X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=9a0def1eabe77ae26d42083e6007c3894ff47ead;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=d89c776fba53541763e45ba03de62d8c3b568c05;hpb=61f35f2177eb22c3d42cafda13db82d4e904b9f0;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index d89c776..9a0def1 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 . */ package jalview.gui; @@ -30,6 +29,8 @@ import jalview.commands.*; import jalview.datamodel.*; import jalview.io.*; import jalview.schemes.*; +import jalview.util.GroupUrlLink; +import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.UrlLink; /** @@ -94,6 +95,8 @@ public class PopupMenu extends JPopupMenu JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); + JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem(); + JMenu editMenu = new JMenu(); JMenuItem cut = new JMenuItem(); @@ -131,16 +134,31 @@ public class PopupMenu extends JPopupMenu // JMenuItem annotationMenuItem = new JMenuItem(); + JMenu groupLinksMenu; + /** * Creates a new PopupMenu object. * * @param ap - * DOCUMENT ME! + * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) { + this(ap, seq, links, null); + } + + /** + * + * @param ap + * @param seq + * @param links + * @param groupLinks + */ + public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, + Vector groupLinks) + { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to // edit or annotate a particular residue. Therefore display the residue menu @@ -378,10 +396,15 @@ public class PopupMenu extends JPopupMenu { conservationMenuItem.setSelected(true); } - + displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); showColourText.setSelected(sg.getColourText()); showBoxes.setSelected(sg.getDisplayBoxes()); + // add any groupURLs to the groupURL submenu and make it visible + if (groupLinks != null && groupLinks.size() > 0) + { + buildGroupURLMenu(sg, groupLinks); + } } else { @@ -402,8 +425,9 @@ public class PopupMenu extends JPopupMenu if (links != null && links.size() > 0) { - JMenu linkMenu = new JMenu("Link"); + JMenu linkMenu = new JMenu("Link"); + Vector linkset = new Vector(); for (int i = 0; i < links.size(); i++) { String link = links.elementAt(i).toString(); @@ -434,7 +458,7 @@ public class PopupMenu extends JPopupMenu // collect id string too String id = seq.getName(); String descr = seq.getDescription(); - if (descr!=null && descr.length()<1) + if (descr != null && descr.length() < 1) { descr = null; } @@ -456,7 +480,12 @@ public class PopupMenu extends JPopupMenu { for (int u = 0; u < urls.length; u += 2) { - addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) + { + linkset.addElement(urls[u] + "|" + urls[u + 1]); + addshowLink(linkMenu, label + "|" + urls[u], + urls[u + 1]); + } } } } @@ -469,29 +498,41 @@ public class PopupMenu extends JPopupMenu { for (int u = 0; u < urls.length; u += 2) { - addshowLink(linkMenu, label, urls[u + 1]); + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) + { + linkset.addElement(urls[u] + "|" + urls[u + 1]); + addshowLink(linkMenu, label, urls[u + 1]); + } + } + } + } + // Create urls from description but only for URL links which are regex + // links + if (descr != null && urlLink.getRegexReplace() != null) + { + // create link for this URL from description where regex matches + String[] urls = urlLink.makeUrls(descr, true); + if (urls != null) + { + for (int u = 0; u < urls.length; u += 2) + { + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) + { + linkset.addElement(urls[u] + "|" + urls[u + 1]); + addshowLink(linkMenu, label, urls[u + 1]); + } } } } - // hard-disable construction of URLs from regexes that match the description - // TODO: introduce a Cache preferences option to dis/en/able URl generation from description -// if (descr != null) -// { -// // create link for this URL from description where regex matches -// String[] urls = urlLink.makeUrls(descr, false); -// if (urls != null) -// { -// for (int u = 0; u < urls.length; u += 2) -// { -// addshowLink(linkMenu, label, urls[u + 1]); -// } -// } -// } } else { - // Add a non-dynamic link - addshowLink(linkMenu, label, urlLink.getUrl_prefix()); + if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) + { + linkset.addElement(label + "|" + urlLink.getUrl_prefix()); + // Add a non-dynamic link + addshowLink(linkMenu, label, urlLink.getUrl_prefix()); + } } } if (sequence != null) @@ -505,14 +546,161 @@ public class PopupMenu extends JPopupMenu } } + private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) + { + + // TODO: usability: thread off the generation of group url content so root + // menu appears asap + // sequence only URLs + // ID/regex match URLs + 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. + SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); + String[][] idandseqs = GroupUrlLink.formStrings(seqs); + Hashtable commonDbrefs = new Hashtable(); + for (int sq = 0; sq < seqs.length; sq++) + { + + int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq] + .findPosition(sg.getEndRes()); + // just collect ids from dataset sequence + // 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(); + } + DBRefEntry[] dbr = sqi.getDBRef(); + if (dbr != null && dbr.length > 0) + { + for (int d = 0; d < dbr.length; d++) + { + String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); + Object[] sarray = (Object[]) commonDbrefs.get(src); + if (sarray == null) + { + sarray = new Object[2]; + sarray[0] = new int[] + { 0 }; + sarray[1] = new String[seqs.length]; + + 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]++; + } + } + } + } + } + // 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 < groupLinks.size(); i++) + { + String link = groupLinks.elementAt(i).toString(); + 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(); + boolean usingNames = false; + // Now see which parts of the group apply for this URL + String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget()); + Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase()); + String[] seqstr, ids; // input to makeUrl + if (idset != null) + { + 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++) + { + if (allids[sq] != null) + { + ids[idcount] = allids[sq]; + seqstr[idcount++] = idandseqs[1][sq]; + } + } + } + else + { + // just use the id/seq set + seqstr = idandseqs[1]; + ids = idandseqs[0]; + usingNames = true; + } + // and try and make the groupURL! + + Object[] urlset = null; + try + { + urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview" + + System.currentTimeMillis(), false); + } catch (UrlStringTooLongException e) + { + } + if (urlset != null) + { + int type = urlLink.getGroupURLType() & 3; + // 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) + ")") : ""), + urlLink, urlset); + addMenu = true; + } + } + if (addMenu) + { + groupLinksMenu = new JMenu("Group Links"); + for (int m = 0; m < linkMenus.length; m++) + { + if (linkMenus[m] != null + && linkMenus[m].getMenuComponentCount() > 0) + { + groupLinksMenu.add(linkMenus[m]); + } + } + + groupMenu.add(groupLinksMenu); + } + } + /** * add a show URL menu item to the given linkMenu * * @param linkMenu - * @param label - - * menu label string - * @param url - - * url to open + * @param label + * - menu label string + * @param url + * - url to open */ private void addshowLink(JMenu linkMenu, String label, final String url) { @@ -538,10 +726,59 @@ public class PopupMenu extends JPopupMenu } /** + * add a late bound groupURL item to the given linkMenu + * + * @param linkMenu + * @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, + final GroupUrlLink urlgenerator, final Object[] urlstub) + { + JMenuItem item = new JMenuItem(label); + item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix() + + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO: + // put + // in + // info + // about + // what + // is + // being + // sent. + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + try + { + showLink(urlgenerator.constructFrom(urlstub)); + } catch (UrlStringTooLongException e) + { + } + } + + }).start(); + } + }); + + linkMenu.add(item); + } + + /** * DOCUMENT ME! * * @throws Exception - * DOCUMENT ME! + * DOCUMENT ME! */ private void jbInit() throws Exception { @@ -617,6 +854,15 @@ public class PopupMenu extends JPopupMenu showColourText_actionPerformed(); } }); + displayNonconserved.setText("Show Nonconserved"); + displayNonconserved.setState(true); + displayNonconserved.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showNonconserved_actionPerformed(); + } + }); editMenu.setText("Edit"); cut.setText("Cut"); cut.addActionListener(new ActionListener() @@ -782,6 +1028,7 @@ public class PopupMenu extends JPopupMenu jMenu1.add(showText); jMenu1.add(showColourText); jMenu1.add(outline); + jMenu1.add(displayNonconserved); structureMenu.add(pdbMenu); structureMenu.add(viewStructureMenu); // structureMenu.add(colStructureMenu); @@ -902,11 +1149,18 @@ public class PopupMenu extends JPopupMenu }); } + protected void showNonconserved_actionPerformed() + { + getGroup().setShowNonconserved(displayNonconserved.isSelected()); + refresh(); + } + /** - * DOCUMENT ME! + * call to refresh view after settings change */ void refresh() { + ap.updateAnnotation(); ap.paintAlignment(true); PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); @@ -916,7 +1170,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void clustalColour_actionPerformed() { @@ -931,7 +1185,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void zappoColour_actionPerformed() { @@ -943,7 +1197,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void taylorColour_actionPerformed() { @@ -955,7 +1209,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void hydrophobicityColour_actionPerformed() { @@ -967,7 +1221,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void helixColour_actionPerformed() { @@ -979,7 +1233,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void strandColour_actionPerformed() { @@ -991,7 +1245,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void