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

[jalview.git] / src / jalview / util / UrlLink.java

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 218da6c..0d92759 100644 (file)
--- 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)