-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.util;\r
-\r
-import java.util.Vector;\r
-\r
-public class UrlLink\r
-{\r
- /**\r
- * helper class to parse URL Link strings taken from applet parameters or\r
- * jalview properties file using the com.stevesoft.pat.Regex implementation.\r
- * Jalview 2.4 extension allows regular expressions to be used to parse ID\r
- * strings and replace the result in the URL. Regex's operate on the whole ID\r
- * string given to the matchURL method, if no regex is supplied, then only\r
- * text following the first pipe symbol will be susbstituted. Usage\r
- * documentation todo.\r
- */\r
- private String url_suffix, url_prefix, target, label, regexReplace;\r
-\r
- private boolean dynamic = false;\r
-\r
- private String invalidMessage = null;\r
-\r
- /**\r
- * parse the given linkString of the form '<label>|<url>' into parts url may\r
- * contain a string $SEQUENCE_ID<=optional regex=>$ where <=optional regex=>\r
- * must be of the form =/<perl style regex>/=$\r
- * \r
- * @param link\r
- */\r
- public UrlLink(String link)\r
- {\r
- int sep = link.indexOf("|"), psqid = link.indexOf("$SEQUENCE_ID");\r
- if (psqid > -1)\r
- {\r
- dynamic = true;\r
- int p = sep;\r
- do\r
- {\r
- sep = p;\r
- p = link.indexOf("|", sep + 1);\r
- } while (p > sep && p < psqid);\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
- // Parse URL : Whole URL string first\r
- url_prefix = link.substring(sep + 1, psqid);\r
- if (link.indexOf("$SEQUENCE_ID=/") == psqid\r
- && (p = link.indexOf("/=$", psqid + 14)) > psqid + 14)\r
- {\r
- // Extract Regex and suffix\r
- url_suffix = link.substring(p + 3);\r
- regexReplace = link.substring(psqid + 14, p);\r
- try\r
- {\r
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"\r
- + regexReplace + "/");\r
- if (rg == null)\r
- {\r
- invalidMessage = "Invalid Regular Expression : '"\r
- + regexReplace + "'\n";\r
- }\r
- } catch (Exception e)\r
- {\r
- invalidMessage = "Invalid Regular Expression : '" + regexReplace\r
- + "'\n";\r
- }\r
- }\r
- else\r
- {\r
- regexReplace = null;\r
- // verify format is really correct.\r
- if (link.indexOf("$SEQUENCE_ID$") == psqid)\r
- {\r
- url_suffix = link.substring(psqid + 13);\r
- regexReplace = null;\r
- }\r
- else\r
- {\r
- invalidMessage = "Warning: invalid regex structure for URL link : "\r
- + link;\r
- }\r
- }\r
- }\r
- else\r
- {\r
- target = link.substring(0, sep);\r
- label = link.substring(0, sep = link.lastIndexOf("|"));\r
- url_prefix = link.substring(sep + 1);\r
- regexReplace = null; // implies we trim any prefix if necessary //\r
- // regexReplace=".*\\|?(.*)";\r
- url_suffix = null;\r
- }\r
- }\r
-\r
- /**\r
- * @return the url_suffix\r
- */\r
- public String getUrl_suffix()\r
- {\r
- return url_suffix;\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 regexReplace\r
- */\r
- public String getRegexReplace()\r
- {\r
- return regexReplace;\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 idstring\r
- * @param onlyIfMatches\r
- * - when true url strings are only made if regex is defined and\r
- * matches\r
- * @return String[] { part of idstring substituted, full substituted url , ..\r
- * next part, next url..}\r
- */\r
- public String[] makeUrls(String idstring, boolean onlyIfMatches)\r
- {\r
- if (dynamic)\r
- {\r
- if (regexReplace != null)\r
- {\r
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"\r
- + regexReplace + "/");\r
- if (rg.search(idstring))\r
- {\r
- int ns = rg.numSubs();\r
