*/
package jalview.util;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import java.util.Hashtable;
+/**
+ * This class is not implemented because Preferences never puts anything in
+ * groupURLLinks.
+ *
+ * @author hansonr
+ *
+ */
public class GroupUrlLink
{
+ @SuppressWarnings("serial")
public class UrlStringTooLongException extends Exception
{
public UrlStringTooLongException(int lng)
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)
+ * tokens that can be replaced in the URL.
*/
- public static final int DATASETID = 4;
-
+ private static final String[] tokens = new String[] { "SEQUENCEIDS",
+ "SEQUENCES", "DATASETID" };
+
+ // /**
+ // * test for GroupURLType bitfield (with default tokens)
+ // */
+ // private static final int SEQUENCEIDS = 1;
+ //
+ // /**
+ // * test for GroupURLType bitfield (with default tokens)
+ // */
+ // private static final int SEQUENCES = 2;
+ //
+ // /**
+ // * test for GroupURLType bitfield (with default tokens)
+ // */
+ // private static final int DATASETID = 4;
+ //
// private int idseg = -1, seqseg = -1;
/**
+ *
+ * called by PopupMenu.buildGroupURLMenu()
+ *
* 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
}
/**
+ *
+ * called by PopupMenu.addShowLink()
+ *
* @return the url_prefix
*/
public String getUrl_prefix()
}
/**
+ * called by PopupMenu.buildGroupURLMenu()
+ *
* @return the target
*/
public String getTarget()
}
/**
+ *
+ * called by PopupMenu.buildGroupURLMenu()
+ *
* @return the label
*/
public String getLabel()
}
/**
- * @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]);
- }
-
- /**
+ *
+ * called by PopupMenu.buildGroupURLMenu()
+ *
* @return the invalidMessage
*/
public String getInvalidMessage()
}
/**
+ * called by PopupMenu.buildGroupURLMenu()
+ *
* Check if URL string was parsed properly.
*
* @return boolean - if false then <code>getInvalidMessage</code> returns an
}
/**
- * 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
+ * called by PopupMenu.buildGroupURLMenu()
+ *
+ * This method is never called, because PopupMenu.buildGroupMenu() is never
+ * called. It relates to the popup menu for the idPanel.
+ *
+ * @param ids
+ * @param seqstr
+ * @param string
* @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 } }
+ * @return URL stub objects ready to pass to constructFrom in the form of
+ * Object[] { int[], boolean[], Hashtable<String, String[]>,
+ * boolean[] }
* @throws UrlStringTooLongException
*/
- public Object[] makeUrls(String[] idstrings, String[] seqstrings,
- String dsstring, boolean onlyIfMatches)
- throws UrlStringTooLongException
+ public Object[] makeUrlStubs(String[] ids, String[] seqstr, String string,
+ boolean onlyIfMatches) throws UrlStringTooLongException
{
- Hashtable rstrings = replacementArgs(idstrings, seqstrings, dsstring);
- return makeUrls(rstrings, onlyIfMatches);
+ Hashtable<String, String[]> rstrings = replacementArgs(ids, seqstr,
+ string);
+ boolean createFullURL = false;
+ Object[] stubs = makeUrlsIf(createFullURL, rstrings, onlyIfMatches);
+ // stubs is just { int[] boolean[] }
+ return stubs == null ? null
+ : new Object[]
+ { stubs[0], stubs[1], rstrings,
+ new boolean[]
+ { onlyIfMatches } }; // int[] boolean[] Hashtable boolean[]
}
/**
* @param dsstring
* @return
*/
- private Hashtable replacementArgs(String[] idstrings, String[] seqstrings,
- String dsstring)
+ private Hashtable<String, String[]> replacementArgs(String[] idstrings,
+ String[] seqstrings, String dsstring)
{
- Hashtable rstrings = new Hashtable();
+ Hashtable<String, String[]> rstrings = new Hashtable<>();
rstrings.put(tokens[0], idstrings);
rstrings.put(tokens[1], seqstrings);
rstrings.put(tokens[2], new String[] { dsstring });
return rstrings;
}
- public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)
- throws UrlStringTooLongException
- {
- return makeUrlsIf(true, repstrings, onlyIfMatches);
- }
-
/**
+ * Called from PopupMenu.addShowLink action listener
*
- * @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.
