From cec2422864f7a07513a5e6da8673885e6740d29a Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 2 Nov 2016 10:03:15 +0000
Subject: [PATCH 1/1] JAL-2282 Code tidy

---
 src/jalview/util/UrlLink.java |  155 ++++++++++++++++++++++++-----------------
 1 file changed, 92 insertions(+), 63 deletions(-)

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 0d92759..b8e3eeb 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -39,19 +39,33 @@ public class UrlLink
    * Jalview 2.4 extension allows regular expressions to be used to parse ID
    * strings and replace the result in the URL. Regex's operate on the whole ID
    * string given to the matchURL method, if no regex is supplied, then only
-   * text following the first pipe symbol will be susbstituted. Usage
+   * text following the first pipe symbol will be substituted. Usage
    * documentation todo.
    */
-  private String url_suffix, url_prefix, target, label, regexReplace;
+
+  // Internal constants
+  private static final String SEP = "|";
+
+  private static final String DELIM = "$";
+
+  private String urlSuffix;
+
+  private String urlPrefix;
+
+  private String target;
+
+  private String label;
+
+  private String regexReplace;
 
   private boolean dynamic = false;
 
-  private boolean uses_db_accession = false;
+  private boolean usesDBaccession = false;
 
   private String invalidMessage = null;
 
   /**
-   * parse the given linkString of the form '<label>|<url>' into parts url may
+   * parse the given linkString of the form '<label>SEP<url>' into parts url may
    * contain a string $SEQUENCE_ID<=optional regex=>$ where <=optional regex=>
    * must be of the form =/<perl style regex>/=$
    * 
@@ -59,13 +73,13 @@ public class UrlLink
    */
   public UrlLink(String link)
   {
-    int sep = link.indexOf("|");
-    int psqid = link.indexOf("$" + DB_ACCESSION);
-    int nsqid = link.indexOf("$" + SEQUENCE_ID);
+    int sep = link.indexOf(SEP);
+    int psqid = link.indexOf(DELIM + DB_ACCESSION);
+    int nsqid = link.indexOf(DELIM + SEQUENCE_ID);
     if (psqid > -1)
     {
       dynamic = true;
-      uses_db_accession = true;
+      usesDBaccession = true;
 
       sep = parseTargetAndLabel(sep, psqid, link);
 
@@ -81,12 +95,11 @@ public class UrlLink
     else
     {
       target = link.substring(0, sep);
-      sep = link.lastIndexOf("|");
+      sep = link.lastIndexOf(SEP);
       label = link.substring(0, sep);
-      url_prefix = link.substring(sep + 1).trim();
+      urlPrefix = link.substring(sep + 1).trim();
       regexReplace = null; // implies we trim any prefix if necessary //
-      // regexReplace=".*\\|?(.*)";
-      url_suffix = null;
+      urlSuffix = null;
     }
 
     label = label.trim();
@@ -100,7 +113,7 @@ public class UrlLink
    */
   public String getUrl_suffix()
   {
-    return url_suffix;
+    return urlSuffix;
   }
 
   /**
@@ -108,7 +121,7 @@ public class UrlLink
    */
   public String getUrl_prefix()
   {
-    return url_prefix;
+    return urlPrefix;
   }
 
