-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.util;\r
-\r
-import jalview.datamodel.Sequence;\r
-import jalview.datamodel.SequenceI;\r
-\r
-import java.util.Hashtable;\r
-import java.util.Vector;\r
-\r
-public class GroupUrlLink\r
-{\r
- /**\r
- * Helper class based on the UrlLink class which enables URLs to be\r
- * constructed from sequences or IDs associated with a group of sequences. URL\r
- * definitions consist of a pipe separated string containing a <label>|<url\r
- * construct>|<separator character>[|<sequence separator character>]. The url\r
- * construct includes regex qualified tokens which are replaced with seuqence\r
- * IDs ($SEQUENCE_IDS$) and/or seuqence regions ($SEQUENCES$) that are\r
- * extracted from the group. See <code>UrlLink</code> for more information\r
- * about the approach, and the original implementation.\r
- * Documentation to come. Note - groupUrls can be very big!\r
- */\r
- private String url_prefix, target, label;\r
-\r
- /**\r
- * these are all filled in order of the occurence of each token in the url\r
- * string template\r
- */\r
- private String url_suffix[], separators[], regexReplace[];\r
-\r
- private String invalidMessage = null;\r
-\r
- /**\r
- * tokens that can be replaced in the URL.\r
- */\r
- private static String[] tokens;\r
-\r
- /**\r
- * position of each token (which can appear once only) in the url\r
- */\r
- private int[] segs;\r
-\r
- /**\r
- * contains tokens in the order they appear in the URL template.\r
- */\r
- private String[] mtch;\r
- static\r
- {\r
- if (tokens == null)\r
- {\r
- tokens = new String[]\r
- { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };\r
- }\r
- }\r
-\r
- // private int idseg = -1, seqseg = -1;\r
-\r
- /**\r
- * parse the given linkString of the form '<label>|<url>|separator\r
- * char[|optional sequence separator char]' into parts. url may contain a\r
- * string $SEQUENCEIDS<=optional regex=>$ where <=optional regex=> must be of\r
- * the form =/<perl style regex>/=$ or $SEQUENCES<=optional regex=>$ or\r
- * $SEQUENCES<=optional regex=>$.\r
- * \r
- * @param link\r
- */\r
- public GroupUrlLink(String link)\r
- {\r
- int sep = link.indexOf("|");\r
- segs = new int[tokens.length];\r
- int ntoks = 0;\r
- for (int i = 0; i < segs.length; i++)\r
- {\r
- if ((segs[i] = link.indexOf("$" + tokens[i])) > -1)\r
- {\r
- ntoks++;\r
- }\r
- }\r
- // expect at least one token\r
- if (ntoks == 0)\r
- {\r
- invalidMessage = "Group URL string must contain at least one of ";\r
- for (int i = 0; i < segs.length; i++)\r
- {\r
- invalidMessage += " '$" + tokens[i] + "[=/regex=/]$'";\r
- }\r
- return;\r
- }\r
-\r
- int[] ptok = new int[ntoks + 1];\r
- String[] tmtch = new String[ntoks + 1];\r
- mtch = new String[ntoks];\r
- for (int i = 0, t = 0; i < segs.length; i++)\r
- {\r
- if (segs[i] > -1)\r
- {\r
- ptok[t] = segs[i];\r
- tmtch[t++] = tokens[i];\r
- }\r
- }\r
- ptok[ntoks] = link.length();\r
- tmtch[ntoks] = "$$$$$$$$$";\r
- jalview.util.QuickSort.sort(ptok, tmtch);\r
- for (int i = 0; i < ntoks; i++)\r
- {\r
- mtch[i] = tmtch[i]; // TODO: check order is ascending\r
- }\r
- /*\r
- * replaces the specific code below {}; if (psqids > -1 && pseqs > -1) { if\r
- * (psqids > pseqs) { idseg = 1; seqseg = 0;\r
- * \r
- * ptok = new int[] { pseqs, psqids, link.length() }; mtch = new String[] {\r
- * "$SEQUENCES", "$SEQUENCEIDS" }; } else { idseg = 0; seqseg = 1; ptok =\r
- * new int[] { psqids, pseqs, link.length() }; mtch = new String[] {\r
- * "$SEQUENCEIDS", "$SEQUENCES" }; } } else { if (psqids != -1) { idseg = 0;\r
- * ptok = new int[] { psqids, link.length() }; mtch = new String[] {\r
- * "$SEQUENCEIDS" }; } else { seqseg = 0; ptok = new int[] { pseqs,\r
- * link.length() }; mtch = new String[] { "$SEQUENCES" }; } }\r
- */\r
-\r
- int p = sep;\r
- // first get the label and target part before the first |\r
- do\r
- {\r
- sep = p;\r
- p = link.indexOf("|", sep + 1);\r
- } while (p > sep && p < ptok[0]);\r
- // Assuming that the URL itself does not contain any '|' symbols\r
- // sep now contains last pipe symbol position prior to any regex symbols\r
- label = link.substring(0, sep);\r
- if (label.indexOf("|") > -1)\r
- {\r
- // | terminated database name / www target at start of Label\r
- target = label.substring(0, label.indexOf("|"));\r
- }\r
- else if (label.indexOf(" ") > 2)\r
- {\r
- // space separated Label - matches database name\r
- target = label.substring(0, label.indexOf(" "));\r
- }\r
- else\r
- {\r
- target = label;\r
- }\r
- // Now Parse URL : Whole URL string first\r
- url_prefix = link.substring(sep + 1, ptok[0]);\r
- url_suffix = new String[mtch.length];\r
- regexReplace = new String[mtch.length];\r
- // and loop through tokens\r
- for (int pass = 0; pass < mtch.length; pass++)\r
- {\r
- int mlength = 3 + mtch[pass].length();\r
- if (link.indexOf("$" + mtch[pass] + "=/") == ptok[pass]\r
- && (p = link.indexOf("/=$", ptok[pass] + mlength)) > ptok[pass]\r
- + mlength)\r
- {\r
- // Extract Regex and suffix\r
- if (ptok[pass + 1] < p + 3)\r
