Factored URL Link constants out into UrlConstants file.

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index ed96b55..2cb3060 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -20,6 +20,9 @@
  */
 package jalview.appletgui;
 
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SRS_STRING;
+
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -82,19 +85,16 @@ public class IdPanel extends Panel implements MouseListener,
     }
     {
       // upgrade old SRS link
-      int srsPos = links
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      int srsPos = links.indexOf(SRS_STRING);
       if (srsPos > -1)
       {
-        links.setElementAt(
-                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                srsPos);
+        links.setElementAt(EMBLEBI_STRING, srsPos);
       }
     }
     if (links.size() < 1)
     {
       links = new java.util.Vector();
-      links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+      links.addElement(EMBLEBI_STRING);
     }
   }
 

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8dbe5e2..b43989a 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,6 +20,10 @@
  */
 package jalview.gui;
 
+import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SRS_STRING;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
@@ -110,10 +114,7 @@ public class Preferences extends GPreferences
   public static List<String> groupURLLinks;
   static
   {
-    String string = Cache
-            .getDefault(
-                    "SEQUENCE_LINKS",
-                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+    String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
     sequenceURLLinks = new Vector<String>();
 
     try
@@ -124,7 +125,7 @@ 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("$" + SEQUENCE_ID + "$");
         while (rxstart == -1 && url.indexOf("/=$") == -1)
         {
           url = url + "|" + st.nextToken();
@@ -137,14 +138,10 @@ public class Preferences extends GPreferences
     }
     {
       // upgrade old SRS link
-      int srsPos = sequenceURLLinks
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      int srsPos = sequenceURLLinks.indexOf(SRS_STRING);
       if (srsPos > -1)
       {
-        sequenceURLLinks
-                .setElementAt(
-                        "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                        srsPos);
+        sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
       }
     }
 

diff --git a/src/jalview/util/UrlConstants.java b/src/jalview/util/UrlConstants.java
new file mode 100644 (file)
index 0000000..fc6dfdd
--- /dev/null
+++ b/src/jalview/util/UrlConstants.java
@@ -0,0 +1,54 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+/**
+ * A class to hold constants relating to Url links used in Jalview
+ */
+public class UrlConstants
+{
+  /*
+   * 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=$SEQUENCE_ID$";
+
+  /*
+   * Default sequence URL link string for SRS 
+   */
+  public static final String SRS_STRING = "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry";
+
+  /*
+   * Sequence ID string
+   */
+  public static final String SEQUENCE_ID = "SEQUENCE_ID";
+
+  /*
+   * Sequence Name string
+   */
+  public static final String SEQUENCE_NAME = "SEQUENCE_NAME";
+
+  /*
+   * not instantiable
+   */
+  private UrlConstants()
+  {
+  }
+}

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 4297090..e196c8c 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -20,6 +20,8 @@
  */
 package jalview.util;
 
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+
 import java.util.Vector;
 
 public class UrlLink
@@ -48,7 +50,7 @@ public class UrlLink
    */
   public UrlLink(String link)
   {
-    int sep = link.indexOf("|"), psqid = link.indexOf("$SEQUENCE_ID");
+    int sep = link.indexOf("|"), psqid = link.indexOf("$" + SEQUENCE_ID);
     if (psqid > -1)
     {
       dynamic = true;
@@ -77,7 +79,7 @@ public class UrlLink
       }
       // Parse URL : Whole URL string first
       url_prefix = link.substring(sep + 1, psqid);
-      if (link.indexOf("$SEQUENCE_ID=/") == psqid
+      if (link.indexOf("$" + SEQUENCE_ID + "=/") == psqid
               && (p = link.indexOf("/=$", psqid + 14)) > psqid + 14)
       {
         // Extract Regex and suffix
@@ -102,7 +104,7 @@ public class UrlLink
       {
         regexReplace = null;
         // verify format is really correct.
-        if (link.indexOf("$SEQUENCE_ID$") == psqid)
+        if (link.indexOf("$" + SEQUENCE_ID + "$") == psqid)
         {
           url_suffix = link.substring(psqid + 13);
           regexReplace = null;
@@ -295,12 +297,13 @@ public class UrlLink
     }
   }
 
+  @Override
   public String toString()
   {
     return label
             + "|"
             + url_prefix
-            + (dynamic ? ("$SEQUENCE_ID" + ((regexReplace != null) ? "="
+            + (dynamic ? ("$" + SEQUENCE_ID + ((regexReplace != null) ? "="
                     + regexReplace + "=$" : "$")) : "")
             + ((url_suffix == null) ? "" : url_suffix);
 
@@ -341,7 +344,8 @@ 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/$SEQUENCE_ID=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
+    "NESTED|http://nested/$" + SEQUENCE_ID
+            + "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
     String[] idstrings = new String[] {
     /*
      * //"LGUL_human", //"QWIQW_123123", "uniprot|why_do+_12313_foo",