-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 <http://www.gnu.org/licenses/>.
*/
package jalview.ws;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
import java.awt.Component;
import java.awt.Cursor;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.io.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
import java.net.URL;
+import java.net.URLEncoder;
+import java.nio.charset.Charset;
+import java.nio.charset.CharsetEncoder;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
+import java.util.regex.Pattern;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
+import org.apache.axis.utils.StringUtils;
+import org.apache.http.client.utils.URLEncodedUtils;
+import org.apache.http.entity.StringEntity;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
+import com.lowagie.text.html.HtmlEncoder;
+
/**
* Lightweight runnable to discover dynamic 'one way' group URL services
+ *
* @author JimP
- *
+ *
*/
-public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSMenuEntryProviderI
+public class EnfinEnvision2OneWay extends DefaultHandler implements
+ Runnable, WSMenuEntryProviderI
{
- private static EnfinEnvision2OneWay groupURLLinksGatherer=null;
- public static EnfinEnvision2OneWay getInstance() {
- if (groupURLLinksGatherer==null) {
+ private static EnfinEnvision2OneWay groupURLLinksGatherer = null;
+
+ public static EnfinEnvision2OneWay getInstance()
+ {
+ if (groupURLLinksGatherer == null)
+ {
groupURLLinksGatherer = new EnfinEnvision2OneWay();
}
return groupURLLinksGatherer;
}
- private void waitForCompletion() {
+
+ private void waitForCompletion()
+ {
if (groupURLLinksGatherer.isRunning())
{
- // wait around and show a visual delay indicator
- Cursor oldCursor = Desktop.instance.getCursor();
- Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- while (groupURLLinksGatherer.isRunning())
- {
- try {
- Thread.sleep(100);
- } catch (InterruptedException e ){};
+ // wait around and show a visual delay indicator
+ Cursor oldCursor = Desktop.instance.getCursor();
+ Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ while (groupURLLinksGatherer.isRunning())
+ {
+ try
+ {
+ Thread.sleep(100);
+ } catch (InterruptedException e)
+ {
+ }
+ ;
+ }
+ Desktop.instance.setCursor(oldCursor);
}
- Desktop.instance.setCursor(oldCursor);
- }
}
- public Vector getEnvisionServiceGroupURLS() {
+
+ public Vector getEnvisionServiceGroupURLS()
+ {
waitForCompletion();
return groupURLLinks;
}
+
/**
- * indicate if
+ * indicate if
*/
- private static String BACKGROUND="BACKGROUNDPARAM";
+ private static String BACKGROUND = "BACKGROUNDPARAM";
+
/**
- * contains null strings or one of the above constants - indicate if this URL is a special case.
+ * contains null strings or one of the above constants - indicate if this URL
+ * is a special case.
*/
private Vector additionalPar = new Vector();
+
/**
* the enfin service URL
*/
- private String enfinService=null;
- private String description=null;
+ private String enfinService = null;
+
+ private String description = null;
+
private String wfname;
- /* (non-Javadoc)
- * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String, java.lang.String)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
+ * java.lang.String, java.lang.String)
*/
public void endElement(String uri, String localName, String qName)
throws SAXException
{
-
-// System.err.println("End element: : '"+uri+" "+localName+" "+qName);
- if (qName.equalsIgnoreCase("workflow") && description!=null && description.length()>0)
+
+ // System.err.println("End element: : '"+uri+" "+localName+" "+qName);
+ if (qName.equalsIgnoreCase("workflow") && description != null
+ && description.length() > 0)
{
- //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
- //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
- System.err.println("Adding entry for "+wfname+" "+description);
- if (wfname.toLowerCase().indexOf("funcnet")==-1)
+ // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
+ // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
+ System.err.println("Adding entry for " + wfname + " " + description);
+ if (wfname.toLowerCase().indexOf("funcnet") == -1)
{
+ description = Pattern.compile("\\s+",Pattern.MULTILINE).matcher(description).replaceAll(" ");
groupURLdescr.addElement(description);
groupURLdescr.addElement(description);
- groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
- groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
+ String urlstub=wfname;
+ if (wfname.indexOf(" ")>-1)
+ {
+ // make the name safe!
+ try {
+ urlstub = URLEncoder.encode(wfname,"utf-8");
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ groupURLLinks
+ .addElement(wfname
+ + "|"
+ + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
+ + urlstub
+ + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
+ groupURLLinks
+ .addElement(wfname
+ + "|"
+ + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
+ + urlstub
+ + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
}
}
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
*/
public void characters(char[] ch, int start, int length)
throws SAXException
{
- if (description!=null) {
- for (int i=start; i<start+length; i++) {
- description+=ch[i];
+ if (description != null)
+ {
+ for (int i = start; i < start + length; i++)
+ {
+ description += ch[i];
}
}
}
- /* (non-Javadoc)
- * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String,
+ * java.lang.String, java.lang.String, org.xml.sax.Attributes)
*/
public void startElement(String uri, String localName, String qName,
Attributes attributes) throws SAXException
if (qName.equalsIgnoreCase("description"))
{
description = "";
- }
-
-
- //System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
+ }
+
+ // System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
// super.startElement(uri,localName,qname,attributes);
}
- private boolean started=false;
- private boolean running=false;
+ private boolean started = false;
+
+ private boolean running = false;
+
private Vector groupURLLinks = null;
+
private Vector groupURLdescr = null;
- private static String[] allowedDb=new String[] {"UNIPROT","EMBL","PDB"} ;
-
- public EnfinEnvision2OneWay() {
+
+ private static String[] allowedDb = new String[]
+ { "UNIPROT", "EMBL", "PDB" };
+
+ public EnfinEnvision2OneWay()
+ {
groupURLLinks = new Vector();
groupURLdescr = new Vector();
-
- enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE", "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
+
+ enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE",
+ "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
new Thread(this).start();
}
{
started = true;
running = true;
- try {
+ try
+ {
SAXParserFactory spf = SAXParserFactory.newInstance();
SAXParser sp = spf.newSAXParser();
- sp.parse(new URL(enfinService).openStream(), this);
+ sp.parse(new URL(enfinService).openStream(), this);
} catch (Exception e)
{
- Cache.log.warn("Exception when discovering One Way services: ",e);
- }
- catch (Error e)
+ Cache.log.warn("Exception when discovering One Way services: ", e);
+ } catch (Error e)
{
- Cache.log.warn("Error when discovering One Way services: ",e);
+ Cache.log.warn("Error when discovering One Way services: ", e);
}
running = false;
Cache.log.debug("Finished running.");
/**
* have we finished running yet ?
+ *
* @return false if we have been run.
*/
public boolean isRunning()
{
-
+
// TODO Auto-generated method stub
return !started || running;
}
- public static void main(String[] args){
+
+ public static void main(String[] args)
+ {
Cache.initLogger();
EnfinEnvision2OneWay ow = new EnfinEnvision2OneWay();
while (ow.isRunning())
{
- try {
+ try
+ {
Thread.sleep(50);
- } catch (Exception e){};
-
+ } catch (Exception e)
+ {
+ }
+ ;
+
}
- for (int i=0;i<ow.groupURLLinks.size();i++) {
- System.err.println("Description"+ow.groupURLdescr.elementAt(i)+"Service URL: "+ow.groupURLLinks.elementAt(i));
+ for (int i = 0; i < ow.groupURLLinks.size(); i++)
+ {
+ System.err.println("Description" + ow.groupURLdescr.elementAt(i)
+ + "Service URL: " + ow.groupURLLinks.elementAt(i));
}
}
- /// Copied from jalview.gui.PopupMenu
+
+ // / Copied from jalview.gui.PopupMenu
/**
* add a late bound URL service item to the given menu
*
* @param linkMenu
- * @param label -
- * menu label string
- * @param urlgenerator GroupURLLink used to generate URL
- * @param urlstub Object array returned from the makeUrlStubs function.
+ * @param label
+ * - menu label string
+ * @param urlgenerator
+ * GroupURLLink used to generate URL
+ * @param urlstub
+ * Object array returned from the makeUrlStubs function.
