X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FUrlLink.java;h=872f43299199b219530c5ee0f057390f2f1874dd;hb=0eb7bbd7c1c29eae73f872693ae033003be1031c;hp=e955a6f71b0502e029d358ccabdc35346f6623e9;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index e955a6f..872f432 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -1,22 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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;
 
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SEQUENCE_NAME;
+
 import java.util.Vector;
 
 public class UrlLink
@@ -34,6 +40,8 @@ public class UrlLink
 
   private boolean dynamic = false;
 
+  private boolean uses_seq_id = false;
+
   private String invalidMessage = null;
 
   /**
@@ -45,81 +53,40 @@ public class UrlLink
    */
   public UrlLink(String link)
   {
-    int sep = link.indexOf("|"), psqid = link.indexOf("$SEQUENCE_ID");
+    int sep = link.indexOf("|");
+    int psqid = link.indexOf("$" + SEQUENCE_ID);
+    int nsqid = link.indexOf("$" + SEQUENCE_NAME);
     if (psqid > -1)
     {
       dynamic = true;
-      int p = sep;
-      do
-      {
-        sep = p;
-        p = link.indexOf("|", sep + 1);
-      } while (p > sep && p < psqid);
-      // Assuming that the URL itself does not contain any '|' symbols
-      // sep now contains last pipe symbol position prior to any regex symbols
-      label = link.substring(0, sep);
-      if (label.indexOf("|") > -1)
-      {
-        // | terminated database name / www target at start of Label
-        target = label.substring(0, label.indexOf("|"));
-      }
-      else if (label.indexOf(" ") > 2)
-      {
-        // space separated Label - matches database name
-        target = label.substring(0, label.indexOf(" "));
-      }
-      else
-      {
-        target = label;
-      }
-      // Parse URL : Whole URL string first
-      url_prefix = link.substring(sep + 1, psqid);
-      if (link.indexOf("$SEQUENCE_ID=/") == psqid
-              && (p = link.indexOf("/=$", psqid + 14)) > psqid + 14)
-      {
-        // Extract Regex and suffix
-        url_suffix = link.substring(p + 3);
-        regexReplace = link.substring(psqid + 14, p);
-        try
-        {
-          com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
-                  + regexReplace + "/");
-          if (rg == null)
-          {
-            invalidMessage = "Invalid Regular Expression : '"
-                    + regexReplace + "'\n";
-          }
-        } catch (Exception e)
-        {
-          invalidMessage = "Invalid Regular Expression : '" + regexReplace
-                  + "'\n";
-        }
-      }
-      else
-      {
-        regexReplace = null;
-        // verify format is really correct.
-        if (link.indexOf("$SEQUENCE_ID$") == psqid)
-        {
-          url_suffix = link.substring(psqid + 13);
-          regexReplace = null;
-        }
-        else
-        {
-          invalidMessage = "Warning: invalid regex structure for URL link : "
-                  + link;
-        }
-      }
+      uses_seq_id = true;
+
+      sep = parseTargetAndLabel(sep, psqid, link);
+
+      parseUrl(link, SEQUENCE_ID, psqid, sep);
+    }
+    else if (nsqid > -1)
+    {
+      dynamic = true;
+      sep = parseTargetAndLabel(sep, nsqid, link);
+
+      parseUrl(link, SEQUENCE_NAME, nsqid, sep);
     }
     else
     {
       target = link.substring(0, sep);
-      label = link.substring(0, sep = link.lastIndexOf("|"));
+      sep = link.lastIndexOf("|");
+      label = link.substring(0, sep);
       url_prefix = link.substring(sep + 1);
       regexReplace = null; // implies we trim any prefix if necessary //
       // regexReplace=".*\\|?(.*)";
       url_suffix = 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
   }
 
   /**
@@ -205,8 +172,7 @@ public class UrlLink
           if (ns == 0)
           {
             // take whole regex
-            return new String[]
-            { rg.stringMatched(),
+            return new String[] { rg.stringMatched(),
                 url_prefix + rg.stringMatched() + url_suffix };
           } /*
              * else if (ns==1) { // take only subgroup match return new String[]
@@ -285,25 +251,130 @@ public class UrlLink
       }
 
       // just return simple url substitution.
-      return new String[]
-      { idstring, url_prefix + idstring + url_suffix };
+      return new String[] { idstring, url_prefix + idstring + url_suffix };
     }
     else
     {
-      return new String[]
-      { "", url_prefix };
+      return new String[] { "", url_prefix };
     }
   }
 
