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 protected MenuItem clustalColour = new MenuItem();
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36 protected MenuItem zappoColour = new MenuItem();
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37 protected MenuItem taylorColour = new MenuItem();
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38 protected MenuItem hydrophobicityColour = new MenuItem();
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39 protected MenuItem helixColour = new MenuItem();
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40 protected MenuItem strandColour = new MenuItem();
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41 protected MenuItem turnColour = new MenuItem();
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42 protected MenuItem buriedColour = new MenuItem();
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43 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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44 protected MenuItem userDefinedColour = new MenuItem();
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45 protected MenuItem PIDColour = new MenuItem();
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46 protected MenuItem BLOSUM62Colour = new MenuItem();
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47 MenuItem noColourmenuItem = new MenuItem();
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48 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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50 final AlignmentPanel ap;
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51 MenuItem unGroupMenuItem = new MenuItem();
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52 MenuItem nucleotideMenuItem = new MenuItem();
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53 Menu colourMenu = new Menu();
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54 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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55 CheckboxMenuItem showText = new CheckboxMenuItem();
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56 CheckboxMenuItem showColourText = new CheckboxMenuItem();
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57 Menu editMenu = new Menu("Edit");
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58 MenuItem copy = new MenuItem("Copy (Jalview Only)");
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59 MenuItem cut = new MenuItem("Cut (Jalview Only)");
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60 MenuItem toUpper = new MenuItem("To Upper Case");
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61 MenuItem toLower = new MenuItem("To Lower Case");
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62 MenuItem toggleCase = new MenuItem("Toggle Case");
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63 Menu outputmenu = new Menu();
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64 Menu seqMenu = new Menu();
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65 MenuItem pdb = new MenuItem();
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66 MenuItem hideSeqs = new MenuItem();
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67 MenuItem repGroup = new MenuItem();
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68 MenuItem sequenceName = new MenuItem("Edit Name/Description");
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71 MenuItem revealAll = new MenuItem();
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72 Menu menu1 = new Menu();
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74 Dialog editNameDialog;
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75 Button okDialog = new Button("Accept");
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76 Button cancelDialog = new Button("Cancel");;
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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; i++)
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101 MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
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103 item.addActionListener(this);
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104 outputmenu.add(item);
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107 SequenceGroup sg = ap.av.getSelectionGroup();
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109 if (sg != null && sg.getSize()>0)
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111 showText.setState(sg.getDisplayText());
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112 showColourText.setState(sg.getColourText());
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113 showBoxes.setState(sg.getDisplayBoxes());
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114 if (!ap.av.alignment.getGroups().contains(sg))
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116 groupMenu.remove(unGroupMenuItem);
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128 Menu linkMenu = new Menu("Link");
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131 for(int i=0; i<links.size(); i++)
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133 link = links.elementAt(i).toString();
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134 final String target = link.substring(0, link.indexOf("|"));
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135 item = new MenuItem(target);
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139 if (link.indexOf("$SEQUENCE_ID$") > -1)
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141 String id = seq.getName();
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142 if (id.indexOf("|") > -1)
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143 id = id.substring(id.lastIndexOf("|") + 1);
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145 url = link.substring(link.indexOf("|") + 1,
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146 link.indexOf("$SEQUENCE_ID$"))
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148 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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151 url = link.substring(link.lastIndexOf("|")+1);
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153 item.addActionListener(new java.awt.event.ActionListener()
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155 public void actionPerformed(ActionEvent e)
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157 ap.alignFrame.showURL(url, target);
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160 linkMenu.add(item);
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163 seqMenu.add(linkMenu);
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169 seqMenu.setLabel(seq.getName());
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170 repGroup.setLabel("Represent Group with " + seq.getName());
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175 if(!ap.av.hasHiddenRows)
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179 public void itemStateChanged(ItemEvent evt)
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181 if(evt.getSource()==abovePIDColour)
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182 abovePIDColour_itemStateChanged();
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183 else if(evt.getSource()==showColourText)
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184 showColourText_itemStateChanged();
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185 else if(evt.getSource()==showText)
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186 showText_itemStateChanged();
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187 else if(evt.getSource()==showBoxes)
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188 showBoxes_itemStateChanged() ;
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191 public void actionPerformed(ActionEvent evt)
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193 Object source = evt.getSource();
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194 if(source==clustalColour)
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195 clustalColour_actionPerformed();
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196 else if(source==zappoColour)
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197 zappoColour_actionPerformed();
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198 else if(source==taylorColour)
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199 taylorColour_actionPerformed();
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200 else if(source==hydrophobicityColour)
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201 hydrophobicityColour_actionPerformed();
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202 else if(source==helixColour)
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203 helixColour_actionPerformed();
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204 else if(source==strandColour)
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205 strandColour_actionPerformed();
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206 else if(source==turnColour)
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207 turnColour_actionPerformed();
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208 else if(source==buriedColour)
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209 buriedColour_actionPerformed();
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210 else if(source==nucleotideMenuItem)
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211 nucleotideMenuItem_actionPerformed();
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213 else if (source == userDefinedColour)
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214 userDefinedColour_actionPerformed();
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215 else if (source == PIDColour)
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216 PIDColour_actionPerformed();
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217 else if (source == BLOSUM62Colour)
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218 BLOSUM62Colour_actionPerformed();
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219 else if (source == noColourmenuItem)
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220 noColourmenuItem_actionPerformed();
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221 else if (source == conservationMenuItem)
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222 conservationMenuItem_itemStateChanged();
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223 else if (source == unGroupMenuItem)
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224 unGroupMenuItem_actionPerformed();
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226 else if(source == sequenceName)
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228 else if (source==okDialog || source==cancelDialog)
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230 editNameDialog.setVisible(false);
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231 if(source==cancelDialog)
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232 editNameDialog = null;
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234 else if(source == pdb)
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236 else if(source == hideSeqs)
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237 hideSequences(false);
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238 else if(source == repGroup)
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239 hideSequences(true);
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240 else if(source == revealAll)
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242 ap.av.showAllHiddenSeqs();
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245 else if(source==copy)
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246 ap.alignFrame.copy_actionPerformed();
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247 else if(source==cut)
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248 ap.alignFrame.cut_actionPerformed();
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249 else if(source==toUpper || source==toLower || source==toggleCase)
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251 SequenceGroup sg = ap.av.getSelectionGroup();
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252 Vector regions = new Vector();
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255 int start = sg.getStartRes();
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256 int end = sg.getEndRes() + 1;
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260 if (ap.av.hasHiddenColumns)
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263 start = ap.av.colSel.adjustForHiddenColumns(start);
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265 end = ap.av.colSel.getHiddenBoundaryRight(start);
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267 end = sg.getEndRes() + 1;
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268 if (end > sg.getEndRes())
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269 end = sg.getEndRes() + 1;
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272 regions.addElement(new int[]
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275 if (ap.av.hasHiddenColumns)
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277 start = ap.av.colSel.adjustForHiddenColumns(end);
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278 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
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281 while (end < sg.getEndRes());
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283 int[][] startEnd = new int[regions.size()][2];
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284 for (int i = 0; i < regions.size(); i++)
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286 startEnd[i] = (int[]) regions.elementAt(i);
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290 String description;
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293 if(source==toggleCase)
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295 description = "Toggle Case";
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296 caseChange = ChangeCaseCommand.TOGGLE_CASE;
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298 else if(source==toUpper)
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300 description = "To Upper Case";
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301 caseChange = ChangeCaseCommand.TO_UPPER;
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305 description = "To Lower Case";
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306 caseChange = ChangeCaseCommand.TO_LOWER;
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309 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
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310 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange
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313 ap.alignFrame.addHistoryItem(caseCommand);
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316 ap.av.firePropertyChange("alignment", null,
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317 ap.av.getAlignment().getSequences());
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326 void outputText(ActionEvent e)
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328 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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330 Frame frame = new Frame();
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332 jalview.bin.JalviewLite.addFrame(frame,
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333 "Selection output - " + e.getActionCommand(),
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336 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
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337 e.getActionCommand(),
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338 new Alignment( ap.av.getSelectionAsNewSequence() ),
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339 ap.av.showJVSuffix));
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345 TextField id = new TextField(seq.getName(), 40);
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346 TextField description = new TextField(seq.getDescription(), 40);
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347 Panel panel = new Panel(new BorderLayout());
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348 Panel panel2 = new Panel(new BorderLayout());
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349 panel2.add(new Label(" Sequence Name "), BorderLayout.WEST);
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350 panel2.add(id, BorderLayout.CENTER);
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351 panel.add(panel2, BorderLayout.NORTH);
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352 panel2 = new Panel(new BorderLayout());
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353 panel2.add(new Label("Sequence Description "), BorderLayout.WEST);
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354 panel2.add(description, BorderLayout.CENTER);
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355 panel.add(panel2, BorderLayout.CENTER);
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357 panel2 = new Panel(new FlowLayout());
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359 panel2.add(okDialog);
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360 panel2.add(cancelDialog);
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362 panel.add(panel2, BorderLayout.SOUTH);
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364 editNameDialog = new Dialog(ap.alignFrame,
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365 "Edit Sequence Name / Description",
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368 editNameDialog.add(panel, BorderLayout.NORTH);
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370 editNameDialog.setBounds(ap.alignFrame.getBounds().x
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371 +(ap.alignFrame.getSize().width-500)/2 ,
