2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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25 import java.awt.event.*;
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27 import jalview.analysis.*;
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28 import jalview.commands.*;
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29 import jalview.datamodel.*;
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30 import jalview.schemes.*;
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32 public class APopupMenu
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33 extends java.awt.PopupMenu implements ActionListener, ItemListener
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35 Menu groupMenu = new Menu();
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36 MenuItem editGroupName = new MenuItem();
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37 protected MenuItem clustalColour = new MenuItem();
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38 protected MenuItem zappoColour = new MenuItem();
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39 protected MenuItem taylorColour = new MenuItem();
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40 protected MenuItem hydrophobicityColour = new MenuItem();
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41 protected MenuItem helixColour = new MenuItem();
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42 protected MenuItem strandColour = new MenuItem();
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43 protected MenuItem turnColour = new MenuItem();
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44 protected MenuItem buriedColour = new MenuItem();
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45 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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46 protected MenuItem userDefinedColour = new MenuItem();
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47 protected MenuItem PIDColour = new MenuItem();
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48 protected MenuItem BLOSUM62Colour = new MenuItem();
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49 MenuItem noColourmenuItem = new MenuItem();
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50 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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52 final AlignmentPanel ap;
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53 MenuItem unGroupMenuItem = new MenuItem();
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54 MenuItem nucleotideMenuItem = new MenuItem();
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55 Menu colourMenu = new Menu();
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56 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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57 CheckboxMenuItem showText = new CheckboxMenuItem();
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58 CheckboxMenuItem showColourText = new CheckboxMenuItem();
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59 Menu editMenu = new Menu("Edit");
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60 MenuItem copy = new MenuItem("Copy (Jalview Only)");
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61 MenuItem cut = new MenuItem("Cut (Jalview Only)");
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62 MenuItem toUpper = new MenuItem("To Upper Case");
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63 MenuItem toLower = new MenuItem("To Lower Case");
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64 MenuItem toggleCase = new MenuItem("Toggle Case");
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65 Menu outputmenu = new Menu();
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66 Menu seqMenu = new Menu();
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67 MenuItem pdb = new MenuItem();
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68 MenuItem hideSeqs = new MenuItem();
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69 MenuItem repGroup = new MenuItem();
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70 MenuItem sequenceName = new MenuItem("Edit Name/Description");
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71 MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
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74 MenuItem revealAll = new MenuItem();
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75 Menu menu1 = new Menu();
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77 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
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79 ///////////////////////////////////////////////////////////
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80 // If this is activated from the sequence panel, the user may want to
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81 // edit or annotate a particular residue. Therefore display the residue menu
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83 // If from the IDPanel, we must display the sequence menu
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84 //////////////////////////////////////////////////////////
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95 e.printStackTrace();
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98 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
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101 MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.
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102 WRITEABLE_FORMATS[i]);
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104 item.addActionListener(this);
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105 outputmenu.add(item);
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108 SequenceGroup sg = ap.av.getSelectionGroup();
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110 if (sg != null && sg.getSize() > 0)
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112 editGroupName.setLabel(sg.getName());
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113 showText.setState(sg.getDisplayText());
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114 showColourText.setState(sg.getColourText());
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115 showBoxes.setState(sg.getDisplayBoxes());
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116 if (!ap.av.alignment.getGroups().contains(sg))
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118 groupMenu.remove(unGroupMenuItem);
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130 Menu linkMenu = new Menu("Link");
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133 for (int i = 0; i < links.size(); i++)
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135 link = links.elementAt(i).toString();
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136 final String target = link.substring(0, link.indexOf("|"));
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137 item = new MenuItem(target);
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141 if (link.indexOf("$SEQUENCE_ID$") > -1)
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143 String id = seq.getName();
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144 if (id.indexOf("|") > -1)
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146 id = id.substring(id.lastIndexOf("|") + 1);
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149 url = link.substring(link.indexOf("|") + 1,
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150 link.indexOf("$SEQUENCE_ID$"))
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152 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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156 url = link.substring(link.lastIndexOf("|") + 1);
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159 item.addActionListener(new java.awt.event.ActionListener()
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161 public void actionPerformed(ActionEvent e)
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163 ap.alignFrame.showURL(url, target);
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166 linkMenu.add(item);
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170 seqMenu.add(linkMenu);
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179 seqMenu.setLabel(seq.getName());
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180 repGroup.setLabel("Represent Group with " + seq.getName());
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187 if (!ap.av.hasHiddenRows)
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193 public void itemStateChanged(ItemEvent evt)
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195 if (evt.getSource() == abovePIDColour)
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197 abovePIDColour_itemStateChanged();
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199 else if (evt.getSource() == showColourText)
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201 showColourText_itemStateChanged();
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203 else if (evt.getSource() == showText)
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205 showText_itemStateChanged();
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207 else if (evt.getSource() == showBoxes)
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209 showBoxes_itemStateChanged();
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213 public void actionPerformed(ActionEvent evt)
