X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=7e8c5730e5f4ace5f284ccc15e9f24de35a60dd9;hb=2f4f1d8fb6878271b64f327bc58c895f458137af;hp=604f4ab17d5ae0294bffdd86ad23a7613b29cfac;hpb=94f7397e4369deba3ec5743f9d28c14566fdfad2;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java old mode 100755 new mode 100644 index 604f4ab..7e8c573 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,20 +1,20 @@ /* - * 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 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -22,21 +22,23 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; -import MCview.*; import jalview.analysis.*; 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; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.118 $ */ public class PopupMenu extends JPopupMenu { @@ -68,6 +70,11 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); @@ -78,8 +85,12 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; + JMenuItem sequenceDetails = new JMenuItem(); + + JMenuItem sequenceSelDetails = new JMenuItem(); + SequenceI sequence; + JMenuItem createGroupMenuItem = new JMenuItem(); JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); @@ -94,6 +105,8 @@ public class PopupMenu extends JPopupMenu JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); + JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem(); + JMenu editMenu = new JMenu(); JMenuItem cut = new JMenuItem(); @@ -131,16 +144,31 @@ 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, final SequenceI 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 @@ -164,6 +192,8 @@ public class PopupMenu extends JPopupMenu colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { @@ -189,11 +219,11 @@ public class PopupMenu extends JPopupMenu e.printStackTrace(); } + JMenuItem menuItem; if (seq != null) { sequenceMenu.setText(sequence.getName()); - JMenuItem menuItem; if (seq.getDatasetSequence().getPDBId() != null && seq.getDatasetSequence().getPDBId().size() > 0) { @@ -210,33 +240,13 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - Vector seqs = new Vector(); - for (int i = 0; i < ap.av.alignment.getHeight(); i++) - { - Vector pdbs = ap.av.alignment.getSequenceAt(i) - .getDatasetSequence().getPDBId(); - if (pdbs == null) - continue; - - for (int p = 0; p < pdbs.size(); p++) - { - PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); - if (p1.getId().equals(pdb.getId())) - { - if (!seqs.contains(ap.av.alignment.getSequenceAt(i))) - seqs.addElement(ap.av.alignment.getSequenceAt(i)); - - continue; - } - } - } - - SequenceI[] seqs2 = new SequenceI[seqs.size()]; - seqs.toArray(seqs2); - - new AppJmol(pdb, seqs2, null, ap); + // TODO re JAL-860: optionally open dialog or provide a menu entry + // allowing user to open just one structure per sequence + new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] + { pdb })[0], null, ap); // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); } + }); viewStructureMenu.add(menuItem); @@ -251,10 +261,68 @@ public class PopupMenu extends JPopupMenu } else { - structureMenu.remove(viewStructureMenu); + if (ap.av.getAlignment().isNucleotide() == false) + { + structureMenu.remove(viewStructureMenu); + } // structureMenu.remove(colStructureMenu); } + if (ap.av.getAlignment().isNucleotide() == true) + { + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + for (int i = 0; i < aa.length; i++) + { + if (aa[i].getRNAStruc() != null) + { + final String rnastruc = aa[i].getRNAStruc(); + final String structureLine = aa[i].label; + menuItem = new JMenuItem(); + menuItem.setText("2D RNA " + structureLine); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new AppVarna(structureLine, seq, seq.getSequenceAsString(), + rnastruc, seq.getName(), ap); + } + }); + viewStructureMenu.add(menuItem); + } + } + + // SequenceFeatures[] test = seq.getSequenceFeatures(); + + if (seq.getAnnotation() != null) + { + AlignmentAnnotation seqAnno[] = seq.getAnnotation(); + for (int i = 0; i < seqAnno.length; i++) + { + if (seqAnno[i].getRNAStruc() != null) + { + final String rnastruc = seqAnno[i].getRNAStruc(); + + // TODO: make rnastrucF a bit more nice + menuItem = new JMenuItem(); + menuItem.setText("2D RNA - " + seq.getName()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: VARNA does'nt print gaps in the sequence + new AppVarna(seq.getName() + " structure", seq, seq + .getSequenceAsString(), rnastruc, seq.getName(), + ap); + } + }); + viewStructureMenu.add(menuItem); + } + } + } + + } + menuItem = new JMenuItem("Hide Sequences"); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -279,9 +347,9 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows) + if (ap.av.hasHiddenRows()) { - final int index = ap.av.alignment.findIndex(seq); + final int index = ap.av.getAlignment().findIndex(seq); if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) @@ -300,7 +368,12 @@ public class PopupMenu extends JPopupMenu }); add(menuItem); } - + } + } + // for the case when no sequences are even visible + if (ap.av.hasHiddenRows()) + { + { menuItem = new JMenuItem("Reveal All"); menuItem.addActionListener(new ActionListener() { @@ -320,10 +393,12 @@ public class PopupMenu extends JPopupMenu } SequenceGroup sg = ap.av.getSelectionGroup(); + boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false; - if (sg != null) - { - groupName.setText(sg.getName()); + if (sg != null && sg.getSize() > 0) + { + groupName.setText("Name: " + sg.getName()); + groupName.setText("Edit name and description of current group."); if (sg.cs instanceof ZappoColourScheme) { @@ -369,6 +444,14 @@ public class PopupMenu extends JPopupMenu { clustalColour.setSelected(true); } + else if (sg.cs instanceof PurinePyrimidineColourScheme) + { + purinePyrimidineColour.setSelected(true); + } + /* + * else if (sg.cs instanceof CovariationColourScheme) { + * covariationColour.setSelected(true); } + */ else { noColourmenuItem.setSelected(true); @@ -378,10 +461,60 @@ 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); + } + // Add a 'show all structures' for the current selection + Hashtable pdbe = new Hashtable(); + SequenceI sqass = null; + for (SequenceI sq : ap.av.getSequenceSelection()) + { + Vector pes = (Vector) sq.getDatasetSequence() + .getPDBId(); + if (pes != null) + { + for (PDBEntry pe : pes) + { + pdbe.put(pe.getId(), pe); + if (sqass == null) + { + sqass = sq; + } + } + } + } + if (pdbe.size() > 0) + { + final PDBEntry[] pe = pdbe.values().toArray( + new PDBEntry[pdbe.size()]); + final JMenuItem gpdbview; + if (pdbe.size() == 1) + { + structureMenu.add(gpdbview = new JMenuItem("View structure for " + + sqass.getDisplayId(false))); + } + else + { + structureMenu.add(gpdbview = new JMenuItem("View all " + + pdbe.size() + " structures.")); + } + gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment."); + gpdbview.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new AppJmol(ap, pe, ap.av.collateForPDB(pe)); + } + }); + } } else { @@ -389,9 +522,15 @@ public class PopupMenu extends JPopupMenu editMenu.setVisible(false); } - if (!ap.av.alignment.getGroups().contains(sg)) + if (!isDefinedGroup) { + createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); + jMenu1.setText("Edit New Group"); + } else { + createGroupMenuItem.setVisible(false); + unGroupMenuItem.setVisible(true); + jMenu1.setText("Edit Group"); } if (seq == null) @@ -402,8 +541,9 @@ 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(); @@ -424,17 +564,17 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (urlLink.isDynamic()) + if (seq != null && urlLink.isDynamic()) { // collect matching db-refs - DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq - .getDBRef(), new String[] - { urlLink.getTarget() }); + DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( + seq.getDBRef(), new String[] + { urlLink.getTarget() }); // 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 +596,12 @@ 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]); + } } } } @@ -469,12 +614,17 @@ 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 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); @@ -482,15 +632,23 @@ 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]); + } } } } } 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) @@ -504,14 +662,161 @@ 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) { @@ -537,10 +842,59 @@ 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 { @@ -563,6 +917,23 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); + sequenceDetails.setText("Sequence Details ..."); + sequenceDetails.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceDetails_actionPerformed(); + } + }); + sequenceSelDetails.setText("Sequence Details ..."); + sequenceSelDetails + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); PIDColour.setFocusPainted(false); unGroupMenuItem.setText("Remove Group"); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() @@ -572,6 +943,14 @@ public class PopupMenu extends JPopupMenu unGroupMenuItem_actionPerformed(); } }); + createGroupMenuItem.setText("Create Group"); + createGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + createGroupMenuItem_actionPerformed(); + } + }); outline.setText("Border colour"); outline.addActionListener(new java.awt.event.ActionListener() @@ -616,6 +995,15 @@ 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() @@ -711,22 +1099,25 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); + /* * annotationMenuItem.setText("By Annotation"); * annotationMenuItem.addActionListener(new ActionListener() { public void * actionPerformed(ActionEvent actionEvent) { * annotationMenuItem_actionPerformed(actionEvent); } }); */ - + groupMenu.add(sequenceSelDetails); add(groupMenu); - add(sequenceMenu); this.add(structureMenu); groupMenu.add(editMenu); groupMenu.add(outputMenu); groupMenu.add(sequenceFeature); + groupMenu.add(createGroupMenuItem); + groupMenu.add(unGroupMenuItem); groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); + sequenceMenu.add(sequenceDetails); colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); @@ -740,6 +1131,11 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); + if (ap.getAlignment().isNucleotide()) + { + colourMenu.add(purinePyrimidineColour); + } + // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -775,12 +1171,12 @@ public class PopupMenu extends JPopupMenu pdbMenu.add(enterPDB); pdbMenu.add(discoverPDB); jMenu1.add(groupName); - jMenu1.add(unGroupMenuItem); jMenu1.add(colourMenu); jMenu1.add(showBoxes); jMenu1.add(showText); jMenu1.add(showColourText); jMenu1.add(outline); + jMenu1.add(displayNonconserved); structureMenu.add(pdbMenu); structureMenu.add(viewStructureMenu); // structureMenu.add(colStructureMenu); @@ -890,6 +1286,21 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); + purinePyrimidineColour.setText("Purine/Pyrimidine"); + purinePyrimidineColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + /* + * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * covariationColour_actionPerformed(); } }); + */ + conservationMenuItem.setText("Conservation"); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() @@ -901,11 +1312,56 @@ public class PopupMenu extends JPopupMenu }); } + protected void sequenceSelectionDetails_actionPerformed() + { + createSequenceDetailsReport(ap.av.getSequenceSelection()); + } + + protected void sequenceDetails_actionPerformed() + { + createSequenceDetailsReport(new SequenceI[] + { sequence }); + } + + public void createSequenceDetailsReport(SequenceI[] sequences) + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + StringBuffer contents = new StringBuffer(); + for (SequenceI seq : sequences) + { + contents.append("

Annotation for " + seq.getDisplayId(true) + + "

"); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : null); + contents.append("

"); + } + cap.setText("" + contents.toString() + ""); + + Desktop.instance.addInternalFrame(cap, "Sequence Details for " + + (sequences.length == 1 ? sequences[0].getDisplayId(true) + : "Selection"), 500, 400); + + } + + 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()); @@ -915,14 +1371,12 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg - .getSequences(ap.av.hiddenRepSequences), ap.av.alignment - .getWidth()); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); refresh(); } @@ -930,7 +1384,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void zappoColour_actionPerformed() { @@ -942,7 +1396,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void taylorColour_actionPerformed() { @@ -954,7 +1408,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void hydrophobicityColour_actionPerformed() { @@ -966,7 +1420,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void helixColour_actionPerformed() { @@ -978,7 +1432,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void strandColour_actionPerformed() { @@ -990,7 +1444,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void turnColour_actionPerformed() { @@ -1002,7 +1456,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void buriedColour_actionPerformed() { @@ -1014,7 +1468,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void nucleotideMenuItem_actionPerformed() { @@ -1022,11 +1476,21 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + + /* + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void abovePIDColour_actionPerformed() { @@ -1038,9 +1502,9 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -1062,7 +1526,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void userDefinedColour_actionPerformed(ActionEvent e) { @@ -1086,15 +1550,15 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1102,7 +1566,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void BLOSUM62Colour_actionPerformed() { @@ -1110,9 +1574,9 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1121,7 +1585,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed() { @@ -1133,7 +1597,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed() { @@ -1146,12 +1610,12 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg - .getSequences(ap.av.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1); + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); + c.verdict(false, ap.av.getConsPercGaps()); sg.cs.setConservation(c); @@ -1175,11 +1639,11 @@ public class PopupMenu extends JPopupMenu return; } - AnnotationColourGradient acg = new AnnotationColourGradient(sequence - .getAnnotation()[0], null, + AnnotationColourGradient acg = new AnnotationColourGradient( + sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); - acg.predefinedColours = true; + acg.setPredefinedColours(true); sg.cs = acg; refresh(); @@ -1189,15 +1653,16 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void groupName_actionPerformed() { SequenceGroup sg = getGroup(); - EditNameDialog dialog = new EditNameDialog(sg.getName(), sg - .getDescription(), " Group Name ", "Group Description ", - "Edit Group Name/Description"); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), " Group Name ", + "Group Description ", "Edit Group Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -1206,12 +1671,13 @@ 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() { @@ -1219,7 +1685,7 @@ public class PopupMenu extends JPopupMenu // this method won't add a new group if it already exists if (sg != null) { - ap.av.alignment.addGroup(sg); + ap.av.getAlignment().addGroup(sg); } return