- if (ns == 0)\r
- {\r
- // take whole regex\r
- return new String[]\r
- { rg.stringMatched(),\r
- url_prefix + rg.stringMatched() + url_suffix };\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
- 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
- Vector subs = new Vector();\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
- String mtch = "";\r
- while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))\r
- {\r
- if (rg.matchedFrom(r) > -1)\r
- {\r
- mtch += rg.stringMatched(r);\r
- }\r
- r++;\r
- }\r
- if (mtch.length() > 0)\r
- {\r
- subs.addElement(mtch);\r
- subs.addElement(url_prefix + mtch + url_suffix);\r
- }\r
- s = r;\r
- }\r
- else\r
- {\r
- if (rg.matchedFrom(s) > -1)\r
- {\r
- subs.addElement(rg.stringMatched(s));\r
- subs.addElement(url_prefix + rg.stringMatched(s)\r
- + url_suffix);\r
- }\r
- s++;\r
- }\r
- }\r
-\r
- String[] res = new String[subs.size()];\r
- for (int r = 0, rs = subs.size(); r < rs; r++)\r
- {\r
- res[r] = (String) subs.elementAt(r);\r
- }\r
- subs.removeAllElements();\r
- return res;\r
- }\r
- }\r
- if (onlyIfMatches)\r
- {\r
- return null;\r
- }\r
- }\r
- /* Otherwise - trim off any 'prefix' - pre 2.4 Jalview behaviour */\r
- if (idstring.indexOf("|") > -1)\r
- {\r
- idstring = idstring.substring(idstring.lastIndexOf("|") + 1);\r
- }\r
-\r
- // just return simple url substitution.\r
- return new String[]\r
- { idstring, url_prefix + idstring + url_suffix };\r
- }\r
- else\r
- {\r
- return new String[]\r
- { "", url_prefix };\r
- }\r
- }\r
-\r
- public String toString()\r
- {\r
- return label\r
- + "|"\r
- + url_prefix\r
- + (dynamic ? ("$SEQUENCE_ID" + ((regexReplace != null) ? "="\r
- + regexReplace + "=$" : "$")) : "")\r
- + ((url_suffix == null) ? "" : url_suffix);\r
-\r
- }\r
-\r
- private static void testUrls(UrlLink ul, String idstring, String[] urls)\r
- {\r
-\r
- if (urls == null)\r
- {\r
- System.out.println("Created NO urls.");\r
- }\r
- else\r
- {\r
- System.out.println("Created " + (urls.length / 2) + " Urls.");\r
- for (int uls = 0; uls < urls.length; uls += 2)\r
- {\r
- System.out.println("URL Replacement text : " + urls[uls]\r
- + " : URL : " + urls[uls + 1]);\r
- }\r
- }\r
- }\r
-\r
- public static void main(String argv[])\r
- {\r
- String[] links = new String[]\r
- {\r
- /*\r
- * "AlinkT|Target|http://foo.foo.soo/",\r
- * "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",\r
- * "myUrl2|http://$SEQUENCE_ID=/(([0-9]+).+([A-Za-z]+))/=$.someserver.org/foo"\r
- * ,\r
- * "myUrl3|http://$SEQUENCE_ID=/([0-9]+).+([A-Za-z]+)/=$.someserver.org/foo"\r
- * , "myUrl4|target|http://$SEQUENCE_ID$.someserver.org/foo|too",\r
- * "PF1|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(?:PFAM:)?(.+)/=$"\r
- * ,\r
- * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$"\r
- * ,\r
- * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"\r
- * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",\r
- */\r
- "NESTED|http://nested/$SEQUENCE_ID=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };\r
- String[] idstrings = new String[]\r
- {\r
- /*\r
- * //"LGUL_human", //"QWIQW_123123", "uniprot|why_do+_12313_foo",\r
- * //"123123312", "123123 ABCDE foo", "PFAM:PF23943",\r
- */\r
- "Label:gi|9234|pdb|102L|A" };\r
- // TODO: test the setLabel method.\r
- for (int i = 0; i < links.length; i++)\r
- {\r
- UrlLink ul = new UrlLink(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 : "\r
- + ul.getUrl_prefix()\r
- + "\n suf : "\r
- + ul.getUrl_suffix()\r
