Jalview 2.8 Source Header

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

diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index 27b81d4..714e12d 100644 (file)
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * 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 
@@ -25,6 +25,22 @@ import java.util.Vector;
 
 public class GroupUrlLink
 {
+  public class UrlStringTooLongException extends Exception
+  {
+    public UrlStringTooLongException(int lng)
+    {
+      urlLength = lng;
+    }
+
+    public int urlLength;
+
+    public String toString()
+    {
+      return "Generated url is estimated to be too long (" + urlLength
+              + ")";
+    }
+  }
+
   /**
    * Helper class based on the UrlLink class which enables URLs to be
    * constructed from sequences or IDs associated with a group of sequences. URL
@@ -69,6 +85,21 @@ public class GroupUrlLink
     }
   }
 
+  /**
+   * test for GroupURLType bitfield (with default tokens)
+   */
+  public static final int SEQUENCEIDS = 1;
+
+  /**
+   * test for GroupURLType bitfield (with default tokens)
+   */
+  public static final int SEQUENCES = 2;
+
+  /**
+   * test for GroupURLType bitfield (with default tokens)
+   */
+  public static final int DATASETID = 4;
+
   // private int idseg = -1, seqseg = -1;
 
   /**
@@ -334,9 +365,11 @@ public class GroupUrlLink
    * @return null or Object[] { int[] { number of seqs substituted},boolean[] {
    *         which seqs were substituted }, StringBuffer[] { substituted lists
    *         for each token }, String[] { url } }
+   * @throws UrlStringTooLongException
    */
   public Object[] makeUrls(String[] idstrings, String[] seqstrings,
           String dsstring, boolean onlyIfMatches)
+          throws UrlStringTooLongException
   {
     Hashtable rstrings = replacementArgs(idstrings, seqstrings, dsstring);
     return makeUrls(rstrings, onlyIfMatches);
@@ -367,6 +400,7 @@ public class GroupUrlLink
   }
 
   public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)
+          throws UrlStringTooLongException
   {
     return makeUrlsIf(true, repstrings, onlyIfMatches);
   }
@@ -378,9 +412,10 @@ public class GroupUrlLink
    * @param string
    * @param b
    * @return URL stub objects ready to pass to constructFrom
+   * @throws UrlStringTooLongException
    */
   public Object[] makeUrlStubs(String[] ids, String[] seqstr,
-          String string, boolean b)
+          String string, boolean b) throws UrlStringTooLongException
   {
     Hashtable rstrings = replacementArgs(ids, seqstr, string);
     Object[] stubs = makeUrlsIf(false, rstrings, b);
@@ -400,8 +435,10 @@ public class GroupUrlLink
    * 
    * @param stubs
    * @return URL string.
+   * @throws UrlStringTooLongException
    */
   public String constructFrom(Object[] stubs)
+          throws UrlStringTooLongException
   {
     Object[] results = makeUrlsIf(true, (Hashtable) stubs[2],
             ((boolean[]) stubs[3])[0]);
@@ -419,9 +456,11 @@ public class GroupUrlLink
    *         seqs }, boolean[] { which matched }, (if createFullUrl also has
    *         StringBuffer[] { segment generated from inputs that is used in URL
    *         }, String[] { url })}
+   * @throws UrlStringTooLongException
    */
   protected Object[] makeUrlsIf(boolean createFullUrl,
           Hashtable repstrings, boolean onlyIfMatches)
+          throws UrlStringTooLongException
   {
     int pass = 0;
 
@@ -515,6 +554,11 @@ public class GroupUrlLink
             rematchat = rg.matchedTo();
             thismatched[sq] |= true;
             urllength += rg.charsMatched(); // count length
+            if ((urllength + 32) > Platform.getMaxCommandLineLength())
+            {
+              throw new UrlStringTooLongException(urllength);
+            }
+
             if (!createFullUrl)
             {
               continue; // don't bother making the URL replacement text.
@@ -641,8 +685,7 @@ public class GroupUrlLink
     // platform
     if ((urllength + 32) > Platform.getMaxCommandLineLength())
     {
-      System.err.println("URL estimated to be too long " + urllength);
-      return null;
+      throw new UrlStringTooLongException(urllength);
     }
     if (!createFullUrl)
     {
@@ -811,13 +854,27 @@ public class GroupUrlLink
 
         System.out
                 .println("<insert input id and sequence strings here> Without onlyIfMatches:");
-        Object[] urls = ul.makeUrls(seqsandids[0], seqsandids[1],
-                "mydataset", false);
-        testUrls(ul, seqsandids, urls);
+        Object[] urls;
+        try
+        {
+          urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
+                  false);
+          testUrls(ul, seqsandids, urls);
+        } catch (UrlStringTooLongException ex)
+        {
+          System.out.println("too long exception " + ex);
+        }
         System.out
                 .println("<insert input id and sequence strings here> With onlyIfMatches set:");
-        urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset", true);
-        testUrls(ul, seqsandids, urls);
+        try
+        {
+          urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
+                  true);
+          testUrls(ul, seqsandids, urls);
+        } catch (UrlStringTooLongException ex)
+        {
+          System.out.println("too long exception " + ex);
+        }
       }
       else
       {