X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=da95ae0bbb2f6c54365be56f85bd1ec689259c16;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=3aa08aa07ba64c9985dd52196b41e10d72ef8ca3;hpb=d442a525b14f6dc79da8054226ca593a0aee315b;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java old mode 100755 new mode 100644 index 3aa08aa..da95ae0 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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. - * - * 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 - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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 . */ package jalview.gui; @@ -22,6 +21,7 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import MCview.*; @@ -30,79 +30,142 @@ 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 +public class PopupMenu extends JPopupMenu { JMenu groupMenu = new JMenu(); + JMenuItem groupName = new JMenuItem(); + protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem hydrophobicityColour = new - JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); + protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + AlignmentPanel ap; + JMenu sequenceMenu = new JMenu(); + JMenuItem sequenceName = new JMenuItem(); + Sequence sequence; + JMenuItem unGroupMenuItem = new JMenuItem(); + JMenuItem outline = new JMenuItem(); + JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); + JMenu colourMenu = new JMenu(); + JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); + JCheckBoxMenuItem showText = new JCheckBoxMenuItem(); + JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); + + JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem(); + JMenu editMenu = new JMenu(); + JMenuItem cut = new JMenuItem(); + JMenuItem copy = new JMenuItem(); + JMenuItem upperCase = new JMenuItem(); + JMenuItem lowerCase = new JMenuItem(); + JMenuItem toggle = new JMenuItem(); + JMenu pdbMenu = new JMenu(); + JMenuItem pdbFromFile = new JMenuItem(); + JMenuItem enterPDB = new JMenuItem(); + JMenuItem discoverPDB = new JMenuItem(); + JMenu outputMenu = new JMenu(); + JMenuItem sequenceFeature = new JMenuItem(); + JMenuItem textColour = new JMenuItem(); + JMenu jMenu1 = new JMenu(); + JMenu structureMenu = new JMenu(); + JMenu viewStructureMenu = new JMenu(); - // JMenu colStructureMenu = new JMenu(); + + // JMenu colStructureMenu = new JMenu(); JMenuItem editSequence = new JMenuItem(); - // JMenuItem annotationMenuItem = new JMenuItem(); + + // JMenuItem annotationMenuItem = new JMenuItem(); + + JMenu groupLinksMenu; /** * Creates a new PopupMenu object. - * - * @param ap DOCUMENT ME! - * @param seq DOCUMENT ME! + * + * @param ap + * DOCUMENT ME! + * @param seq + * 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 // // If from the IDPanel, we must display the sequence menu - ////////////////////////////////////////////////////////// + // //////////////////////////////////////////////////////// this.ap = ap; sequence = seq; @@ -123,8 +186,8 @@ public class PopupMenu for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { - JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[ - i]); + JMenuItem item = new JMenuItem( + jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); item.addActionListener(new java.awt.event.ActionListener() { @@ -140,22 +203,21 @@ public class PopupMenu try { jbInit(); - } - catch (Exception e) + } catch (Exception e) { e.printStackTrace(); } + JMenuItem menuItem; if (seq != null) { sequenceMenu.setText(sequence.getName()); - JMenuItem menuItem; if (seq.getDatasetSequence().getPDBId() != null - && seq.getDatasetSequence().getPDBId().size()>0) + && seq.getDatasetSequence().getPDBId().size() > 0) { - java.util.Enumeration e = seq.getDatasetSequence().getPDBId(). - elements(); + java.util.Enumeration e = seq.getDatasetSequence().getPDBId() + .elements(); while (e.hasMoreElements()) { @@ -167,51 +229,27 @@ public class PopupMenu { 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 1) + && ap.av.getSelectionGroup().getSize() > 1) { menuItem = new JMenuItem("Represent Group with " + seq.getName()); menuItem.addActionListener(new java.awt.event.ActionListener() @@ -242,8 +280,8 @@ public class PopupMenu { final int index = ap.av.alignment.findIndex(seq); - if (ap.av.adjustForHiddenSeqs(index) - - ap.av.adjustForHiddenSeqs(index - 1) > 1) + if (ap.av.adjustForHiddenSeqs(index) + - ap.av.adjustForHiddenSeqs(index - 1) > 1) { menuItem = new JMenuItem("Reveal Sequences"); menuItem.addActionListener(new ActionListener() @@ -259,7 +297,11 @@ public class PopupMenu }); add(menuItem); } - + } + } + // for the case when no sequences are even visible + if (ap.av.hasHiddenRows) { + { menuItem = new JMenuItem("Reveal All"); menuItem.addActionListener(new ActionListener() { @@ -280,9 +322,10 @@ public class PopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg != null) + if (sg != null&& sg.getSize()>0) { - groupName.setText(sg.getName()); + groupName.setText("Name: "+sg.getName()); + groupName.setText("Edit name and description of current group."); if (sg.cs instanceof ZappoColourScheme) { @@ -337,10 +380,53 @@ public class PopupMenu { 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 { @@ -359,20 +445,25 @@ public class PopupMenu structureMenu.setVisible(false); } - if (links != null && links.size() > 0) + if (seq !