- {\r
- // tokens are not allowed inside other tokens - e.g. inserting a\r
- // $sequences$ into the regex match for the sequenceid\r
- invalidMessage = "Token regexes cannot contain other regexes (did you terminate the $"\r
- + mtch[pass] + " regex with a '/=$' ?";\r
- return;\r
- }\r
- url_suffix[pass] = link.substring(p + 3, ptok[pass + 1]);\r
- regexReplace[pass] = link.substring(ptok[pass] + mlength, p);\r
- try\r
- {\r
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"\r
- + regexReplace[pass] + "/");\r
- if (rg == null)\r
- {\r
- invalidMessage = "Invalid Regular Expression : '"\r
- + regexReplace[pass] + "'\n";\r
- }\r
- } catch (Exception e)\r
- {\r
- invalidMessage = "Invalid Regular Expression : '"\r
- + regexReplace[pass] + "'\n";\r
- }\r
- }\r
- else\r
- {\r
- regexReplace[pass] = null;\r
- // verify format is really correct.\r
- if ((p = link.indexOf("$" + mtch[pass] + "$")) == ptok[pass])\r
- {\r
- url_suffix[pass] = link.substring(p + mtch[pass].length() + 2,\r
- ptok[pass + 1]);\r
- }\r
- else\r
- {\r
- invalidMessage = "Warning: invalid regex structure (after '"\r
- + mtch[0] + "') for URL link : " + link;\r
- }\r
- }\r
- }\r
- int pass = 0;\r
- separators = new String[url_suffix.length];\r
- String suffices = url_suffix[url_suffix.length - 1], lastsep = ",";\r
- // have a look in the last suffix for any more separators.\r
- while ((p = suffices.indexOf('|')) > -1)\r
- {\r
- separators[pass] = suffices.substring(p + 1);\r
- if (pass == 0)\r
- {\r
- // trim the original suffix string\r
- url_suffix[url_suffix.length - 1] = suffices.substring(0, p);\r
- }\r
- else\r
- {\r
- lastsep = (separators[pass - 1] = separators[pass - 1].substring(0,\r
- p));\r
- }\r
- suffices = separators[pass];\r
- pass++;\r
- }\r
- if (pass > 0)\r
- {\r
- lastsep = separators[pass - 1];\r
- }\r
- // last separator is always used for all the remaining separators\r
- while (pass < separators.length)\r
- {\r
- separators[pass++] = lastsep;\r
- }\r
- }\r
-\r
- /**\r
- * @return the url_suffix\r
- */\r
- public String getUrl_suffix()\r
- {\r
- return url_suffix[url_suffix.length - 1];\r
- }\r
-\r
- /**\r
- * @return the url_prefix\r
- */\r
- public String getUrl_prefix()\r
- {\r
- return url_prefix;\r
- }\r
-\r
- /**\r
- * @return the target\r
- */\r
- public String getTarget()\r
- {\r
- return target;\r
- }\r
-\r
- /**\r
- * @return the label\r
- */\r
- public String getLabel()\r
- {\r
- return label;\r
- }\r
-\r
- /**\r
- * @return the sequence ID regexReplace\r
- */\r
- public String getIDRegexReplace()\r
- {\r
- return _replaceFor(tokens[0]);\r
- }\r
-\r
- private String _replaceFor(String token)\r
- {\r
- for (int i = 0; i < mtch.length; i++)\r
- if (segs[i] > -1 && mtch[i].equals(token))\r
- {\r
- return regexReplace[i];\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * @return the sequence ID regexReplace\r
- */\r
- public String getSeqRegexReplace()\r
- {\r
- return _replaceFor(tokens[1]);\r
- }\r
-\r
- /**\r
- * @return the invalidMessage\r
- */\r
- public String getInvalidMessage()\r
- {\r
- return invalidMessage;\r
- }\r
-\r
- /**\r
- * Check if URL string was parsed properly.\r
- * \r
- * @return boolean - if false then <code>getInvalidMessage</code> returns an\r
- * error message\r
- */\r
- public boolean isValid()\r
- {\r
- return invalidMessage == null;\r
- }\r
-\r
- /**\r
- * return one or more URL strings by applying regex to the given idstring\r
- * \r
- * @param idstrings\r
- * array of id strings to pass to service\r
- * @param seqstrings\r
- * array of seq strings to pass to service\r
- * @param onlyIfMatches\r
- * - when true url strings are only made if regex is defined and\r
- * matches for all qualified tokens in groupURL - TODO: consider if\r
- * onlyIfMatches is really a useful parameter!\r
- * @return null or Object[] { int[] { number of seqs substituted},boolean[] {\r
- * which seqs were substituted }, StringBuffer[] { substituted lists\r
- * for each token }, String[] { url } }\r
- */\r
- public Object[] makeUrls(String[] idstrings, String[] seqstrings,\r
- String dsstring, boolean onlyIfMatches)\r
- {\r
- Hashtable rstrings = replacementArgs(idstrings, seqstrings, dsstring);\r
- return makeUrls(rstrings, onlyIfMatches);\r
- }\r
-\r
- /**\r
- * gathers input into a hashtable\r
- * @param idstrings\r
- * @param seqstrings\r
- * @param dsstring\r
- * @return\r
- */\r
- private Hashtable replacementArgs(String[] idstrings,\r
- String[] seqstrings, String dsstring)\r
- {\r
- Hashtable rstrings = new Hashtable();\r
- rstrings.put(tokens[0], idstrings);\r
- rstrings.put(tokens[1], seqstrings);\r
- rstrings.put(tokens[2], new String[]\r
- { dsstring });\r
- if (idstrings.length != seqstrings.length)\r
- {\r
- throw new Error(\r
- "idstrings and seqstrings contain one string each per sequence.");\r
- }\r
- return rstrings;\r
- }\r
-\r
- public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)\r
- {\r
- return makeUrlsIf(true,repstrings,onlyIfMatches);\r
- }\r
- /**\r
- * \r
- * @param ids\r
- * @param seqstr\r
- * @param string\r
- * @param b\r
- * @return URL stub objects ready to pass to constructFrom \r
- */\r
- public Object[] makeUrlStubs(String[] ids, String[] seqstr,\r
- String string, boolean b)\r
- {\r
- Hashtable rstrings = replacementArgs(ids, seqstr, string);\r
- Object[] stubs = makeUrlsIf(false, rstrings, b);\r
- if (stubs!=null)\r
- {\r
- return new Object[] { stubs[0], stubs[1], rstrings, new boolean[] { b } };\r
- }\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- /**\r
- * generate the URL for the given URL stub object array returned from makeUrlStubs\r
- * @param stubs\r
- * @return URL string.\r
- */\r
- public String constructFrom(Object[] stubs)\r
- {\r
- Object[] results = makeUrlsIf(true, (Hashtable) stubs[2], ((boolean[])stubs[3])[0]); \r
- return ((String[]) results[3])[0];\r
- }\r
- /**\r
- * conditionally generate urls or stubs for a given input.\r
- * @param createFullUrl set to false if you only want to test if URLs would be generated.\r
- * @param repstrings\r
- * @param onlyIfMatches\r
- * @return null if no url is generated. Object[] { int[] { number of matches seqs }, boolean[] { which matched }, (if createFullUrl also has StringBuffer[] { segment generated from inputs that is used in URL }, String[] { url })}\r
- */\r
- protected Object[] makeUrlsIf(boolean createFullUrl, Hashtable repstrings, boolean onlyIfMatches)\r
- {\r
- int pass = 0;\r
- \r
- // prepare string arrays in correct order to be assembled into URL input\r
- String[][] idseq = new String[mtch.length][]; // indexed by pass\r
- int mins = 0, maxs = 0; // allowed two values, 1 or n-sequences.\r
- for (int i = 0; i < mtch.length; i++)\r
- {\r
- idseq[i] = (String[]) repstrings.get(mtch[i]);\r
- if (idseq[i].length >= 1)\r
- {\r
- if (mins == 0 && idseq[i].length == 1)\r
- {\r
- mins = 1;\r
- }\r
- if (maxs < 2)\r
- {\r
- maxs = idseq[i].length;\r
- }\r
- else\r
- {\r
- if (maxs != idseq[i].length)\r
- {\r
- throw new Error(\r
- "Cannot have mixed length replacement vectors. Replacement vector for "\r
- + (mtch[i]) + " is " + idseq[i].length\r
- + " strings long, and have already seen a "\r
- + maxs + " length vector.");\r
- }\r
- }\r
- }\r
- else\r
- {\r
- throw new Error(\r
- "Cannot have zero length vector of replacement strings - either 1 value or n values.");\r
- }\r
- }\r
- // iterate through input, collating segments to be inserted into url\r
- StringBuffer matched[] = new StringBuffer[idseq.length];\r
- // and precompile regexes\r
- com.stevesoft.pat.Regex[] rgxs = new com.stevesoft.pat.Regex[matched.length];\r
- for (pass = 0; pass < matched.length; pass++)\r
- {\r
- matched[pass] = new StringBuffer();\r
- if (regexReplace[pass] != null)\r
- {\r
- rgxs[pass] = com.stevesoft.pat.Regex.perlCode("/" + regexReplace[pass]\r
- + "/");\r
- }\r
- else\r
- {\r
- rgxs[pass] = null;\r
- }\r
- }\r
- // tot up the invariant lengths for this url\r
- int urllength = url_prefix.length();\r
- for (pass=0;pass<matched.length; pass++)\r
- {\r
- urllength+=url_suffix[pass].length();\r
- }\r
-\r
- // flags to record which of the input sequences were actually used to generate the\r
- // url\r
- boolean[] thismatched = new boolean[maxs];\r
- int seqsmatched = 0;\r
- for (int sq = 0; sq < maxs; sq++)\r
- {\r
- // initialise flag for match\r
- thismatched[sq] = false;\r
- StringBuffer[] thematches = new StringBuffer[rgxs.length];\r
- for (pass = 0; pass < rgxs.length; pass++)\r
- {\r
- thematches[pass] = new StringBuffer(); // initialise - in case there are no more\r
- // matches.\r
- // if a regex is provided, then it must match for all sequences in all\r
- // tokens for it to be considered.\r
- if (idseq[pass].length <= sq)\r
- {\r
- // no more replacement strings to try for this token\r
- continue;\r
- }\r
- if (rgxs[pass] != null)\r
- {\r
- com.stevesoft.pat.Regex rg = rgxs[pass];\r
- int rematchat = 0;\r
- // concatenate all matches of re in the given string!\r
- while (rg.searchFrom(idseq[pass][sq], rematchat))\r
- {\r
- rematchat = rg.matchedTo();\r
- thismatched[sq] |= true;\r
- urllength+=rg.charsMatched(); // count length\r
- if (!createFullUrl)\r
- {\r
- continue; // don't bother making the URL replacement text.\r
- }\r
- // do we take the cartesian products of the substituents ?\r
- int ns = rg.numSubs();\r
- if (ns == 0)\r
- {\r
- thematches[pass].append(rg.stringMatched());// take whole regex\r
- }\r
- /*\r
- * else if (ns==1) { // take only subgroup match return new String[]\r
- * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix\r
- * }; }\r
- */\r
- // deal with multiple submatch case - for moment we do the simplest\r
- // - concatenate the matched regions, instead of creating a complete\r
- // list for each alternate match over all sequences.\r
- // TODO: specify a 'replace pattern' - next refinement\r
- else\r
- {\r
- // debug\r
- /*for (int s = 0; s <= rg.numSubs(); s++)\r
- {\r
- System.err.println("Sub " + s + " : " + rg.matchedFrom(s)\r
- + " : " + rg.matchedTo(s) + " : '"\r
- + rg.stringMatched(s) + "'");\r
