2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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23 import java.awt.event.*;
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24 import java.util.Vector;
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26 import jalview.analysis.*;
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27 import jalview.datamodel.*;
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28 import jalview.schemes.*;
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29 import jalview.commands.ChangeCaseCommand;
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31 public class APopupMenu
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32 extends java.awt.PopupMenu implements ActionListener, ItemListener
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34 Menu groupMenu = new Menu();
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35 MenuItem editGroupName = new MenuItem();
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36 protected MenuItem clustalColour = new MenuItem();
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37 protected MenuItem zappoColour = new MenuItem();
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38 protected MenuItem taylorColour = new MenuItem();
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39 protected MenuItem hydrophobicityColour = new MenuItem();
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40 protected MenuItem helixColour = new MenuItem();
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41 protected MenuItem strandColour = new MenuItem();
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42 protected MenuItem turnColour = new MenuItem();
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43 protected MenuItem buriedColour = new MenuItem();
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44 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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45 protected MenuItem userDefinedColour = new MenuItem();
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46 protected MenuItem PIDColour = new MenuItem();
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47 protected MenuItem BLOSUM62Colour = new MenuItem();
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48 MenuItem noColourmenuItem = new MenuItem();
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49 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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51 final AlignmentPanel ap;
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52 MenuItem unGroupMenuItem = new MenuItem();
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53 MenuItem nucleotideMenuItem = new MenuItem();
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54 Menu colourMenu = new Menu();
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55 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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56 CheckboxMenuItem showText = new CheckboxMenuItem();
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57 CheckboxMenuItem showColourText = new CheckboxMenuItem();
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58 Menu editMenu = new Menu("Edit");
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59 MenuItem copy = new MenuItem("Copy (Jalview Only)");
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60 MenuItem cut = new MenuItem("Cut (Jalview Only)");
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61 MenuItem toUpper = new MenuItem("To Upper Case");
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62 MenuItem toLower = new MenuItem("To Lower Case");
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63 MenuItem toggleCase = new MenuItem("Toggle Case");
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64 Menu outputmenu = new Menu();
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65 Menu seqMenu = new Menu();
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66 MenuItem pdb = new MenuItem();
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67 MenuItem hideSeqs = new MenuItem();
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68 MenuItem repGroup = new MenuItem();
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69 MenuItem sequenceName = new MenuItem("Edit Name/Description");
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72 MenuItem revealAll = new MenuItem();
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73 Menu menu1 = new Menu();
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75 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
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77 ///////////////////////////////////////////////////////////
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78 // If this is activated from the sequence panel, the user may want to
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79 // edit or annotate a particular residue. Therefore display the residue menu
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81 // If from the IDPanel, we must display the sequence menu
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82 //////////////////////////////////////////////////////////
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93 e.printStackTrace();
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96 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
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98 MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
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100 item.addActionListener(this);
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101 outputmenu.add(item);
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104 SequenceGroup sg = ap.av.getSelectionGroup();
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106 if (sg != null && sg.getSize()>0)
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108 editGroupName.setLabel(sg.getName());
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109 showText.setState(sg.getDisplayText());
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110 showColourText.setState(sg.getColourText());
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111 showBoxes.setState(sg.getDisplayBoxes());
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112 if (!ap.av.alignment.getGroups().contains(sg))
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114 groupMenu.remove(unGroupMenuItem);
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126 Menu linkMenu = new Menu("Link");
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129 for(int i=0; i<links.size(); i++)
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131 link = links.elementAt(i).toString();
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132 final String target = link.substring(0, link.indexOf("|"));
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133 item = new MenuItem(target);
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137 if (link.indexOf("$SEQUENCE_ID$") > -1)
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139 String id = seq.getName();
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140 if (id.indexOf("|") > -1)
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141 id = id.substring(id.lastIndexOf("|") + 1);
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143 url = link.substring(link.indexOf("|") + 1,
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144 link.indexOf("$SEQUENCE_ID$"))
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146 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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149 url = link.substring(link.lastIndexOf("|")+1);
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151 item.addActionListener(new java.awt.event.ActionListener()
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153 public void actionPerformed(ActionEvent e)
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155 ap.alignFrame.showURL(url, target);
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158 linkMenu.add(item);
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161 seqMenu.add(linkMenu);
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167 seqMenu.setLabel(seq.getName());
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168 repGroup.setLabel("Represent Group with " + seq.getName());
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173 if(!ap.av.hasHiddenRows)
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177 public void itemStateChanged(ItemEvent evt)
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179 if(evt.getSource()==abovePIDColour)
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180 abovePIDColour_itemStateChanged();
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181 else if(evt.getSource()==showColourText)
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182 showColourText_itemStateChanged();
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183 else if(evt.getSource()==showText)
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184 showText_itemStateChanged();
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185 else if(evt.getSource()==showBoxes)
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186 showBoxes_itemStateChanged() ;
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189 public void actionPerformed(ActionEvent evt)
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191 Object source = evt.getSource();
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192 if(source==clustalColour)
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193 clustalColour_actionPerformed();
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194 else if(source==zappoColour)
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195 zappoColour_actionPerformed();
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196 else if(source==taylorColour)
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197 taylorColour_actionPerformed();
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198 else if(source==hydrophobicityColour)
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199 hydrophobicityColour_actionPerformed();
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200 else if(source==helixColour)
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201 helixColour_actionPerformed();
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202 else if(source==strandColour)
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203 strandColour_actionPerformed();
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204 else if(source==turnColour)
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205 turnColour_actionPerformed();
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206 else if(source==buriedColour)
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207 buriedColour_actionPerformed();
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208 else if(source==nucleotideMenuItem)
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209 nucleotideMenuItem_actionPerformed();
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211 else if (source == userDefinedColour)
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212 userDefinedColour_actionPerformed();
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213 else if (source == PIDColour)
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214 PIDColour_actionPerformed();
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215 else if (source == BLOSUM62Colour)
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216 BLOSUM62Colour_actionPerformed();
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217 else if (source == noColourmenuItem)
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218 noColourmenuItem_actionPerformed();
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219 else if (source == conservationMenuItem)
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220 conservationMenuItem_itemStateChanged();
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221 else if (source == unGroupMenuItem)
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222 unGroupMenuItem_actionPerformed();
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224 else if(source == sequenceName)
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226 else if(source == pdb)
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228 else if(source == hideSeqs)
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229 hideSequences(false);
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230 else if(source == repGroup)
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231 hideSequences(true);
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232 else if(source == revealAll)
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234 ap.av.showAllHiddenSeqs();
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237 else if(source==editGroupName)
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239 EditNameDialog dialog = new EditNameDialog(
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240 getGroup().getName(),
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241 getGroup().getDescription(),
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243 "Group Description",
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245 "Edit Group Name / Description");
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250 getGroup().setName(dialog.getName().replace(' ', '_'));
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251 getGroup().setDescription(dialog.getDescription());
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255 else if(source==copy)
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256 ap.alignFrame.copy_actionPerformed();
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257 else if(source==cut)
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258 ap.alignFrame.cut_actionPerformed();
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259 else if(source==toUpper || source==toLower || source==toggleCase)
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261 SequenceGroup sg = ap.av.getSelectionGroup();
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262 Vector regions = new Vector();
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265 int start = sg.getStartRes();
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266 int end = sg.getEndRes() + 1;
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270 if (ap.av.hasHiddenColumns)
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273 start = ap.av.colSel.adjustForHiddenColumns(start);
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275 end = ap.av.colSel.getHiddenBoundaryRight(start);
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277 end = sg.getEndRes() + 1;
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278 if (end > sg.getEndRes())
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279 end = sg.getEndRes() + 1;
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282 regions.addElement(new int[]
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285 if (ap.av.hasHiddenColumns)
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287 start = ap.av.colSel.adjustForHiddenColumns(end);
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288 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
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291 while (end < sg.getEndRes());
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293 int[][] startEnd = new int[regions.size()][2];
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294 for (int i = 0; i < regions.size(); i++)
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296 startEnd[i] = (int[]) regions.elementAt(i);
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300 String description;
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303 if(source==toggleCase)
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305 description = "Toggle Case";
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306 caseChange = ChangeCaseCommand.TOGGLE_CASE;
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308 else if(source==toUpper)
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310 description = "To Upper Case";
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311 caseChange = ChangeCaseCommand.TO_UPPER;
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315 description = "To Lower Case";
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316 caseChange = ChangeCaseCommand.TO_LOWER;
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319 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
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320 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange
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323 ap.alignFrame.addHistoryItem(caseCommand);
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326 ap.av.firePropertyChange("alignment", null,
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327 ap.av.getAlignment().getSequences());
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336 void outputText(ActionEvent e)
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338 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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340 Frame frame = new Frame();
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342 jalview.bin.JalviewLite.addFrame(frame,
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343 "Selection output - " + e.getActionCommand(),
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346 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
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347 e.getActionCommand(),
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348 new Alignment( ap.av.getSelectionAsNewSequence() ),
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349 ap.av.showJVSuffix));
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355 EditNameDialog dialog = new EditNameDialog(
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357 seq.getDescription(),
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359 "Sequence Description",
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361 "Edit Sequence Name / Description");
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365 seq.setName(dialog.getName());
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366 seq.setDescription(dialog.getDescription());
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373 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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374 cap.setText("Paste your PDB file here.");
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375 cap.setPDBImport(seq);
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376 Frame frame = new Frame();
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378 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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381 private void jbInit()
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384 groupMenu.setLabel("Group");
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385 groupMenu.setLabel("Selection");
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387 editGroupName.addActionListener(this);
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388 unGroupMenuItem.setLabel("Remove Group");
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389 unGroupMenuItem.addActionListener(this);
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391 nucleotideMenuItem.setLabel("Nucleotide");
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392 nucleotideMenuItem.addActionListener(this);
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393 conservationMenuItem.addItemListener(this);
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394 abovePIDColour.addItemListener(this);
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395 colourMenu.setLabel("Group Colour");
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396 showBoxes.setLabel("Boxes");
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397 showBoxes.setState(true);
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398 showBoxes.addItemListener(this);
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399 sequenceName.addActionListener(this);
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401 showText.setLabel("Text");
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402 showText.addItemListener(this);
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403 showColourText.setLabel("Colour Text");
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404 showColourText.addItemListener(this);
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405 outputmenu.setLabel("Output to Textbox...");
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406 seqMenu.setLabel("Sequence");
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407 pdb.setLabel("View PDB Structure");
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408 hideSeqs.setLabel("Hide Sequences");
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409 repGroup.setLabel("Represent Group with");
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410 revealAll.setLabel("Reveal All");
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411 menu1.setLabel("Group");
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414 this.add(hideSeqs);
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415 this.add(revealAll);
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416 groupMenu.add(editGroupName);
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417 groupMenu.add(editMenu);
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418 groupMenu.add(outputmenu);
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419 groupMenu.add(menu1);
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420 colourMenu.add(noColourmenuItem);
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421 colourMenu.add(clustalColour);
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422 colourMenu.add(BLOSUM62Colour);
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423 colourMenu.add(PIDColour);
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424 colourMenu.add(zappoColour);
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425 colourMenu.add(taylorColour);
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426 colourMenu.add(hydrophobicityColour);
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427 colourMenu.add(helixColour);
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428 colourMenu.add(strandColour);
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429 colourMenu.add(turnColour);
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430 colourMenu.add(buriedColour);
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431 colourMenu.add(nucleotideMenuItem);
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432 colourMenu.add(userDefinedColour);
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433 colourMenu.addSeparator();
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434 colourMenu.add(abovePIDColour);
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435 colourMenu.add(conservationMenuItem);
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437 noColourmenuItem.setLabel("None");
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438 noColourmenuItem.addActionListener(this);
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440 clustalColour.setLabel("Clustalx colours");
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441 clustalColour.addActionListener(this);
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442 zappoColour.setLabel("Zappo");
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443 zappoColour.addActionListener(this);
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444 taylorColour.setLabel("Taylor");
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445 taylorColour.addActionListener(this);
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446 hydrophobicityColour.setLabel("Hydrophobicity");
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447 hydrophobicityColour.addActionListener(this);
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448 helixColour.setLabel("Helix propensity");
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449 helixColour.addActionListener(this);
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450 strandColour.setLabel("Strand propensity");
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451 strandColour.addActionListener(this);
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452 turnColour.setLabel("Turn propensity");
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453 turnColour.addActionListener(this);
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454 buriedColour.setLabel("Buried Index");
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455 buriedColour.addActionListener(this);
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456 abovePIDColour.setLabel("Above % Identity");
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458 userDefinedColour.setLabel("User Defined");
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459 userDefinedColour.addActionListener(this);
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460 PIDColour.setLabel("Percentage Identity");
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461 PIDColour.addActionListener(this);
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462 BLOSUM62Colour.setLabel("BLOSUM62");
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463 BLOSUM62Colour.addActionListener(this);
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464 conservationMenuItem.setLabel("Conservation");
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466 editMenu.add(copy);
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467 copy.addActionListener(this);
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469 cut.addActionListener(this);
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470 editMenu.add(toUpper);
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471 toUpper.addActionListener(this);
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472 editMenu.add(toLower);
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473 toLower.addActionListener(this);
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474 editMenu.add(toggleCase);
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475 seqMenu.add(sequenceName);
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477 seqMenu.add(repGroup);
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478 menu1.add(unGroupMenuItem);
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479 menu1.add(colourMenu);
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480 menu1.add(showBoxes);
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481 menu1.add(showText);