+ * 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 })}
+ * @return URL string
* @throws UrlStringTooLongException
*/
+ @SuppressWarnings("unchecked")
public String constructFrom(Object[] stubs)
throws UrlStringTooLongException
{
- Object[] results = makeUrlsIf(true, (Hashtable) stubs[2],
- ((boolean[]) stubs[3])[0]);
- return ((String[]) results[3])[0];
+ // Object[] {
+ // int[] { number of matches seqs },
+ // boolean[] { which matched }
+ // }
+
+ boolean createFullURL = true;
+ Hashtable<String, String[]> repstrings = (Hashtable<String, String[]>) stubs[2];
+ boolean onlyIfMatches = ((boolean[]) stubs[3])[0];
+ String url = ((String[]) makeUrlsIf(createFullURL, repstrings,
+ onlyIfMatches)[3])[0];
+ return url;
}
/**
* }, String[] { url })}
* @throws UrlStringTooLongException
*/
- protected Object[] makeUrlsIf(boolean createFullUrl, Hashtable repstrings,
+ private Object[] makeUrlsIf(boolean createFullUrl,
+ Hashtable<String, String[]> repstrings,
boolean onlyIfMatches) throws UrlStringTooLongException
{
int pass = 0;
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]);
+ idseq[i] = repstrings.get(mtch[i]);
if (idseq[i].length >= 1)
{
if (mins == 0 && idseq[i].length == 1)
{
// just return the essential info about what the URL would be generated
// from
- return new Object[] { new int[] { seqsmatched }, thismatched };
+ return new Object[] { new int[] { seqsmatched }, thismatched // boolean[]
+ };
}
// otherwise, create the URL completely.
}
}
- return new Object[] { new int[] { seqsmatched }, thismatched, matched,
+ // full return
+ return new Object[] { new int[] { seqsmatched }, thismatched, // boolean[]
+ matched, // StringBuffer[]
new String[]
{ submiturl.toString() } };
}
/**
*
+ * Called by PopupMenu.addShowLinks()
+ *
* @param urlstub
* @return number of distinct sequence (id or seuqence) replacements predicted
* for this stub
}
/**
+ * called by PopupMenu.buildGroupURLMenu()
+ *
* get token types present in this url as a bitfield indicating presence of
* each token from tokens (LSB->MSB).
*
return r;
}
+ /**
+ * called by PopupMenu.buildGroupURLMenu()
+ *
+ * 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;
+ }
+
+ // commented out test code
+ //
+ // /**
+ // *
+ // * @param argv
+ // * @j2sIgnore
+ // */
+ // public static void main(String argv[])
+ // {
+ // // note - JAL-1383 - these services are all dead
+ // 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());
+ // }
+ // }
+ // }
+ // /**
+ // * @return the sequence ID regexReplace
+ // */
+ // private String getIDRegexReplace()
+ // {
+ // String token = tokens[0];
+ // 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
+ // */
+ // private String getSeqRegexReplace()
+ // {
+ // return _replaceFor(tokens[1]);
+ // }
+ //
+ // /**
+ // * 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 void setLabel(String newlabel)
+ // {
+ // this.label = newlabel;
+ // }
+ // /**
+ // * 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
+ // */
+ // private Object[] makeUrls(String[] idstrings, String[] seqstrings,
+ // String dsstring, boolean onlyIfMatches)
+ // throws UrlStringTooLongException
+ // {
+ // Hashtable<String, String[]> rstrings = replacementArgs(idstrings,
+ // seqstrings, dsstring);
+ // return makeUrls(rstrings, onlyIfMatches);
+ // }
+ //
+ // /**
+ // *
+ // * @param repstrings
+ // * @param onlyIfMatches
+ // * @return Object[] {int[], boolean[], StringBuffer[], String[] }
+ // * @throws UrlStringTooLongException
+ // */
+ // private Object[] makeUrls(Hashtable<String, String[]> repstrings,
+ // boolean onlyIfMatches)
+ // throws UrlStringTooLongException
+ // {
+ // return makeUrlsIf(true, repstrings, onlyIfMatches);
+ // }
+ //
+
@Override
public String toString()
{
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]);
- }
- }
-
- /**
- *
- * @param argv
- * @j2sIgnore
- */
- public static void main(String argv[])
- {
- // note - JAL-1383 - these services are all dead
- 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