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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31 import jalview.io.AppletFormatAdapter;
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33 public class APopupMenu
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34 extends java.awt.PopupMenu implements ActionListener, ItemListener
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36 Menu groupMenu = new Menu();
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37 MenuItem editGroupName = new MenuItem();
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38 protected MenuItem clustalColour = new MenuItem();
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39 protected MenuItem zappoColour = new MenuItem();
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40 protected MenuItem taylorColour = new MenuItem();
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41 protected MenuItem hydrophobicityColour = new MenuItem();
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42 protected MenuItem helixColour = new MenuItem();
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43 protected MenuItem strandColour = new MenuItem();
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44 protected MenuItem turnColour = new MenuItem();
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45 protected MenuItem buriedColour = new MenuItem();
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46 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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47 protected MenuItem userDefinedColour = new MenuItem();
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48 protected MenuItem PIDColour = new MenuItem();
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49 protected MenuItem BLOSUM62Colour = new MenuItem();
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50 MenuItem noColourmenuItem = new MenuItem();
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51 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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53 final AlignmentPanel ap;
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54 MenuItem unGroupMenuItem = new MenuItem();
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55 MenuItem nucleotideMenuItem = new MenuItem();
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56 Menu colourMenu = new Menu();
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57 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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58 CheckboxMenuItem showText = new CheckboxMenuItem();
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59 CheckboxMenuItem showColourText = new CheckboxMenuItem();
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60 Menu editMenu = new Menu("Edit");
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61 MenuItem copy = new MenuItem("Copy (Jalview Only)");
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62 MenuItem cut = new MenuItem("Cut (Jalview Only)");
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63 MenuItem toUpper = new MenuItem("To Upper Case");
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64 MenuItem toLower = new MenuItem("To Lower Case");
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65 MenuItem toggleCase = new MenuItem("Toggle Case");
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66 Menu outputmenu = new Menu();
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67 Menu seqMenu = new Menu();
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68 MenuItem pdb = new MenuItem();
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69 MenuItem hideSeqs = new MenuItem();
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70 MenuItem repGroup = new MenuItem();
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71 MenuItem sequenceName = new MenuItem("Edit Name/Description");
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72 MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
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75 MenuItem revealAll = new MenuItem();
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76 Menu menu1 = new Menu();
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78 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
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80 ///////////////////////////////////////////////////////////
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81 // If this is activated from the sequence panel, the user may want to
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82 // edit or annotate a particular residue. Therefore display the residue menu
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84 // If from the IDPanel, we must display the sequence menu
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85 //////////////////////////////////////////////////////////
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96 e.printStackTrace();
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99 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
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102 MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.
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103 WRITEABLE_FORMATS[i]);
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105 item.addActionListener(this);
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106 outputmenu.add(item);
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109 SequenceGroup sg = ap.av.getSelectionGroup();
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111 if (sg != null && sg.getSize() > 0)
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113 editGroupName.setLabel(sg.getName());
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114 showText.setState(sg.getDisplayText());
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115 showColourText.setState(sg.getColourText());
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116 showBoxes.setState(sg.getDisplayBoxes());
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117 if (!ap.av.alignment.getGroups().contains(sg))
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119 groupMenu.remove(unGroupMenuItem);
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131 Menu linkMenu = new Menu("Link");
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134 for (int i = 0; i < links.size(); i++)
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136 link = links.elementAt(i).toString();
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137 final String target = link.substring(0, link.indexOf("|"));
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138 item = new MenuItem(target);
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142 if (link.indexOf("$SEQUENCE_ID$") > -1)
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144 String id = seq.getName();
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145 if (id.indexOf("|") > -1)
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147 id = id.substring(id.lastIndexOf("|") + 1);
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150 url = link.substring(link.indexOf("|") + 1,
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151 link.indexOf("$SEQUENCE_ID$"))
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153 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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157 url = link.substring(link.lastIndexOf("|") + 1);
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160 item.addActionListener(new java.awt.event.ActionListener()
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162 public void actionPerformed(ActionEvent e)
