From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 2 Nov 2016 09:39:10 +0000 (+0000)
Subject: JAL-2282 Renamed internal use of sequence id / db accession for
X-Git-Tag: Release_2_10_1^2~18^2~2^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8c53a6c0bda186beb949efd99cecbb815eab2210;p=jalview.git

JAL-2282 Renamed internal use of sequence id / db accession for
consistency
---

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index b6353c3..182f20e 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -247,7 +247,7 @@ public class IdPanel extends Panel implements MouseListener,
         continue;
       }
 
-      if (urlLink.usesSeqId())
+      if (urlLink.usesDBAccession())
       {
         // this URL requires an accession id, not the name of a sequence
         url = null;
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index acc2a9f..e321a74 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -226,7 +226,7 @@ public class IdPanel extends JPanel implements MouseListener,
         continue;
       }
 
-      if (urlLink.usesSeqId())
+      if (urlLink.usesDBAccession())
       {
         // this URL requires an accession id, not the name of a sequence
         url = null;
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index be0ac05..4f094e1 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -21,8 +21,8 @@
 package jalview.gui;
 
 import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.DB_ACCESSION;
 import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SEQUENCE_NAME;
 import static jalview.util.UrlConstants.SRS_STRING;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
@@ -126,10 +126,10 @@ public class Preferences extends GPreferences
         String name = st.nextToken();
         String url = st.nextToken();
         // check for '|' within a regex
-        int rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
+        int rxstart = url.indexOf("$" + DB_ACCESSION + "$");
         if (rxstart == -1)
         {
-          rxstart = url.indexOf("$" + SEQUENCE_NAME + "$");
+          rxstart = url.indexOf("$" + SEQUENCE_ID + "$");
         }
         while (rxstart == -1 && url.indexOf("/=$") == -1)
         {
diff --git a/src/jalview/util/UrlConstants.java b/src/jalview/util/UrlConstants.java
index b70edf5..1910bff 100644
--- a/src/jalview/util/UrlConstants.java
+++ b/src/jalview/util/UrlConstants.java
@@ -29,12 +29,12 @@ public class UrlConstants
   /*
    * Sequence ID string
    */
-  public static final String SEQUENCE_ID = "DB_ACCESSION";
+  public static final String DB_ACCESSION = "DB_ACCESSION";
 
   /*
    * Sequence Name string
    */
-  public static final String SEQUENCE_NAME = "SEQUENCE_ID";
+  public static final String SEQUENCE_ID = "SEQUENCE_ID";
 
   /*
    * Default sequence URL link string for EMBL-EBI search
diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 218da6c..0d92759 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -20,8 +20,8 @@
  */
 package jalview.util;
 
+import static jalview.util.UrlConstants.DB_ACCESSION;
 import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SEQUENCE_NAME;
 
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
@@ -46,7 +46,7 @@ public class UrlLink
 
   private boolean dynamic = false;
 
-  private boolean uses_seq_id = false;
+  private boolean uses_db_accession = false;
 
   private String invalidMessage = null;
 
@@ -60,23 +60,23 @@ public class UrlLink
   public UrlLink(String link)
   {
     int sep = link.indexOf("|");
-    int psqid = link.indexOf("$" + SEQUENCE_ID);
-    int nsqid = link.indexOf("$" + SEQUENCE_NAME);
+    int psqid = link.indexOf("$" + DB_ACCESSION);
+    int nsqid = link.indexOf("$" + SEQUENCE_ID);
     if (psqid > -1)
     {
       dynamic = true;
-      uses_seq_id = true;
+      uses_db_accession = true;
 
       sep = parseTargetAndLabel(sep, psqid, link);
 
-      parseUrl(link, SEQUENCE_ID, psqid, sep);
+      parseUrl(link, DB_ACCESSION, psqid, sep);
     }
     else if (nsqid > -1)
     {
       dynamic = true;
       sep = parseTargetAndLabel(sep, nsqid, link);
 
