f0bdd08f403d">
test/jalview/gui/AlignViewportTest.java
</a>
</li>
<li class="file-stats">
<a href="#cbe188801783d7791385c45539e030afcc7472fc">
test/jalview/gui/AlignmentPanelTest.java
</a>
</li>
<li class="file-stats">
<a href="#37286118eb7ca9c3bf9622c16d7b0747d9e9b1f3">
test/jalview/gui/AnnotationChooserTest.java
</a>
</li>
<li class="file-stats">
<a href="#1a886d124577d6b1b38df46cdafaf76e3cc441b0">
test/jalview/gui/AnnotationColumnChooserTest.java
</a>
</li>
<li class="file-stats">
<a href="#fe658344d564cb03c609e3183484828426e9b30d">
test/jalview/gui/AnnotationLabelsTest.java
</a>
</li>
<li class="file-stats">
<a href="#104a4863bb0f86c90d1ad63ef79c5aeb546b2f79">
test/jalview/gui/AnnotationLabelsTest2.java
</a>
</li>
<li class="file-stats">
<a href="#257f9f30098d8d412644d1aa1b8d634fa845831b">
test/jalview/gui/AnnotationPanelTest.java
</a>
</li>
<li class="file-stats">
<a href="#2d739ad7473b6ce8bce0b5da4acf39f85ed3e7ab">
test/jalview/gui/AnnotationRowFilterTest.java
</a>
</li>
<li class="file-stats">
<a href="#d968ac15da8a8feb4932516ad4b384485b367ca9">
test/jalview/gui/AppVarnaTest.java
</a>
</li>
<li class="file-stats">
<a href="#7ffea87f30246b410f8d0083cc1df718ac97f6cb">
test/jalview/gui/AssociatePDBFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#e8510adf18986e8669da0e1293f35677d4877916">
test/jalview/gui/CalculationChooserTest.java
</a>
</li>
<li class="file-stats">
<a href="#879be67b271637c20934d5bbe224751b9fd1156d">
test/jalview/gui/ColourMenuHelperTest.java
</a>
</li>
<li class="file-stats">
<a href="#205b89e67a31b92c10cc386393d5a4f61458c708">
test/jalview/gui/DesktopTests.java
</a>
</li>
<li class="file-stats">
<a href="#ed53aa6c1aa329b16a5253923b7b85d0d2608921">
test/jalview/gui/FeatureSettingsTest.java
</a>
</li>
<li class="file-stats">
<a href="#dd2d8d624ad05b73c89f91ef244e3ed9ac5db08d">
test/jalview/gui/FontChooserTest.java
</a>
</li>
<li class="file-stats">
<a href="#90bd81c4030efa0431f75afde613b393b056d020">
test/jalview/gui/FreeUpMemoryTest.java
</a>
</li>
<li class="file-stats">
<a href="#cb53204062cbdb5ef8d554bcee02744062587c25">
test/jalview/gui/HelpTest.java
</a>
</li>
<li class="file-stats">
<a href="#173a5468a9aec504f3823af56221bc20eee95fbc">
test/jalview/gui/JAL1353bugdemo.java
</a>
</li>
<li class="file-stats">
<a href="#c9f8e982105e7ca4c9ebcbe22ea02136e3eb2bd6">
test/jalview/gui/JvOptionPaneTest.java
</a>
</li>
<li class="file-stats">
<a href="#ea20c4b21926e8d0bf893f253c8511d3f8dfa154">
test/jalview/gui/JvSwingUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#9750a609473c2f515649bf51585fb468e12e0850">
test/jalview/gui/MouseEventDemo.java
</a>
</li>
<li class="file-stats">
<a href="#46aa8c6fdc48110fa4cf2bd00d45ed3fd52f01b2">
test/jalview/gui/PaintRefresherTest.java
</a>
</li>
<li class="file-stats">
<a href="#f2f813108ba95028e3272afa491bdeb45b2638d4">
test/jalview/gui/PairwiseAlignmentPanelTest.java
</a>
</li>
<li class="file-stats">
<a href="#8d7df39ee90e695f59171a749cc6da52ff118536">