- + "\n : "\r
- + ((ul.getRegexReplace() != null) ? ul.getRegexReplace()\r
- : ""));\r
- for (int ids = 0; ids < idstrings.length; ids++)\r
- {\r
- System.out.println("ID String : " + idstrings[ids]\r
- + "\nWithout onlyIfMatches:");\r
- String[] urls = ul.makeUrls(idstrings[ids], false);\r
- testUrls(ul, idstrings[ids], urls);\r
- System.out.println("With onlyIfMatches set.");\r
- urls = ul.makeUrls(idstrings[ids], true);\r
- testUrls(ul, idstrings[ids], urls);\r
- }\r
- }\r
- else\r
- {\r
- System.err.println("Invalid URLLink : " + links[i] + " : "\r
- + ul.getInvalidMessage());\r
- }\r
- }\r
- }\r
-\r
- public boolean isDynamic()\r
- {\r
- // TODO Auto-generated method stub\r
- return dynamic;\r
- }\r
-\r
- public void setLabel(String newlabel)\r
- {\r
- this.label = newlabel;\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+import static jalview.util.UrlConstants.DB_ACCESSION;
+import static jalview.util.UrlConstants.DELIM;
+import static jalview.util.UrlConstants.SEP;
+import static jalview.util.UrlConstants.SEQUENCE_ID;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+public class UrlLink
+{
+ /**
+ * helper class to parse URL Link strings taken from applet parameters or
+ * jalview properties file using the com.stevesoft.pat.Regex implementation.
+ * Jalview 2.4 extension allows regular expressions to be used to parse ID
+ * strings and replace the result in the URL. Regex's operate on the whole ID
+ * string given to the matchURL method, if no regex is supplied, then only
+ * text following the first pipe symbol will be substituted. Usage
+ * documentation todo.
+ */
+
+ private static final String EQUALS = "=";
+
+ private static final String SPACE = " ";
+
+ private String urlSuffix;
+
+ private String urlPrefix;
+
+ private String target;
+
+ private String label;
+
+ private String dbname;
+
+ private String regexReplace;
+
+ private boolean dynamic = false;
+
+ private boolean usesDBaccession = false;
+
+ private String invalidMessage = null;
+
+ /**
+ * parse the given linkString of the form '<label>SEP<url>' into parts url may
+ * contain a string $SEQUENCE_ID<=optional regex=>$ where <=optional regex=>
+ * must be of the form =/<perl style regex>/=$
+ *
+ * @param link
+ */
+ public UrlLink(String link)
+ {
+ int sep = link.indexOf(SEP);
+ int psqid = link.indexOf(DELIM + DB_ACCESSION);
+ int nsqid = link.indexOf(DELIM + SEQUENCE_ID);
+ if (psqid > -1)
+ {
+ dynamic = true;
+ usesDBaccession = true;
+
+ sep = parseLabel(sep, psqid, link);
+
+ int endOfRegex = parseUrl(link, DB_ACCESSION, psqid, sep);
+ parseTarget(link, sep, endOfRegex);
+ }
+ else if (nsqid > -1)
+ {
+ dynamic = true;
+ sep = parseLabel(sep, nsqid, link);
+
+ int endOfRegex = parseUrl(link, SEQUENCE_ID, nsqid, sep);
+
+ parseTarget(link, sep, endOfRegex);
+ }
+ else
+ {
+ label = link.substring(0, sep).trim();
+
+ // if there's a third element in the url link string
+ // it is the target name, otherwise target=label
+ int lastsep = link.lastIndexOf(SEP);
+ if (lastsep != sep)
+ {
+ urlPrefix = link.substring(sep + 1, lastsep).trim();
+ target = link.substring(lastsep + 1).trim();
+ }
+ else
+ {
+ urlPrefix = link.substring(sep + 1).trim();
+ target = label;
+ }
+
+ regexReplace = null; // implies we trim any prefix if necessary //
+ urlSuffix = null;
+ }
+
+ label = label.trim();
+ target = target.trim();
+ }
+
+ /**
+ * Alternative constructor for separate name, link and description
+ *
+ * @param name
