import jalview.commands.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.UrlLink;
import jalview.io.AppletFormatAdapter;
public class APopupMenu
for (int i = 0; i < links.size(); i++)
{
link = links.elementAt(i).toString();
- final String target = link.substring(0, link.indexOf("|"));
-
- final String url;
+ UrlLink urlLink = new UrlLink(link);
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String target = urlLink.getTarget(); // link.substring(0, link.indexOf("|"));
+ final String label = urlLink.getLabel();
+ if (urlLink.isDynamic())
+ {
+ // collect matching db-refs
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target});
+ // collect id string too
+ String id = seq.getName();
+ if (dbr!=null)
+ {
+ for (int r=0;r<dbr.length; r++)
+ {
+ if (id!=null && dbr[r].getAccessionId().equals(id))
+ {
+ // suppress duplicate link creation for the bare sequence ID string with this link
+ id = null;
+ }
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
+ if (urls!=null)
+ {
+ for (int u=0; u<urls.length; u+=2)
+ {
+ addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
+ }
+ }
+ }
+ }
+ if (id!=null)
+ {
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls!=null)
+ {
+ for (int u=0; u<urls.length; u+=2)
+ {
+ addshowLink(linkMenu, label,urls[u+1]);
+ }
+ }
+ // addshowLink(linkMenu, target, url_pref + id + url_suff);
+ }
+ } else {
+ addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
+ }
+ /*final String url;
+
if (link.indexOf("$SEQUENCE_ID$") > -1)
{
// Substitute SEQUENCE_ID string and any matching database reference accessions
}
} else {
addshowLink(linkMenu, target, link.substring(link.lastIndexOf("|")+1));
- }
+ } */
}
if (seq != null)
import jalview.datamodel.*;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.UrlLink;
/**
* DOCUMENT ME!
for (int i = 0; i < links.size(); i++)
{
String link = links.elementAt(i).toString();
- final String label = link.substring(0, link.indexOf("|"));
-
-
- if (link.indexOf("$SEQUENCE_ID$") > -1)
+ UrlLink urlLink = new UrlLink(link);
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ if (urlLink.isDynamic())
{
- // Substitute SEQUENCE_ID string and any matching database reference accessions
- String url_pref = link.substring(link.indexOf("|") + 1,
- link.indexOf("$SEQUENCE_ID$"));
-
- String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
// collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{label});
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{urlLink.getTarget()});
// collect id string too
String id = seq.getName();
- if (id.indexOf("|") > -1)
- {
- id = id.substring(id.lastIndexOf("|") + 1);
- }
-
if (dbr!=null)
{
for (int r=0;r<dbr.length; r++)
{
- if (dbr[r].getAccessionId().equals(id))
+ if (id!=null && dbr[r].getAccessionId().equals(id))
{
// suppress duplicate link creation for the bare sequence ID string with this link
id = null;
}
- addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(),
- url_pref+dbr[r].getAccessionId()+url_suff);
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
+ if (urls!=null)
+ {
+ for (int u=0; u<urls.length; u+=2)
+ {
+ addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
+ }
+ }
}
}
if (id!=null)
{
// create Bare ID link for this RUL
- addshowLink(linkMenu, label, url_pref + id + url_suff);
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls!=null)
+ {
+ for (int u=0; u<urls.length; u+=2)
+ {
+ addshowLink(linkMenu, label, urls[u+1]);
+ }
+ }
}
- }
- else
+ } else
{
// Add a non-dynamic link
- addshowLink(linkMenu, label, link.substring(link.lastIndexOf("|") + 1));
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());
}
}
if (sequence != null)
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
+ item.setToolTipText("open URL: "+url);
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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.jbgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-public class GSequenceLink\r
- extends Panel\r
-{\r
- public GSequenceLink()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.setLayout(gridBagLayout1);\r
- nameTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- nameTB.setBounds(new Rectangle(77, 10, 310, 23));\r
- nameTB.addKeyListener(new KeyAdapter()\r
- {\r
- public void keyTyped(KeyEvent e)\r
- {\r
- nameTB_keyTyped(e);\r
- }\r
- });\r
- urlTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- urlTB.setText("http://www.");\r
- urlTB.setBounds(new Rectangle(78, 40, 309, 23));\r
- urlTB.addKeyListener(new KeyAdapter()\r
- {\r
- public void keyTyped(KeyEvent e)\r
- {\r
- urlTB_keyTyped(e);\r
- }\r
- });\r
- jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);\r
- jLabel1.setText("Link Name");\r
- jLabel1.setBounds(new Rectangle(4, 10, 71, 24));\r
- jLabel2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel2.setHorizontalAlignment(SwingConstants.TRAILING);\r
- jLabel2.setText("URL");\r
- jLabel2.setBounds(new Rectangle(17, 37, 54, 27));\r
- jLabel3.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
- jLabel3.setText("Use $SEQUENCE_ID$ to specify where sequence id is in URL");\r
- jLabel3.setBounds(new Rectangle(21, 72, 351, 15));\r
