René's URL Explorer Experiment


Title: Issue of Biojava protein comparision tool · Issue #1096 · biojava/biojava · GitHub

Open Graph Title: Issue of Biojava protein comparision tool · Issue #1096 · biojava/biojava

X Title: Issue of Biojava protein comparision tool · Issue #1096 · biojava/biojava

Description: Dear Biojava team, When I was using the Biojava tool to perform tertiary structure alignment of proteins recently, I found that there was a problem of missing parameters in the protein comparison tool, which is important for automation. ...

Open Graph Description: Dear Biojava team, When I was using the Biojava tool to perform tertiary structure alignment of proteins recently, I found that there was a problem of missing parameters in the protein comparison t...

X Description: Dear Biojava team, When I was using the Biojava tool to perform tertiary structure alignment of proteins recently, I found that there was a problem of missing parameters in the protein comparison t...

Opengraph URL: https://github.com/biojava/biojava/issues/1096

X: @github

direct link

Domain: github.com


Hey, it has json ld scripts:
{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Issue of Biojava protein comparision tool","articleBody":"Dear Biojava team,\r\n\r\nWhen I was using the Biojava tool to perform tertiary structure alignment of proteins recently, I found that there was a problem of missing parameters in the protein comparison tool, which is important for automation.\r\n\r\n**Insufficient parameter occurs when calling FatCat program.**\r\nBiojava 7.1.1/4.0.0 -alignPair function failure \r\nI read the help manual. According to the documentation and the past command line examples, I entered the command line as follow and it should not be missing any parameter. However in the latest version and all versions after 6.0.0 can not use this parameter -alignPair, may I ask is it invalid?\r\n![image](https://github.com/biojava/biojava/assets/145386695/63ba2c4a-9763-4855-bc41-0114d98a08bc)\r\n![image](https://github.com/biojava/biojava/assets/145386695/9d176cb5-1eeb-4c51-b439-64fcb2d96436)\r\n\r\n\r\n\r\n**One more question of invalid of autoFetch function invalid in earliest version comparison tool**\r\nBiojava 7.1.1(latest version) autoFetch parameter run success\r\n![image](https://github.com/biojava/biojava/assets/145386695/6ff7c966-bd73-4264-929d-a92305f9d7ca)\r\n\r\nBut Biojava 4.0.0 autoFetch parameter run failure— time out\r\n![image](https://github.com/biojava/biojava/assets/145386695/14b8e35d-6ed7-45da-ad1f-f70d7f0c9c8c)\r\n\r\nI think maybe because the FatCat update and then the network protocal maybe different and the autofetch function need update also. So may I ask why 4.0.0 can not be used but latest version can be used?\r\n\r\nLooking forward to your guidance and suggestions on these matters.  Many thanks for any advice you can give.\r\n","author":{"url":"https://github.com/B246371-2023","@type":"Person","name":"B246371-2023"},"datePublished":"2024-07-03T05:03:44.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":2},"url":"https://github.com/1096/biojava/issues/1096"}

route-pattern/_view_fragments/issues/show/:user_id/:repository/:id/issue_layout(.:format)
route-controllervoltron_issues_fragments
route-actionissue_layout
fetch-noncev2:39fa3247-882f-30b6-ed32-d41ee4e81207
current-catalog-service-hash81bb79d38c15960b92d99bca9288a9108c7a47b18f2423d0f6438c5b7bcd2114
request-idC36E:373426:6791AF:8A812D:697311B6
html-safe-nonce627a31e89195455702bbc7a1ba4071bd9aa4afe041a09597b8010c9dfcd58ab6
visitor-payloadeyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiJDMzZFOjM3MzQyNjo2NzkxQUY6OEE4MTJEOjY5NzMxMUI2IiwidmlzaXRvcl9pZCI6IjU4Mzc1Mjk0MDc5OTUxODc2MzgiLCJyZWdpb25fZWRnZSI6ImlhZCIsInJlZ2lvbl9yZW5kZXIiOiJpYWQifQ==
visitor-hmacc3a06bbe1c3f053b8ac86fe3ef28798f9e98c22ad31788583cdb9826c19aa094
hovercard-subject-tagissue:2387678163
github-keyboard-shortcutsrepository,issues,copilot
google-site-verificationApib7-x98H0j5cPqHWwSMm6dNU4GmODRoqxLiDzdx9I
octolytics-urlhttps://collector.github.com/github/collect
analytics-location///voltron/issues_fragments/issue_layout
fb:app_id1401488693436528
apple-itunes-appapp-id=1477376905, app-argument=https://github.com/_view_fragments/issues/show/biojava/biojava/1096/issue_layout
twitter:imagehttps://opengraph.githubassets.com/c0718a63b823a078eb4dd3f69aae6c19458016133af64889a73f1391042e994c/biojava/biojava/issues/1096
twitter:cardsummary_large_image
og:imagehttps://opengraph.githubassets.com/c0718a63b823a078eb4dd3f69aae6c19458016133af64889a73f1391042e994c/biojava/biojava/issues/1096
og:image:altDear Biojava team, When I was using the Biojava tool to perform tertiary structure alignment of proteins recently, I found that there was a problem of missing parameters in the protein comparison t...
og:image:width1200
og:image:height600
og:site_nameGitHub
og:typeobject
og:author:usernameB246371-2023
hostnamegithub.com
expected-hostnamegithub.com
None44ab3188c1dcfe3be0f9c3feca2e04e14fb79f120939ce2395e4f15ab96ec1d4
turbo-cache-controlno-preview
go-importgithub.com/biojava/biojava git https://github.com/biojava/biojava.git
octolytics-dimension-user_id237402
octolytics-dimension-user_loginbiojava
octolytics-dimension-repository_id9199359
octolytics-dimension-repository_nwobiojava/biojava
octolytics-dimension-repository_publictrue
octolytics-dimension-repository_is_forkfalse
octolytics-dimension-repository_network_root_id9199359
octolytics-dimension-repository_network_root_nwobiojava/biojava
turbo-body-classeslogged-out env-production page-responsive
disable-turbofalse
browser-stats-urlhttps://api.github.com/_private/browser/stats
browser-errors-urlhttps://api.github.com/_private/browser/errors
releasea5e2b48bd1260476599758f5d253b5d24092ab84
ui-targetfull
theme-color#1e2327
color-schemelight dark

Links:

Skip to contenthttps://github.com/biojava/biojava/issues/1096#start-of-content
https://github.com/
Sign in https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fbiojava%2Fbiojava%2Fissues%2F1096
GitHub CopilotWrite better code with AIhttps://github.com/features/copilot
GitHub SparkBuild and deploy intelligent appshttps://github.com/features/spark
GitHub ModelsManage and compare promptshttps://github.com/features/models
MCP RegistryNewIntegrate external toolshttps://github.com/mcp
ActionsAutomate any workflowhttps://github.com/features/actions
CodespacesInstant dev environmentshttps://github.com/features/codespaces
IssuesPlan and track workhttps://github.com/features/issues
Code ReviewManage code changeshttps://github.com/features/code-review
GitHub Advanced SecurityFind and fix vulnerabilitieshttps://github.com/security/advanced-security
Code securitySecure your code as you buildhttps://github.com/security/advanced-security/code-security
Secret protectionStop leaks before they starthttps://github.com/security/advanced-security/secret-protection
Why GitHubhttps://github.com/why-github
Documentationhttps://docs.github.com
Bloghttps://github.blog
Changeloghttps://github.blog/changelog
Marketplacehttps://github.com/marketplace
View all featureshttps://github.com/features
Enterpriseshttps://github.com/enterprise
Small and medium teamshttps://github.com/team
Startupshttps://github.com/enterprise/startups
Nonprofitshttps://github.com/solutions/industry/nonprofits
App Modernizationhttps://github.com/solutions/use-case/app-modernization
DevSecOpshttps://github.com/solutions/use-case/devsecops
DevOpshttps://github.com/solutions/use-case/devops
CI/CDhttps://github.com/solutions/use-case/ci-cd
View all use caseshttps://github.com/solutions/use-case
Healthcarehttps://github.com/solutions/industry/healthcare
Financial serviceshttps://github.com/solutions/industry/financial-services
Manufacturinghttps://github.com/solutions/industry/manufacturing
Governmenthttps://github.com/solutions/industry/government
View all industrieshttps://github.com/solutions/industry
View all solutionshttps://github.com/solutions
AIhttps://github.com/resources/articles?topic=ai
Software Developmenthttps://github.com/resources/articles?topic=software-development
DevOpshttps://github.com/resources/articles?topic=devops
Securityhttps://github.com/resources/articles?topic=security
View all topicshttps://github.com/resources/articles
Customer storieshttps://github.com/customer-stories
Events & webinarshttps://github.com/resources/events
Ebooks & reportshttps://github.com/resources/whitepapers
Business insightshttps://github.com/solutions/executive-insights
GitHub Skillshttps://skills.github.com
Documentationhttps://docs.github.com
Customer supporthttps://support.github.com
Community forumhttps://github.com/orgs/community/discussions
Trust centerhttps://github.com/trust-center
Partnershttps://github.com/partners
GitHub SponsorsFund open source developershttps://github.com/sponsors
Security Labhttps://securitylab.github.com
Maintainer Communityhttps://maintainers.github.com
Acceleratorhttps://github.com/accelerator
Archive Programhttps://archiveprogram.github.com
Topicshttps://github.com/topics
Trendinghttps://github.com/trending
Collectionshttps://github.com/collections
Enterprise platformAI-powered developer platformhttps://github.com/enterprise
GitHub Advanced SecurityEnterprise-grade security featureshttps://github.com/security/advanced-security
Copilot for BusinessEnterprise-grade AI featureshttps://github.com/features/copilot/copilot-business
Premium SupportEnterprise-grade 24/7 supporthttps://github.com/premium-support
Pricinghttps://github.com/pricing
Search syntax tipshttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
documentationhttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
Sign in https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fbiojava%2Fbiojava%2Fissues%2F1096
Sign up https://github.com/signup?ref_cta=Sign+up&ref_loc=header+logged+out&ref_page=%2F%3Cuser-name%3E%2F%3Crepo-name%3E%2Fvoltron%2Fissues_fragments%2Fissue_layout&source=header-repo&source_repo=biojava%2Fbiojava
Reloadhttps://github.com/biojava/biojava/issues/1096
Reloadhttps://github.com/biojava/biojava/issues/1096
Reloadhttps://github.com/biojava/biojava/issues/1096
biojava https://github.com/biojava
biojavahttps://github.com/biojava/biojava
Notifications https://github.com/login?return_to=%2Fbiojava%2Fbiojava
Fork 395 https://github.com/login?return_to=%2Fbiojava%2Fbiojava
Star 623 https://github.com/login?return_to=%2Fbiojava%2Fbiojava
Code https://github.com/biojava/biojava
Issues 67 https://github.com/biojava/biojava/issues
Pull requests 2 https://github.com/biojava/biojava/pulls
Actions https://github.com/biojava/biojava/actions
Security 0 https://github.com/biojava/biojava/security
Insights https://github.com/biojava/biojava/pulse
Code https://github.com/biojava/biojava
Issues https://github.com/biojava/biojava/issues
Pull requests https://github.com/biojava/biojava/pulls
Actions https://github.com/biojava/biojava/actions
Security https://github.com/biojava/biojava/security
Insights https://github.com/biojava/biojava/pulse
New issuehttps://github.com/login?return_to=https://github.com/biojava/biojava/issues/1096
New issuehttps://github.com/login?return_to=https://github.com/biojava/biojava/issues/1096
#1098https://github.com/biojava/biojava/pull/1098
Issue of Biojava protein comparision toolhttps://github.com/biojava/biojava/issues/1096#top
#1098https://github.com/biojava/biojava/pull/1098
bugBugs and bugfixeshttps://github.com/biojava/biojava/issues?q=state%3Aopen%20label%3A%22bug%22
https://github.com/B246371-2023
https://github.com/B246371-2023
B246371-2023https://github.com/B246371-2023
on Jul 3, 2024https://github.com/biojava/biojava/issues/1096#issue-2387678163
https://private-user-images.githubusercontent.com/145386695/345286474-63ba2c4a-9763-4855-bc41-0114d98a08bc.png?jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3NjkxNDkxNTQsIm5iZiI6MTc2OTE0ODg1NCwicGF0aCI6Ii8xNDUzODY2OTUvMzQ1Mjg2NDc0LTYzYmEyYzRhLTk3NjMtNDg1NS1iYzQxLTAxMTRkOThhMDhiYy5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjYwMTIzJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI2MDEyM1QwNjE0MTRaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT02MTllN2QyNDI1MmIyMDJmODJiNjVjMmYwZDBiYzU3NzhlZWQwMThjM2QyOTBhM2FiYWIxNDQ3YWJhMjBlMmVlJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCJ9.0Put1cSZTGNWWwPXCbTZfJREBxEiM8OeTZUyLDWFLYo
https://private-user-images.githubusercontent.com/145386695/345286557-9d176cb5-1eeb-4c51-b439-64fcb2d96436.png?jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3NjkxNDkxNTQsIm5iZiI6MTc2OTE0ODg1NCwicGF0aCI6Ii8xNDUzODY2OTUvMzQ1Mjg2NTU3LTlkMTc2Y2I1LTFlZWItNGM1MS1iNDM5LTY0ZmNiMmQ5NjQzNi5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjYwMTIzJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI2MDEyM1QwNjE0MTRaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1iYmNlNTk3OWZiY2M5OTVmMjk5NzRlYTQ4YzRkZjliOTMwNmY4ZDc2Y2UwYjcwMDNlYjgzYzNkNTgyNjRjNDM1JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCJ9.Va9ln8RzMbkS1FyhIy0QRVZcZFh2v2WQCS6yNL1B69g
https://private-user-images.githubusercontent.com/145386695/345286597-6ff7c966-bd73-4264-929d-a92305f9d7ca.png?jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3NjkxNDkxNTQsIm5iZiI6MTc2OTE0ODg1NCwicGF0aCI6Ii8xNDUzODY2OTUvMzQ1Mjg2NTk3LTZmZjdjOTY2LWJkNzMtNDI2NC05MjlkLWE5MjMwNWY5ZDdjYS5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjYwMTIzJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI2MDEyM1QwNjE0MTRaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT05ZGNjZDgzMWMyOWY4NDRlMTExMWEzZjczMWZlNjdhYjVlOGRlMjE1ZTI5ZTFlOGExY2I2YWU2NWEyZmNlN2U0JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCJ9.0TmDHmkVkvkZ1PmpEUiH3SLuGmQm6HbqEm-V-Wv6cpc
https://private-user-images.githubusercontent.com/145386695/345286632-14b8e35d-6ed7-45da-ad1f-f70d7f0c9c8c.png?jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3NjkxNDkxNTQsIm5iZiI6MTc2OTE0ODg1NCwicGF0aCI6Ii8xNDUzODY2OTUvMzQ1Mjg2NjMyLTE0YjhlMzVkLTZlZDctNDVkYS1hZDFmLWY3MGQ3ZjBjOWM4Yy5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjYwMTIzJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI2MDEyM1QwNjE0MTRaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT0zYjA2MzNkNzNiZjM5ZGEyMjE1ZjIzNjQ1MTk0MDU1NWNlM2YwOTNlYThiZmE2M2E2OGQwMjdmODVmOTJlMmJlJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCJ9.2tsfG-TUA_5BOOCwwGIcbEmqFi3ZkrfvCMHq2Kjx7qI
bugBugs and bugfixeshttps://github.com/biojava/biojava/issues?q=state%3Aopen%20label%3A%22bug%22
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

Viewport: width=device-width


URLs of crawlers that visited me.