*/
- private void addshowLink(JMenu linkMenu, String label, String descr, final GroupUrlLink urlgenerator, final Object[] urlstub)
+ private void addshowLink(JMenu linkMenu, String label, String descr,
+ String dbname, final GroupUrlLink urlgenerator,
+ final Object[] urlstub)
{
- Component[] jmi=linkMenu.getMenuComponents();
- for (int i=0; i<jmi.length; i++)
+ Component[] jmi = linkMenu.getMenuComponents();
+ for (int i = 0; i < jmi.length; i++)
{
- if (jmi[i] instanceof JMenuItem && ((JMenuItem)jmi[i]).getText().equalsIgnoreCase(label))
+ if (jmi[i] instanceof JMenuItem
+ && ((JMenuItem) jmi[i]).getText().equalsIgnoreCase(label))
{
// don't add this - its a repeat of an existing URL.
return;
}
}
+ try {
+ descr = HtmlEncoder.encode(descr);
+ } catch (Exception e){};
+
+ boolean seqsorids = (urlgenerator.getGroupURLType() & urlgenerator.SEQUENCEIDS) == 0;
+ int i = urlgenerator.getNumberInvolved(urlstub);
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("Submit ("+urlgenerator.getNumberInvolved(urlstub)+" seqs) to workflow: "+descr);
+ //
+ if (dbname == null || dbname.trim().length() == 0)
+ {
+ dbname = "";
+ }
+ item.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
+ + (seqsorids ? "sequence" : "sequence id")
+ + (i > 1 ? "s" : "")
+
+ + " to<br/>" + descr) + "</html>");
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
public void run()
{
- showLink(urlgenerator.constructFrom(urlstub));
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException ex)
+ {
+ Cache.log.warn("Not showing link: URL is too long!", ex);
+ }
}
}).start();
/**
* open the given link in a new browser window
+ *
* @param url
*/
public void showLink(String url)
ex.printStackTrace();
}
}
+
/**
* called by a web service menu instance when it is opened.
+ *
* @param enfinServiceMenu
* @param alignFrame
*/
private void buildGroupLinkMenu(JMenu enfinServiceMenu,
AlignFrame alignFrame)
{
+ if (running || !started)
+ {
+ return;
+ }
SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
- if (sg==null) {
+ if (sg == null)
+ {
// consider visible regions here/
}
enfinServiceMenu.removeAll();
- JMenu entries = buildGroupURLMenu(seqs,sg);
- if (entries!=null)
+ JMenu entries = buildGroupURLMenu(seqs, sg);
+ if (entries != null)
{
- for (int i=0,iSize=entries.getMenuComponentCount();i<iSize;i++)
+ for (int i = 0, iSize = entries.getMenuComponentCount(); i < iSize; i++)
{
// transfer - menu component is removed from entries automatically
enfinServiceMenu.add(entries.getMenuComponent(0));
}
// entries.removeAll();
enfinServiceMenu.setEnabled(true);
- } else {
+ }
+ else
+ {
enfinServiceMenu.setEnabled(false);
}
}
/**
* construct a dynamic enfin services menu given a sequence selection
+ *
* @param seqs
* @param sg
* @param groupLinks
*/
private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
{
-
- // TODO: usability: thread off the generation of group url content so root menu appears asap
+ if (groupURLdescr == null || groupURLLinks == null)
+ return null;
+ // TODO: usability: thread off the generation of group url content so root
+ // menu appears asap
// sequence only URLs
// ID/regex match URLs
JMenu groupLinksMenu = new JMenu("Group Link");
- JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
- for (int sq = 0; sq<seqs.length;sq++) {
+ for (int sq = 0; sq < seqs.length; sq++)
+ {
- int start,end;
- if (sg!=null) {
+ int start, end;
+ if (sg != null)
+ {
start = seqs[sq].findPosition(sg.getStartRes());
- end=seqs[sq].findPosition(sg.getEndRes());
- } else {
+ end = seqs[sq].findPosition(sg.getEndRes());
+ }
+ else
+ {
// get total width of alignment.
start = seqs[sq].getStart();
end = seqs[sq].findPosition(seqs[sq].getLength());
}
- // we skip sequences which do not have any non-gaps in the region of interest
- if (start>end)
+ // we skip sequences which do not have any non-gaps in the region of
+ // interest
+ if (start > end)
{
continue;
}
// just collect ids from dataset sequence
- // TODO: check if IDs collected from selecton group intersects with the current selection, too
+ // TODO: check if IDs collected from selecton group intersects with the
+ // current selection, too
SequenceI sqi = seqs[sq];
- while (sqi.getDatasetSequence()!=null) {
- sqi = sqi.getDatasetSequence(); }
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
DBRefEntry[] dbr = sqi.getDBRef();
- if (dbr!=null && dbr.length>0)
+ if (dbr != null && dbr.length > 0)
{
- for (int d=0;d<dbr.length;d++)
+ for (int d = 0; d < dbr.length; d++)
{
- String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
Object[] sarray = (Object[]) commonDbrefs.get(src);
- if (sarray==null)
+ if (sarray == null)
{
sarray = new Object[2];
- sarray[0] = new int[] { 0 };
+ sarray[0] = new int[]
+ { 0 };
sarray[1] = new String[seqs.length];
-
- commonDbrefs.put(src,sarray);
+
+ commonDbrefs.put(src, sarray);
}
-
- if (((String[])sarray[1])[sq]==null) {
- if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
- ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
- ((int[])sarray[0])[0]++;
+
+ if (((String[]) sarray[1])[sq] == null)
+ {
+ if (!dbr[d].hasMap()
+ || (dbr[d].getMap().locateMappedRange(start, end) != null))
+ {
+ ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+ ((int[]) sarray[0])[0]++;
}
}
}
}
}
// now create group links for all distinct ID/sequence sets.