- }*/\r
- // try to collate subgroup matches\r
- StringBuffer subs = new StringBuffer();\r
- // have to loop through submatches, collating them at top level\r
- // match\r
- int s = 0; // 1;\r
- while (s <= ns)\r
- {\r
- if (s + 1 <= ns && rg.matchedTo(s) > -1\r
- && rg.matchedTo(s + 1) > -1\r
- && rg.matchedTo(s + 1) < rg.matchedTo(s))\r
- {\r
- // s is top level submatch. search for submatches enclosed by\r
- // this one\r
- int r = s + 1;\r
- StringBuffer rmtch = new StringBuffer();\r
- while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))\r
- {\r
- if (rg.matchedFrom(r) > -1)\r
- {\r
- rmtch.append(rg.stringMatched(r));\r
- }\r
- r++;\r
- }\r
- if (rmtch.length() > 0)\r
- {\r
- subs.append(rmtch); // simply concatenate\r
- }\r
- s = r;\r
- }\r
- else\r
- {\r
- if (rg.matchedFrom(s) > -1)\r
- {\r
- subs.append(rg.stringMatched(s)); // concatenate\r
- }\r
- s++;\r
- }\r
- }\r
- thematches[pass].append(subs);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- // are we only supposed to take regex matches ?\r
- if (!onlyIfMatches)\r
- {\r
- thismatched[sq] |= true;\r
- urllength+=idseq[pass][sq].length(); // tot up length\r
- if (createFullUrl)\r
- {\r
- thematches[pass] = new StringBuffer(idseq[pass][sq]); // take whole string -\r
- // regardless - probably not a\r
- // good idea!\r
- /*\r
- * TODO: do some boilerplate trimming of the fields to make them\r
- * sensible e.g. trim off any 'prefix' in the id string (see UrlLink\r
- * for the below) - pre 2.4 Jalview behaviour if\r
- * (idstring.indexOf("|") > -1) { idstring =\r
- * idstring.substring(idstring.lastIndexOf("|") + 1); }\r
- */\r
- }\r
- \r
- }\r
- }\r
- }\r
-\r
- // check if we are going to add this sequence's results ? all token\r
- // replacements must be valid for this to happen!\r
- // (including single value replacements - eg. dataset name)\r
- if (thismatched[sq])\r
- {\r
- if (createFullUrl) {\r
- for (pass = 0; pass < matched.length; pass++)\r
- {\r
- if (idseq[pass].length > 1 && matched[pass].length() > 0)\r
- {\r
- matched[pass].append(separators[pass]);\r
- }\r
- matched[pass].append(thematches[pass]);\r
- }\r
- }\r
- seqsmatched++;\r
- }\r
- }\r
- // finally, if any sequences matched, then form the URL and return\r
- if (seqsmatched==0 || (createFullUrl && matched[0].length() == 0))\r
- {\r
- // no matches - no url generated\r
- return null;\r
- }\r
- // check if we are beyond the feasible command line string limit for this platform\r
- if ((urllength+32)>Platform.getMaxCommandLineLength())\r
- {\r
- System.err.println("URL estimated to be too long "+urllength);\r
- return null;\r
- }\r
- if (!createFullUrl)\r
- {\r
- // just return the essential info about what the URL would be generated from\r
- return new Object[]\r
- { new int[]\r
- { seqsmatched }, thismatched};\r
- }\r
- // otherwise, create the URL completely.\r
- \r
- StringBuffer submiturl = new StringBuffer();\r
- submiturl.append(url_prefix);\r
- for (pass = 0; pass < matched.length; pass++)\r
- {\r
- submiturl.append(matched[pass]);\r
- if (url_suffix[pass] != null)\r
- {\r
- submiturl.append(url_suffix[pass]);\r
- }\r
- }\r
-\r
- return new Object[]\r
- { new int[]\r
- { seqsmatched }, thismatched, matched, new String[]\r
- { submiturl.toString() } };\r
- }\r
-\r
- /**\r
- * \r
- * @param urlstub\r
- * @return number of distinct sequence (id or seuqence) replacements predicted for this stub\r
- */\r
- public int getNumberInvolved(Object[] urlstub)\r
- {\r
- return ((int[])urlstub[0])[0]; // returns seqsmatched from makeUrlsIf(false,...)\r
- }\r
-\r
- /**\r
- * get token types present in this url as a bitfield indicating presence of each token from tokens (LSB->MSB).\r
- * @return groupURL class as integer\r
- */\r
- public int getGroupURLType()\r
- {\r
- int r = 0;\r
- for (int pass = 0; pass < tokens.length; pass++)\r
- {\r
- for (int i = 0; i < mtch.length; i++)\r
- {\r
- if (mtch[i].equals(tokens[pass]))\r
- {\r
- r += 1 << pass;\r
- }\r
- }\r
- }\r
- return r;\r
- }\r
-\r
- public String toString()\r
- {\r
- StringBuffer result = new StringBuffer();\r
- result.append(label + "|" + url_prefix);\r
- int r;\r
- for (r = 0; r < url_suffix.length; r++)\r
- {\r
- result.append("$");\r
- result.append(mtch[r]);\r
- if (regexReplace[r] != null)\r
- {\r
- result.append("=/");\r
- result.append(regexReplace[r]);\r
- result.append("/=");\r
- }\r
- result.append("$");\r
- result.append(url_suffix[r]);\r
- }\r
- for (r = 0; r < separators.length; r++)\r
- {\r
- result.append("|");\r
- result.append(separators[r]);\r
- }\r
- return result.toString();\r
- }\r
-\r
- /**\r
- * report stats about the generated url string given an input set\r
- * \r
- * @param ul\r
- * @param idstring\r
- * @param url\r
- */\r
- private static void testUrls(GroupUrlLink ul, String[][] idstring,\r
- Object[] url)\r
- {\r
-\r
- if (url == null)\r
- {\r
- System.out.println("Created NO urls.");\r
- }\r
- else\r
- {\r
- System.out.println("Created a url from " + ((int[]) url[0])[0]\r