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164 ap.alignFrame.showURL(url, target);
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167 linkMenu.add(item);
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171 seqMenu.add(linkMenu);
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180 seqMenu.setLabel(seq.getName());
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181 repGroup.setLabel("Represent Group with " + seq.getName());
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188 if (!ap.av.hasHiddenRows)
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194 public void itemStateChanged(ItemEvent evt)
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196 if (evt.getSource() == abovePIDColour)
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198 abovePIDColour_itemStateChanged();
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200 else if (evt.getSource() == showColourText)
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202 showColourText_itemStateChanged();
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204 else if (evt.getSource() == showText)
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206 showText_itemStateChanged();
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208 else if (evt.getSource() == showBoxes)
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210 showBoxes_itemStateChanged();
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214 public void actionPerformed(ActionEvent evt)
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216 Object source = evt.getSource();
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217 if (source == clustalColour)
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219 clustalColour_actionPerformed();
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221 else if (source == zappoColour)
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223 zappoColour_actionPerformed();
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225 else if (source == taylorColour)
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227 taylorColour_actionPerformed();
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229 else if (source == hydrophobicityColour)
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231 hydrophobicityColour_actionPerformed();
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233 else if (source == helixColour)
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235 helixColour_actionPerformed();
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237 else if (source == strandColour)
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239 strandColour_actionPerformed();
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241 else if (source == turnColour)
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243 turnColour_actionPerformed();
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245 else if (source == buriedColour)
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247 buriedColour_actionPerformed();
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249 else if (source == nucleotideMenuItem)
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251 nucleotideMenuItem_actionPerformed();
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254 else if (source == userDefinedColour)
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256 userDefinedColour_actionPerformed();
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258 else if (source == PIDColour)
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260 PIDColour_actionPerformed();
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262 else if (source == BLOSUM62Colour)
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264 BLOSUM62Colour_actionPerformed();
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266 else if (source == noColourmenuItem)
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268 noColourmenuItem_actionPerformed();
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270 else if (source == conservationMenuItem)
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272 conservationMenuItem_itemStateChanged();
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274 else if (source == unGroupMenuItem)
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276 unGroupMenuItem_actionPerformed();
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279 else if (source == sequenceName)
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283 else if (source == pdb)
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287 else if (source == hideSeqs)
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289 hideSequences(false);
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291 else if (source == repGroup)
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293 hideSequences(true);
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295 else if (source == revealAll)
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297 ap.av.showAllHiddenSeqs();
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300 else if (source == editGroupName)
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302 EditNameDialog dialog = new EditNameDialog(
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303 getGroup().getName(),
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304 getGroup().getDescription(),
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306 "Group Description",
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308 "Edit Group Name / Description",
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314 getGroup().setName(dialog.getName().replace(' ', '_'));
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315 getGroup().setDescription(dialog.getDescription());
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319 else if (source == copy)
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321 ap.alignFrame.copy_actionPerformed();
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323 else if (source == cut)
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325 ap.alignFrame.cut_actionPerformed();
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327 else if (source == toUpper || source == toLower || source == toggleCase)
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329 SequenceGroup sg = ap.av.getSelectionGroup();
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330 Vector regions = new Vector();
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333 int start = sg.getStartRes();
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334 int end = sg.getEndRes() + 1;
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338 if (ap.av.hasHiddenColumns)
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342 start = ap.av.colSel.adjustForHiddenColumns(start);
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345 end = ap.av.colSel.getHiddenBoundaryRight(start);
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348 end = sg.getEndRes() + 1;
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350 if (end > sg.getEndRes())
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352 end = sg.getEndRes() + 1;
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356 regions.addElement(new int[]
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359 if (ap.av.hasHiddenColumns)
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361 start = ap.av.colSel.adjustForHiddenColumns(end);
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362 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
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365 while (end < sg.getEndRes());
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367 int[][] startEnd = new int[regions.size()][2];