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482 menu1.add(showColourText);
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483 toggleCase.addActionListener(this);
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484 pdb.addActionListener(this);
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485 hideSeqs.addActionListener(this);
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486 repGroup.addActionListener(this);
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487 revealAll.addActionListener(this);
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492 ap.seqPanel.seqCanvas.repaint();
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493 if(ap.overviewPanel!=null)
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494 ap.overviewPanel.updateOverviewImage();
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497 protected void clustalColour_actionPerformed()
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499 SequenceGroup sg = getGroup();
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500 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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501 ap.av.alignment.getWidth());
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505 protected void zappoColour_actionPerformed()
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507 getGroup().cs = new ZappoColourScheme();
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511 protected void taylorColour_actionPerformed()
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513 getGroup().cs = new TaylorColourScheme();
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517 protected void hydrophobicityColour_actionPerformed()
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519 getGroup().cs = new HydrophobicColourScheme();
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523 protected void helixColour_actionPerformed()
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525 getGroup().cs = new HelixColourScheme();
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529 protected void strandColour_actionPerformed()
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531 getGroup().cs = new StrandColourScheme();
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535 protected void turnColour_actionPerformed()
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537 getGroup().cs = new TurnColourScheme();
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541 protected void buriedColour_actionPerformed()
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543 getGroup().cs = new BuriedColourScheme();
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547 public void nucleotideMenuItem_actionPerformed()
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549 getGroup().cs = new NucleotideColourScheme();
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553 protected void abovePIDColour_itemStateChanged()
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555 SequenceGroup sg = getGroup();
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559 if (abovePIDColour.getState())
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561 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
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562 ap.av.alignment.getWidth()));
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563 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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564 getGroup().getName());
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566 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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568 SliderPanel.showPIDSlider();
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571 else // remove PIDColouring
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573 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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580 protected void userDefinedColour_actionPerformed()
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582 new UserDefinedColours(ap, getGroup());
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585 protected void PIDColour_actionPerformed()
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587 SequenceGroup sg = getGroup();
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588 sg.cs = new PIDColourScheme();
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589 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
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590 ap.av.alignment.getWidth()));
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594 protected void BLOSUM62Colour_actionPerformed()
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596 SequenceGroup sg = getGroup();
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598 sg.cs = new Blosum62ColourScheme();
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600 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
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601 ap.av.alignment.getWidth()));
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606 protected void noColourmenuItem_actionPerformed()
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608 getGroup().cs = null;
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612 protected void conservationMenuItem_itemStateChanged()
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614 SequenceGroup sg = getGroup();
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618 if (conservationMenuItem.getState())
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621 Conservation c = new Conservation("Group",
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622 ResidueProperties.propHash, 3,
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623 sg.getSequences(ap.av.hiddenRepSequences), 0,
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624 ap.av.alignment.getWidth());
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627 c.verdict(false, ap.av.ConsPercGaps);
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629 sg.cs.setConservation(c);
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631 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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632 SliderPanel.showConservationSlider();
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634 else // remove ConservationColouring
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636 sg.cs.setConservation(null);
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643 SequenceGroup getGroup()
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645 SequenceGroup sg = ap.av.getSelectionGroup();
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647 // this method won't add a new group if it already exists
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649 ap.av.alignment.addGroup(sg);
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654 void unGroupMenuItem_actionPerformed()
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656 SequenceGroup sg = ap.av.getSelectionGroup();
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657 ap.av.alignment.deleteGroup(sg);
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658 ap.av.setSelectionGroup(null);
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662 public void showColourText_itemStateChanged()
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664 getGroup().setColourText(showColourText.getState());
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668 public void showText_itemStateChanged()
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670 getGroup().setDisplayText(showText.getState());
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674 public void showBoxes_itemStateChanged()
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676 getGroup().setDisplayBoxes(showBoxes.getState());
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680 void hideSequences(boolean representGroup)
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682 SequenceGroup sg = ap.av.getSelectionGroup();
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683 if(sg==null || sg.getSize()<1)
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685 ap.av.hideSequence(new SequenceI[]{seq});
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689 ap.av.setSelectionGroup(null);
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691 if (representGroup)
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693 ap.av.hideRepSequences(seq, sg);
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698 int gsize = sg.getSize();
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701 hseqs = new SequenceI[gsize];
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704 for (int i = 0; i < gsize; i++)
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706 hseqs[index++] = sg.getSequenceAt(i);
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709 ap.av.hideSequence(hseqs);
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