- + "out of " + idstring[0].length + " sequences.");\r
- System.out.println("Sequences that did not match:");\r
- for (int sq = 0; sq < idstring[0].length; sq++)\r
- {\r
- if (!((boolean[]) url[1])[sq])\r
- {\r
- System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "\r
- + idstring[1][sq]);\r
- }\r
- }\r
- System.out.println("Sequences that DID match:");\r
- for (int sq = 0; sq < idstring[0].length; sq++)\r
- {\r
- if (((boolean[]) url[1])[sq])\r
- {\r
- System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "\r
- + idstring[1][sq]);\r
- }\r
- }\r
- System.out.println("The generated URL:");\r
- System.out.println(((String[]) url[3])[0]);\r
- }\r
- }\r
-\r
- public static void main(String argv[])\r
- {\r
- String[] links = new String[]\r
- {\r
- "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",\r
- "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCES$&inputType=1|,",\r
- "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,",\r
- "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",\r
- "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",\r
- "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",\r
- "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|,",\r
- "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|,"\r
- /*\r
- * http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?input=P38389,P38398\r
- * &inputType=0&workflow=Enfin%20Default%20Workflow&datasetName=\r
- * linkInDatasetFromPRIDE\r
- */\r
- };\r
-\r
- SequenceI[] seqs = new SequenceI[]\r
- { new Sequence("StupidLabel:gi|9234|pdb|102L|A",\r
- "asdiasdpasdpadpwpadasdpaspdw"), };\r
- String[][] seqsandids = formStrings(seqs);\r
- for (int i = 0; i < links.length; i++)\r
- {\r
- GroupUrlLink ul = new GroupUrlLink(links[i]);\r
- if (ul.isValid())\r
- {\r
- System.out.println("\n\n\n");\r
- System.out.println("Link " + i + " " + links[i] + " : "\r
- + ul.toString());\r
- System.out.println(" pref : " + ul.getUrl_prefix());\r
- System.out.println(" IdReplace : " + ul.getIDRegexReplace());\r
- System.out.println(" SeqReplace : " + ul.getSeqRegexReplace());\r
- System.out.println(" Suffixes : " + ul.getUrl_suffix());\r
-\r
- System.out\r
- .println("<insert input id and sequence strings here> Without onlyIfMatches:");\r
- Object[] urls = ul.makeUrls(seqsandids[0], seqsandids[1],\r
- "mydataset", false);\r
- testUrls(ul, seqsandids, urls);\r
- System.out\r
- .println("<insert input id and sequence strings here> With onlyIfMatches set:");\r
- urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset", true);\r
- testUrls(ul, seqsandids, urls);\r
- }\r
- else\r
- {\r
- System.err.println("Invalid URLLink : " + links[i] + " : "\r
- + ul.getInvalidMessage());\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * covenience method to generate the id and sequence string vector from a set\r
- * of seuqences using each sequence's getName() and getSequenceAsString()\r
- * method\r
- * \r
- * @param seqs\r
- * @return String[][] {{sequence ids},{sequence strings}}\r
- */\r
- public static String[][] formStrings(SequenceI[] seqs)\r
- {\r
- String[][] idset = new String[2][seqs.length];\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- idset[0][i] = seqs[i].getName();\r
- idset[1][i] = seqs[i].getSequenceAsString();\r
- }\r
- return idset;\r
- }\r
-\r
- public void setLabel(String newlabel)\r
- {\r
- this.label = newlabel;\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.util;
+
+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;
+
+ 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
+ * definitions consist of a pipe separated string containing a <label>|<url
+ * construct>|<separator character>[|<sequence separator character>]. The url
+ * construct includes regex qualified tokens which are replaced with seuqence
+ * IDs ($SEQUENCE_IDS$) and/or seuqence regions ($SEQUENCES$) that are
+ * extracted from the group. See <code>UrlLink</code> for more information
+ * about the approach, and the original implementation. Documentation to come.
+ * Note - groupUrls can be very big!
+ */
+ private String url_prefix, target, label;
+
+ /**
+ * these are all filled in order of the occurence of each token in the url
+ * string template
+ */
+ private String url_suffix[], separators[], regexReplace[];
+
+ private String invalidMessage = null;
+
+ /**
+ * tokens that can be replaced in the URL.
+ */
+ private static String[] tokens;
+
+ /**
+ * position of each token (which can appear once only) in the url
+ */
+ private int[] segs;
+
+ /**
+ * contains tokens in the order they appear in the URL template.
+ */
+ private String[] mtch;
+ static
+ {
+ if (tokens == null)
+ {
+ 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;
+
+ /**
+ * parse the given linkString of the form '<label>|<url>|separator
+ * char[|optional sequence separator char]' into parts. url may contain a
+ * string $SEQUENCEIDS<=optional regex=>$ where <=optional regex=> must be of
+ * the form =/<perl style regex>/=$ or $SEQUENCES<=optional regex=>$ or
+ * $SEQUENCES<=optional regex=>$.