- boolean addMenu = false; // indicates if there are any group links to give to user
- for (int i = 0; i < groupURLLinks.size(); i++) {
- String link = groupURLLinks.elementAt(i).toString();
- String descr = groupURLdescr.elementAt(i).toString();
-// boolean specialCase = additionalPar.elementAt(i).toString().equals(BACKGROUND);
- GroupUrlLink urlLink = null;
- try
- {
- urlLink = new GroupUrlLink(link);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
- + "'", foo);
- continue;
- }
- ;
- if (!urlLink.isValid())
+ Hashtable<String, JMenu[]> gurlMenus = new Hashtable<String, JMenu[]>();
+ /**
+ * last number of sequences where URL generation failed
+ */
+ int[] nsqtype = new int[]
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
+ for (int i = 0; i < groupURLLinks.size(); i++)
+ {
+ String link = (String) groupURLLinks.elementAt(i);
+ String descr = (String) groupURLdescr.elementAt(i);
+
+ // boolean specialCase =
+ // additionalPar.elementAt(i).toString().equals(BACKGROUND);
+ GroupUrlLink urlLink = null;
+ try
+ {
+ urlLink = new GroupUrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ // create/recover the sub menus that might be populated for this link.
+ JMenu[] wflinkMenus = gurlMenus.get(label);
+ if (wflinkMenus == null)
+ {
+ // three types of url that might be
+ // created.
+ wflinkMenus = new JMenu[]
+ { null, new JMenu("IDS"), new JMenu("Sequences"),
+ new JMenu("IDS and Sequences") };
+ gurlMenus.put(label, wflinkMenus);
+ }
+
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget;
+ String[] seqstr, ids; // input to makeUrl
+ for (int t = 0; t < allowedDb.length; t++)
+ {
+ ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+ Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+ if (idset != null)
{
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
- final String label = urlLink.getLabel();
- boolean usingNames = false;
- // Now see which parts of the group apply for this URL
- String ltarget;
- String[] seqstr,ids; // input to makeUrl
- for (int t=0;t<allowedDb.length; t++) {
- ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
- if (idset!=null)
+ int numinput = ((int[]) idset[0])[0];
+ String[] allids = ((String[]) idset[1]);
+ seqstr = new String[numinput];
+ ids = new String[numinput];
+ if (nsqtype[urlLink.getGroupURLType()] > 0
+ && numinput >= nsqtype[urlLink.getGroupURLType()])
{
- int numinput = ((int[])idset[0])[0];
- String[] allids = ((String[])idset[1]);
- seqstr = new String[numinput];
- ids = new String[numinput];
- for (int sq=0,idcount=0;sq<seqs.length;sq++)
+ continue;
+ }
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
+ {
+ if (allids[sq] != null)
{
- if (allids[sq]!=null) {
- ids[idcount] = allids[sq];
- seqstr[idcount++] = idandseqs[1][sq];
- }
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
}
- addMenu = addMenu | createAndAddLinks(linkMenus,false,urlLink,label,ltarget,descr, ids,seqstr);
+ }
+ try
+ {
+ createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
+ descr, ids, seqstr);
+ } catch (UrlStringTooLongException ex)
+ {
+ nsqtype[urlLink.getGroupURLType()] = numinput;
}
}
- // also do names only.
- seqstr = idandseqs[1];
- ids = idandseqs[0];
- addMenu = addMenu | createAndAddLinks(linkMenus,true,urlLink,label,"Names",descr, ids,seqstr);
}
- if (addMenu)
+ // also do names only.