   /**
@@ -155,6 +168,34 @@ public class UrlLink
   }
 
   /**
+   * 
+   * @return whether link is dynamic
+   */
+  public boolean isDynamic()
+  {
+    return dynamic;
+  }
+
+  /**
+   * 
+   * @return whether link uses DB Accession id
+   */
+  public boolean usesDBAccession()
+  {
+    return usesDBaccession;
+  }
+
+  /**
+   * Set the label
+   * 
+   * @param newlabel
+   */
+  public void setLabel(String newlabel)
+  {
+    this.label = newlabel;
+  }
+
+  /**
    * return one or more URL strings by applying regex to the given idstring
    * 
    * @param idstring
@@ -179,7 +220,7 @@ public class UrlLink
           {
             // take whole regex
             return new String[] { rg.stringMatched(),
-                url_prefix + rg.stringMatched() + url_suffix };
+                urlPrefix + rg.stringMatched() + urlSuffix };
           } /*
              * else if (ns==1) { // take only subgroup match return new String[]
              * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
@@ -220,7 +261,7 @@ public class UrlLink
                 if (mtch.length() > 0)
                 {
                   subs.addElement(mtch);
-                  subs.addElement(url_prefix + mtch + url_suffix);
+                  subs.addElement(urlPrefix + mtch + urlSuffix);
                 }
                 s = r;
               }
@@ -229,8 +270,8 @@ public class UrlLink
                 if (rg.matchedFrom(s) > -1)
                 {
                   subs.addElement(rg.stringMatched(s));
-                  subs.addElement(url_prefix + rg.stringMatched(s)
-                          + url_suffix);
+                  subs.addElement(urlPrefix + rg.stringMatched(s)
+                          + urlSuffix);
                 }
                 s++;
               }
@@ -251,31 +292,31 @@ public class UrlLink
         }
       }
       /* Otherwise - trim off any 'prefix' - pre 2.4 Jalview behaviour */
-      if (idstring.indexOf("|") > -1)
+      if (idstring.indexOf(SEP) > -1)
       {
-        idstring = idstring.substring(idstring.lastIndexOf("|") + 1);
+        idstring = idstring.substring(idstring.lastIndexOf(SEP) + 1);
       }
 
       // just return simple url substitution.
-      return new String[] { idstring, url_prefix + idstring + url_suffix };
+      return new String[] { idstring, urlPrefix + idstring + urlSuffix };
     }
     else
     {
-      return new String[] { "", url_prefix };
+      return new String[] { "", urlPrefix };
     }
   }
 
   @Override
   public String toString()
   {
-    String var = (uses_db_accession ? DB_ACCESSION : SEQUENCE_ID);
+    String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
 
     return label
-            + "|"
-            + url_prefix
-            + (dynamic ? ("$" + var + ((regexReplace != null) ? "="
-                    + regexReplace + "=$" : "$")) : "")
-            + ((url_suffix == null) ? "" : url_suffix);
+            + SEP
+            + urlPrefix
+            + (dynamic ? (DELIM + var + ((regexReplace != null) ? "="
+                    + regexReplace + "=" + DELIM : DELIM)) : "")
+            + ((urlSuffix == null) ? "" : urlSuffix);
   }
 
   /**
@@ -295,15 +336,15 @@ public class UrlLink
     do
     {
       sep = p;
-      p = link.indexOf("|", sep + 1);
+      p = link.indexOf(SEP, sep + 1);
     } while (p > sep && p < psqid);
-    // Assuming that the URL itself does not contain any '|' symbols
+    // Assuming that the URL itself does not contain any SEP symbols
     // sep now contains last pipe symbol position prior to any regex symbols
     label = link.substring(0, sep);
-    if (label.indexOf("|") > -1)
+    if (label.indexOf(SEP) > -1)
     {
-      // | terminated database name / www target at start of Label
-      target = label.substring(0, label.indexOf("|"));
+      // SEP terminated database name / www target at start of Label
+      target = label.substring(0, label.indexOf(SEP));
     }
     else if (label.indexOf(" ") > 2)
     {
@@ -331,13 +372,13 @@ public class UrlLink
    */
   protected void parseUrl(String link, String varName, int sqidPos, int sep)
   {
-    url_prefix = link.substring(sep + 1, sqidPos).trim();
+    urlPrefix = link.substring(sep + 1, sqidPos).trim();
 
     // delimiter at start of regex: e.g. $SEQUENCE_ID=/
-    String startDelimiter = "$" + varName + "=/";
+    String startDelimiter = DELIM + varName + "=/";
 
     // delimiter at end of regex: /=$
-    String endDelimiter = "/=$";
+    String endDelimiter = "/=" + DELIM;
 
     int startLength = startDelimiter.length();
 