+  @Override
   public String toString()
   {
+    String var = (uses_seq_id ? SEQUENCE_ID : SEQUENCE_NAME);
+
     return label
             + "|"
             + url_prefix
-            + (dynamic ? ("$SEQUENCE_ID" + ((regexReplace != null) ? "="
+            + (dynamic ? ("$" + var + ((regexReplace != null) ? "="
                     + regexReplace + "=$" : "$")) : "")
             + ((url_suffix == null) ? "" : url_suffix);
+  }
+
+  /**
+   * 
+   * @param firstSep
+   *          Location of first occurrence of separator in link string
+   * @param psqid
+   *          Position of sequence id or name in link string
+   * @param link
+   *          Link string containing database name and url
+   * @return Position of last separator symbol prior to any regex symbols
+   */
+  protected int parseTargetAndLabel(int firstSep, int psqid, String link)
+  {
+    int p = firstSep;
+    int sep = firstSep;
+    do
+    {
+      sep = p;
+      p = link.indexOf("|", sep + 1);
+    } while (p > sep && p < psqid);
+    // Assuming that the URL itself does not contain any '|' symbols
+    // sep now contains last pipe symbol position prior to any regex symbols
+    label = link.substring(0, sep);
+    if (label.indexOf("|") > -1)
+    {
+      // | terminated database name / www target at start of Label
+      target = label.substring(0, label.indexOf("|"));
+    }
+    else if (label.indexOf(" ") > 2)
+    {
+      // space separated Label - matches database name
+      target = label.substring(0, label.indexOf(" "));
+    }
+    else
+    {
+      target = label;
+    }
+    return sep;
+  }
+
+  /**
+   * Parse the URL part of the link string
+   * 
+   * @param link
+   *          Link string containing database name and url
+   * @param varName
+   *          Name of variable in url string (e.g. SEQUENCE_ID, SEQUENCE_NAME)
+   * @param sqidPos
+   *          Position of id or name in link string
+   * @param sep
+   *          Position of separator in link string
+   */
+  protected void parseUrl(String link, String varName, int sqidPos, int sep)
+  {
+    url_prefix = link.substring(sep + 1, sqidPos);
+
+    // delimiter at start of regex: e.g. $SEQUENCE_ID=/
+    String startDelimiter = "$" + varName + "=/";
+
+    // delimiter at end of regex: /=$
+    String endDelimiter = "/=$";
 
+    int startLength = startDelimiter.length();
+
+    // Parse URL : Whole URL string first
+    int p = link.indexOf(endDelimiter, sqidPos + startLength);
+
+    if (link.indexOf(startDelimiter) == sqidPos
+            && (p > sqidPos + startLength))
+    {
+      // Extract Regex and suffix
+      url_suffix = link.substring(p + endDelimiter.length());
+      regexReplace = link.substring(sqidPos + startLength, p);
+      try
+      {
+        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
+                + regexReplace + "/");
+        if (rg == null)
+        {
+          invalidMessage = "Invalid Regular Expression : '" + regexReplace
+                  + "'\n";
+        }
+      } catch (Exception e)
+      {
+        invalidMessage = "Invalid Regular Expression : '" + regexReplace
+                + "'\n";
+      }
+    }
+    else
+    {
+      // no regex
+      regexReplace = null;
+      // verify format is really correct.
+      if (link.indexOf("$" + varName + "$") == sqidPos)
+      {
+        url_suffix = link.substring(sqidPos + startLength - 1);
+        regexReplace = null;
+      }
+      else
+      {
+        invalidMessage = "Warning: invalid regex structure for URL link : "
+                + link;
+      }
+    }
   }
 
   private static void testUrls(UrlLink ul, String idstring, String[] urls)
@@ -326,8 +397,7 @@ public class UrlLink
 
   public static void main(String argv[])
   {
-    String[] links = new String[]
-    {
+    String[] links = new String[] {
     /*
      * "AlinkT|Target|http://foo.foo.soo/",
      * "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",
@@ -342,9 +412,9 @@ 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" };
-    String[] idstrings = new String[]
-    {
+    "NESTED|http://nested/$" + SEQUENCE_ID
+            + "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
+    String[] idstrings = new String[] {
     /*
      * //"LGUL_human", //"QWIQW_123123", "uniprot|why_do+_12313_foo",
      * //"123123312", "123123 ABCDE foo", "PFAM:PF23943",
@@ -391,6 +461,11 @@ public class UrlLink
     return dynamic;
   }
 
+  public boolean usesSeqId()
+  {
+    return uses_seq_id;
+  }
+
   public void setLabel(String newlabel)
   {
     this.label = newlabel;