-      parseUrl(link, SEQUENCE_NAME, nsqid, sep);
+      parseUrl(link, SEQUENCE_ID, nsqid, sep);
     }
     else
     {
@@ -268,7 +268,7 @@ public class UrlLink
   @Override
   public String toString()
   {
-    String var = (uses_seq_id ? SEQUENCE_ID : SEQUENCE_NAME);
+    String var = (uses_db_accession ? DB_ACCESSION : SEQUENCE_ID);
 
     return label
             + "|"
@@ -439,7 +439,7 @@ public class UrlLink
       descr = null;
     }
 
-    if (usesSeqId()) // link is ID
+    if (usesDBAccession()) // link is ID
     {
       // collect matching db-refs
       DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
@@ -455,7 +455,7 @@ public class UrlLink
         }
       }
     }
-    else if (!usesSeqId() && id != null) // link is name
+    else if (!usesDBAccession() && id != null) // link is name
     {
       // create Bare ID link for this URL
       createBareURLLink(id, false, linkset);
@@ -533,7 +533,7 @@ public class UrlLink
      * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"
      * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",
      */
-    "NESTED|http://nested/$" + SEQUENCE_ID
+    "NESTED|http://nested/$" + DB_ACCESSION
             + "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
     String[] idstrings = new String[] {
     /*
@@ -581,9 +581,9 @@ public class UrlLink
     return dynamic;
   }
 
-  public boolean usesSeqId()
+  public boolean usesDBAccession()
   {
-    return uses_seq_id;
+    return uses_db_accession;
   }
 
   public void setLabel(String newlabel)
diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 9e49828..7b1eac1 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -20,8 +20,8 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.DB_ACCESSION;
 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;
@@ -461,14 +461,14 @@ public class PopupMenuTest
 
     // 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/$" + SEQUENCE_ID
+            + SEQUENCE_ID + "$");
+    links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
             + "$");
     links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
-            + SEQUENCE_ID + "$");
+            + DB_ACCESSION + "$");
     // Gene3D entry tests for case (in)sensitivity
     links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
-            + SEQUENCE_ID + "$&mode=protein");
+            + DB_ACCESSION + "$&mode=protein");
 
     // make seq0 dbrefs
     refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
diff --git a/test/jalview/util/UrlLinkTest.java b/test/jalview/util/UrlLinkTest.java
index 875dd7f..c98d8ce 100644
--- a/test/jalview/util/UrlLinkTest.java
+++ b/test/jalview/util/UrlLinkTest.java
@@ -20,8 +20,8 @@
  */
 package jalview.util;
 
+import static jalview.util.UrlConstants.DB_ACCESSION;
 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.assertNull;
@@ -61,28 +61,28 @@ public class UrlLinkTest
   @Test(groups = { "Functional" })
   public void testUrlLinkCreationNoRegex()
   {
-    // SEQUENCE_NAME
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    // SEQUENCE_ID
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + DELIM + URL_SUFFIX);
     assertEquals(DB.toUpperCase(), ul.getTarget());
     assertEquals(DB, ul.getLabel());
     assertEquals(URL_PREFIX, ul.getUrl_prefix());
     assertEquals(URL_SUFFIX, ul.getUrl_suffix());
     assertTrue(ul.isDynamic());
-    assertFalse(ul.usesSeqId());
+    assertFalse(ul.usesDBAccession());
     assertNull(ul.getRegexReplace());
     assertTrue(ul.isValid());
     assertNull(ul.getInvalidMessage());
 