+ *
+ * @param link
+ */
+ public GroupUrlLink(String link)
+ {
+ int sep = link.indexOf("|");
+ segs = new int[tokens.length];
+ int ntoks = 0;
+ for (int i = 0; i < segs.length; i++)
+ {
+ if ((segs[i] = link.indexOf("$" + tokens[i])) > -1)
+ {
+ ntoks++;
+ }
+ }
+ // expect at least one token
+ if (ntoks == 0)
+ {
+ invalidMessage = "Group URL string must contain at least one of ";
+ for (int i = 0; i < segs.length; i++)
+ {
+ invalidMessage += " '$" + tokens[i] + "[=/regex=/]$'";
+ }
+ return;
+ }
+
+ int[] ptok = new int[ntoks + 1];
+ String[] tmtch = new String[ntoks + 1];
+ mtch = new String[ntoks];
+ for (int i = 0, t = 0; i < segs.length; i++)
+ {
+ if (segs[i] > -1)
+ {
+ ptok[t] = segs[i];
+ tmtch[t++] = tokens[i];
+ }
+ }
+ ptok[ntoks] = link.length();
+ tmtch[ntoks] = "$$$$$$$$$";
+ jalview.util.QuickSort.sort(ptok, tmtch);
+ for (int i = 0; i < ntoks; i++)
+ {
+ mtch[i] = tmtch[i]; // TODO: check order is ascending
+ }
+ /*
+ * replaces the specific code below {}; if (psqids > -1 && pseqs > -1) { if
+ * (psqids > pseqs) { idseg = 1; seqseg = 0;
+ *
+ * ptok = new int[] { pseqs, psqids, link.length() }; mtch = new String[] {
+ * "$SEQUENCES", "$SEQUENCEIDS" }; } else { idseg = 0; seqseg = 1; ptok =
+ * new int[] { psqids, pseqs, link.length() }; mtch = new String[] {
+ * "$SEQUENCEIDS", "$SEQUENCES" }; } } else { if (psqids != -1) { idseg = 0;
+ * ptok = new int[] { psqids, link.length() }; mtch = new String[] {
+ * "$SEQUENCEIDS" }; } else { seqseg = 0; ptok = new int[] { pseqs,
+ * link.length() }; mtch = new String[] { "$SEQUENCES" }; } }
+ */
+
+ int p = sep;
+ // first get the label and target part before the first |
+ do
+ {
+ sep = p;
+ p = link.indexOf("|", sep + 1);
+ } while (p > sep && p < ptok[0]);
+ // Assuming that the URL itself does not contain any '|' symbols
+ // sep now contains last pipe symbol position prior to any regex symbols
+ label = link.substring(0, sep);
+ if (label.indexOf("|") > -1)
+ {
+ // | terminated database name / www target at start of Label
+ target = label.substring(0, label.indexOf("|"));
+ }
+ else if (label.indexOf(" ") > 2)
+ {
+ // space separated Label - matches database name
+ target = label.substring(0, label.indexOf(" "));
+ }
+ else
+ {
+ target = label;
+ }
+ // Now Parse URL : Whole URL string first
+ url_prefix = link.substring(sep + 1, ptok[0]);
+ url_suffix = new String[mtch.length];
+ regexReplace = new String[mtch.length];
+ // and loop through tokens
+ 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)
+ {
+ // Extract Regex and suffix
+ if (ptok[pass + 1] < p + 3)
+ {
+ // tokens are not allowed inside other tokens - e.g. inserting a
+ // $sequences$ into the regex match for the sequenceid
+ invalidMessage = "Token regexes cannot contain other regexes (did you terminate the $"
+ + mtch[pass] + " regex with a '/=$' ?";
+ return;
+ }
+ url_suffix[pass] = link.substring(p + 3, ptok[pass + 1]);
+ regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
+ try
+ {
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
+ + regexReplace[pass] + "/");
+ if (rg == null)
+ {
+ invalidMessage = "Invalid Regular Expression : '"
+ + regexReplace[pass] + "'\n";
+ }
+ } catch (Exception e)
+ {
+ invalidMessage = "Invalid Regular Expression : '"
+ + regexReplace[pass] + "'\n";
+ }
+ }
+ else
+ {
+ regexReplace[pass] = null;
+ // verify format is really correct.
+ if ((p = link.indexOf("$" + mtch[pass] + "$")) == ptok[pass])
+ {
+ url_suffix[pass] = link.substring(p + mtch[pass].length() + 2,
+ ptok[pass + 1]);
+ }
+ else
+ {
+ invalidMessage = "Warning: invalid regex structure (after '"
+ + mtch[0] + "') for URL link : " + link;
+ }
+ }
+ }
+ int pass = 0;
+ separators = new String[url_suffix.length];
+ String suffices = url_suffix[url_suffix.length - 1], lastsep = ",";
+ // have a look in the last suffix for any more separators.
+ while ((p = suffices.indexOf('|')) > -1)
+ {
+ separators[pass] = suffices.substring(p + 1);
+ if (pass == 0)
+ {
+ // trim the original suffix string
+ url_suffix[url_suffix.length - 1] = suffices.substring(0, p);
+ }
+ else
+ {
+ lastsep = (separators[pass - 1] = separators[pass - 1].substring(0,
+ p));
+ }
+ suffices = separators[pass];
+ pass++;
+ }
+ if (pass > 0)
+ {
+ lastsep = separators[pass - 1];
+ }
+ // last separator is always used for all the remaining separators
+ while (pass < separators.length)
+ {
+ separators[pass++] = lastsep;
+ }
+ }
+
+ /**
+ * @return the url_suffix
+ */
+ public String getUrl_suffix()
+ {
+ return url_suffix[url_suffix.length - 1];
+ }
+
+ /**
+ * @return the url_prefix
+ */
+ public String getUrl_prefix()
+ {
+ return url_prefix;
+ }
+
+ /**
+ * @return the target
+ */
+ public String getTarget()
+ {
+ return target;
+ }
+
+ /**
+ * @return the label
+ */
+ public String getLabel()
+ {
+ return label;
+ }
+
+ /**
+ * @return the sequence ID regexReplace
+ */
+ public String getIDRegexReplace()
+ {
+ return _replaceFor(tokens[0]);
+ }
+
+ 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;
+ }
+
+ /**
+ * @return the sequence ID regexReplace
+ */
+ public String getSeqRegexReplace()
+ {
+ return _replaceFor(tokens[1]);
+ }
+
+ /**
+ * @return the invalidMessage
+ */
+ public String getInvalidMessage()
+ {
+ return invalidMessage;
+ }
+
+ /**
+ * Check if URL string was parsed properly.
