X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FGroupUrlLink.java;h=af0b3083e0c039d77bcfccefa61988fb9ec30fb5;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=27b81d4583134374618fe1de92a0f5515e3d4ead;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index 27b81d4..af0b308 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 ($$Version-Rel$$)
+ * 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 .
+ * 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;
@@ -21,10 +24,26 @@ import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import java.util.Hashtable;
-import java.util.Vector;
public class GroupUrlLink
{
+ public class UrlStringTooLongException extends Exception
+ {
+ public UrlStringTooLongException(int lng)
+ {
+ urlLength = lng;
+ }
+
+ public int urlLength;
+
+ @Override
+ 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
@@ -64,11 +83,25 @@ public class GroupUrlLink
{
if (tokens == null)
{
- tokens = new String[]
- { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
+ tokens = new String[] { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
}
}
+ /**
+ * 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;
/**
@@ -166,9 +199,8 @@ public class GroupUrlLink
for (int pass = 0; pass < mtch.length; pass++)
{
int mlength = 3 + mtch[pass].length();
- if (link.indexOf("$" + mtch[pass] + "=/") == ptok[pass]
- && (p = link.indexOf("/=$", ptok[pass] + mlength)) > ptok[pass]
- + mlength)
+ if (link.indexOf("$" + mtch[pass] + "=/") == ptok[pass] && (p = link
+ .indexOf("/=$", ptok[pass] + mlength)) > ptok[pass] + mlength)
{
// Extract Regex and suffix
if (ptok[pass + 1] < p + 3)
@@ -183,8 +215,8 @@ public class GroupUrlLink
regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
try
{
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace[pass] + "/");
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace[pass] + "/");
if (rg == null)
{
invalidMessage = "Invalid Regular Expression : '"
@@ -286,10 +318,12 @@ public class GroupUrlLink
private String _replaceFor(String token)
{
for (int i = 0; i < mtch.length; i++)
+ {
if (segs[i] > -1 && mtch[i].equals(token))
{
return regexReplace[i];
}
+ }
return null;
}
@@ -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);
@@ -350,23 +386,23 @@ public class GroupUrlLink
* @param dsstring
* @return
*/
- private Hashtable replacementArgs(String[] idstrings,
- String[] seqstrings, String dsstring)
+ private Hashtable replacementArgs(String[] idstrings, String[] seqstrings,
+ String dsstring)
{
Hashtable rstrings = new Hashtable();
rstrings.put(tokens[0], idstrings);
rstrings.put(tokens[1], seqstrings);
- rstrings.put(tokens[2], new String[]
- { dsstring });
+ rstrings.put(tokens[2], new String[] { 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);
}
@@ -378,17 +414,18 @@ 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)
+ public Object[] makeUrlStubs(String[] ids, String[] seqstr, String string,
+ boolean b) throws UrlStringTooLongException
{
Hashtable rstrings = replacementArgs(ids, seqstr, string);
Object[] stubs = makeUrlsIf(false, rstrings, b);
if (stubs != null)
{
- return new Object[]
- { stubs[0], stubs[1], rstrings, new boolean[]
- { b } };
+ return new Object[] { stubs[0], stubs[1], rstrings,
+ new boolean[]
+ { b } };
}
// TODO Auto-generated method stub
return null;
@@ -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 +458,10 @@ 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)
+ protected Object[] makeUrlsIf(boolean createFullUrl, Hashtable repstrings,
+ boolean onlyIfMatches) throws UrlStringTooLongException
{
int pass = 0;
@@ -445,18 +485,19 @@ 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
@@ -468,8 +509,8 @@ public class GroupUrlLink
matched[pass] = new StringBuffer();
if (regexReplace[pass] != null)
{
- rgxs[pass] = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace[pass] + "/");
+ rgxs[pass] = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace[pass] + "/");
}
else
{
@@ -515,6 +556,11 @@ 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.
@@ -539,7 +585,7 @@ public class GroupUrlLink
// debug
/*
* for (int s = 0; s <= rg.numSubs(); s++) {
- * System.err.println("Sub " + s + " : " + rg.matchedFrom(s) +
+ * jalview.bin.Console.errPrintln("Sub " + s + " : " + rg.matchedFrom(s) +
* " : " + rg.matchedTo(s) + " : '" + rg.stringMatched(s) + "'");
* }
*/
@@ -641,16 +687,13 @@ 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)
{
// just return the essential info about what the URL would be generated
// from
- return new Object[]
- { new int[]
- { seqsmatched }, thismatched };
+ return new Object[] { new int[] { seqsmatched }, thismatched };
}
// otherwise, create the URL completely.