turnColour_actionPerformed() { @@ -1003,7 +1257,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void buriedColour_actionPerformed() { @@ -1015,7 +1269,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void nucleotideMenuItem_actionPerformed() { @@ -1027,7 +1281,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void abovePIDColour_actionPerformed() { @@ -1063,7 +1317,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void userDefinedColour_actionPerformed(ActionEvent e) { @@ -1087,7 +1341,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void PIDColour_actionPerformed() { @@ -1103,7 +1357,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void BLOSUM62Colour_actionPerformed() { @@ -1122,7 +1376,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed() { @@ -1134,7 +1388,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed() { @@ -1190,7 +1444,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void groupName_actionPerformed() { @@ -1198,7 +1452,7 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), sg .getDescription(), " Group Name ", "Group Description ", - "Edit Group Name/Description"); + "Edit Group Name/Description", ap.alignFrame); if (!dialog.accept) { @@ -1207,12 +1461,13 @@ public class PopupMenu extends JPopupMenu sg.setName(dialog.getName()); sg.setDescription(dialog.getDescription()); + refresh(); } /** - * DOCUMENT ME! + * Get selection group - adding it to the alignment if necessary. * - * @return DOCUMENT ME! + * @return sequence group to operate on */ SequenceGroup getGroup() { @@ -1230,13 +1485,13 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ void sequenceName_actionPerformed() { EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence .getDescription(), " Sequence Name ", - "Sequence Description ", "Edit Sequence Name/Description"); + "Sequence Description ", "Edit Sequence Name/Description", ap.alignFrame); if (!dialog.accept) { @@ -1268,7 +1523,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ void unGroupMenuItem_actionPerformed() { @@ -1282,7 +1537,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void outline_actionPerformed() { @@ -1302,7 +1557,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showBoxes_actionPerformed() { @@ -1314,7 +1569,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showText_actionPerformed() { @@ -1326,7 +1581,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showColourText_actionPerformed() { @@ -1383,6 +1638,8 @@ public class PopupMenu extends JPopupMenu } ap.av.hideSequence(hseqs); + // refresh(); TODO: ? needed ? + ap.av.sendSelection(); } public void copy_actionPerformed() @@ -1446,17 +1703,19 @@ public class PopupMenu extends JPopupMenu String[] omitHidden = null; System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens - // or we simply trust the user wants - // wysiwig behaviour + // or we simply trust the user wants + // wysiwig behaviour SequenceGroup sg = ap.av.getSelectionGroup(); ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); omitHidden = ap.av.getViewAsString(true); Alignment oal = new Alignment(ap.av.getSequenceSelection()); AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation(); - for (int i = 0; i < nala.length; i++) - { - AlignmentAnnotation na = nala[i]; - oal.addAnnotation(na); + if (nala!=null) { + for (int i = 0; i < nala.length; i++) + { + AlignmentAnnotation na = nala[i]; + oal.addAnnotation(na); + } } cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), oal, omitHidden, csel, sg)); @@ -1553,24 +1812,32 @@ public class PopupMenu extends JPopupMenu return; } - int gSize = sg.getSize(); - SequenceI[] seqs = new SequenceI[gSize]; - SequenceFeature[] features = new SequenceFeature[gSize]; + int rsize = 0, gSize = sg.getSize(); + SequenceI[] rseqs, seqs = new SequenceI[gSize]; + SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; for (int i = 0; i < gSize; i++) { - seqs[i] = sg.getSequenceAt(i).getDatasetSequence(); int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); - features[i] = new SequenceFeature(null, null, null, start, end, - "Jalview"); + if (start <= end) + { + seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); + features[rsize] = new SequenceFeature(null, null, null, start, end, + "Jalview"); + rsize++; + } } - + rseqs = new SequenceI[rsize]; + tfeatures = new SequenceFeature[rsize]; + System.arraycopy(seqs, 0, rseqs, 0, rsize); + System.arraycopy(features, 0, tfeatures, 0, rsize); + features = tfeatures; + seqs = rseqs; if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { - ap.alignFrame.showSeqFeatures.setSelected(true); - ap.av.setShowSequenceFeatures(true); + ap.alignFrame.setShowSeqFeatures(true); ap.highlightSearchResults(null); } } @@ -1615,7 +1882,7 @@ public class PopupMenu extends JPopupMenu EditNameDialog dialog = new EditNameDialog(sequence .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), - null, "Edit Sequence ", null, "Edit Sequence"); + null, "Edit Sequence ", null, "Edit Sequence", ap.alignFrame); if (dialog.accept) {