+ * The string used to match the link to a DB reference id
+ * @param url
+ * The url to link to
+ * @param desc
+ * The description of the associated target DB
+ */
+ public UrlLink(String name, String url, String desc)
+ {
+ this(name + SEP + url + SEP + desc);
+ }
+
+ /**
+ * @return the url_suffix
+ */
+ public String getUrlSuffix()
+ {
+ return urlSuffix;
+ }
+
+ /**
+ * @return the url_prefix
+ */
+ public String getUrlPrefix()
+ {
+ return urlPrefix;
+ }
+
+ /**
+ * @return the target
+ */
+ public String getTarget()
+ {
+ return target;
+ }
+
+ /**
+ * @return the label
+ */
+ public String getLabel()
+ {
+ return label;
+ }
+
+ public String getUrlWithToken()
+ {
+ String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
+
+ return urlPrefix
+ + (dynamic
+ ? (DELIM + var
+ + ((regexReplace != null)
+ ? EQUALS + regexReplace + EQUALS + DELIM
+ : DELIM))
+ : "")
+ + ((urlSuffix == null) ? "" : urlSuffix);
+ }
+
+ /**
+ * @return the regexReplace
+ */
+ public String getRegexReplace()
+ {
+ return regexReplace;
+ }
+
+ /**
+ * @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 whether link is dynamic
+ */
+ public boolean isDynamic()
+ {
+ return dynamic;
+ }
+
+ /**
+ *
+ * @return whether link uses DB Accession id
+ */
+ public boolean usesDBAccession()
+ {
+ return usesDBaccession;
+ }
+
+ /**
+ * Set the label
+ *
+ * @param newlabel
+ */
+ public void setLabel(String newlabel)
+ {
+ this.label = newlabel;
+ }
+
+ /**
+ * Set the target
+ *
+ * @param desc
+ */
+ public void setTarget(String desc)
+ {
+ target = desc;
+ }
+
+ /**
+ * return one or more URL strings by applying regex to the given idstring
+ *
+ * @param idstring
+ * @param onlyIfMatches
+ * - when true url strings are only made if regex is defined and
+ * matches
+ * @return String[] { part of idstring substituted, full substituted url , ..
+ * next part, next url..}
+ */
+ public String[] makeUrls(String idstring, boolean onlyIfMatches)
+ {
+ if (dynamic)
+ {
+ if (regexReplace != null)
+ {
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace + "/");
+ if (rg.search(idstring))
+ {
+ int ns = rg.numSubs();
+ if (ns == 0)
+ {
+ // take whole regex
+ return new String[] { rg.stringMatched(),
+ urlPrefix + rg.stringMatched() + urlSuffix };
+ } /*
+ * else if (ns==1) { // take only subgroup match return new String[]
+ * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
+ * }; }
+ */
+ 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
+ Vector<String> subs = new Vector<String>();
+ // 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;
+ String mtch = "";
+ while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))
+ {
+ if (rg.matchedFrom(r) > -1)
+ {
+ mtch += rg.stringMatched(r);
+ }
+ r++;
+ }
+ if (mtch.length() > 0)
+ {
+ subs.addElement(mtch);
+ subs.addElement(urlPrefix + mtch + urlSuffix);
+ }
+ s = r;
+ }
+ else
+ {
+ if (rg.matchedFrom(s) > -1)
+ {
+ subs.addElement(rg.stringMatched(s));
+ subs.addElement(
+ urlPrefix + rg.stringMatched(s) + urlSuffix);
+ }
+ s++;
+ }
+ }
+
+ String[] res = new String[subs.size()];
+ for (int r = 0, rs = subs.size(); r < rs; r++)
+ {
+ res[r] = subs.elementAt(r);
+ }
+ subs.removeAllElements();
+ return res;
+ }
+ }
+ if (onlyIfMatches)
+ {
+ return null;
+ }
+ }
+ /* Otherwise - trim off any 'prefix' - pre 2.4 Jalview behaviour */
+ if (idstring.indexOf(SEP) > -1)
+ {
+ idstring = idstring.substring(idstring.lastIndexOf(SEP) + 1);
+ }
+
+ // just return simple url substitution.