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368 for (int i = 0; i < regions.size(); i++)
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370 startEnd[i] = (int[]) regions.elementAt(i);
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373 String description;
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376 if (source == toggleCase)
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378 description = "Toggle Case";
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379 caseChange = ChangeCaseCommand.TOGGLE_CASE;
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381 else if (source == toUpper)
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383 description = "To Upper Case";
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384 caseChange = ChangeCaseCommand.TO_UPPER;
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388 description = "To Lower Case";
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389 caseChange = ChangeCaseCommand.TO_LOWER;
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392 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
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393 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
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394 startEnd, caseChange
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397 ap.alignFrame.addHistoryItem(caseCommand);
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399 ap.av.firePropertyChange("alignment", null,
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400 ap.av.getAlignment().getSequences());
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404 else if(source == sequenceFeature)
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406 SequenceGroup sg = ap.av.getSelectionGroup();
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412 int gSize = sg.getSize();
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413 SequenceI[] seqs = new SequenceI[gSize];
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414 SequenceFeature[] features = new SequenceFeature[gSize];
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416 for (int i = 0; i < gSize; i++)
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418 seqs[i] = sg.getSequenceAt(i);
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419 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
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420 int end = sg.findEndRes(sg.getSequenceAt(i));
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421 features[i] = new SequenceFeature(null, null, null, start, end,
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425 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
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426 .createNewFeatures(seqs, features, ap))
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428 ap.alignFrame.sequenceFeatures.setState(true);
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429 ap.av.showSequenceFeatures(true);
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430 ap.highlightSearchResults(null);
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440 void outputText(ActionEvent e)
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442 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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444 Frame frame = new Frame();
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446 jalview.bin.JalviewLite.addFrame(frame,
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447 "Selection output - " + e.getActionCommand(),
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450 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
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451 e.getActionCommand(),
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452 new Alignment(ap.av.getSelectionAsNewSequence()),
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453 ap.av.showJVSuffix));
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459 EditNameDialog dialog = new EditNameDialog(
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461 seq.getDescription(),
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463 "Sequence Description",
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465 "Edit Sequence Name / Description",
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470 seq.setName(dialog.getName());
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471 seq.setDescription(dialog.getDescription());
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472 ap.paintAlignment(false);
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478 if(seq.getPDBId()!=null)
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480 PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement();
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482 if ( ap.av.applet.jmolAvailable )
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483 new jalview.appletgui.AppletJmol(entry,
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487 AppletFormatAdapter.URL);
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490 new MCview.AppletPDBViewer(entry,
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494 AppletFormatAdapter.URL);
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499 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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500 cap.setText("Paste your PDB file here.");
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501 cap.setPDBImport(seq);
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502 Frame frame = new Frame();
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504 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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508 private void jbInit()
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511 groupMenu.setLabel("Group");
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512 groupMenu.setLabel("Selection");
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513 sequenceFeature.addActionListener(this);
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515 editGroupName.addActionListener(this);
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516 unGroupMenuItem.setLabel("Remove Group");
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517 unGroupMenuItem.addActionListener(this);
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519 nucleotideMenuItem.setLabel("Nucleotide");
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520 nucleotideMenuItem.addActionListener(this);
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521 conservationMenuItem.addItemListener(this);
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522 abovePIDColour.addItemListener(this);
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523 colourMenu.setLabel("Group Colour");
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524 showBoxes.setLabel("Boxes");
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525 showBoxes.setState(true);
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526 showBoxes.addItemListener(this);
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527 sequenceName.addActionListener(this);
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529 showText.setLabel("Text");
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530 showText.addItemListener(this);
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531 showColourText.setLabel("Colour Text");
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532 showColourText.addItemListener(this);
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533 outputmenu.setLabel("Output to Textbox...");