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372 ap.alignFrame.getBounds().y
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373 +(ap.alignFrame.getSize().height-120)/2,
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376 editNameDialog.show();
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378 if (editNameDialog != null)
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380 seq.setName(id.getText());
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381 seq.setDescription(description.getText());
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388 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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389 cap.setText("Paste your PDB file here.");
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390 cap.setPDBImport(seq);
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391 Frame frame = new Frame();
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393 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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396 private void jbInit()
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399 groupMenu.setLabel("Group");
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400 groupMenu.setLabel("Selection");
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402 unGroupMenuItem.setLabel("Remove Group");
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403 unGroupMenuItem.addActionListener(this);
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405 nucleotideMenuItem.setLabel("Nucleotide");
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406 nucleotideMenuItem.addActionListener(this);
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407 conservationMenuItem.addItemListener(this);
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408 abovePIDColour.addItemListener(this);
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409 colourMenu.setLabel("Group Colour");
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410 showBoxes.setLabel("Boxes");
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411 showBoxes.setState(true);
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412 showBoxes.addItemListener(this);
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413 sequenceName.addActionListener(this);
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415 showText.setLabel("Text");
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416 showText.addItemListener(this);
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417 showColourText.setLabel("Colour Text");
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418 showColourText.addItemListener(this);
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419 outputmenu.setLabel("Output to Textbox...");
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420 seqMenu.setLabel("Sequence");
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421 pdb.setLabel("View PDB Structure");
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422 hideSeqs.setLabel("Hide Sequences");
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423 repGroup.setLabel("Represent Group with");
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424 revealAll.setLabel("Reveal All");
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425 menu1.setLabel("Group");
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428 this.add(hideSeqs);
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429 this.add(revealAll);
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430 groupMenu.add(editMenu);
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431 groupMenu.add(outputmenu);
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432 groupMenu.add(menu1);
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433 colourMenu.add(noColourmenuItem);
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434 colourMenu.add(clustalColour);
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435 colourMenu.add(BLOSUM62Colour);
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436 colourMenu.add(PIDColour);
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437 colourMenu.add(zappoColour);
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438 colourMenu.add(taylorColour);
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439 colourMenu.add(hydrophobicityColour);
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440 colourMenu.add(helixColour);
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441 colourMenu.add(strandColour);
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442 colourMenu.add(turnColour);
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443 colourMenu.add(buriedColour);
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444 colourMenu.add(nucleotideMenuItem);
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445 colourMenu.add(userDefinedColour);
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446 colourMenu.addSeparator();
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447 colourMenu.add(abovePIDColour);
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448 colourMenu.add(conservationMenuItem);
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450 noColourmenuItem.setLabel("None");
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451 noColourmenuItem.addActionListener(this);
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453 clustalColour.setLabel("Clustalx colours");
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454 clustalColour.addActionListener(this);
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455 zappoColour.setLabel("Zappo");
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456 zappoColour.addActionListener(this);
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457 taylorColour.setLabel("Taylor");
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458 taylorColour.addActionListener(this);
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459 hydrophobicityColour.setLabel("Hydrophobicity");
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460 hydrophobicityColour.addActionListener(this);
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461 helixColour.setLabel("Helix propensity");
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462 helixColour.addActionListener(this);
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463 strandColour.setLabel("Strand propensity");
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464 strandColour.addActionListener(this);
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465 turnColour.setLabel("Turn propensity");
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466 turnColour.addActionListener(this);
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467 buriedColour.setLabel("Buried Index");
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468 buriedColour.addActionListener(this);
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469 abovePIDColour.setLabel("Above % Identity");
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471 userDefinedColour.setLabel("User Defined");
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472 userDefinedColour.addActionListener(this);
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473 PIDColour.setLabel("Percentage Identity");
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474 PIDColour.addActionListener(this);
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475 BLOSUM62Colour.setLabel("BLOSUM62");
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476 BLOSUM62Colour.addActionListener(this);
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477 conservationMenuItem.setLabel("Conservation");
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479 editMenu.add(copy);
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480 copy.addActionListener(this);
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482 cut.addActionListener(this);
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483 editMenu.add(toUpper);
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484 toUpper.addActionListener(this);
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485 editMenu.add(toLower);
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486 toLower.addActionListener(this);
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487 editMenu.add(toggleCase);
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488 seqMenu.add(sequenceName);
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490 seqMenu.add(repGroup);
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491 menu1.add(unGroupMenuItem);
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492 menu1.add(colourMenu);
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493 menu1.add(showBoxes);
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494 menu1.add(showText);
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495 menu1.add(showColourText);
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496 toggleCase.addActionListener(this);