sg; @@ -1229,13 +1695,14 @@ 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"); + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), " Sequence Name ", + "Sequence Description ", "Edit Sequence Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -1267,21 +1734,26 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); + ap.av.getAlignment().deleteGroup(sg); ap.av.setSelectionGroup(null); refresh(); } + void createGroupMenuItem_actionPerformed() + { + getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this + refresh(); + } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void outline_actionPerformed() { @@ -1301,7 +1773,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showBoxes_actionPerformed() { @@ -1313,7 +1785,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showText_actionPerformed() { @@ -1325,7 +1797,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showColourText_actionPerformed() { @@ -1382,6 +1854,7 @@ public class PopupMenu extends JPopupMenu } ap.av.hideSequence(hseqs); + // refresh(); TODO: ? needed ? ap.av.sendSelection(); } @@ -1424,9 +1897,9 @@ public class PopupMenu extends JPopupMenu caseChange = ChangeCaseCommand.TO_LOWER; } - ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg - .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, - caseChange); + ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1440,23 +1913,27 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, "Alignment output - " - + e.getActionCommand(), 600, 500); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, 500); 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[] nala = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (nala != null) { - AlignmentAnnotation na = nala[i]; - oal.addAnnotation(na); + 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)); @@ -1468,47 +1945,19 @@ public class PopupMenu extends JPopupMenu jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Select a PDB file"); - chooser.setToolTipText("Load a PDB file"); + chooser.setDialogTitle("Select a PDB file for " + + sequence.getDisplayId(false)); + chooser.setToolTipText("Load a PDB file and associate it with sequence '" + + sequence.getDisplayId(false) + "'"); int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { - PDBEntry entry = new PDBEntry(); String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - try - { - MCview.PDBfile pdbfile = new MCview.PDBfile(choice, - jalview.io.AppletFormatAdapter.FILE); - - if (pdbfile.id == null) - { - String reply = JOptionPane - .showInternalInputDialog( - Desktop.desktop, - "Couldn't find a PDB id in the file supplied." - + "Please enter an Id to identify this structure.", - "No PDB Id in File", JOptionPane.QUESTION_MESSAGE); - if (reply == null) - { - return; - } - - entry.setId(reply); - } - else - { - entry.setId(pdbfile.id); - } - } catch (java.io.IOException ex) - { - ex.printStackTrace(); - } - - entry.setFile(choice); - sequence.getDatasetSequence().addPDBId(entry); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, + jalview.io.AppletFormatAdapter.FILE, sequence, true); } } @@ -1529,9 +1978,9 @@ public class PopupMenu extends JPopupMenu public void discoverPDB_actionPerformed() { - final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[] + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] { sequence } - : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); + : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { public void run() @@ -1553,24 +2002,32 @@ 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); } } @@ -1586,17 +2043,16 @@ public class PopupMenu extends JPopupMenu public void colourByStructure(String pdbid) { - Annotation[] anots = jalview.structure.StructureSelectionManager - .getStructureSelectionManager().colourSequenceFromStructure( - sequence, pdbid); + Annotation[] anots = ap.av.getStructureSelectionManager() + .colourSequenceFromStructure(sequence, pdbid); AlignmentAnnotation an = new AlignmentAnnotation("Structure", "Coloured by " + pdbid, anots); - ap.av.alignment.addAnnotation(an); + ap.av.getAlignment().addAnnotation(an); an.createSequenceMapping(sequence, 0, true); // an.adjustForAlignment(); - ap.av.alignment.setAnnotationIndex(an, 0); + ap.av.getAlignment().setAnnotationIndex(an, 0); ap.adjustAnnotationHeight(); @@ -1613,17 +2069,18 @@ public class PopupMenu extends JPopupMenu if (sequence == null) sequence = (Sequence) sg.getSequenceAt(0); - EditNameDialog dialog = new EditNameDialog(sequence - .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), - null, "Edit Sequence ", null, "Edit Sequence"); + EditNameDialog dialog = new EditNameDialog( + sequence.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1), null, "Edit Sequence ", null, + "Edit Sequence", ap.alignFrame); if (dialog.accept) { EditCommand editCommand = new EditCommand("Edit Sequences", EditCommand.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), sg - .getSequencesAsArray(ap.av.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1, ap.av.alignment); + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand);