X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FUrlLink.java;h=3ee64329521fe8af4b8d201a508c2858a0e70612;hb=cd06f45d5fedf6fcc87c0d77aa6c2b1fb6ea7a46;hp=0968d360e68ca6ac5c9bb74ce3c2daa998a72387;hpb=bb90751010ab798f54dabddb8cfb6f51e847072c;p=jalview.git

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 0968d36..3ee6432 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -20,12 +20,14 @@
  */
 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;
 
+import java.util.Arrays;
+import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
@@ -37,19 +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_seq_id = 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>/=$
    * 
@@ -57,40 +73,37 @@ public class UrlLink
    */
   public UrlLink(String link)
   {
-    int sep = link.indexOf("|");
-    int psqid = link.indexOf("$" + SEQUENCE_ID);
-    int nsqid = link.indexOf("$" + SEQUENCE_NAME);
+    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_seq_id = true;
+      usesDBaccession = 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
     {
       target = link.substring(0, sep);
-      sep = link.lastIndexOf("|");
+      sep = link.lastIndexOf(SEP);
       label = link.substring(0, sep);
-      url_prefix = link.substring(sep + 1);
+      urlPrefix = link.substring(sep + 1).trim();
       regexReplace = null; // implies we trim any prefix if necessary //
-      // regexReplace=".*\\|?(.*)";
-      url_suffix = null;
+      urlSuffix = null;
     }
 
     label = label.trim();
     target = target.trim();
-    target = target.toUpperCase(); // DBRefEntry uppercases DB names
-    // NB getCanonicalName might be better but does not currently change case
   }
 
   /**
@@ -98,7 +111,7 @@ public class UrlLink
    */
   public String getUrl_suffix()
   {
-    return url_suffix;
+    return urlSuffix;
   }
 
   /**
@@ -106,7 +119,7 @@ public class UrlLink
    */
   public String getUrl_prefix()
   {
-    return url_prefix;
+    return urlPrefix;
   }
 
   /**
@@ -153,6 +166,34 @@ 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
@@ -177,7 +218,7 @@ 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
@@ -218,7 +259,7 @@ public class UrlLink
                 if (mtch.length() > 0)
                 {
                   subs.addElement(mtch);
-                  subs.addElement(url_prefix + mtch + url_suffix);
+                  subs.addElement(urlPrefix + mtch + urlSuffix);
                 }
                 s = r;
               }
@@ -227,8 +268,8 @@ 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++;
               }
@@ -249,31 +290,31 @@ 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_seq_id ? SEQUENCE_ID : SEQUENCE_NAME);
+    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);
   }
 
   /**
@@ -293,15 +334,15 @@ 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)
     {
@@ -329,13 +370,13 @@ public class UrlLink
    */
   protected void parseUrl(String link, String varName, int sqidPos, int sep)
   {
-    url_prefix = link.substring(sep + 1, sqidPos);
+    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();
 
@@ -346,7 +387,7 @@ 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
       {
@@ -368,9 +409,9 @@ 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
@@ -382,13 +423,16 @@ public class UrlLink
   }
 
   /**
+   * Create a set of URL links for a sequence
    * 
-   * @param urlLink
    * @param seq
+   *          The sequence to create links for
    * @param linkset
+   *          Map of links: key = id + SEP + link, value = [target, label, id,
+   *          link]
    */
   public void createLinksFromSeq(final SequenceI seq,
-          Map<String, String[]> linkset)
+          Map<String, List<String>> linkset)
   {
     if (seq != null && dynamic)
     {
@@ -404,25 +448,30 @@ public class UrlLink
    * Create a static URL link
    * 
    * @param linkset
+   *          Map of links: key = id + SEP + link, value = [target, label, id,
+   *          link]
    */
-  public void createStaticLink(Map<String, String[]> linkset)
+  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(), new String[] { "", label,
-          "", getUrl_prefix() });
+      linkset.put(label + SEP + getUrl_prefix(),
+              Arrays.asList(target, label, null, getUrl_prefix()));
     }
   }
 
   /**
-   * Create a dynamic URL link
+   * Create dynamic URL links
    * 
    * @param seq
+   *          The sequence to create links for
    * @param linkset
+   *          Map of links: key = id + SEP + link, value = [target, label, id,
+   *          link]
    */
-  public void createDynamicLinks(final SequenceI seq,
-          Map<String, String[]> linkset)
+  protected void createDynamicLinks(final SequenceI seq,
+          Map<String, List<String>> linkset)
   {
     // collect id string too
     String id = seq.getName();
@@ -432,7 +481,7 @@ 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(),
@@ -444,14 +493,14 @@ public class UrlLink
         for (int r = 0; r < dbr.length; r++)
         {
           // create Bare ID link for this URL
-          createBareURLLink(dbr[r].getAccessionId(), linkset, true);
+          createBareURLLink(dbr[r].getAccessionId(), true, linkset);
         }
       }
     }
-    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, linkset, false);
+      createBareURLLink(id, false, linkset);
     }
 
     // Create urls from description but only for URL links which are regex
@@ -459,31 +508,33 @@ public class UrlLink
     if (descr != null && getRegexReplace() != null)
     {
       // create link for this URL from description where regex matches
-      createBareURLLink(descr, linkset, false);
+      createBareURLLink(descr, false, linkset);
     }
   }
 
   /*
    * Create a bare URL Link
+   * Returns map where key = id + SEP + link, and value = [target, label, id, link]
    */
-  protected void createBareURLLink(String id,
-          Map<String, String[]> linkset, Boolean combineLabel)
+  protected void createBareURLLink(String id, Boolean combineLabel,
+          Map<String, List<String>> linkset)
   {
     String[] urls = makeUrls(id, true);
     if (urls != null)
     {
       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)
           {
-            thisLabel = label + "|" + urls[u];
+            // incorporate label with idstring
+            thisLabel = label + SEP + urls[u];
           }
 
-          linkset.put(urls[u] + "|" + urls[u + 1], new String[] { target,
-              thisLabel, urls[u], urls[u + 1] });
+          linkset.put(urls[u] + SEP + urls[u + 1],
+                  Arrays.asList(target, thisLabel, urls[u], urls[u + 1]));
         }
       }
     }
@@ -524,7 +575,7 @@ 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[] {
     /*
@@ -566,19 +617,4 @@ public class UrlLink
       }
     }
   }
-
-  public boolean isDynamic()
-  {
-    return dynamic;
-  }
-
-  public boolean usesSeqId()
-  {
-    return uses_seq_id;
-  }
-
-  public void setLabel(String newlabel)
-  {
-    this.label = newlabel;
-  }
 }