X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FGroupUrlLink.java;h=e8af4cd7e2e8bb54117e6a9583ba3147203694a0;hb=1cb953ba4613be2af16e73eb131abf0f3d8d4234;hp=27b81d4583134374618fe1de92a0f5515e3d4ead;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index 27b81d4..e8af4cd 100644
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -1,19 +1,22 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
@@ -25,6 +28,22 @@ 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 +88,21 @@ 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 +368,11 @@ 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);
@@ -360,13 +396,13 @@ public class GroupUrlLink
{ dsstring });
if (idstrings.length != seqstrings.length)
{
- throw new Error(
- "idstrings and seqstrings contain one string each per sequence.");
+ throw new Error(MessageManager.getString("error.idstring_seqstrings_only_one_per_sequence"));
}
return rstrings;
}
public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)
+ throws UrlStringTooLongException
{
return makeUrlsIf(true, repstrings, onlyIfMatches);
}
@@ -378,9 +414,10 @@ 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 +437,10 @@ 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 +458,11 @@ 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;
@@ -445,18 +486,14 @@ public class GroupUrlLink
{
if (maxs != idseq[i].length)
{
- throw new Error(
- "Cannot have mixed length replacement vectors. Replacement vector for "
- + (mtch[i]) + " is " + idseq[i].length
- + " strings long, and have already seen a "
- + maxs + " length vector.");
+ throw new Error(MessageManager.formatMessage("error.cannot_have_mixed_length_replacement_vectors",
+ new String[]{(mtch[i]), Integer.valueOf(idseq[i].length).toString(),Integer.valueOf(maxs).toString()}));
}
}
}
else
{
- throw new Error(
- "Cannot have zero length vector of replacement strings - either 1 value or n values.");
+ throw new Error(MessageManager.getString("error.cannot_have_zero_length_vector_replacement_strings"));
}
}
// iterate through input, collating segments to be inserted into url
@@ -515,6 +552,11 @@ 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 +683,7 @@ 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)
{
@@ -775,6 +816,7 @@ public class GroupUrlLink
public static void main(String argv[])
{
+ // note - JAL-1383 - these services are all dead
String[] links = new String[]
{
"EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
@@ -811,13 +853,27 @@ public class GroupUrlLink
System.out
.println(" 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(" 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
{