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ if (nsqtype[urlLink.getGroupURLType()] > 0
+ && idandseqs[0].length >= nsqtype[urlLink.getGroupURLType()])
+ {
+ continue;
+ }
+
+ try
+ {
+ createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
+ ids, seqstr);
+ } catch (UrlStringTooLongException ex)
+ {
+ nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
+ }
+ }
+ boolean anyadded = false; // indicates if there are any group links to give
+ // to user
+ for (Map.Entry<String, JMenu[]> menues : gurlMenus.entrySet())
{
- groupLinksMenu = new JMenu("Group Links");
- for (int m=0;m<linkMenus.length; m++)
+ JMenu grouplinkset = new JMenu(menues.getKey());
+ JMenu[] wflinkMenus = menues.getValue();
+ for (int m = 0; m < wflinkMenus.length; m++)
{
- if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
+ if (wflinkMenus[m] != null
+ && wflinkMenus[m].getMenuComponentCount() > 0)
{
- groupLinksMenu.add(linkMenus[m]);
+ anyadded = true;
+ grouplinkset.add(wflinkMenus[m]);
}
}
-
+ groupLinksMenu.add(grouplinkset);
+ }
+ if (anyadded)
+ {
return groupLinksMenu;
}
return null;
}
private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
- GroupUrlLink urlLink, String label, String ltarget, String descr, String[] ids,
- String[] seqstr)
+ GroupUrlLink urlLink, String label, String ltarget, String descr,
+ String[] ids, String[] seqstr) throws UrlStringTooLongException
{
- Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
- if (urlset!=null)
+ Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+ + System.currentTimeMillis(), false);
+
+ if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
- //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
+ // System.out.println(urlLink.getGroupURLType()
+ // +" "+((String[])urlset[3])[0]);
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), descr, urlLink, urlset);
+ addshowLink(
+ linkMenus[type],
+ label
+ + " "
+ + (ltarget == null ? (((type & 1) == 1 ? "ID"
+ : "Sequence") + (urlLink
+ .getNumberInvolved(urlset) > 1 ? "s" : ""))
+ : (usingNames ? (((type & 1) == 1) ? "(Names)"
+ : "")
+ : ("(" + ltarget + ")"))), descr,
+ usingNames ? null : label, urlLink, urlset);
return true;
}
return false;
}
- /// end of stuff copied from popupmenu
- public void attachWSMenuEntry(final JMenu wsmenu, final AlignFrame alignFrame)
+
+ // / end of stuff copied from popupmenu
+ public void attachWSMenuEntry(final JMenu wsmenu,
+ final AlignFrame alignFrame)
{
final JMenu enfinServiceMenu = new JMenu("Envision 2");
wsmenu.add(enfinServiceMenu);
enfinServiceMenu.setEnabled(false);
wsmenu.addMenuListener(new MenuListener()
- {
- // this listener remembers when the menu was first selected, and
- // doesn't rebuild the session list until it has been cleared and
- // reselected again.
- boolean refresh = true;
+ {
+ // this listener remembers when the menu was first selected, and
+ // doesn't rebuild the session list until it has been cleared and
+ // reselected again.
+ boolean refresh = true;
- public void menuCanceled(MenuEvent e)
- {
- refresh = true;
- }
+ public void menuCanceled(MenuEvent e)
+ {
+ refresh = true;
+ }
- public void menuDeselected(MenuEvent e)
- {
- refresh = true;
- }
+ public void menuDeselected(MenuEvent e)
+ {
+ refresh = true;
+ }
- public void menuSelected(MenuEvent e)
+ public void menuSelected(MenuEvent e)
+ {
+ if (refresh && !isRunning())
{
- if (refresh)
+ new Thread(new Runnable()
{
- try {
- buildGroupLinkMenu(enfinServiceMenu,alignFrame);
- } catch (OutOfMemoryError ex)
+ public void run()
{
- Cache.log.error("Out of memory when calculating the Envision2 links.",ex);
- enfinServiceMenu.setEnabled(false);
+ try
+ {
+ buildGroupLinkMenu(enfinServiceMenu, alignFrame);
+ } catch (OutOfMemoryError ex)
+ {
+ Cache.log
+ .error("Out of memory when calculating the Envision2 links.",
+ ex);
+ enfinServiceMenu.setEnabled(false);
+ }
}
- refresh = false;
- }
+ }).start();
+ refresh = false;
}
- });
-
-
+ }
+ });
+
}
}
git://source.jalview.org / jalview.git / blobdiff