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Jalview 2.6 source licence
[jalview.git]
/
src
/
jalview
/
ws
/
EnfinEnvision2OneWay.java
diff --git
a/src/jalview/ws/EnfinEnvision2OneWay.java
b/src/jalview/ws/EnfinEnvision2OneWay.java
index
ae2792c
..
f40831c
100644
(file)
--- a/
src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/
src/jalview/ws/EnfinEnvision2OneWay.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-25,6
+25,7
@@
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvSwingUtils;
import jalview.util.GroupUrlLink;
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.Component;
import java.awt.Cursor;
@@
-318,7
+319,12
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
public void run()
{
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();
}
}).start();
@@
-360,6
+366,10
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
private void buildGroupLinkMenu(JMenu enfinServiceMenu,
AlignFrame 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)
SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
if (sg == null)
@@
-394,7
+404,8
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
*/
private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
{
*/
private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
{
-
+ 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
// TODO: usability: thread off the generation of group url content so root
// menu appears asap
// sequence only URLs
@@
-462,10
+473,14
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
}
// now create group links for all distinct ID/sequence sets.
Hashtable<String, JMenu[]> gurlMenus = new Hashtable<String, JMenu[]>();
}
// now create group links for all distinct ID/sequence sets.
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++)
{
for (int i = 0; i < groupURLLinks.size(); i++)
{
- String link = groupURLLinks.elementAt(i).toString();
- String descr = groupURLdescr.elementAt(i).toString();
+ String link = (String) groupURLLinks.elementAt(i);
+ String descr = (String) groupURLdescr.elementAt(i);
// boolean specialCase =
// additionalPar.elementAt(i).toString().equals(BACKGROUND);
// boolean specialCase =
// additionalPar.elementAt(i).toString().equals(BACKGROUND);
@@
-512,6
+527,10
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
String[] allids = ((String[]) idset[1]);
seqstr = new String[numinput];
ids = new String[numinput];
String[] allids = ((String[]) idset[1]);
seqstr = new String[numinput];
ids = new String[numinput];
+ if (nsqtype[urlLink.getGroupURLType()]>0 && numinput>=nsqtype[urlLink.getGroupURLType()])
+ {
+ continue;
+ }
for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
{
if (allids[sq] != null)
for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
{
if (allids[sq] != null)
@@
-520,15
+539,28
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
seqstr[idcount++] = idandseqs[1][sq];
}
}
seqstr[idcount++] = idandseqs[1][sq];
}
}
- createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
+ try {createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
descr, ids, seqstr);
descr, ids, seqstr);
+ } catch (UrlStringTooLongException ex)
+ {
+ nsqtype[urlLink.getGroupURLType()] = numinput;
+ }
}
}
// also do names only.
seqstr = idandseqs[1];
ids = idandseqs[0];
}
}
// also do names only.
seqstr = idandseqs[1];
ids = idandseqs[0];
- createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
+ if (nsqtype[urlLink.getGroupURLType()]>0 && idandseqs[0].length>=nsqtype[urlLink.getGroupURLType()])
+ {
+ continue;
+ }
+
+ try {createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
ids, seqstr);
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
}
boolean anyadded = false; // indicates if there are any group links to give
// to user
@@
-556,10
+588,11
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
GroupUrlLink urlLink, String label, String ltarget, String descr,
private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
GroupUrlLink urlLink, String label, String ltarget, String descr,
- String[] ids, String[] seqstr)
+ String[] ids, String[] seqstr) throws UrlStringTooLongException
{
{
- Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+ Object[] urlset= urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+ System.currentTimeMillis(), false);
+ System.currentTimeMillis(), false);
+
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
@@
-582,7
+615,6
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
}
return false;
}
}
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)
@@
-609,8
+641,10
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
public void menuSelected(MenuEvent e)
{
public void menuSelected(MenuEvent e)
{
- if (refresh)
+ if (refresh && !isRunning())
{
{
+ new Thread(new Runnable() {
+ public void run() {
try
{
buildGroupLinkMenu(enfinServiceMenu, alignFrame);
try
{
buildGroupLinkMenu(enfinServiceMenu, alignFrame);
@@
-621,6
+655,7
@@
public class EnfinEnvision2OneWay extends DefaultHandler implements
ex);
enfinServiceMenu.setEnabled(false);
}
ex);
enfinServiceMenu.setEnabled(false);
}
+ }}).start();
refresh = false;
}
}
refresh = false;
}
}