-    // SEQUENCE_ID
-    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM
+    // DB_ACCESSION
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
             + URL_SUFFIX);
     assertEquals(DB.toUpperCase(), ul.getTarget());
     assertEquals(DB, ul.getLabel());
     assertEquals(URL_PREFIX, ul.getUrl_prefix());
     assertEquals(URL_SUFFIX, ul.getUrl_suffix());
     assertTrue(ul.isDynamic());
-    assertTrue(ul.usesSeqId());
+    assertTrue(ul.usesDBAccession());
     assertNull(ul.getRegexReplace());
     assertTrue(ul.isValid());
     assertNull(ul.getInvalidMessage());
@@ -93,7 +93,7 @@ public class UrlLinkTest
     assertEquals(DB, ul.getLabel());
     assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix());
     assertFalse(ul.isDynamic());
-    assertFalse(ul.usesSeqId());
+    assertFalse(ul.usesDBAccession());
     assertNull(ul.getRegexReplace());
     assertTrue(ul.isValid());
     assertNull(ul.getInvalidMessage());
@@ -105,43 +105,43 @@ public class UrlLinkTest
   @Test(groups = { "Functional" })
   public void testUrlLinkCreationWithRegex()
   {
-    // SEQUENCE_NAME
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    // SEQUENCE_ID
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + REGEX_NESTED + DELIM + URL_SUFFIX);
     assertEquals(DB.toUpperCase(), ul.getTarget());
     assertEquals(DB, ul.getLabel());
     assertEquals(URL_PREFIX, ul.getUrl_prefix());
     assertEquals(URL_SUFFIX, ul.getUrl_suffix());
     assertTrue(ul.isDynamic());
-    assertFalse(ul.usesSeqId());
+    assertFalse(ul.usesDBAccession());
     assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
             ul.getRegexReplace());
     assertTrue(ul.isValid());
     assertNull(ul.getInvalidMessage());
 
-    // SEQUENCE_ID
-    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+    // DB_ACCESSION
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
             + REGEX_NESTED + DELIM + URL_SUFFIX);
     assertEquals(DB.toUpperCase(), ul.getTarget());
     assertEquals(DB, ul.getLabel());
     assertEquals(URL_PREFIX, ul.getUrl_prefix());
     assertEquals(URL_SUFFIX, ul.getUrl_suffix());
     assertTrue(ul.isDynamic());
-    assertTrue(ul.usesSeqId());
+    assertTrue(ul.usesDBAccession());
     assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
             ul.getRegexReplace());
     assertTrue(ul.isValid());
     assertNull(ul.getInvalidMessage());
 
     // invalid regex
-    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
             + REGEX_RUBBISH + DELIM + URL_SUFFIX);
     assertEquals(DB.toUpperCase(), ul.getTarget());
     assertEquals(DB, ul.getLabel());
     assertEquals(URL_PREFIX, ul.getUrl_prefix());
     assertEquals(URL_SUFFIX, ul.getUrl_suffix());
     assertTrue(ul.isDynamic());
-    assertTrue(ul.usesSeqId());
+    assertTrue(ul.usesDBAccession());
     assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
             ul.getRegexReplace());
     assertFalse(ul.isValid());
@@ -159,7 +159,7 @@ public class UrlLinkTest
   public void testMakeUrlNoRegex()
   {
     // Single non-regex
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + DELIM + URL_SUFFIX);
     String idstring = "FER_CAPAA";
     String[] urls = ul.makeUrls(idstring, true);
@@ -183,7 +183,7 @@ public class UrlLinkTest
   public void testMakeUrlWithRegex()
   {
     // Unused regex
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION
             + REGEX_NESTED + DELIM + URL_SUFFIX);
     String idstring = "FER_CAPAA";
     String[] urls = ul.makeUrls(idstring, true);
@@ -259,7 +259,7 @@ public class UrlLinkTest
   @Test(groups = { "Functional" })
   public void testCreateLinksFromNullSequence()
   {
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + DELIM + URL_SUFFIX);
 
     Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
@@ -307,11 +307,11 @@ public class UrlLinkTest
 
     // 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/$" + SEQUENCE_ID
+            + SEQUENCE_ID + "$");
+    links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
             + "$");
     links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
-            + SEQUENCE_ID + "$");
+            + DB_ACCESSION + "$");
 
     // make seq0 dbrefs
     refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527"));
@@ -329,7 +329,7 @@ public class UrlLinkTest
     seq0.createDatasetSequence();
 
     // Test where link takes a sequence id as replacement
-    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_NAME
+    UrlLink ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID
             + DELIM + URL_SUFFIX);
 
     Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
@@ -392,7 +392,7 @@ public class UrlLinkTest
             "http://www.ebi.ac.uk/interpro/entry/IPR012675");
 
     // Test where there are no matching dbrefs for the link
-    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + SEQUENCE_ID + DELIM
+    ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
             + URL_SUFFIX);
     linkset = new LinkedHashMap<String, List<String>>();
     ul.createLinksFromSeq(seq0, linkset);