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215 Object source = evt.getSource();
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216 if (source == clustalColour)
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218 clustalColour_actionPerformed();
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220 else if (source == zappoColour)
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222 zappoColour_actionPerformed();
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224 else if (source == taylorColour)
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226 taylorColour_actionPerformed();
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228 else if (source == hydrophobicityColour)
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230 hydrophobicityColour_actionPerformed();
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232 else if (source == helixColour)
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234 helixColour_actionPerformed();
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236 else if (source == strandColour)
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238 strandColour_actionPerformed();
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240 else if (source == turnColour)
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242 turnColour_actionPerformed();
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244 else if (source == buriedColour)
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246 buriedColour_actionPerformed();
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248 else if (source == nucleotideMenuItem)
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250 nucleotideMenuItem_actionPerformed();
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253 else if (source == userDefinedColour)
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255 userDefinedColour_actionPerformed();
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257 else if (source == PIDColour)
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259 PIDColour_actionPerformed();
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261 else if (source == BLOSUM62Colour)
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263 BLOSUM62Colour_actionPerformed();
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265 else if (source == noColourmenuItem)
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267 noColourmenuItem_actionPerformed();
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269 else if (source == conservationMenuItem)
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271 conservationMenuItem_itemStateChanged();
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273 else if (source == unGroupMenuItem)
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275 unGroupMenuItem_actionPerformed();
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278 else if (source == sequenceName)
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282 else if (source == pdb)
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286 else if (source == hideSeqs)
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288 hideSequences(false);
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290 else if (source == repGroup)
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292 hideSequences(true);
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294 else if (source == revealAll)
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296 ap.av.showAllHiddenSeqs();
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299 else if (source == editGroupName)
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301 EditNameDialog dialog = new EditNameDialog(
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302 getGroup().getName(),
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303 getGroup().getDescription(),
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305 "Group Description",
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307 "Edit Group Name / Description",
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313 getGroup().setName(dialog.getName().replace(' ', '_'));
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314 getGroup().setDescription(dialog.getDescription());
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318 else if (source == copy)
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320 ap.alignFrame.copy_actionPerformed();
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322 else if (source == cut)
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324 ap.alignFrame.cut_actionPerformed();
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326 else if (source == toUpper || source == toLower || source == toggleCase)
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328 SequenceGroup sg = ap.av.getSelectionGroup();
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329 Vector regions = new Vector();
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332 int start = sg.getStartRes();
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333 int end = sg.getEndRes() + 1;
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337 if (ap.av.hasHiddenColumns)
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341 start = ap.av.colSel.adjustForHiddenColumns(start);
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344 end = ap.av.colSel.getHiddenBoundaryRight(start);
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347 end = sg.getEndRes() + 1;
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349 if (end > sg.getEndRes())
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351 end = sg.getEndRes() + 1;
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355 regions.addElement(new int[]
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358 if (ap.av.hasHiddenColumns)
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360 start = ap.av.colSel.adjustForHiddenColumns(end);
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361 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
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364 while (end < sg.getEndRes());
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366 int[][] startEnd = new int[regions.size()][2];
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367 for (int i = 0; i < regions.size(); i++)
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369 startEnd[i] = (int[]) regions.elementAt(i);
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372 String description;
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375 if (source == toggleCase)
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377 description = "Toggle Case";
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378 caseChange = ChangeCaseCommand.TOGGLE_CASE;
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380 else if (source == toUpper)
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382 description = "To Upper Case";
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383 caseChange = ChangeCaseCommand.TO_UPPER;
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387 description = "To Lower Case";
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388 caseChange = ChangeCaseCommand.TO_LOWER;
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391 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
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392 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
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393 startEnd, caseChange
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396 ap.alignFrame.addHistoryItem(caseCommand);
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398 ap.av.firePropertyChange("alignment", null,
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399 ap.av.getAlignment().getSequences());
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403 else if(source == sequenceFeature)
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405 SequenceGroup sg = ap.av.getSelectionGroup();
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411 int gSize = sg.getSize();
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412 SequenceI[] seqs = new SequenceI[gSize];
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413 SequenceFeature[] features = new SequenceFeature[gSize];
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415 for (int i = 0; i < gSize; i++)
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417 seqs[i] = sg.getSequenceAt(i);
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418 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
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419 int end = sg.findEndRes(sg.getSequenceAt(i));
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420 features[i] = new SequenceFeature(null, null, null, start, end,
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424 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
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425 .createNewFeatures(seqs, features, ap))
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427 ap.alignFrame.sequenceFeatures.setState(true);
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428 ap.av.showSequenceFeatures(true);
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429 ap.highlightSearchResults(null);
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439 void outputText(ActionEvent e)
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441 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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443 Frame frame = new Frame();