+ *
+ * @return boolean - if false then <code>getInvalidMessage</code> returns an
+ * error message
+ */
+ public boolean isValid()
+ {
+ return invalidMessage == null;
+ }
+
+ /**
+ * return one or more URL strings by applying regex to the given idstring
+ *
+ * @param idstrings
+ * array of id strings to pass to service
+ * @param seqstrings
+ * array of seq strings to pass to service
+ * @param onlyIfMatches
+ * - when true url strings are only made if regex is defined and
+ * matches for all qualified tokens in groupURL - TODO: consider if
+ * onlyIfMatches is really a useful parameter!
+ * @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);
+ }
+
+ /**
+ * gathers input into a hashtable
+ *
+ * @param idstrings
+ * @param seqstrings
+ * @param dsstring
+ * @return
+ */
+ 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 });
+ if (idstrings.length != seqstrings.length)
+ {
+ throw new Error(
+ "idstrings and seqstrings contain one string each per sequence.");
+ }
+ return rstrings;
+ }
+
+ public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)
+ throws UrlStringTooLongException
+ {
+ return makeUrlsIf(true, repstrings, onlyIfMatches);
+ }
+
+ /**
+ *
+ * @param ids
+ * @param seqstr
+ * @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) 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 } };
+ }
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * generate the URL for the given URL stub object array returned from
+ * makeUrlStubs
+ *
+ * @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]);
+ return ((String[]) results[3])[0];
+ }
+
+ /**
+ * conditionally generate urls or stubs for a given input.
+ *
+ * @param createFullUrl
+ * set to false if you only want to test if URLs would be generated.
+ * @param repstrings
+ * @param onlyIfMatches
+ * @return null if no url is generated. Object[] { int[] { number of matches
+ * 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;
+
+ // prepare string arrays in correct order to be assembled into URL input
+ String[][] idseq = new String[mtch.length][]; // indexed by pass
+ int mins = 0, maxs = 0; // allowed two values, 1 or n-sequences.
+ for (int i = 0; i < mtch.length; i++)
+ {
+ idseq[i] = (String[]) repstrings.get(mtch[i]);
+ if (idseq[i].length >= 1)
+ {
+ if (mins == 0 && idseq[i].length == 1)
+ {
+ mins = 1;
+ }
+ if (maxs < 2)
+ {
+ maxs = idseq[i].length;
+ }
+ else
+ {
+ 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.");
+ }
+ }
+ }
+ else
+ {
+ throw new Error(
+ "Cannot have zero length vector of replacement strings - either 1 value or n values.");
+ }
+ }
+ // iterate through input, collating segments to be inserted into url
+ StringBuffer matched[] = new StringBuffer[idseq.length];
+ // and precompile regexes
+ com.stevesoft.pat.Regex[] rgxs = new com.stevesoft.pat.Regex[matched.length];
+ for (pass = 0; pass < matched.length; pass++)
+ {
+ matched[pass] = new StringBuffer();
+ if (regexReplace[pass] != null)
+ {
+ rgxs[pass] = com.stevesoft.pat.Regex.perlCode("/"
+ + regexReplace[pass] + "/");
+ }
+ else
+ {
+ rgxs[pass] = null;
+ }
+ }
+ // tot up the invariant lengths for this url
+ int urllength = url_prefix.length();
+ for (pass = 0; pass < matched.length; pass++)
+ {
+ urllength += url_suffix[pass].length();
+ }
+
+ // flags to record which of the input sequences were actually used to
+ // generate the
+ // url
+ boolean[] thismatched = new boolean[maxs];
+ int seqsmatched = 0;
+ for (int sq = 0; sq < maxs; sq++)
+ {
+ // initialise flag for match
+ thismatched[sq] = false;
+ StringBuffer[] thematches = new StringBuffer[rgxs.length];
+ for (pass = 0; pass < rgxs.length; pass++)
+ {
+ thematches[pass] = new StringBuffer(); // initialise - in case there are
+ // no more
+ // matches.
+ // if a regex is provided, then it must match for all sequences in all
+ // tokens for it to be considered.
+ if (idseq[pass].length <= sq)
+ {
+ // no more replacement strings to try for this token
+ continue;
+ }
+ if (rgxs[pass] != null)
+ {
+ com.stevesoft.pat.Regex rg = rgxs[pass];
+ int rematchat = 0;
+ // concatenate all matches of re in the given string!
+ while (rg.searchFrom(idseq[pass][sq], rematchat))
+ {
+ 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.
+ }
+ // do we take the cartesian products of the substituents ?
+ int ns = rg.numSubs();
+ if (ns == 0)
+ {
+ thematches[pass].append(rg.stringMatched());// take whole regex
+ }
+ /*
+ * else if (ns==1) { // take only subgroup match return new String[]
+ * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
+ * }; }
+ */
+ // deal with multiple submatch case - for moment we do the simplest
+ // - concatenate the matched regions, instead of creating a complete
+ // list for each alternate match over all sequences.
+ // TODO: specify a 'replace pattern' - next refinement
+ else
+ {
+ // debug
+ /*
+ * for (int s = 0; s <= rg.numSubs(); s++) {
+ * System.err.println("Sub " + s + " : " + rg.matchedFrom(s) +
+ * " : " + rg.matchedTo(s) + " : '" + rg.stringMatched(s) + "'");
+ * }
+ */
+ // try to collate subgroup matches
+ StringBuffer subs = new StringBuffer();
+ // have to loop through submatches, collating them at top level
+ // match
+ int s = 0; // 1;
+ while (s <= ns)
+ {
+ if (s + 1 <= ns && rg.matchedTo(s) > -1
+ && rg.matchedTo(s + 1) > -1
+ && rg.matchedTo(s + 1) < rg.matchedTo(s))
+ {
+ // s is top level submatch. search for submatches enclosed by
+ // this one
+ int r = s + 1;
+ StringBuffer rmtch = new StringBuffer();
+ while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))
+ {
+ if (rg.matchedFrom(r) > -1)
+ {
+ rmtch.append(rg.stringMatched(r));
+ }
+ r++;
+ }
+ if (rmtch.length() > 0)
+ {
+ subs.append(rmtch); // simply concatenate
+ }
+ s = r;
+ }
+ else
+ {
+ if (rg.matchedFrom(s) > -1)
+ {
+ subs.append(rg.stringMatched(s)); // concatenate
+ }
+ s++;
+ }
+ }
+ thematches[pass].append(subs);
+ }
+ }
+ }
+ else
+ {
+ // are we only supposed to take regex matches ?