- jPanel1.setBorder(BorderFactory.createEtchedBorder());\r
- jPanel1.setLayout(null);\r
- jPanel1.add(jLabel1);\r
- jPanel1.add(nameTB);\r
- jPanel1.add(urlTB);\r
- jPanel1.add(jLabel2);\r
- jPanel1.add(jLabel3);\r
- this.add(jPanel1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0\r
- , GridBagConstraints.CENTER,\r
- GridBagConstraints.BOTH,\r
- new Insets(5, 4, 6, 5), 390, 100));\r
- }\r
-\r
- public void setName(String name)\r
- {\r
- nameTB.setText(name);\r
- }\r
-\r
- public void setURL(String url)\r
- {\r
- urlTB.setText(url);\r
- }\r
-\r
- public String getName()\r
- {\r
- return nameTB.getText();\r
- }\r
-\r
- public String getURL()\r
- {\r
- return urlTB.getText();\r
- }\r
-\r
- public boolean checkValid()\r
- {\r
- if (urlTB.getText().indexOf("$SEQUENCE_ID$") == -1)\r
- {\r
- JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,\r
- "Sequence URL must contain $SEQUENCE_ID$",\r
- "URL not valid",\r
- JOptionPane.WARNING_MESSAGE);\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- JTextField nameTB = new JTextField();\r
- JTextField urlTB = new JTextField();\r
- JLabel jLabel1 = new JLabel();\r
- JLabel jLabel2 = new JLabel();\r
- JLabel jLabel3 = new JLabel();\r
- JPanel jPanel1 = new JPanel();\r
- GridBagLayout gridBagLayout1 = new GridBagLayout();\r
- public void nameTB_keyTyped(KeyEvent e)\r
- {\r
- if (e.getKeyChar() == '|')\r
- {\r
- e.consume();\r
- }\r
- }\r
-\r
- public void urlTB_keyTyped(KeyEvent e)\r
- {\r
- if (e.getKeyChar() == '|' || e.getKeyChar() == ' ')\r
- {\r
- e.consume();\r
- }\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.jbgui;
+
+import jalview.util.UrlLink;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+public class GSequenceLink
+ extends Panel
+{
+ public GSequenceLink()
+ {
+ try
+ {
+ jbInit();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ private void jbInit()
+ throws Exception
+ {
+ this.setLayout(gridBagLayout1);
+ nameTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ nameTB.setBounds(new Rectangle(77, 10, 310, 23));
+ nameTB.addKeyListener(new KeyAdapter()
+ {
+ public void keyTyped(KeyEvent e)
+ {
+ nameTB_keyTyped(e);
+ }
+ });
+ urlTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ urlTB.setText("http://www.");
+ urlTB.setBounds(new Rectangle(78, 40, 309, 23));
+ urlTB.addKeyListener(new KeyAdapter()
+ {
+ public void keyTyped(KeyEvent e)
+ {
+ urlTB_keyTyped(e);
+ }
+ });
+ jLabel1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
+ jLabel1.setText("Link Name");
+ jLabel1.setBounds(new Rectangle(4, 10, 71, 24));
+ jLabel2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ jLabel2.setHorizontalAlignment(SwingConstants.TRAILING);
+ jLabel2.setText("URL");
+ jLabel2.setBounds(new Rectangle(17, 37, 54, 27));
+ jLabel3.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ jLabel3.setText("Use $SEQUENCE_ID$ to specify where sequence id is in URL");
+ jLabel3.setBounds(new Rectangle(21, 72, 351, 15));
+ jPanel1.setBorder(BorderFactory.createEtchedBorder());
+ jPanel1.setLayout(null);
+ jPanel1.add(jLabel1);
+ jPanel1.add(nameTB);
+ jPanel1.add(urlTB);
+ jPanel1.add(jLabel2);
+ jPanel1.add(jLabel3);
+ this.add(jPanel1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0
+ , GridBagConstraints.CENTER,
+ GridBagConstraints.BOTH,
+ new Insets(5, 4, 6, 5), 390, 100));
+ }
+
+ public void setName(String name)
+ {
+ nameTB.setText(name);
+ }
+
+ public void setURL(String url)
+ {
+ urlTB.setText(url);
+ }
+
+ public String getName()
+ {
+ return nameTB.getText();
+ }
+
+ public String getURL()
+ {
+ return urlTB.getText();
+ }
+
+ public boolean checkValid()
+ {
+ UrlLink ul = new UrlLink("foo|"+urlTB.getText().trim());
+ if (ul.isValid()&&ul.isDynamic())
+ {
+ return true;
+ }
+
+ JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
+ "Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQUENCE_ID=/<regex>/=$",
+ "URL not valid",
+ JOptionPane.WARNING_MESSAGE);
+ return false;
+ }
+
+ JTextField nameTB = new JTextField();
+ JTextField urlTB = new JTextField();
+ JLabel jLabel1 = new JLabel();
+ JLabel jLabel2 = new JLabel();
+ JLabel jLabel3 = new JLabel();
+ JPanel jPanel1 = new JPanel();
+ GridBagLayout gridBagLayout1 = new GridBagLayout();
+ public void nameTB_keyTyped(KeyEvent e)
+ {
+ if (e.getKeyChar() == '|')
+ {
+ e.consume();
+ }
+ }
+
+ public void urlTB_keyTyped(KeyEvent e)
+ {
+ if (e.getKeyChar() == '|' || e.getKeyChar() == ' ')
+ {
+ e.consume();
+ }
+
+ }
+}
--- /dev/null
+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.\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
+ * \r
+ * @return true if URL string could not be parsed properly.\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
+ 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]+))/=$.someserver.org/foo",\r
+ * "myUrl3|http://$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:)?(.+)/=$",\r
+ * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$",\r
+ * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$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
+\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
git://source.jalview.org / jalview.git / commitdiff