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445 jalview.bin.JalviewLite.addFrame(frame,
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446 "Selection output - " + e.getActionCommand(),
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449 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
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450 e.getActionCommand(),
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451 new Alignment(ap.av.getSelectionAsNewSequence()),
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452 ap.av.showJVSuffix));
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458 EditNameDialog dialog = new EditNameDialog(
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460 seq.getDescription(),
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462 "Sequence Description",
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464 "Edit Sequence Name / Description",
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469 seq.setName(dialog.getName());
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470 seq.setDescription(dialog.getDescription());
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471 ap.paintAlignment(false);
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477 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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478 cap.setText("Paste your PDB file here.");
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479 cap.setPDBImport(seq);
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480 Frame frame = new Frame();
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482 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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485 private void jbInit()
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488 groupMenu.setLabel("Group");
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489 groupMenu.setLabel("Selection");
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490 sequenceFeature.addActionListener(this);
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492 editGroupName.addActionListener(this);
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493 unGroupMenuItem.setLabel("Remove Group");
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494 unGroupMenuItem.addActionListener(this);
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496 nucleotideMenuItem.setLabel("Nucleotide");
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497 nucleotideMenuItem.addActionListener(this);
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498 conservationMenuItem.addItemListener(this);
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499 abovePIDColour.addItemListener(this);
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500 colourMenu.setLabel("Group Colour");
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501 showBoxes.setLabel("Boxes");
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502 showBoxes.setState(true);
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503 showBoxes.addItemListener(this);
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504 sequenceName.addActionListener(this);
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506 showText.setLabel("Text");
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507 showText.addItemListener(this);
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508 showColourText.setLabel("Colour Text");
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509 showColourText.addItemListener(this);
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510 outputmenu.setLabel("Output to Textbox...");
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511 seqMenu.setLabel("Sequence");
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512 pdb.setLabel("View PDB Structure");
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513 hideSeqs.setLabel("Hide Sequences");
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514 repGroup.setLabel("Represent Group with");
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515 revealAll.setLabel("Reveal All");
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516 menu1.setLabel("Group");
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519 this.add(hideSeqs);
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520 this.add(revealAll);
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521 groupMenu.add(editGroupName);
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522 groupMenu.add(editMenu);
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523 groupMenu.add(outputmenu);
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524 groupMenu.add(sequenceFeature);
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525 groupMenu.add(menu1);
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527 colourMenu.add(noColourmenuItem);
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528 colourMenu.add(clustalColour);
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529 colourMenu.add(BLOSUM62Colour);
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530 colourMenu.add(PIDColour);
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531 colourMenu.add(zappoColour);
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532 colourMenu.add(taylorColour);
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533 colourMenu.add(hydrophobicityColour);
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534 colourMenu.add(helixColour);
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535 colourMenu.add(strandColour);
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536 colourMenu.add(turnColour);
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537 colourMenu.add(buriedColour);
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538 colourMenu.add(nucleotideMenuItem);
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539 colourMenu.add(userDefinedColour);
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540 colourMenu.addSeparator();
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541 colourMenu.add(abovePIDColour);
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542 colourMenu.add(conservationMenuItem);
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544 noColourmenuItem.setLabel("None");
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545 noColourmenuItem.addActionListener(this);
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547 clustalColour.setLabel("Clustalx colours");
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548 clustalColour.addActionListener(this);
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549 zappoColour.setLabel("Zappo");
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550 zappoColour.addActionListener(this);
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551 taylorColour.setLabel("Taylor");
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552 taylorColour.addActionListener(this);
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553 hydrophobicityColour.setLabel("Hydrophobicity");
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554 hydrophobicityColour.addActionListener(this);
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555 helixColour.setLabel("Helix propensity");
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556 helixColour.addActionListener(this);
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557 strandColour.setLabel("Strand propensity");
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558 strandColour.addActionListener(this);
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559 turnColour.setLabel("Turn propensity");
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560 turnColour.addActionListener(this);
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561 buriedColour.setLabel("Buried Index");
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562 buriedColour.addActionListener(this);
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563 abovePIDColour.setLabel("Above % Identity");
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565 userDefinedColour.setLabel("User Defined");
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566 userDefinedColour.addActionListener(this);
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567 PIDColour.setLabel("Percentage Identity");
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568 PIDColour.addActionListener(this);
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569 BLOSUM62Colour.setLabel("BLOSUM62");
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570 BLOSUM62Colour.addActionListener(this);
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571 conservationMenuItem.setLabel("Conservation");
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573 editMenu.add(copy);
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574 copy.addActionListener(this);
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576 cut.addActionListener(this);
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577 editMenu.add(toUpper);
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578 toUpper.addActionListener(this);
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579 editMenu.add(toLower);
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580 toLower.addActionListener(this);
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581 editMenu.add(toggleCase);
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582 seqMenu.add(sequenceName);