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534 seqMenu.setLabel("Sequence");
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535 pdb.setLabel("View PDB Structure");
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536 hideSeqs.setLabel("Hide Sequences");
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537 repGroup.setLabel("Represent Group with");
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538 revealAll.setLabel("Reveal All");
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539 menu1.setLabel("Group");
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542 this.add(hideSeqs);
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543 this.add(revealAll);
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544 groupMenu.add(editGroupName);
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545 groupMenu.add(editMenu);
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546 groupMenu.add(outputmenu);
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547 groupMenu.add(sequenceFeature);
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548 groupMenu.add(menu1);
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550 colourMenu.add(noColourmenuItem);
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551 colourMenu.add(clustalColour);
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552 colourMenu.add(BLOSUM62Colour);
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553 colourMenu.add(PIDColour);
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554 colourMenu.add(zappoColour);
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555 colourMenu.add(taylorColour);
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556 colourMenu.add(hydrophobicityColour);
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557 colourMenu.add(helixColour);
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558 colourMenu.add(strandColour);
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559 colourMenu.add(turnColour);
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560 colourMenu.add(buriedColour);
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561 colourMenu.add(nucleotideMenuItem);
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562 colourMenu.add(userDefinedColour);
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563 colourMenu.addSeparator();
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564 colourMenu.add(abovePIDColour);
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565 colourMenu.add(conservationMenuItem);
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567 noColourmenuItem.setLabel("None");
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568 noColourmenuItem.addActionListener(this);
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570 clustalColour.setLabel("Clustalx colours");
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571 clustalColour.addActionListener(this);
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572 zappoColour.setLabel("Zappo");
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573 zappoColour.addActionListener(this);
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574 taylorColour.setLabel("Taylor");
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575 taylorColour.addActionListener(this);
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576 hydrophobicityColour.setLabel("Hydrophobicity");
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577 hydrophobicityColour.addActionListener(this);
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578 helixColour.setLabel("Helix propensity");
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579 helixColour.addActionListener(this);
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580 strandColour.setLabel("Strand propensity");
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581 strandColour.addActionListener(this);
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582 turnColour.setLabel("Turn propensity");
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583 turnColour.addActionListener(this);
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584 buriedColour.setLabel("Buried Index");
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585 buriedColour.addActionListener(this);
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586 abovePIDColour.setLabel("Above % Identity");
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588 userDefinedColour.setLabel("User Defined");
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589 userDefinedColour.addActionListener(this);
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590 PIDColour.setLabel("Percentage Identity");
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591 PIDColour.addActionListener(this);
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592 BLOSUM62Colour.setLabel("BLOSUM62");
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593 BLOSUM62Colour.addActionListener(this);
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594 conservationMenuItem.setLabel("Conservation");
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596 editMenu.add(copy);
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597 copy.addActionListener(this);
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599 cut.addActionListener(this);
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600 editMenu.add(toUpper);
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601 toUpper.addActionListener(this);
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602 editMenu.add(toLower);
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603 toLower.addActionListener(this);
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604 editMenu.add(toggleCase);
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605 seqMenu.add(sequenceName);
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607 seqMenu.add(repGroup);
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608 menu1.add(unGroupMenuItem);
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609 menu1.add(colourMenu);
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610 menu1.add(showBoxes);
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611 menu1.add(showText);
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612 menu1.add(showColourText);
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613 toggleCase.addActionListener(this);
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614 pdb.addActionListener(this);
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615 hideSeqs.addActionListener(this);
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616 repGroup.addActionListener(this);
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617 revealAll.addActionListener(this);
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622 ap.paintAlignment(true);
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625 protected void clustalColour_actionPerformed()
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627 SequenceGroup sg = getGroup();
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628 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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629 ap.av.alignment.getWidth());
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633 protected void zappoColour_actionPerformed()
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635 getGroup().cs = new ZappoColourScheme();
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639 protected void taylorColour_actionPerformed()
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641 getGroup().cs = new TaylorColourScheme();
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645 protected void hydrophobicityColour_actionPerformed()
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647 getGroup().cs = new HydrophobicColourScheme();
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651 protected void helixColour_actionPerformed()
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653 getGroup().cs = new HelixColourScheme();
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657 protected void strandColour_actionPerformed()
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659 getGroup().cs = new StrandColourScheme();
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663 protected void turnColour_actionPerformed()
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665 getGroup().cs = new TurnColourScheme();
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669 protected void buriedColour_actionPerformed()
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671 getGroup().cs = new BuriedColourScheme();
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675 public void nucleotideMenuItem_actionPerformed()
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677 getGroup().cs = new NucleotideColourScheme();
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681 protected void abovePIDColour_itemStateChanged()
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683 SequenceGroup sg = getGroup();
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689 if (abovePIDColour.getState())
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691 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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692 hiddenRepSequences), 0,
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693 ap.av.alignment.getWidth()));
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694 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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695 getGroup().getName());
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697 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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699 SliderPanel.showPIDSlider();
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702 else // remove PIDColouring
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704 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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711 protected void userDefinedColour_actionPerformed()
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713 new UserDefinedColours(ap, getGroup());
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716 protected void PIDColour_actionPerformed()
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718 SequenceGroup sg = getGroup();
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719 sg.cs = new PIDColourScheme();
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720 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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721 hiddenRepSequences), 0,
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722 ap.av.alignment.getWidth()));
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726 protected void BLOSUM62Colour_actionPerformed()
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728 SequenceGroup sg = getGroup();
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730 sg.cs = new Blosum62ColourScheme();
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732 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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733 hiddenRepSequences), 0,
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734 ap.av.alignment.getWidth()));
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739 protected void noColourmenuItem_actionPerformed()
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741 getGroup().cs = null;
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745 protected void conservationMenuItem_itemStateChanged()
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747 SequenceGroup sg = getGroup();
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753 if (conservationMenuItem.getState())
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756 Conservation c = new Conservation("Group",
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757 ResidueProperties.propHash, 3,
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758 sg.getSequences(ap.av.
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759 hiddenRepSequences), 0,
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760 ap.av.alignment.getWidth());
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763 c.verdict(false, ap.av.ConsPercGaps);
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765 sg.cs.setConservation(c);
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767 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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768 SliderPanel.showConservationSlider();
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770 else // remove ConservationColouring
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772 sg.cs.setConservation(null);
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778 SequenceGroup getGroup()
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780 SequenceGroup sg = ap.av.getSelectionGroup();
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782 // this method won't add a new group if it already exists
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785 ap.av.alignment.addGroup(sg);
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791 void unGroupMenuItem_actionPerformed()
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793 SequenceGroup sg = ap.av.getSelectionGroup();
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794 ap.av.alignment.deleteGroup(sg);
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795 ap.av.setSelectionGroup(null);
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796 ap.paintAlignment(true);
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799 public void showColourText_itemStateChanged()
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801 getGroup().setColourText(showColourText.getState());
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805 public void showText_itemStateChanged()
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807 getGroup().setDisplayText(showText.getState());
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811 public void showBoxes_itemStateChanged()
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813 getGroup().setDisplayBoxes(showBoxes.getState());
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817 void hideSequences(boolean representGroup)
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819 SequenceGroup sg = ap.av.getSelectionGroup();
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820 if (sg == null || sg.getSize() < 1)
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822 ap.av.hideSequence(new SequenceI[]
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827 ap.av.setSelectionGroup(null);
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829 if (representGroup)
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831 ap.av.hideRepSequences(seq, sg);
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836 int gsize = sg.getSize();
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839 hseqs = new SequenceI[gsize];
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842 for (int i = 0; i < gsize; i++)
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844 hseqs[index++] = sg.getSequenceAt(i);
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847 ap.av.hideSequence(hseqs);
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