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497 pdb.addActionListener(this);
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498 hideSeqs.addActionListener(this);
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499 repGroup.addActionListener(this);
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500 revealAll.addActionListener(this);
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501 okDialog.addActionListener(this);
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502 cancelDialog.addActionListener(this);
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508 ap.seqPanel.seqCanvas.repaint();
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509 if(ap.overviewPanel!=null)
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510 ap.overviewPanel.updateOverviewImage();
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513 protected void clustalColour_actionPerformed()
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515 SequenceGroup sg = getGroup();
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516 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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517 ap.av.alignment.getWidth());
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521 protected void zappoColour_actionPerformed()
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523 getGroup().cs = new ZappoColourScheme();
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527 protected void taylorColour_actionPerformed()
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529 getGroup().cs = new TaylorColourScheme();
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533 protected void hydrophobicityColour_actionPerformed()
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535 getGroup().cs = new HydrophobicColourScheme();
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539 protected void helixColour_actionPerformed()
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541 getGroup().cs = new HelixColourScheme();
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545 protected void strandColour_actionPerformed()
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547 getGroup().cs = new StrandColourScheme();
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551 protected void turnColour_actionPerformed()
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553 getGroup().cs = new TurnColourScheme();
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557 protected void buriedColour_actionPerformed()
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559 getGroup().cs = new BuriedColourScheme();
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563 public void nucleotideMenuItem_actionPerformed()
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565 getGroup().cs = new NucleotideColourScheme();
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569 protected void abovePIDColour_itemStateChanged()
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571 SequenceGroup sg = getGroup();
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575 if (abovePIDColour.getState())
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577 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
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578 ap.av.alignment.getWidth()));
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579 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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580 getGroup().getName());
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582 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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584 SliderPanel.showPIDSlider();
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587 else // remove PIDColouring
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589 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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596 protected void userDefinedColour_actionPerformed()
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598 new UserDefinedColours(ap, getGroup());
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601 protected void PIDColour_actionPerformed()
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603 SequenceGroup sg = getGroup();
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604 sg.cs = new PIDColourScheme();
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605 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
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606 ap.av.alignment.getWidth()));
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610 protected void BLOSUM62Colour_actionPerformed()
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612 SequenceGroup sg = getGroup();
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614 sg.cs = new Blosum62ColourScheme();
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616 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,
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617 ap.av.alignment.getWidth()));
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622 protected void noColourmenuItem_actionPerformed()
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624 getGroup().cs = null;
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628 protected void conservationMenuItem_itemStateChanged()
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630 SequenceGroup sg = getGroup();
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634 if (conservationMenuItem.getState())
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637 Conservation c = new Conservation("Group",
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638 ResidueProperties.propHash, 3,
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639 sg.getSequences(ap.av.hiddenRepSequences), 0,
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640 ap.av.alignment.getWidth());
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643 c.verdict(false, ap.av.ConsPercGaps);
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645 sg.cs.setConservation(c);
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647 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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648 SliderPanel.showConservationSlider();
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650 else // remove ConservationColouring
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652 sg.cs.setConservation(null);
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659 SequenceGroup getGroup()
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661 SequenceGroup sg = ap.av.getSelectionGroup();
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663 // this method won't add a new group if it already exists
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665 ap.av.alignment.addGroup(sg);
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670 void unGroupMenuItem_actionPerformed()
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672 SequenceGroup sg = ap.av.getSelectionGroup();
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673 ap.av.alignment.deleteGroup(sg);
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674 ap.av.setSelectionGroup(null);
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678 public void showColourText_itemStateChanged()
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680 getGroup().setColourText(showColourText.getState());
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684 public void showText_itemStateChanged()
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686 getGroup().setDisplayText(showText.getState());
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690 public void showBoxes_itemStateChanged()
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692 getGroup().setDisplayBoxes(showBoxes.getState());
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696 void hideSequences(boolean representGroup)
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698 SequenceGroup sg = ap.av.getSelectionGroup();
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699 if(sg==null || sg.getSize()<1)
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701 ap.av.hideSequence(new SequenceI[]{seq});
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705 ap.av.setSelectionGroup(null);
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707 if (representGroup)
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709 ap.av.hideRepSequences(seq, sg);
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714 int gsize = sg.getSize();
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717 hseqs = new SequenceI[gsize];
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720 for (int i = 0; i < gsize; i++)
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722 hseqs[index++] = sg.getSequenceAt(i);
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725 ap.av.hideSequence(hseqs);
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