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584 seqMenu.add(repGroup);
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585 menu1.add(unGroupMenuItem);
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586 menu1.add(colourMenu);
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587 menu1.add(showBoxes);
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588 menu1.add(showText);
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589 menu1.add(showColourText);
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590 toggleCase.addActionListener(this);
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591 pdb.addActionListener(this);
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592 hideSeqs.addActionListener(this);
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593 repGroup.addActionListener(this);
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594 revealAll.addActionListener(this);
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599 ap.paintAlignment(true);
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602 protected void clustalColour_actionPerformed()
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604 SequenceGroup sg = getGroup();
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605 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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606 ap.av.alignment.getWidth());
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610 protected void zappoColour_actionPerformed()
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612 getGroup().cs = new ZappoColourScheme();
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616 protected void taylorColour_actionPerformed()
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618 getGroup().cs = new TaylorColourScheme();
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622 protected void hydrophobicityColour_actionPerformed()
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624 getGroup().cs = new HydrophobicColourScheme();
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628 protected void helixColour_actionPerformed()
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630 getGroup().cs = new HelixColourScheme();
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634 protected void strandColour_actionPerformed()
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636 getGroup().cs = new StrandColourScheme();
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640 protected void turnColour_actionPerformed()
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642 getGroup().cs = new TurnColourScheme();
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646 protected void buriedColour_actionPerformed()
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648 getGroup().cs = new BuriedColourScheme();
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652 public void nucleotideMenuItem_actionPerformed()
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654 getGroup().cs = new NucleotideColourScheme();
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658 protected void abovePIDColour_itemStateChanged()
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660 SequenceGroup sg = getGroup();
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666 if (abovePIDColour.getState())
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668 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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669 hiddenRepSequences), 0,
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670 ap.av.alignment.getWidth()));
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671 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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672 getGroup().getName());
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674 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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676 SliderPanel.showPIDSlider();
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679 else // remove PIDColouring
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681 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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688 protected void userDefinedColour_actionPerformed()
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690 new UserDefinedColours(ap, getGroup());
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693 protected void PIDColour_actionPerformed()
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695 SequenceGroup sg = getGroup();
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696 sg.cs = new PIDColourScheme();
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697 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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698 hiddenRepSequences), 0,
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699 ap.av.alignment.getWidth()));
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703 protected void BLOSUM62Colour_actionPerformed()
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705 SequenceGroup sg = getGroup();
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707 sg.cs = new Blosum62ColourScheme();
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709 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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710 hiddenRepSequences), 0,
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711 ap.av.alignment.getWidth()));
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716 protected void noColourmenuItem_actionPerformed()
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718 getGroup().cs = null;
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722 protected void conservationMenuItem_itemStateChanged()
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724 SequenceGroup sg = getGroup();
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730 if (conservationMenuItem.getState())
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733 Conservation c = new Conservation("Group",
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734 ResidueProperties.propHash, 3,
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735 sg.getSequences(ap.av.
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736 hiddenRepSequences), 0,
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737 ap.av.alignment.getWidth());
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740 c.verdict(false, ap.av.ConsPercGaps);
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742 sg.cs.setConservation(c);
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744 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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745 SliderPanel.showConservationSlider();
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747 else // remove ConservationColouring
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749 sg.cs.setConservation(null);
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755 SequenceGroup getGroup()
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757 SequenceGroup sg = ap.av.getSelectionGroup();
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759 // this method won't add a new group if it already exists
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762 ap.av.alignment.addGroup(sg);
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768 void unGroupMenuItem_actionPerformed()
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770 SequenceGroup sg = ap.av.getSelectionGroup();
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771 ap.av.alignment.deleteGroup(sg);
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772 ap.av.setSelectionGroup(null);
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773 ap.paintAlignment(true);
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776 public void showColourText_itemStateChanged()
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778 getGroup().setColourText(showColourText.getState());
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782 public void showText_itemStateChanged()
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784 getGroup().setDisplayText(showText.getState());
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788 public void showBoxes_itemStateChanged()
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790 getGroup().setDisplayBoxes(showBoxes.getState());
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794 void hideSequences(boolean representGroup)
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796 SequenceGroup sg = ap.av.getSelectionGroup();
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797 if (sg == null || sg.getSize() < 1)
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799 ap.av.hideSequence(new SequenceI[]
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804 ap.av.setSelectionGroup(null);
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806 if (representGroup)
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808 ap.av.hideRepSequences(seq, sg);
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813 int gsize = sg.getSize();
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816 hseqs = new SequenceI[gsize];
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819 for (int i = 0; i < gsize; i++)
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821 hseqs[index++] = sg.getSequenceAt(i);
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824 ap.av.hideSequence(hseqs);
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