+ return new String[] { idstring, urlPrefix + idstring + urlSuffix };
+ }
+ else
+ {
+ return new String[] { "", urlPrefix };
+ }
+ }
+
+ @Override
+ public String toString()
+ {
+ return label + SEP + getUrlWithToken();
+ }
+
+ /**
+ * @return delimited string containing label, url and target
+ */
+ public String toStringWithTarget()
+ {
+ return label + SEP + getUrlWithToken() + SEP + target;
+ }
+
+ /**
+ * Parse the label from the link string
+ *
+ * @param firstSep
+ * Location of first occurrence of separator in link string
+ * @param psqid
+ * Position of sequence id or name in link string
+ * @param link
+ * Link string containing database name and url
+ * @return Position of last separator symbol prior to any regex symbols
+ */
+ protected int parseLabel(int firstSep, int psqid, String link)
+ {
+ int p = firstSep;
+ int sep = firstSep;
+ do
+ {
+ sep = p;
+ p = link.indexOf(SEP, sep + 1);
+ } while (p > sep && p < psqid);
+ // Assuming that the URL itself does not contain any SEP symbols
+ // sep now contains last pipe symbol position prior to any regex symbols
+ label = link.substring(0, sep);
+
+ return sep;
+ }
+
+ /**
+ * Parse the target from the link string
+ *
+ * @param link
+ * Link string containing database name and url
+ * @param sep
+ * Location of first separator symbol
+ * @param endOfRegex
+ * Location of end of any regular expression in link string
+ */
+ protected void parseTarget(String link, int sep, int endOfRegex)
+ {
+ int lastsep = link.lastIndexOf(SEP);
+
+ if ((lastsep != sep) && (lastsep > endOfRegex))
+ {
+ // final element in link string is the target
+ target = link.substring(lastsep + 1).trim();
+ }
+ else
+ {
+ target = label;
+ }
+
+ if (target.indexOf(SEP) > -1)
+ {
+ // SEP terminated database name / www target at start of Label
+ target = target.substring(0, target.indexOf(SEP));
+ }
+ else if (target.indexOf(SPACE) > 2)
+ {
+ // space separated label - first word matches database name
+ target = target.substring(0, target.indexOf(SPACE));
+ }
+ }
+
+ /**
+ * Parse the URL part of the link string
+ *
+ * @param link
+ * Link string containing database name and url
+ * @param varName
+ * Name of variable in url string (e.g. SEQUENCE_ID, SEQUENCE_NAME)
+ * @param sqidPos
+ * Position of id or name in link string
+ * @param sep
+ * Position of separator in link string
+ * @return Location of end of any regex in link string
+ */
+ protected int parseUrl(String link, String varName, int sqidPos, int sep)
+ {
+ urlPrefix = link.substring(sep + 1, sqidPos).trim();
+
+ // delimiter at start of regex: e.g. $SEQUENCE_ID=/
+ String startDelimiter = DELIM + varName + "=/";
+
+ // delimiter at end of regex: /=$
+ String endDelimiter = "/=" + DELIM;
+
+ int startLength = startDelimiter.length();
+
+ // Parse URL : Whole URL string first
+ int p = link.indexOf(endDelimiter, sqidPos + startLength);
+
+ if (link.indexOf(startDelimiter) == sqidPos
+ && (p > sqidPos + startLength))
+ {
+ // Extract Regex and suffix
+ urlSuffix = link.substring(p + endDelimiter.length());
+ regexReplace = link.substring(sqidPos + startLength, p);
+ try
+ {
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace + "/");
+ if (rg == null)
+ {
+ invalidMessage = "Invalid Regular Expression : '" + regexReplace
+ + "'\n";
+ }
+ } catch (Exception e)
+ {
+ invalidMessage = "Invalid Regular Expression : '" + regexReplace
+ + "'\n";
+ }
+ }
+ else
+ {
+ // no regex
+ regexReplace = null;
+ // verify format is really correct.
