*/
package jalview.util;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import java.util.Hashtable;
-import com.stevesoft.pat.Regex;
-
-/**
- * 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" };
+ }
+ }
/**
- * tokens that can be replaced in the URL.
+ * test for GroupURLType bitfield (with default tokens)
+ */
+ public static final int SEQUENCEIDS = 1;
+
+ /**
+ * test for GroupURLType bitfield (with default tokens)
*/
- 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;
- //
+ 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;
/**
- *
- * 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
regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
try
{
- Regex rg = Platform.newRegexPerl("/" + regexReplace[pass] + "/");
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace[pass] + "/");
if (rg == null)
{
invalidMessage = "Invalid Regular Expression : '"
}
/**
- *
- * 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()
}
/**
- *
- * called by PopupMenu.buildGroupURLMenu()
- *
+ * @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()
}
/**
- * 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
*
- * 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 idstrings
+ * array of id strings to pass to service
+ * @param seqstrings
+ * array of seq strings to pass to service
* @param onlyIfMatches
- * @return URL stub objects ready to pass to constructFrom in the form of
- * Object[] { int[], boolean[], Hashtable<String, String[]>,
- * boolean[] }
+ * - 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[] makeUrlStubs(String[] ids, String[] seqstr, String string,
- boolean onlyIfMatches) throws UrlStringTooLongException
+ public Object[] makeUrls(String[] idstrings, String[] seqstrings,
+ String dsstring, boolean onlyIfMatches)
+ throws UrlStringTooLongException
{
- 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[]
+ Hashtable rstrings = replacementArgs(idstrings, seqstrings, dsstring);
+ return makeUrls(rstrings, onlyIfMatches);
}
/**
* @param dsstring
* @return
*/
- private Hashtable<String, String[]> replacementArgs(String[] idstrings,
- String[] seqstrings, String dsstring)
+ private Hashtable replacementArgs(String[] idstrings, String[] seqstrings,
+ String dsstring)
{
- Hashtable<String, String[]> rstrings = new Hashtable<>();
+ Hashtable 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
- * 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
+ * @return URL string.
* @throws UrlStringTooLongException
*/
- @SuppressWarnings("unchecked")
public String constructFrom(Object[] stubs)
throws UrlStringTooLongException
{
- // 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;
+ Object[] results = makeUrlsIf(true, (Hashtable) stubs[2],
+ ((boolean[]) stubs[3])[0]);
+ return ((String[]) results[3])[0];
}
/**
* }, String[] { url })}
* @throws UrlStringTooLongException
*/
- private Object[] makeUrlsIf(boolean createFullUrl,
- Hashtable<String, String[]> repstrings,
+ protected Object[] makeUrlsIf(boolean createFullUrl, Hashtable 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] = repstrings.get(mtch[i]);
+ idseq[i] = (String[]) repstrings.get(mtch[i]);
if (idseq[i].length >= 1)
{
if (mins == 0 && idseq[i].length == 1)
// iterate through input, collating segments to be inserted into url
StringBuffer matched[] = new StringBuffer[idseq.length];
// and precompile regexes
- Regex[] rgxs = new Regex[matched.length];
+ 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] = Platform.newRegexPerl("/" + regexReplace[pass] + "/");
+ rgxs[pass] = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace[pass] + "/");
}
else
{
{
// just return the essential info about what the URL would be generated
// from
- return new Object[] { new int[] { seqsmatched }, thismatched // boolean[]
- };
+ return new Object[] { new int[] { seqsmatched }, thismatched };
}
// otherwise, create the URL completely.
}
}
- // full return
- return new Object[] { new int[] { seqsmatched }, thismatched, // boolean[]
- matched, // StringBuffer[]
+ return new Object[] { new int[] { seqsmatched }, thismatched, matched,
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