+ if (!onlyIfMatches)
+ {
+ thismatched[sq] |= true;
+ urllength += idseq[pass][sq].length(); // tot up length
+ if (createFullUrl)
+ {
+ thematches[pass] = new StringBuffer(idseq[pass][sq]); // take
+ // whole
+ // string -
+ // regardless - probably not a
+ // good idea!
+ /*
+ * TODO: do some boilerplate trimming of the fields to make them
+ * sensible e.g. trim off any 'prefix' in the id string (see
+ * UrlLink for the below) - pre 2.4 Jalview behaviour if
+ * (idstring.indexOf("|") > -1) { idstring =
+ * idstring.substring(idstring.lastIndexOf("|") + 1); }
+ */
+ }
+
+ }
+ }
+ }
+
+ // check if we are going to add this sequence's results ? all token
+ // replacements must be valid for this to happen!
+ // (including single value replacements - eg. dataset name)
+ if (thismatched[sq])
+ {
+ if (createFullUrl)
+ {
+ for (pass = 0; pass < matched.length; pass++)
+ {
+ if (idseq[pass].length > 1 && matched[pass].length() > 0)
+ {
+ matched[pass].append(separators[pass]);
+ }
+ matched[pass].append(thematches[pass]);
+ }
+ }
+ seqsmatched++;
+ }
+ }
+ // finally, if any sequences matched, then form the URL and return
+ if (seqsmatched == 0 || (createFullUrl && matched[0].length() == 0))
+ {
+ // no matches - no url generated
+ return null;
+ }
+ // check if we are beyond the feasible command line string limit for this
+ // platform
+ if ((urllength + 32) > Platform.getMaxCommandLineLength())
+ {
+ 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 };
+ }
+ // otherwise, create the URL completely.
+
+ StringBuffer submiturl = new StringBuffer();
+ submiturl.append(url_prefix);
+ for (pass = 0; pass < matched.length; pass++)
+ {
+ submiturl.append(matched[pass]);
+ if (url_suffix[pass] != null)
+ {
+ submiturl.append(url_suffix[pass]);
+ }
+ }
+
+ return new Object[]
+ { new int[]
+ { seqsmatched }, thismatched, matched, new String[]
+ { submiturl.toString() } };
+ }
+
+ /**
+ *
+ * @param urlstub
+ * @return number of distinct sequence (id or seuqence) replacements predicted
+ * for this stub
+ */
+ public int getNumberInvolved(Object[] urlstub)
+ {
+ return ((int[]) urlstub[0])[0]; // returns seqsmatched from
+ // makeUrlsIf(false,...)
+ }
+
+ /**
+ * get token types present in this url as a bitfield indicating presence of
+ * each token from tokens (LSB->MSB).
+ *
+ * @return groupURL class as integer
+ */
+ public int getGroupURLType()
+ {
+ int r = 0;
+ for (int pass = 0; pass < tokens.length; pass++)
+ {
+ for (int i = 0; i < mtch.length; i++)
+ {
+ if (mtch[i].equals(tokens[pass]))
+ {
+ r += 1 << pass;
+ }
+ }
+ }
+ return r;
+ }
+
+ public String toString()
+ {
+ StringBuffer result = new StringBuffer();
+ result.append(label + "|" + url_prefix);
+ int r;
+ for (r = 0; r < url_suffix.length; r++)
+ {
+ result.append("$");
+ result.append(mtch[r]);
+ if (regexReplace[r] != null)
+ {
+ result.append("=/");
+ result.append(regexReplace[r]);
+ result.append("/=");
+ }
+ result.append("$");
+ result.append(url_suffix[r]);
+ }
+ for (r = 0; r < separators.length; r++)
+ {
+ result.append("|");
+ result.append(separators[r]);
+ }
+ return result.toString();
+ }
+
+ /**
+ * report stats about the generated url string given an input set
+ *
+ * @param ul
+ * @param idstring
+ * @param url
+ */
+ private static void testUrls(GroupUrlLink ul, String[][] idstring,
+ Object[] url)
+ {
+
+ if (url == null)
+ {
+ System.out.println("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:");
+ 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]);
+ }
+ }
+ System.out.println("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]);
+ }
+ }
+ System.out.println("The generated URL:");
+ System.out.println(((String[]) url[3])[0]);
+ }
+ }
+
+ public static void main(String argv[])
+ {
+ 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|,",
+ "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
+ "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
+ "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
+ */
+ };
+
+ 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:");
+ 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:");
+ 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
+ {
+ System.err.println("Invalid URLLink : " + links[i] + " : "
+ + ul.getInvalidMessage());
+ }
+ }
+ }
+
+ /**
+ * covenience method to generate the id and sequence string vector from a set
+ * of seuqences using each sequence's getName() and getSequenceAsString()
+ * method
+ *
+ * @param seqs
+ * @return String[][] {{sequence ids},{sequence strings}}
+ */
+ public static String[][] formStrings(SequenceI[] seqs)
+ {
+ String[][] idset = new String[2][seqs.length];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ idset[0][i] = seqs[i].getName();
+ idset[1][i] = seqs[i].getSequenceAsString();
+ }
+ return idset;
+ }
+
+ public void setLabel(String newlabel)
+ {
+ this.label = newlabel;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff