/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
public int urlLength;
+ @Override
public String toString()
{
return "Generated url is estimated to be too long (" + urlLength
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)
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 : '"
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;
}
* @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[2], new String[] { dsstring });
if (idstrings.length != seqstrings.length)
{
- throw new Error(
- MessageManager
- .getString("error.idstring_seqstrings_only_one_per_sequence"));
+ throw new Error(MessageManager.getString(
+ "error.idstring_seqstrings_only_one_per_sequence"));
}
return rstrings;
}
* @return URL stub objects ready to pass to constructFrom
* @throws UrlStringTooLongException
*/
- public Object[] makeUrlStubs(String[] ids, String[] seqstr,
- String string, boolean b) throws UrlStringTooLongException
+ 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 } };
+ new boolean[]
+ { b } };
}
// TODO Auto-generated method stub
return null;
* }, String[] { url })}
* @throws UrlStringTooLongException
*/
- protected Object[] makeUrlsIf(boolean createFullUrl,
- Hashtable repstrings, boolean onlyIfMatches)
- throws UrlStringTooLongException
+ protected Object[] makeUrlsIf(boolean createFullUrl, Hashtable repstrings,
+ boolean onlyIfMatches) throws UrlStringTooLongException
{
int pass = 0;
{
throw new Error(MessageManager.formatMessage(
"error.cannot_have_mixed_length_replacement_vectors",
- new String[] { (mtch[i]),
+ new String[]
+ { (mtch[i]),
Integer.valueOf(idseq[i].length).toString(),
Integer.valueOf(maxs).toString() }));
}
}
else
{
- throw new Error(
- MessageManager
- .getString("error.cannot_have_zero_length_vector_replacement_strings"));
+ throw new Error(MessageManager.getString(
+ "error.cannot_have_zero_length_vector_replacement_strings"));
}
}
// iterate through input, collating segments to be inserted into url
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
{
// 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) + "'");
* }
*/
}
return new Object[] { new int[] { seqsmatched }, thismatched, matched,
- new String[] { submiturl.toString() } };
+ new String[]
+ { submiturl.toString() } };
}
/**
return r;
}
+ @Override
public String toString()
{
StringBuffer result = new StringBuffer();
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[])
{
// note - JAL-1383 - these services are all dead
"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("<insert input id and sequence strings here> Without onlyIfMatches:");
+ 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(
+ "<insert input id and sequence strings here> Without onlyIfMatches:");
Object[] urls;
try
{
testUrls(ul, seqsandids, urls);
} catch (UrlStringTooLongException ex)
{
- System.out.println("too long exception " + ex);
+ jalview.bin.Console.outPrintln("too long exception " + ex);
}
- System.out
- .println("<insert input id and sequence strings here> With onlyIfMatches set:");
+ jalview.bin.Console.outPrintln(
+ "<insert input id and sequence strings here> With onlyIfMatches set:");
try
{
urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
testUrls(ul, seqsandids, urls);
} catch (UrlStringTooLongException ex)
{
- System.out.println("too long exception " + 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());
}
}
}
git://source.jalview.org / jalview.git / blobdiff