X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FGroupUrlLink.java;h=a26dfbb6277bfe040d0e04c23df7eedb5a075ae9;hb=c17981672620e0b780a2338bd0c74e55cf9ddec2;hp=1654aef1650f5c1e9bc4fcf97cfb8fa7d958323d;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java index 1654aef..a26dfbb 100644 --- a/src/jalview/util/GroupUrlLink.java +++ b/src/jalview/util/GroupUrlLink.java @@ -1,19 +1,21 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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. * * 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; @@ -22,7 +24,6 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import java.util.Hashtable; -import java.util.Vector; public class GroupUrlLink { @@ -81,8 +82,7 @@ public class GroupUrlLink { if (tokens == null) { - tokens = new String[] - { "SEQUENCEIDS", "SEQUENCES", "DATASETID" }; + tokens = new String[] { "SEQUENCEIDS", "SEQUENCES", "DATASETID" }; } } @@ -198,9 +198,8 @@ 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) @@ -215,8 +214,8 @@ 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 : '" @@ -384,18 +383,17 @@ 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; } @@ -415,16 +413,16 @@ public class GroupUrlLink * @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 } }; + return new Object[] { stubs[0], stubs[1], rstrings, + new boolean[] + { b } }; } // TODO Auto-generated method stub return null; @@ -459,9 +457,8 @@ public class GroupUrlLink * }, 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; @@ -485,18 +482,19 @@ 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 @@ -508,8 +506,8 @@ 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 { @@ -692,9 +690,7 @@ public class GroupUrlLink { // 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. @@ -709,10 +705,9 @@ 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() } }; } /** @@ -820,8 +815,7 @@ public class GroupUrlLink public static void main(String argv[]) { // note - JAL-1383 - these services are all dead - String[] links = new String[] - { + 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|,", @@ -830,16 +824,16 @@ 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++) { @@ -847,15 +841,15 @@ public class GroupUrlLink if (ul.isValid()) { System.out.println("\n\n\n"); - System.out.println("Link " + i + " " + links[i] + " : " - + ul.toString()); + 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:"); + System.out.println( + " Without onlyIfMatches:"); Object[] urls; try { @@ -866,8 +860,8 @@ public class GroupUrlLink { System.out.println("too long exception " + ex); } - System.out - .println(" With onlyIfMatches set:"); + System.out.println( + " With onlyIfMatches set:"); try { urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",