=null && 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(); UrlLink urlLink = null; - try { + try + { urlLink = new UrlLink(link); - } catch (Exception foo) { - jalview.bin.Cache.log.error("Exception for URLLink '"+link+"'",foo); + } catch (Exception foo) + { + jalview.bin.Cache.log.error("Exception for URLLink '" + link + + "'", foo); continue; - }; + } + ; if (!urlLink.isValid()) { jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); @@ -383,45 +474,87 @@ public class PopupMenu { // 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(); - if (dbr!=null) + String descr = seq.getDescription(); + if (descr != null && descr.length() < 1) { - for (int r=0;r 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) { JMenuItem item = new JMenuItem(label); - item.setToolTipText("open URL: "+url); + item.setToolTipText("open URL: " + url); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - new Thread(new Runnable() { + new Thread(new Runnable() + { public void run() { showLink(url); } - + }).start(); } }); - linkMenu.add(item); + linkMenu.add(item); + } + + /** + * 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! + * + * @throws Exception + * DOCUMENT ME! */ - private void jbInit() - throws Exception + private void jbInit() throws Exception { groupMenu.setText("Group"); groupMenu.setText("Selection"); @@ -543,6 +876,15 @@ public class PopupMenu 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() @@ -629,7 +971,7 @@ public class PopupMenu jMenu1.setText("Group"); structureMenu.setText("Structure"); viewStructureMenu.setText("View Structure"); - // colStructureMenu.setText("Colour By Structure"); + // colStructureMenu.setText("Colour By Structure"); editSequence.setText("Edit Sequence..."); editSequence.addActionListener(new ActionListener() { @@ -638,14 +980,12 @@ public class PopupMenu editSequence_actionPerformed(actionEvent); } }); - /* annotationMenuItem.setText("By Annotation"); - annotationMenuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent actionEvent) - { - annotationMenuItem_actionPerformed(actionEvent); - } - });*/ + /* + * annotationMenuItem.setText("By Annotation"); + * annotationMenuItem.addActionListener(new ActionListener() { public void + * actionPerformed(ActionEvent actionEvent) { + * annotationMenuItem_actionPerformed(actionEvent); } }); + */ add(groupMenu); @@ -673,13 +1013,12 @@ public class PopupMenu if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours. - getUserColourSchemes().keys(); + java.util.Enumeration userColours = jalview.gui.UserDefinedColours + .getUserColourSchemes().keys(); while (userColours.hasMoreElements()) { - JMenuItem item = new JMenuItem(userColours. - nextElement().toString()); + JMenuItem item = new JMenuItem(userColours.nextElement().toString()); item.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) @@ -694,7 +1033,7 @@ public class PopupMenu colourMenu.addSeparator(); colourMenu.add(abovePIDColour); colourMenu.add(conservationMenuItem); - //colourMenu.add(annotationMenuItem); + // colourMenu.add(annotationMenuItem); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); @@ -711,9 +1050,10 @@ public class PopupMenu jMenu1.add(showText); jMenu1.add(showColourText); jMenu1.add(outline); + jMenu1.add(displayNonconserved); structureMenu.add(pdbMenu); structureMenu.add(viewStructureMenu); - // structureMenu.add(colStructureMenu); + // structureMenu.add(colStructureMenu); noColourmenuItem.setText("None"); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -748,13 +1088,14 @@ public class PopupMenu } }); hydrophobicityColour.setText("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(); - } - }); + hydrophobicityColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(); + } + }); helixColour.setText("Helix propensity"); helixColour.addActionListener(new java.awt.event.ActionListener() { @@ -820,20 +1161,28 @@ public class PopupMenu } }); conservationMenuItem.setText("Conservation"); - conservationMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); - } - }); + conservationMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); + } + }); + } + + 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()); @@ -841,21 +1190,24 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * 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.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); refresh(); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void zappoColour_actionPerformed() { @@ -865,8 +1217,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void taylorColour_actionPerformed() { @@ -876,8 +1229,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void hydrophobicityColour_actionPerformed() { @@ -887,8 +1241,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void helixColour_actionPerformed() { @@ -898,8 +1253,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void strandColour_actionPerformed() { @@ -909,8 +1265,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void turnColour_actionPerformed() { @@ -920,8 +1277,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void buriedColour_actionPerformed() { @@ -931,8 +1289,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void nucleotideMenuItem_actionPerformed() { @@ -942,8 +1301,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void abovePIDColour_actionPerformed() { @@ -956,17 +1316,18 @@ public class PopupMenu if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, - getGroup().getName()); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + .getName()); sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); } - else // remove PIDColouring + else + // remove PIDColouring { sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); } @@ -976,8 +1337,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void userDefinedColour_actionPerformed(ActionEvent e) { @@ -989,8 +1351,8 @@ public class PopupMenu } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours. - getUserColourSchemes().get(e.getActionCommand()); + UserColourScheme udc = (UserColourScheme) UserDefinedColours + .getUserColourSchemes().get(e.getActionCommand()); sg.cs = udc; } @@ -999,24 +1361,25 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * 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.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void BLOSUM62Colour_actionPerformed() { @@ -1024,18 +1387,18 @@ public class PopupMenu 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.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed() { @@ -1045,8 +1408,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed() { @@ -1059,11 +1423,9 @@ public class PopupMenu 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.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); c.verdict(false, ap.av.ConsPercGaps); @@ -1073,7 +1435,8 @@ public class PopupMenu SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } - else // remove ConservationColouring + else + // remove ConservationColouring { sg.cs.setConservation(null); } @@ -1090,7 +1453,8 @@ public class PopupMenu } AnnotationColourGradient acg = new AnnotationColourGradient( - sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); + sequence.getAnnotation()[0], null, + AnnotationColourGradient.NO_THRESHOLD); acg.predefinedColours = true; sg.cs = acg; @@ -1100,18 +1464,18 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * 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"); + sg.getDescription(), " Group Name ", + "Group Description ", "Edit Group Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -1120,12 +1484,13 @@ public class PopupMenu sg.setName(dialog.getName()); sg.setDescription(dialog.getDescription()); + refresh(); } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Get selection group - adding it to the alignment if necessary. + * + * @return sequence group to operate on */ SequenceGroup getGroup() { @@ -1141,16 +1506,16 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ void sequenceName_actionPerformed() { EditNameDialog dialog = new EditNameDialog(sequence.getName(), - sequence.getDescription(), - " Sequence Name ", - "Sequence Description ", - "Edit Sequence Name/Description"); + sequence.getDescription(), " Sequence Name ", + "Sequence Description ", "Edit Sequence Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -1162,9 +1527,9 @@ public class PopupMenu if (dialog.getName().indexOf(" ") > -1) { JOptionPane.showMessageDialog(ap, - "Spaces have been converted to \"_\"", - "No spaces allowed in Sequence Name", - JOptionPane.WARNING_MESSAGE); + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); @@ -1173,15 +1538,16 @@ public class PopupMenu sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ void unGroupMenuItem_actionPerformed() { @@ -1193,14 +1559,15 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); Color col = JColorChooser.showDialog(this, "Select Outline Colour", - Color.BLUE); + Color.BLUE); if (col != null) { @@ -1212,8 +1579,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void showBoxes_actionPerformed() { @@ -1223,8 +1591,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void showText_actionPerformed() { @@ -1234,8 +1603,9 @@ public class PopupMenu /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void showColourText_actionPerformed() { @@ -1248,15 +1618,14 @@ public class PopupMenu try { jalview.util.BrowserLauncher.openURL(url); - } - catch (Exception ex) + } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Unixers: Couldn't find default web browser." - + - "\nAdd the full path to your browser in Preferences.", - "Web browser not found", - JOptionPane.WARNING_MESSAGE); + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + "Unixers: Couldn't find default web browser." + + "\nAdd the full path to your browser in Preferences.", + "Web browser not found", JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -1268,7 +1637,7 @@ public class PopupMenu if (sg == null || sg.getSize() < 1) { ap.av.hideSequence(new SequenceI[] - {sequence}); + { sequence }); return; } @@ -1293,6 +1662,8 @@ public class PopupMenu } ap.av.hideSequence(hseqs); + // refresh(); TODO: ? needed ? + ap.av.sendSelection(); } public void copy_actionPerformed() @@ -1312,8 +1683,8 @@ public class PopupMenu if (sg != null) { - int[][] startEnd = ap.av.getVisibleRegionBoundaries( - sg.getStartRes(), sg.getEndRes() + 1); + int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), + sg.getEndRes() + 1); String description; int caseChange; @@ -1334,15 +1705,14 @@ public class PopupMenu 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.hiddenRepSequences), startEnd, + caseChange); ap.alignFrame.addHistoryItem(caseCommand); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); } } @@ -1352,77 +1722,46 @@ public class PopupMenu CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, - "Alignment output - " + e.getActionCommand(), 600, - 500); + "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 + System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens + // 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 0) { PDBEntry entry = new PDBEntry(); entry.setId(id.toUpperCase()); - sequence.getDatasetSequence() - .addPDBId(entry); + sequence.getDatasetSequence().addPDBId(entry); } } public void discoverPDB_actionPerformed() { - SequenceI[] sequences = - ap.av.selectionGroup == null ? - new Sequence[]{sequence} - : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment); - new jalview.ws.DBRefFetcher(sequences, - ap.alignFrame).fetchDBRefs(false); + final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[] + { sequence } + : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); + Thread discpdb = new Thread(new Runnable() + { + public void run() + { + + new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) + .fetchDBRefs(false); + } + + }); + discpdb.start(); } public void sequenceFeature_actionPerformed() @@ -1460,23 +1806,32 @@ public class PopupMenu 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++; + } } - - if (ap.seqPanel.seqCanvas.getFeatureRenderer() - .amendFeatures(seqs, features, true, ap)) - { - ap.alignFrame.showSeqFeatures.setSelected(true); - ap.av.setShowSequenceFeatures(true); + 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.setShowSeqFeatures(true); ap.highlightSearchResults(null); } } @@ -1492,57 +1847,51 @@ public class PopupMenu 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); + AlignmentAnnotation an = new AlignmentAnnotation("Structure", + "Coloured by " + pdbid, anots); ap.av.alignment.addAnnotation(an); an.createSequenceMapping(sequence, 0, true); - //an.adjustForAlignment(); - ap.av.alignment.setAnnotationIndex(an,0); + // an.adjustForAlignment(); + ap.av.alignment.setAnnotationIndex(an, 0); ap.adjustAnnotationHeight(); sequence.addAlignmentAnnotation(an); - } + } public void editSequence_actionPerformed(ActionEvent actionEvent) { - SequenceGroup sg = ap.av.getSelectionGroup(); + SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg!=null) - { - if (sequence == null) - sequence = (Sequence) sg.getSequenceAt(0); + if (sg != null) + { + 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 - ); + 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.alignFrame.addHistoryItem(editCommand); + ap.alignFrame.addHistoryItem(editCommand); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - } + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); } + } } - }