@@ -665,10 +708,9 @@ public class GroupUrlLink
}
}
- return new Object[]
- { new int[]
- { seqsmatched }, thismatched, matched, new String[]
- { submiturl.toString() } };
+ return new Object[] { new int[] { seqsmatched }, thismatched, matched,
+ new String[]
+ { submiturl.toString() } };
}
/**
@@ -705,6 +747,7 @@ public class GroupUrlLink
return r;
}
+ @Override
public String toString()
{
StringBuffer result = new StringBuffer();
@@ -744,39 +787,45 @@ public class GroupUrlLink
if (url == null)
{
- System.out.println("Created NO urls.");
+ jalview.bin.Console.outPrintln("Created NO urls.");
}
else
{
- System.out.println("Created a url from " + ((int[]) url[0])[0]
- + "out of " + idstring[0].length + " sequences.");
- System.out.println("Sequences that did not match:");
+ jalview.bin.Console
+ .outPrintln("Created a url from " + ((int[]) url[0])[0]
+ + "out of " + idstring[0].length + " sequences.");
+ jalview.bin.Console.outPrintln("Sequences that did not match:");
for (int sq = 0; sq < idstring[0].length; sq++)
{
if (!((boolean[]) url[1])[sq])
{
- System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
- + idstring[1][sq]);
+ jalview.bin.Console.outPrintln("Seq " + sq + ": "
+ + idstring[0][sq] + "\t: " + idstring[1][sq]);
}
}
- System.out.println("Sequences that DID match:");
+ jalview.bin.Console.outPrintln("Sequences that DID match:");
for (int sq = 0; sq < idstring[0].length; sq++)
{
if (((boolean[]) url[1])[sq])
{
- System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
- + idstring[1][sq]);
+ jalview.bin.Console.outPrintln("Seq " + sq + ": "
+ + idstring[0][sq] + "\t: " + idstring[1][sq]);
}
}
- System.out.println("The generated URL:");
- System.out.println(((String[]) url[3])[0]);
+ jalview.bin.Console.outPrintln("The generated URL:");
+ jalview.bin.Console.outPrintln(((String[]) url[3])[0]);
}
}
+ /**
+ *
+ * @param argv
+ * @j2sIgnore
+ */
public static void main(String argv[])
{
- String[] links = new String[]
- {
+ // 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|,",
"EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCES$&inputType=1|,",
"EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,",
@@ -785,44 +834,60 @@ public class GroupUrlLink
"EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
"EnVision2 Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([a-zA-Z]+)/=$&inputType=1|,",
"EnVision2 Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/[A-Za-z]+/=$&inputType=1|,"
- /*
- * http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?input=P38389,P38398
- * &inputType=0&workflow=Enfin%20Default%20Workflow&datasetName=
- * linkInDatasetFromPRIDE
- */
+ /*
+ * http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?input=P38389,P38398
+ * &inputType=0&workflow=Enfin%20Default%20Workflow&datasetName=
+ * linkInDatasetFromPRIDE
+ */
};
- SequenceI[] seqs = new SequenceI[]
- { new Sequence("StupidLabel:gi|9234|pdb|102L|A",
- "asdiasdpasdpadpwpadasdpaspdw"), };
+ SequenceI[] seqs = new SequenceI[] {
+ new Sequence("StupidLabel:gi|9234|pdb|102L|A",
+ "asdiasdpasdpadpwpadasdpaspdw"), };
String[][] seqsandids = formStrings(seqs);
for (int i = 0; i < links.length; i++)
{
GroupUrlLink ul = new GroupUrlLink(links[i]);
if (ul.isValid())
{
- System.out.println("\n\n\n");
- System.out.println("Link " + i + " " + links[i] + " : "
- + ul.toString());
- System.out.println(" pref : " + ul.getUrl_prefix());
- System.out.println(" IdReplace : " + ul.getIDRegexReplace());
- System.out.println(" SeqReplace : " + ul.getSeqRegexReplace());
- System.out.println(" Suffixes : " + ul.getUrl_suffix());
-
- System.out
- .println(" Without onlyIfMatches:");
- Object[] urls = ul.makeUrls(seqsandids[0], seqsandids[1],
- "mydataset", false);
- testUrls(ul, seqsandids, urls);
- System.out
- .println(" With onlyIfMatches set:");
- urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset", true);
- testUrls(ul, seqsandids, urls);
+ jalview.bin.Console.outPrintln("\n\n\n");
+ jalview.bin.Console.outPrintln(
+ "Link " + i + " " + links[i] + " : " + ul.toString());
+ jalview.bin.Console.outPrintln(" pref : " + ul.getUrl_prefix());
+ jalview.bin.Console
+ .outPrintln(" IdReplace : " + ul.getIDRegexReplace());
+ jalview.bin.Console
+ .outPrintln(" SeqReplace : " + ul.getSeqRegexReplace());
+ jalview.bin.Console.outPrintln(" Suffixes : " + ul.getUrl_suffix());
+
+ jalview.bin.Console.outPrintln(
+ " Without onlyIfMatches:");
+ Object[] urls;
+ try
+ {
+ urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
+ false);
+ testUrls(ul, seqsandids, urls);
+ } catch (UrlStringTooLongException ex)
+ {
+ jalview.bin.Console.outPrintln("too long exception " + ex);
+ }
+ jalview.bin.Console.outPrintln(
+ " With onlyIfMatches set:");
+ try
+ {
+ urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
+ true);
+ testUrls(ul, seqsandids, urls);
+ } catch (UrlStringTooLongException ex)
+ {
+ jalview.bin.Console.outPrintln("too long exception " + ex);
+ }
}
else
{
- System.err.println("Invalid URLLink : " + links[i] + " : "
- + ul.getInvalidMessage());
+ jalview.bin.Console.errPrintln("Invalid URLLink : " + links[i]
+ + " : " + ul.getInvalidMessage());
}
}
}