test/jalview/gui/PopupMenuTest.java
</a>
</li>
<li class="file-stats">
<a href="#968a4169548b317f634aa0290cdb533d15469464">
test/jalview/gui/ProgressBarTest.java
</a>
</li>
<li class="file-stats">
<a href="#2775bb4cdac6cc2d072bc22539721801e4022d21">
test/jalview/gui/QuitHandlerTest.java
</a>
</li>
<li class="file-stats">
<a href="#3e7932e6285a9955c17b6c42acaefed815fb01db">
test/jalview/gui/ScalePanelTest.java
</a>
</li>
<li class="file-stats">
<a href="#5993aa53414ab8c070ccb065f50b78aee8c93eec">
test/jalview/gui/SeqCanvasTest.java
</a>
</li>
<li class="file-stats">
<a href="#74be1026e6edf74a2183956b0b48b7dfac1d3627">
test/jalview/gui/SeqPanelTest.java
</a>
</li>
<li class="file-stats">
<a href="#9f8789304292a6efbf0ee78d28bc8907687ccf0c">
test/jalview/gui/SequenceRendererTest.java
</a>
</li>
<li class="file-stats">
<a href="#3c672fa5c32a62f4f42c2e7ca369c006aef3bd29">
test/jalview/gui/StructureChooserTest.java
</a>
</li>
<li class="file-stats">
<a href="#9259502c4d1470655cc175360360191e6db9cda9">
test/jalview/gui/StructureViewerTest.java
</a>
</li>
<li class="file-stats">
<a href="#e1dd4b84735111051fd693d96f66a8d370c820d9">
test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
</a>
</li>
<li class="file-stats">
<a href="#ec74e79e86d1fa2f40ce8da634bd52ab1bfd9c38">
test/jalview/io/AnnotatedPDBFileInputTest.java
</a>
</li>
<li class="file-stats">
<a href="#8b2950043023f881b2c737529a2adbc2a4b1e0f6">
test/jalview/io/AnnotationExporterTest.java
</a>
</li>
<li class="file-stats">
<a href="#59193f71bc1ef54c236c5c9a662aec6bd184c75a">
test/jalview/io/AnnotationFileIOTest.java
</a>
</li>
<li class="file-stats">
<a href="#1f08d8c5e1f4939429bfb251e04d05631a15a6e3">
test/jalview/io/BackupFilesTest.java
</a>
</li>
<li class="file-stats">
<a href="#658b06f54e774ed1134b18b4acfa24b770f7bacd">
test/jalview/io/BioJsHTMLOutputTest.java
</a>
</li>
<li class="file-stats">
<a href="#f2ad60603d3412f5456cc0f18cedb2da955ebb61">
test/jalview/io/ClustalFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#0f55b2e09312fbbde03abf019bc572ee3ed1e5c7">
test/jalview/io/CrossRef2xmlTests.java
</a>
</li>
<li class="file-stats">
<a href="#a8a63625dca4cbf36f68cab4a6a6bb17f550a9bb">
test/jalview/io/EmblFlatFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#d2ca4c598247f9bb382cb0fc2a89bb5f733b0b17">
test/jalview/io/FeaturesFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#d562c0679dd01f34cbeedfe44c393557313c2da6">
test/jalview/io/FileFormatsTest.java
</a>
</li>
<li class="file-stats">
<a href="#14fd3f4ec1cfdfe9125f6416e3122fb5f88a18a4">
test/jalview/io/FileIOTester.java
</a>
</li>
<li class="file-stats">
<a href="#23f0987caf31e4930ff203643b7e86bb8a1de4dd">
test/jalview/io/FileLoaderTest.java
</a>
</li>
<li class="file-stats">
<a href="#4a285dc2ad388dea9e0eb6918069fd16cde03437">
test/jalview/io/FormatAdapterTest.java
</a>
</li>
<li class="file-stats">
<a href="#b92b049b40f5b767b0ea3c562786862f8602daf0">
test/jalview/io/GenBankFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#1bfd0f97a1cc735a5d362ca3295c84c3a2cf0217">
test/jalview/io/HtmlFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#89c2684ee56a55ae5f53fc843380a4aeb40de2cb">
test/jalview/io/IdentifyFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#4d0ccbdbd3c55a4481eabfc52a3f4f5884b68859">
test/jalview/io/JSONFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#ab1c3ecae9be25e0165fc9a4b74574782bb6ee08">
test/jalview/io/Jalview2xmlBase.java
</a>
</li>
<li class="file-stats">
<a href="#b95aad89d4ec219e2eaa762070a145fa0bacdd11">
test/jalview/io/JalviewExportPropertiesTests.java
</a>
</li>
<li class="file-stats">
<a href="#9592636122415ba9572f6bb40b467ddb584052d7">
test/jalview/io/JalviewFileViewTest.java
</a>
</li>
<li class="file-stats">
<a href="#5728857ee0c082d83c5b6afc3d6e9c4256360825">
test/jalview/io/NewickFileTests.java
</a>
</li>
<li class="file-stats">
<a href="#997291966bc397bb1dfd81224dd0088bba14951f">
test/jalview/io/PfamFormatInputTest.java
</a>
</li>
<li class="file-stats">
<a href="#ef47777f185de42e4edf5642a943e4fd6ff43a0d">
test/jalview/io/PhylipFileTests.java
</a>
</li>
<li class="file-stats">
<a href="#883015ca976a4c77ab4a876c13789bbdd18251a8">
test/jalview/io/RNAMLfileTest.java
</a>
</li>
<li class="file-stats">
<a href="#eaadac23e68c57de6d80771896d9726455779ebf">
test/jalview/io/ScoreMatrixFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#572ee3b7fad06e6c5df6f3f3b6554c87b45712d2">
test/jalview/io/SequenceAnnotationReportTest.java
</a>
</li>
<li class="file-stats">
<a href="#cd6d3022cd06ea5538dbeb98930f7435b7b2c4fa">
test/jalview/io/StockholmFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#93f6323f6ef7f3682ba448e8fe0f24d9647e5a82">
test/jalview/io/TCoffeeScoreFileTest.java
</a>
</li>
<li class="file-stats">
<a href="#65ae02bd53b805087bc1d95d5f758ae1dca240ce">
test/jalview/io/WindowsFileLoadAndSaveTest.java
</a>
</li>
<li class="file-stats">
<a href="#faf993f6cef551b72dc723f8c425897ddec9b868">
test/jalview/io/cache/AppCacheTest.java
</a>
</li>
<li class="file-stats">
<a href="#52a7f375f5a44eb46d6cc5ea8e5e2605f72500f4">
test/jalview/io/cache/JvCacheableInputBoxTest.java
</a>
</li>
<li class="file-stats">
<a href="#54bd1b5f847144b53d7aaf337936f6bc912cb177">
test/jalview/io/gff/ExonerateHelperTest.java
</a>
</li>
<li class="file-stats">
<a href="#00e89600342eb54a58b105d34dc906eb4d26d445">
test/jalview/io/gff/Gff3HelperTest.java
</a>
</li>
<li class="file-stats">
<a href="#c4a4ea0e6b52f594ff59641dedef6fdc47b2eca6">
test/jalview/io/gff/GffHelperBaseTest.java
</a>
</li>
<li class="file-stats">
<a href="#d7e9cb1dad8165b0fcf824d7389e034e8af64c67">
test/jalview/io/gff/GffHelperFactoryTest.java
</a>
</li>
<li class="file-stats">
<a href="#0825bf0cec62928cd0d29147c8854a8f78d019bf">
test/jalview/io/gff/GffTests.java
</a>
</li>
<li class="file-stats">
<a href="#0eda101267480a05a11a6560dac9367215991964">
test/jalview/io/gff/InterProScanHelperTest.java
</a>
</li>
<li class="file-stats">
<a href="#3fdc332da4ff70033dfc6510d1093da2ef6417e2">
test/jalview/io/gff/SequenceOntologyLiteTest.java
</a>
</li>
<li class="file-stats">
<a href="#e6875ff94c5499d67a4dc852dd2860a63e3536a8">
test/jalview/io/vcf/VCFLoaderTest.java
</a>
</li>
<li class="file-stats">
<a href="#6163f787ba826b3149ee690d01783fe0ae1bacc8">
test/jalview/math/MatrixTest.java
</a>
</li>
<li class="file-stats">
<a href="#5669e23a4d61c892cb82c69dd668189f7eac1cf9">
test/jalview/math/RotatableMatrixTest.java
</a>
</li>
<li class="file-stats">
<a href="#1a2933fb65b3d96e3dabc9225513acc1770b02c3">
test/jalview/math/SparseMatrixTest.java
</a>
</li>
<li class="file-stats">
<a href="#c7af0ae75208a5678958d6d1471b8a11cd6c1226">
test/jalview/project/Jalview2xmlTests.java
</a>
</li>
<li class="file-stats">
<a href="#28c2284c68eef843aa5b4e5fbcf9f812c354e386">
test/jalview/renderer/ContactGeometryTest.java
</a>
</li>
<li class="file-stats">
<a href="#b1266df09febf9a3f1d3c3a65db74c3aed410c9f">
test/jalview/renderer/OverviewRendererTest.java
</a>
</li>
<li class="file-stats">
<a href="#839910bce095620a0623da6ab99dc3d1551b236a">
test/jalview/renderer/OverviewResColourFinderTest.java
</a>
</li>
<li class="file-stats">
<a href="#e342b2bff234ae13a767940102fe07ad27519b27">
test/jalview/renderer/ResidueColourFinderTest.java
</a>
</li>
<li class="file-stats">
<a href="#221a172f88b1df293afd19b7cd3d14ad57c98b6d">
test/jalview/renderer/ResidueShaderTest.java
</a>
</li>
<li class="file-stats">
<a href="#18f40ad2d89486675b18d8d17cb849afb000b6e6">
test/jalview/renderer/ScaleRendererTest.java
</a>
</li>
<li class="file-stats">
<a href="#052c858b5b6460fb820fd7884566265cd5f30c0c">
test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
</a>
</li>
<li class="file-stats">
<a href="#83468a4235e8de782e83630cc92b9b4bcef08aa3">
test/jalview/renderer/seqfeatures/FeatureRendererTest.java
</a>
</li>
<li class="file-stats">
<a href="#d44d4b394ad547d5aa8987d9acbecc8544428e91">
test/jalview/schemes/AnnotationColourGradientTest.java
</a>
</li>
<li class="file-stats">
<a href="#8b3fe7c9276146ce3fbab8ff24dc9c7981ba5067">
test/jalview/schemes/Blosum62ColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#3088ecbc88dc9030fdea9e13135d4db890cbaa0f">
test/jalview/schemes/BuriedColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#3fdf87ac2cc89d44781bd5417f1a32b9918d5a4a">
test/jalview/schemes/ClustalxColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#2bc3f2d8f6398a9eb58a845e1c5facdb1176e87c">
test/jalview/schemes/ColourSchemePropertyTest.java
</a>
</li>
<li class="file-stats">
<a href="#9265889cbc99ae42229d88ab4a6767909edb605a">
test/jalview/schemes/ColourSchemesTest.java
</a>
</li>
<li class="file-stats">
<a href="#e3fc18193191196db3b27cf80a5b99e2837016b7">
test/jalview/schemes/FeatureColourTest.java
</a>
</li>
<li class="file-stats">
<a href="#2284752eb26d88d79a79af5f28bc1237626732cd">
test/jalview/schemes/HelixColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#32d60dd3d023732e9c5e7594a7a24b78d943d3fb">
