X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FUrlLink.java;h=5e08b0e1bdd94a4f3bf0be77d86d61728c0ac40f;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=c69287240ed39a8d88095b6323400a03913d63b0;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index c692872..5e08b0e 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -1,398 +1,399 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 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 |' into parts url may
- * contain a string $SEQUENCE_ID<=optional regex=>$ where <=optional regex=>
- * must be of the form =//=$
- *
- * @param link
- */
- public UrlLink(String link)
- {
- int sep = link.indexOf("|"), psqid = link.indexOf("$SEQUENCE_ID");
- if (psqid > -1)
- {
- dynamic = true;
- int p = sep;
- do
- {
- sep = p;
- p = link.indexOf("|", sep + 1);
- } while (p > sep && p < psqid);
- // Assuming that the URL itself does not contain any '|' symbols
- // sep now contains last pipe symbol position prior to any regex symbols
- label = link.substring(0, sep);
- if (label.indexOf("|") > -1)
- {
- // | terminated database name / www target at start of Label
- target = label.substring(0, label.indexOf("|"));
- }
- else if (label.indexOf(" ") > 2)
- {
- // space separated Label - matches database name
- target = label.substring(0, label.indexOf(" "));
- }
- else
- {
- target = label;
- }
- // Parse URL : Whole URL string first
- url_prefix = link.substring(sep + 1, psqid);
- if (link.indexOf("$SEQUENCE_ID=/") == psqid
- && (p = link.indexOf("/=$", psqid + 14)) > psqid + 14)
- {
- // Extract Regex and suffix
- url_suffix = link.substring(p + 3);
- regexReplace = link.substring(psqid + 14, p);
- try
- {
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace + "/");
- if (rg == null)
- {
- invalidMessage = "Invalid Regular Expression : '"
- + regexReplace + "'\n";
- }
- } catch (Exception e)
- {
- invalidMessage = "Invalid Regular Expression : '" + regexReplace
- + "'\n";
- }
- }
- else
- {
- regexReplace = null;
- // verify format is really correct.
- if (link.indexOf("$SEQUENCE_ID$") == psqid)
- {
- url_suffix = link.substring(psqid + 13);
- regexReplace = null;
- }
- else
- {
- invalidMessage = "Warning: invalid regex structure for URL link : "
- + link;
- }
- }
- }
- else
- {
- target = link.substring(0, sep);
- label = link.substring(0, sep = link.lastIndexOf("|"));
- url_prefix = link.substring(sep + 1);
- regexReplace = null; // implies we trim any prefix if necessary //
- // regexReplace=".*\\|?(.*)";
- url_suffix = null;
- }
- }
-
- /**
- * @return the url_suffix
- */
- public String getUrl_suffix()
- {
- return url_suffix;
- }
-
- /**
- * @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 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 getInvalidMessage returns an
- * error message
- */
- public boolean isValid()
- {
- return invalidMessage == null;
- }
-
- /**
- * 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(),
- url_prefix + rg.stringMatched() + url_suffix };
- } /*
- * 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 subs = new Vector();
- // 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(url_prefix + mtch + url_suffix);
- }
- s = r;
- }
- else
- {
- if (rg.matchedFrom(s) > -1)
- {
- subs.addElement(rg.stringMatched(s));
- subs.addElement(url_prefix + rg.stringMatched(s)
- + url_suffix);
- }
- s++;
- }
- }
-
- String[] res = new String[subs.size()];
- for (int r = 0, rs = subs.size(); r < rs; r++)
- {
- res[r] = (String) subs.elementAt(r);
- }
- subs.removeAllElements();
- return res;
- }
- }
- if (onlyIfMatches)
- {
- return null;
- }
- }
- /* Otherwise - trim off any 'prefix' - pre 2.4 Jalview behaviour */
- if (idstring.indexOf("|") > -1)
- {
- idstring = idstring.substring(idstring.lastIndexOf("|") + 1);
- }
-
- // just return simple url substitution.
- return new String[]
- { idstring, url_prefix + idstring + url_suffix };
- }
- else
- {
- return new String[]
- { "", url_prefix };
- }
- }
-
- public String toString()
- {
- return label
- + "|"
- + url_prefix
- + (dynamic ? ("$SEQUENCE_ID" + ((regexReplace != null) ? "="
- + regexReplace + "=$" : "$")) : "")
- + ((url_suffix == null) ? "" : url_suffix);
-
- }
-
- private static void testUrls(UrlLink ul, String idstring, String[] urls)
- {
-
- if (urls == null)
- {
- System.out.println("Created NO urls.");
- }
- else
- {
- System.out.println("Created " + (urls.length / 2) + " Urls.");
- for (int uls = 0; uls < urls.length; uls += 2)
- {
- System.out.println("URL Replacement text : " + urls[uls]
- + " : URL : " + urls[uls + 1]);
- }
- }
- }
-
- public static void main(String argv[])
- {
- String[] links = new String[]
- {
- /*
- * "AlinkT|Target|http://foo.foo.soo/",
- * "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",
- * "myUrl2|http://$SEQUENCE_ID=/(([0-9]+).+([A-Za-z]+))/=$.someserver.org/foo"
- * ,
- * "myUrl3|http://$SEQUENCE_ID=/([0-9]+).+([A-Za-z]+)/=$.someserver.org/foo"
- * , "myUrl4|target|http://$SEQUENCE_ID$.someserver.org/foo|too",
- * "PF1|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(?:PFAM:)?(.+)/=$"
- * ,
- * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$"
- * ,
- * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"
- * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+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 susbstituted. Usage
+ * documentation todo.
+ */
+ private String url_suffix, url_prefix, target, label, regexReplace;
+
+ private boolean dynamic = false;
+
+ private String invalidMessage = null;
+
+ /**
+ * parse the given linkString of the form '|' into parts url may
+ * contain a string $SEQUENCE_ID<=optional regex=>$ where <=optional regex=>
+ * must be of the form =//=$
+ *
+ * @param link
+ */
+ public UrlLink(String link)
+ {
+ int sep = link.indexOf("|"), psqid = link.indexOf("$SEQUENCE_ID");
+ if (psqid > -1)
+ {
+ dynamic = true;
+ int p = sep;
+ do
+ {
+ sep = p;
+ p = link.indexOf("|", sep + 1);
+ } while (p > sep && p < psqid);
+ // Assuming that the URL itself does not contain any '|' symbols
+ // sep now contains last pipe symbol position prior to any regex symbols
+ label = link.substring(0, sep);
+ if (label.indexOf("|") > -1)
+ {
+ // | terminated database name / www target at start of Label
+ target = label.substring(0, label.indexOf("|"));
+ }
+ else if (label.indexOf(" ") > 2)
+ {
+ // space separated Label - matches database name
+ target = label.substring(0, label.indexOf(" "));
+ }
+ else
+ {
+ target = label;
+ }
+ // Parse URL : Whole URL string first
+ url_prefix = link.substring(sep + 1, psqid);
+ if (link.indexOf("$SEQUENCE_ID=/") == psqid
+ && (p = link.indexOf("/=$", psqid + 14)) > psqid + 14)
+ {
+ // Extract Regex and suffix
+ url_suffix = link.substring(p + 3);
+ regexReplace = link.substring(psqid + 14, p);
+ try
+ {
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
+ + regexReplace + "/");
+ if (rg == null)
+ {
+ invalidMessage = "Invalid Regular Expression : '"
+ + regexReplace + "'\n";
+ }
+ } catch (Exception e)
+ {
+ invalidMessage = "Invalid Regular Expression : '" + regexReplace
+ + "'\n";
+ }
+ }
+ else
+ {
+ regexReplace = null;
+ // verify format is really correct.
+ if (link.indexOf("$SEQUENCE_ID$") == psqid)
+ {
+ url_suffix = link.substring(psqid + 13);
+ regexReplace = null;
+ }
+ else
+ {
+ invalidMessage = "Warning: invalid regex structure for URL link : "
+ + link;
+ }
+ }
+ }
+ else
+ {
+ target = link.substring(0, sep);
+ label = link.substring(0, sep = link.lastIndexOf("|"));
+ url_prefix = link.substring(sep + 1);
+ regexReplace = null; // implies we trim any prefix if necessary //
+ // regexReplace=".*\\|?(.*)";
+ url_suffix = null;
+ }
+ }
+
+ /**
+ * @return the url_suffix
+ */
+ public String getUrl_suffix()
+ {
+ return url_suffix;
+ }
+
+ /**
+ * @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 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 getInvalidMessage returns an
+ * error message
+ */
+ public boolean isValid()
+ {
+ return invalidMessage == null;
+ }
+
+ /**
+ * 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(),
+ url_prefix + rg.stringMatched() + url_suffix };
+ } /*
+ * 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 subs = new Vector();
+ // 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(url_prefix + mtch + url_suffix);
+ }
+ s = r;
+ }
+ else
+ {
+ if (rg.matchedFrom(s) > -1)
+ {
+ subs.addElement(rg.stringMatched(s));
+ subs.addElement(url_prefix + rg.stringMatched(s)
+ + url_suffix);
+ }
+ s++;
+ }
+ }
+
+ String[] res = new String[subs.size()];
+ for (int r = 0, rs = subs.size(); r < rs; r++)
+ {
+ res[r] = (String) subs.elementAt(r);
+ }
+ subs.removeAllElements();
+ return res;
+ }
+ }
+ if (onlyIfMatches)
+ {
+ return null;
+ }
+ }
+ /* Otherwise - trim off any 'prefix' - pre 2.4 Jalview behaviour */
+ if (idstring.indexOf("|") > -1)
+ {
+ idstring = idstring.substring(idstring.lastIndexOf("|") + 1);
+ }
+
+ // just return simple url substitution.
+ return new String[]
+ { idstring, url_prefix + idstring + url_suffix };
+ }
+ else
+ {
+ return new String[]
+ { "", url_prefix };
+ }
+ }
+
+ public String toString()
+ {
+ return label
+ + "|"
+ + url_prefix
+ + (dynamic ? ("$SEQUENCE_ID" + ((regexReplace != null) ? "="
+ + regexReplace + "=$" : "$")) : "")
+ + ((url_suffix == null) ? "" : url_suffix);
+
+ }
+
+ private static void testUrls(UrlLink ul, String idstring, String[] urls)
+ {
+
+ if (urls == null)
+ {
+ System.out.println("Created NO urls.");
+ }
+ else
+ {
+ System.out.println("Created " + (urls.length / 2) + " Urls.");
+ for (int uls = 0; uls < urls.length; uls += 2)
+ {
+ System.out.println("URL Replacement text : " + urls[uls]
+ + " : URL : " + urls[uls + 1]);
+ }
+ }
+ }
+
+ public static void main(String argv[])
+ {
+ String[] links = new String[]
+ {
+ /*
+ * "AlinkT|Target|http://foo.foo.soo/",
+ * "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",
+ * "myUrl2|http://$SEQUENCE_ID=/(([0-9]+).+([A-Za-z]+))/=$.someserver.org/foo"
+ * ,
+ * "myUrl3|http://$SEQUENCE_ID=/([0-9]+).+([A-Za-z]+)/=$.someserver.org/foo"
+ * , "myUrl4|target|http://$SEQUENCE_ID$.someserver.org/foo|too",
+ * "PF1|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(?:PFAM:)?(.+)/=$"
+ * ,
+ * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$"
+ * ,
+ * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"
+ * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?