X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FEnfinEnvision2OneWay.java;h=f40831ca2041c7ac2f9ac8f33916fc8365b05a04;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=53d5b4aaec081ad411fa5e7e31f3873b92a39175;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 53d5b4a..f40831c 100644
--- 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.
@@ -23,7 +23,9 @@ import jalview.datamodel.SequenceGroup;
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;
@@ -35,6 +37,7 @@ import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
import javax.swing.JMenu;
@@ -281,7 +284,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
* Object array returned from the makeUrlStubs function.
*/
private void addshowLink(JMenu linkMenu, String label, String descr,
- final GroupUrlLink urlgenerator, final Object[] urlstub)
+ String dbname, final GroupUrlLink urlgenerator, final Object[] urlstub)
{
Component[] jmi = linkMenu.getMenuComponents();
for (int i = 0; i < jmi.length; i++)
@@ -293,10 +296,20 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
return;
}
}
+ 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(""
+ + JvSwingUtils.wrapTooltip("Submit " + i + " " +
+ dbname +" "
+ + (seqsorids ? "sequence" : "sequence id") + (i > 1 ? "s" : "")
+
+ + " to
" + descr) + "");
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -306,7 +319,12 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
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();
@@ -348,6 +366,10 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
private void buildGroupLinkMenu(JMenu enfinServiceMenu,
AlignFrame alignFrame)
{
+ if (running || !started)
+ {
+ return;
+ }
SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
if (sg == null)
@@ -382,16 +404,13 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
*/
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
// 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++)
@@ -453,12 +472,16 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
}
}
// now create group links for all distinct ID/sequence sets.
- boolean addMenu = false; // indicates if there are any group links to give
- // to user
+ Hashtable gurlMenus = new Hashtable();
+ /**
+ * 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 = 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);
GroupUrlLink urlLink = null;
@@ -478,6 +501,18 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
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;
@@ -492,6 +527,10 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
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)
@@ -500,30 +539,48 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
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 (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;
+ }
}
- if (addMenu)
+ boolean anyadded = false; // indicates if there are any group links to give
+ // to user
+ for (Map.Entry 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;
@@ -531,10 +588,11 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
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);
+
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
@@ -542,15 +600,21 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
// +" "+((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
- + " "
- + (usingNames ? (((type & 1) == 1) ? "(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)
@@ -577,8 +641,10 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
public void menuSelected(MenuEvent e)
{
- if (refresh)
+ if (refresh && !isRunning())
{
+ new Thread(new Runnable() {
+ public void run() {
try
{
buildGroupLinkMenu(enfinServiceMenu, alignFrame);
@@ -589,6 +655,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
ex);
enfinServiceMenu.setEnabled(false);
}
+ }}).start();
refresh = false;
}
}