test/jalview/schemes/HydrophobicColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#0260b1aafa221c4f3c01d2c11bf11f8d72b759f0">
test/jalview/schemes/JalviewColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#db9cd02576fadd4638951df8a6075a9350b5934d">
test/jalview/schemes/PIDColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#004b3bae0b7cdf18d82efcf72b8cc1fb91fc5fc7">
test/jalview/schemes/ResidueColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#a43cb08a64505f83396ba36abc43cda58cbf846c">
test/jalview/schemes/ResiduePropertiesTest.java
</a>
</li>
<li class="file-stats">
<a href="#de72100b48aeac2dbcb4156cdc71b4bd48e09b0c">
test/jalview/schemes/StrandColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#f4bda04de9bffd15dcbb75125c218df78d885b1d">
test/jalview/schemes/TurnColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#6420b33156f76c55dfab98f487f1c6f7ef3d6588">
test/jalview/schemes/UserColourSchemeTest.java
</a>
</li>
<li class="file-stats">
<a href="#a405eed0fea6f7aa495637d5eb9b31831f0b6588">
test/jalview/structure/AtomSpecModelTest.java
</a>
</li>
<li class="file-stats">
<a href="#b7f04a014b57e5c7f03a6e8e19ee8b9879e9d6b9">
test/jalview/structure/AtomSpecTest.java
</a>
</li>
<li class="file-stats">
<a href="#1ec61b02c69bf9a95ce18d7897476fd618a86f90">
test/jalview/structure/Mapping.java
</a>
</li>
<li class="file-stats">
<a href="#9987ef6a63b925a079c10ee41265366c614f4870">
test/jalview/structure/StructureCommandTest.java
</a>
</li>
<li class="file-stats">
<a href="#b82f777c4c2e7bea76a6b8dde844e9dc77845495">
test/jalview/structure/StructureMappingTest.java
</a>
</li>
<li class="file-stats">
<a href="#4d00ce5c9b0748eaf86fe52a9b80a4a581177ab5">
test/jalview/structure/StructureSelectionManagerTest.java
</a>
</li>
<li class="file-stats">
<a href="#21bf62d2569846b24fae184f12cb833957ad7533">
test/jalview/structures/models/AAStructureBindingModelTest.java
</a>
</li>
<li class="file-stats">
<a href="#969fd1808a6870816fb820018a8f585309a08eb5">
test/jalview/urls/AppletUrlProviderFactoryTest.java
</a>
</li>
<li class="file-stats">
<a href="#6b8a072a080245e64fc1c1ec637f40c51169daab">
test/jalview/urls/CustomUrlProviderTest.java
</a>
</li>
<li class="file-stats">
<a href="#154a2d6323884d144128106e48cc3c67c28adab0">
test/jalview/urls/DesktopUrlProviderFactoryTest.java
</a>
</li>
<li class="file-stats">
<a href="#675b417d69292c6dd48fbfe60ddbfd839b1a95b7">
test/jalview/urls/IdentifiersUrlProviderTest.java
</a>
</li>
<li class="file-stats">
<a href="#682ef4feb2d695f31ec536fbe996fc415add8ca0">
test/jalview/urls/UrlLinkDisplayTest.java
</a>
</li>
<li class="file-stats">
<a href="#69e76a1cb5e6100bf5a6fdd3e5e938311d6a8342">
test/jalview/urls/UrlLinkTableModelTest.java
</a>
</li>
<li class="file-stats">
<a href="#9bdb4045e62a35a6d42eb61d17968d3fd74d95e7">
test/jalview/urls/UrlProviderTest.java
</a>
</li>
<li class="file-stats">
<a href="#6023feb6fe83b076eb5e574f538fafa7aca427fb">
test/jalview/util/ArrayUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#e43f4a76e21b114d462b10c182f9c63fb9ccb0f3">
test/jalview/util/CaseInsensitiveStringTest.java
</a>
</li>
<li class="file-stats">
<a href="#576ceff6d6815c86f5b380fb72c736f74aba4590">
test/jalview/util/ColorUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#38cee79f1f1c07728e32c7b9a87b3f9d8b70e99b">
test/jalview/util/ComparisonTest.java
</a>
</li>
<li class="file-stats">
<a href="#a0d2662d6878cfca28b61327ffee099527775ebe">
test/jalview/util/DBRefUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#11855597cec19de9e65a01e11ae678228d9048b8">
test/jalview/util/DnaUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#d44529c3bc5ddcbee6c926b684574404f8aeebb8">
test/jalview/util/FileUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#18d779805f49477beeef694596a49f1e2137a4cc">
test/jalview/util/FormatTest.java
</a>
</li>
<li class="file-stats">
<a href="#5564241fd0777ae02f4159a0f8b5b7cd7e11c62c">
test/jalview/util/ImageMakerTest.java
</a>
</li>
<li class="file-stats">
<a href="#e1748623bf6b162b5e1f55beaf5711e1a0e2dc97">
test/jalview/util/JSONUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#e7ed3b99e6cdff2c9e733186a65a26c01b95092d">
test/jalview/util/Log4jTest.java
</a>
</li>
<li class="file-stats">
<a href="#abc20c9bb2064e26a7b1ec5b05413283861a90f4">
test/jalview/util/MapListTest.java
</a>
</li>
<li class="file-stats">
<a href="#991c1d424eb2f11b80bf8c3a47864b8d6a796720">
test/jalview/util/MappingUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#d2e964a4e0d314e2242a1278f2796dd4ccdebdf2">
test/jalview/util/MathUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#e02b7f80e43158d19ea533b8d295a221b0aad2cb">
test/jalview/util/MessageManagerTest.java
</a>
</li>
<li class="file-stats">
<a href="#afd3b5d5a3910c3833718209929dadb782e7bc8d">
test/jalview/util/ParseHtmlBodyAndLinksTest.java
</a>
</li>
<li class="file-stats">
<a href="#f52877e2464839204f785dd10f1a8b03e91756ca">
test/jalview/util/PlatformTest.java
</a>
</li>
<li class="file-stats">
<a href="#084d8c89fa3b732ab2fa226f0cd9145db2d1c668">
test/jalview/util/QuickSortTest.java
</a>
</li>
<li class="file-stats">
<a href="#72ae42e4f4adab30b75316957f87e1bc7f9b0536">
test/jalview/util/SetUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#aab15df24b2b8426cb9fa8e89b859b47630fae3a">
test/jalview/util/ShiftListTest.java
</a>
</li>
<li class="file-stats">
<a href="#a7fe61b92a7d9232178b544cdaa60b91b6c12f97">
test/jalview/util/SparseCountTest.java
</a>
</li>
<li class="file-stats">
<a href="#fd7d21181ffad2d52066a17d5f4a4204f523db81">
test/jalview/util/StringUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#7bb518c561f7c439cb2dd32ee7a20dd66f334def">
test/jalview/util/UrlLinkTest.java
</a>
</li>
<li class="file-stats">
<a href="#c1ebb59c291c0cf4f3a1670924b03520d929772f">
test/jalview/util/dialogrunner/DialogRunnerTest.java
</a>
</li>
<li class="file-stats">
<a href="#a22dc25ab8bbefc7df86f3c2e96774cf9dea21a6">
test/jalview/util/imagemaker/BitmapImageSizeTest.java
</a>
</li>
<li class="file-stats">
