From 8abc6bc1d2dac87289bc2658e7c1be352f1deb9f Mon Sep 17 00:00:00 2001 From: kiramt Date: Mon, 31 Oct 2016 08:14:49 +0000 Subject: [PATCH] Use ACCESSION_ID for database accession id, and SEQUENCE_ID for sequence name. --- src/jalview/gui/Preferences.java | 7 ------- src/jalview/util/UrlConstants.java | 11 +++-------- test/jalview/gui/PopupMenuTest.java | 14 ++++++++++---- 3 files changed, 13 insertions(+), 19 deletions(-) diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index b57b951..be0ac05 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -21,7 +21,6 @@ package jalview.gui; import static jalview.util.UrlConstants.EMBLEBI_STRING; -import static jalview.util.UrlConstants.OLD_EMBLEBI_STRING; import static jalview.util.UrlConstants.SEQUENCE_ID; import static jalview.util.UrlConstants.SEQUENCE_NAME; import static jalview.util.UrlConstants.SRS_STRING; @@ -149,12 +148,6 @@ public class Preferences extends GPreferences { sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos); } - // upgrade old EMBL-EBI link - int emblPos = sequenceURLLinks.indexOf(OLD_EMBLEBI_STRING); - if (emblPos > -1) - { - sequenceURLLinks.setElementAt(EMBLEBI_STRING, emblPos); - } } /** diff --git a/src/jalview/util/UrlConstants.java b/src/jalview/util/UrlConstants.java index ce6d980..b511b8c 100644 --- a/src/jalview/util/UrlConstants.java +++ b/src/jalview/util/UrlConstants.java @@ -29,22 +29,17 @@ public class UrlConstants /* * Sequence ID string */ - public static final String SEQUENCE_ID = "SEQUENCE_ID"; + public static final String SEQUENCE_ID = "ACCESSION_ID"; /* * Sequence Name string */ - public static final String SEQUENCE_NAME = "SEQUENCE_NAME"; + public static final String SEQUENCE_NAME = "SEQUENCE_ID"; /* * Default sequence URL link string for EMBL-EBI search */ - public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$"; - - /* - * Default sequence URL link string for EMBL-EBI search - */ - public static final String OLD_EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"; + public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"; /* * Default sequence URL link string for SRS diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index b4e8629..9e49828 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import static jalview.util.UrlConstants.SEQUENCE_ID; +import static jalview.util.UrlConstants.SEQUENCE_NAME; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; @@ -458,11 +460,15 @@ public class PopupMenuTest List refs = new ArrayList(); // links as might be added into Preferences | Connections dialog - links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$"); - links.add("UNIPROT | http://www.uniprot.org/uniprot/$SEQUENCE_ID$"); - links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$SEQUENCE_ID$"); + links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$" + + SEQUENCE_NAME + "$"); + links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + SEQUENCE_ID + + "$"); + links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$" + + SEQUENCE_ID + "$"); // Gene3D entry tests for case (in)sensitivity - links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$SEQUENCE_ID$&mode=protein"); + links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$" + + SEQUENCE_ID + "$&mode=protein"); // make seq0 dbrefs refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527")); -- 1.7.10.2