@@ -348,7 +389,7 @@ public class UrlLink
             && (p > sqidPos + startLength))
     {
       // Extract Regex and suffix
-      url_suffix = link.substring(p + endDelimiter.length());
+      urlSuffix = link.substring(p + endDelimiter.length());
       regexReplace = link.substring(sqidPos + startLength, p);
       try
       {
@@ -370,9 +411,9 @@ public class UrlLink
       // no regex
       regexReplace = null;
       // verify format is really correct.
-      if (link.indexOf("$" + varName + "$") == sqidPos)
+      if (link.indexOf(DELIM + varName + DELIM) == sqidPos)
       {
-        url_suffix = link.substring(sqidPos + startLength - 1);
+        urlSuffix = link.substring(sqidPos + startLength - 1);
         regexReplace = null;
       }
       else
@@ -389,7 +430,8 @@ public class UrlLink
    * @param seq
    *          The sequence to create links for
    * @param linkset
-   *          Map of links: key = id | link, value = [target, label, id, link]
+   *          Map of links: key = id + SEP + link, value = [target, label, id,
+   *          link]
    */
   public void createLinksFromSeq(final SequenceI seq,
           Map<String, List<String>> linkset)
@@ -408,14 +450,15 @@ public class UrlLink
    * Create a static URL link
    * 
    * @param linkset
-   *          Map of links: key = id | link, value = [target, label, id, link]
+   *          Map of links: key = id + SEP + link, value = [target, label, id,
+   *          link]
    */
   protected void createStaticLink(Map<String, List<String>> linkset)
   {
-    if (!linkset.containsKey(label + "|" + getUrl_prefix()))
+    if (!linkset.containsKey(label + SEP + getUrl_prefix()))
     {
       // Add a non-dynamic link
-      linkset.put(label + "|" + getUrl_prefix(),
+      linkset.put(label + SEP + getUrl_prefix(),
               Arrays.asList(target, label, null, getUrl_prefix()));
     }
   }
@@ -426,7 +469,8 @@ public class UrlLink
    * @param seq
    *          The sequence to create links for
    * @param linkset
-   *          Map of links: key = id | link, value = [target, label, id, link]
+   *          Map of links: key = id + SEP + link, value = [target, label, id,
+   *          link]
    */
   protected void createDynamicLinks(final SequenceI seq,
           Map<String, List<String>> linkset)
@@ -472,7 +516,7 @@ public class UrlLink
 
   /*
    * Create a bare URL Link
-   * Returns map where key = id | link, and value = [target, label, id, link]
+   * Returns map where key = id + SEP + link, and value = [target, label, id, link]
    */
   protected void createBareURLLink(String id, Boolean combineLabel,
           Map<String, List<String>> linkset)
@@ -482,16 +526,16 @@ public class UrlLink
     {
       for (int u = 0; u < urls.length; u += 2)
       {
-        if (!linkset.containsKey(urls[u] + "|" + urls[u + 1]))
+        if (!linkset.containsKey(urls[u] + SEP + urls[u + 1]))
         {
           String thisLabel = label;
           if (combineLabel)
           {
             // incorporate label with idstring
-            thisLabel = label + "|" + urls[u];
+            thisLabel = label + SEP + urls[u];
           }
 
-          linkset.put(urls[u] + "|" + urls[u + 1],
+          linkset.put(urls[u] + SEP + urls[u + 1],
                   Arrays.asList(target, thisLabel, urls[u], urls[u + 1]));
         }
       }
@@ -575,19 +619,4 @@ public class UrlLink
       }
     }
   }
-
-  public boolean isDynamic()
-  {
-    return dynamic;
-  }
-
-  public boolean usesDBAccession()
-  {
-    return uses_db_accession;
-  }
-
-  public void setLabel(String newlabel)
-  {
-    this.label = newlabel;
-  }
 }
-- 
1.7.10.2