<a href="#e30298a62a137f4b53fb7c778920974047111393">
test/jalview/util/matcher/ConditionTest.java
</a>
</li>
<li class="file-stats">
<a href="#550945c7c9604cb558fff6633e2c6ff95396c6b4">
test/jalview/util/matcher/MatcherTest.java
</a>
</li>
<li class="file-stats">
<a href="#c217435f5aac4ef963dfd7b4bca251989b376878">
test/jalview/viewmodel/OverviewDimensionsHideHiddenTest.java
</a>
</li>
<li class="file-stats">
<a href="#677118342b0abf3de676214bebb20a7b892556d2">
test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
</a>
</li>
<li class="file-stats">
<a href="#b7cc562679d0ab0014eb5d2fb4a126fce37d425e">
test/jalview/viewmodel/ViewportRangesTest.java
</a>
</li>
<li class="file-stats">
<a href="#7e3fe29415afd8bba0be825e2f38c1772b245fb7">
test/jalview/viewmodel/styles/ViewStyleTest.java
</a>
</li>
<li class="file-stats">
<a href="#05adeee602bcbfa52ae3fd19f7b3819d73052a6c">
test/jalview/workers/AlignCalcManagerTest.java
</a>
</li>
<li class="file-stats">
<a href="#e47be8986388a09caa5ebd9e45bc453e0905304f">
test/jalview/ws/PDBSequenceFetcherTest.java
</a>
</li>
<li class="file-stats">
<a href="#2a14c8223af606d0f26a8a255c25c3d7f9696f9e">
test/jalview/ws/SequenceFetcherTest.java
</a>
</li>
<li class="file-stats">
<a href="#f8fd0e3070472cc51e47ff5fdc28bb848ac6b865">
test/jalview/ws/dbsources/EmblXmlSourceTest.java
</a>
</li>
<li class="file-stats">
<a href="#cc211f2c0f2f9a0bbfeb68da8dba9edff26a81c7">
test/jalview/ws/dbsources/PfamFullTest.java
</a>
</li>
<li class="file-stats">
<a href="#69ea145120b4d16f9061b1c98cbe8d0aaba43937">
test/jalview/ws/dbsources/PfamSeedTest.java
</a>
</li>
<li class="file-stats">
<a href="#a3ce543aeaebd1239e32428f16bc8f09e73628ba">
test/jalview/ws/dbsources/RemoteFormatTest.java
</a>
</li>
<li class="file-stats">
<a href="#1eb9be0a42377405cd1b052efee939edf78c3269">
test/jalview/ws/dbsources/RfamFullTest.java
</a>
</li>
<li class="file-stats">
<a href="#9cd3fd780207c093b473364e1dfbb45a3cc16a91">
test/jalview/ws/dbsources/RfamSeedTest.java
</a>
</li>
<li class="file-stats">
<a href="#50154f8a90e1f00eeb0b922a8ed462bde65d6d9c">
test/jalview/ws/dbsources/UniprotTest.java
</a>
</li>
<li class="file-stats">
<a href="#f08d3cc0a7c8ae02d341076777990bb3bbc50180">
test/jalview/ws/dbsources/XfamFetcherTest.java
</a>
</li>
<li class="file-stats">
<a href="#671408461913f8713998ba0411cf45e5301aa43d">
test/jalview/ws/ebi/EBIFetchClientTest.java
</a>
</li>
<li class="file-stats">
<a href="#d6d6b55b617cf042cceab2923cdf789a58741025">
test/jalview/ws/gui/Jws2ParamView.java
</a>
</li>
<li class="file-stats">
<a href="#022af5efe05a336f5f08bb461a88bba06aee88f3">
test/jalview/ws/jabaws/DisorderAnnotExportImport.java
</a>
</li>
<li class="file-stats">
<a href="#87197125948f2439943a160b188656a92992fecb">
test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
</a>
</li>
<li class="file-stats">
<a href="#f34a4db191c78e80fdc2f4987fa2da44106093fa">
test/jalview/ws/jabaws/MinJabawsClientTests.java
</a>
</li>
<li class="file-stats">
<a href="#1b12ecab6db4956a5db69abf71e5c80c62b46bf1">
test/jalview/ws/jabaws/RNAStructExportImport.java
</a>
</li>
<li class="file-stats">
<a href="#bee60e8b075430e7ca7b57e128b608a80b52588e">
test/jalview/ws/jws2/ParameterUtilsTest.java
</a>
</li>
<li class="file-stats">
<a href="#6d6ec0157929c4271110614cc89caeeb13203acd">
test/jalview/ws/rest/RestClientTest.java
</a>
</li>
<li class="file-stats">
<a href="#dde4eb85966a6757e8458615c5f5a4e6c6a3cfba">
test/jalview/ws/rest/ShmmrRSBSService.java
</a>
</li>
<li class="file-stats">
<a href="#cfcb2b8d022b902a99f92240704c4cc61f6a8f4b">
test/jalview/ws/seqfetcher/DbRefFetcherTest.java
</a>
</li>
<li class="file-stats">
<a href="#3b07128986ac088dac7d67e601f35adbe6b9e89d">
test/jalview/ws/sifts/SiftsClientTest.java
</a>
</li>
<li class="file-stats">
<a href="#99d3f5acfcdc4cabdfd6ca42cf431be36cd4dd3c">
test/jalview/ws/utils/UrlDownloadClientTest.java
</a>
</li>
<li class="file-stats">
<a href="#9b2bd25e61c17d1b69fec36060afd10e559cc11b">
test/mc_view/AtomTest.java
</a>
</li>
<li class="file-stats">
<a href="#a97c2a8cc81eeaceace53e08a9a3fcba2fa5313b">
test/mc_view/BondTest.java
</a>
</li>
<li class="file-stats">
<a href="#c0949326eb935595327399e02b38e7d6e4b6e2fe">
test/mc_view/PDBChainTest.java
</a>
</li>
<li class="file-stats">
<a href="#0303e3bb73a6857fb51c6495d2dde585ef8f1022">
test/mc_view/PDBfileTest.java
</a>
</li>
<li class="file-stats">
<a href="#f84b53ccbe4cfca11dbaa25d81daf32a1958f558">
test/mc_view/ResidueTest.java
</a>
</li>
<li class="file-stats">
<a href="#062ec074347136fbb4de2c6d56f607c51957007f">
utils/BufferedLineReader.java
</a>
</li>
<li class="file-stats">
<a href="#08b3e7e7217118ce566287416e8cdd33256f856b">
utils/HelpLinksChecker.java
</a>
</li>
<li class="file-stats">
<a href="#6851d5a19f6d9ffb65a65d7d0d37d50a88fac23f">
utils/MessageBundleChecker.java
</a>
</li>
<li class="file-stats">
<a href="#4059368481c27991c94265d8ded67d5db33869a8">
utils/getJavaVersion.java
</a>
</li>
<li class="file-stats">
<a href="#dc822bda48a4056e2b45562b4f1f1f2d2d4162e3">
utils/help2Website.java
</a>
</li>
<li class="file-stats">
<a href="#11054d5fbdb6ba6830467492e231991e5bbad14d">
utils/showJVMVersion.java
</a>
</li>
<li class="file-stats">
<a href="#35210002dcf5661317cb12fec60c0b30b8c45f41">
utils/test/JalviewJSTest.java
</a>
</li>
<li class="file-stats">
<a href="#0dc908ec06a3dea8eead8fbb4f11240bcbb85ad6">
utils/test/Test_Applet_Scroll.java
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>

</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #626168;">

<br>
<a href="https://salsa.debian.org/java-team/jalview/-/commit/ea14fe6f7f1161ec0d5c6d40fe35d9a98d08b670">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
<script type="application/ld+json">{"@context":"http://schema.org","@type":"EmailMessage","action":{"@type":"ViewAction","name":"View Commit","url":"https://salsa.debian.org/java-team/jalview/-/commit/ea14fe6f7f1161ec0d5c6d40fe35d9a98d08b670"}}</script>


</p>
</div>
</body>
</html>