+ if (link.indexOf(DELIM + varName + DELIM) == sqidPos)
+ {
+ int lastsep = link.lastIndexOf(SEP);
+ if (lastsep < sqidPos + startLength - 1)
+ {
+ // the last SEP character was before the regex, ignore
+ lastsep = link.length();
+ }
+ urlSuffix = link.substring(sqidPos + startLength - 1, lastsep)
+ .trim();
+ regexReplace = null;
+ }
+ else
+ {
+ invalidMessage = "Warning: invalid regex structure for URL link : "
+ + link;
+ }
+ }
+
+ return p;
+ }
+
+ /**
+ * Create a set of URL links for a sequence
+ *
+ * @param seq
+ * The sequence to create links for
+ * @param linkset
+ * Map of links: key = id + SEP + link, value = [target, label, id,
+ * link]
+ */
+ public void createLinksFromSeq(final SequenceI seq,
+ Map<String, List<String>> linkset)
+ {
+ if (seq != null && dynamic)
+ {
+ createDynamicLinks(seq, linkset);
+ }
+ else
+ {
+ createStaticLink(linkset);
+ }
+ }
+
+ /**
+ * Create a static URL link
+ *
+ * @param linkset
+ * Map of links: key = id + SEP + link, value = [target, label, id,
+ * link]
+ */
+ protected void createStaticLink(Map<String, List<String>> linkset)
+ {
+ if (!linkset.containsKey(label + SEP + getUrlPrefix()))
+ {
+ // Add a non-dynamic link
+ linkset.put(label + SEP + getUrlPrefix(),
+ Arrays.asList(target, label, null, getUrlPrefix()));
+ }
+ }
+
+ /**
+ * Create dynamic URL links
+ *
+ * @param seq
+ * The sequence to create links for
+ * @param linkset
+ * Map of links: key = id + SEP + link, value = [target, label, id,
+ * link]
+ */
+ protected void createDynamicLinks(final SequenceI seq,
+ Map<String, List<String>> linkset)
+ {
+ // collect id string too
+ String id = seq.getName();
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
+ {
+ descr = null;
+ }
+
+ if (usesDBAccession()) // link is ID
+ {
+ // collect matching db-refs
+ DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
+ new String[]
+ { target });
+
+ // if there are any dbrefs which match up with the link
+ if (dbr != null)
+ {
+ for (int r = 0; r < dbr.length; r++)
+ {
+ // create Bare ID link for this URL
+ createBareURLLink(dbr[r].getAccessionId(), true, linkset);
+ }
+ }
+ }
+ else if (!usesDBAccession() && id != null) // link is name
+ {
+ // create Bare ID link for this URL
+ createBareURLLink(id, false, linkset);
+ }
+
+ // Create urls from description but only for URL links which are regex
+ // links
+ if (descr != null && getRegexReplace() != null)
+ {
+ // create link for this URL from description where regex matches
+ createBareURLLink(descr, false, linkset);
+ }
+ }
+
+ /*
+ * Create a bare URL Link
+ * Returns map where key = id + SEP + link, and value = [target, label, id, link]
+ */
+ protected void createBareURLLink(String id, Boolean combineLabel,
+ Map<String, List<String>> linkset)
+ {
+ String[] urls = makeUrls(id, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.containsKey(urls[u] + SEP + urls[u + 1]))
+ {
+ String thisLabel = label;
+ if (combineLabel)
+ {
+ // incorporate label with idstring
+ thisLabel = label + SEP + urls[u];
+ }
+
+ linkset.put(urls[u] + SEP + urls[u + 1],
+ Arrays.asList(target, thisLabel, urls[u], urls[u + 1]));
+ }
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff