From 35c3de415520c5636e12d47d4043e62e5302e24b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 9 Aug 2017 19:31:29 +0100 Subject: [PATCH] JAL-2425 raw stockholm download URLs --- src/jalview/ws/dbsources/PfamFull.java | 8 +++++++- src/jalview/ws/dbsources/PfamSeed.java | 7 ++++++- src/jalview/ws/dbsources/RfamFull.java | 7 ++++++- src/jalview/ws/dbsources/RfamSeed.java | 3 --- 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java index 3c5373d..12b193d 100644 --- a/src/jalview/ws/dbsources/PfamFull.java +++ b/src/jalview/ws/dbsources/PfamFull.java @@ -39,9 +39,15 @@ public class PfamFull extends Pfam @Override protected String getXFAMURL() { - return "http://pfam.xfam.org/family/alignment/download/format?alnType=full&format=stockholm&order=t&case=l&gaps=default&entry="; + return "http://pfam.xfam.org/family/"; + } + @Override + public String getXFAMURLSUFFIX() + { + return "/alignment/full"; + } /* * (non-Javadoc) * diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java index ba9d1e0..9f07e5d 100644 --- a/src/jalview/ws/dbsources/PfamSeed.java +++ b/src/jalview/ws/dbsources/PfamSeed.java @@ -41,9 +41,14 @@ public class PfamSeed extends Pfam @Override protected String getXFAMURL() { - return "http://pfam.xfam.org/family/alignment/download/format?alnType=seed&format=stockholm&order=t&case=l&gaps=default&entry="; + return "http://pfam.xfam.org/family/"; } + @Override + public String getXFAMURLSUFFIX() + { + return "/alignment/seed"; + } /* * (non-Javadoc) * diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java index e6fc8ff..e263c4b 100644 --- a/src/jalview/ws/dbsources/RfamFull.java +++ b/src/jalview/ws/dbsources/RfamFull.java @@ -41,10 +41,15 @@ public class RfamFull extends Rfam @Override protected String getXFAMURL() { - return "http://rfam.xfam.org/family/alignment/download/format?alnType=full&nseLabels=0&format=stockholm&acc="; + return "http://rfam.xfam.org/family/"; } + @Override + public String getXFAMURLSUFFIX() + { + return "/alignment/full"; + } /* * (non-Javadoc) * diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java index 580ebe2..b2fe72e 100644 --- a/src/jalview/ws/dbsources/RfamSeed.java +++ b/src/jalview/ws/dbsources/RfamSeed.java @@ -42,14 +42,11 @@ public class RfamSeed extends Rfam protected String getXFAMURL() { return "http://rfam.xfam.org/family/"; - // Janelia Farms url - // "http://rfam.janelia.org/cgi-bin/getalignment?type=seed&fmt=stockholm&acc="; } @Override public String getXFAMURLSUFFIX() { - return "/alignment"; } /* -- 1.7.10.2