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(false)>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(true), 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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329 Vector vseqs = new Vector();
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331 String [] selection = ap.av.getViewAsString(true);
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332 SequenceI [] seqs = ap.av.getSelectionAsNewSequence();
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333 if (selection != null)
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335 for (int i = 0; i < selection.length; i++)
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337 Sequence seq = new Sequence(
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340 seqs[i].getStart(), seqs[i].getEnd());
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341 seq.setDescription(seqs[i].getDescription());
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342 vseqs.addElement( seq );
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346 Frame frame = new Frame();
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348 jalview.bin.JalviewLite.addFrame(frame,
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349 "Selection output - " + e.getActionCommand(),
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352 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
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353 e.getActionCommand(),
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355 ap.av.showJVSuffix));
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361 TextField id = new TextField(seq.getName(), 40);
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362 TextField description = new TextField(seq.getDescription(), 40);
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363 Panel panel = new Panel(new BorderLayout());
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364 Panel panel2 = new Panel(new BorderLayout());
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365 panel2.add(new Label(" Sequence Name "), BorderLayout.WEST);
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366 panel2.add(id, BorderLayout.CENTER);
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367 panel.add(panel2, BorderLayout.NORTH);
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368 panel2 = new Panel(new BorderLayout());
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369 panel2.add(new Label("Sequence Description "), BorderLayout.WEST);
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370 panel2.add(description, BorderLayout.CENTER);
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371 panel.add(panel2, BorderLayout.CENTER);
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373 panel2 = new Panel(new FlowLayout());
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375 panel2.add(okDialog);
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376 panel2.add(cancelDialog);
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378 panel.add(panel2, BorderLayout.SOUTH);
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380 editNameDialog = new Dialog(ap.alignFrame,
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381 "Edit Sequence Name / Description",
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384 editNameDialog.add(panel, BorderLayout.NORTH);
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386 editNameDialog.setBounds(ap.alignFrame.getBounds().x
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387 +(ap.alignFrame.getSize().width-500)/2 ,
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388 ap.alignFrame.getBounds().y
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389 +(ap.alignFrame.getSize().height-120)/2,
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392 editNameDialog.show();
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394 if (editNameDialog != null)
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396 seq.setName(id.getText());
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397 seq.setDescription(description.getText());
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404 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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405 cap.setText("Paste your PDB file here.");
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406 cap.setPDBImport(seq);
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407 Frame frame = new Frame();
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409 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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412 private void jbInit()
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415 groupMenu.setLabel("Group");
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416 groupMenu.setLabel("Selection");
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418 unGroupMenuItem.setLabel("Remove Group");
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419 unGroupMenuItem.addActionListener(this);
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421 nucleotideMenuItem.setLabel("Nucleotide");
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422 nucleotideMenuItem.addActionListener(this);
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423 conservationMenuItem.addItemListener(this);
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424 abovePIDColour.addItemListener(this);
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425 colourMenu.setLabel("Group Colour");
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426 showBoxes.setLabel("Boxes");
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427 showBoxes.setState(true);
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428 showBoxes.addItemListener(this);
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429 sequenceName.addActionListener(this);
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431 showText.setLabel("Text");
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432 showText.addItemListener(this);
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433 showColourText.setLabel("Colour Text");
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434 showColourText.addItemListener(this);
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435 outputmenu.setLabel("Output to Textbox...");
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436 seqMenu.setLabel("Sequence");
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437 pdb.setLabel("View PDB Structure");
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438 hideSeqs.setLabel("Hide Sequences");
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439 repGroup.setLabel("Represent Group with");
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440 revealAll.setLabel("Reveal All");
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441 menu1.setLabel("Group");
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444 this.add(hideSeqs);
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445 this.add(revealAll);
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446 groupMenu.add(editMenu);
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447 groupMenu.add(outputmenu);
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448 groupMenu.add(menu1);
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449 colourMenu.add(noColourmenuItem);
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450 colourMenu.add(clustalColour);
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451 colourMenu.add(BLOSUM62Colour);
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452 colourMenu.add(PIDColour);
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453 colourMenu.add(zappoColour);
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454 colourMenu.add(taylorColour);
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455 colourMenu.add(hydrophobicityColour);
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456 colourMenu.add(helixColour);
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457 colourMenu.add(strandColour);
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458 colourMenu.add(turnColour);
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459 colourMenu.add(buriedColour);
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460 colourMenu.add(nucleotideMenuItem);
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461 colourMenu.add(userDefinedColour);
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462 colourMenu.addSeparator();
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463 colourMenu.add(abovePIDColour);
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464 colourMenu.add(conservationMenuItem);
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466 noColourmenuItem.setLabel("None");
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467 noColourmenuItem.addActionListener(this);
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469 clustalColour.setLabel("Clustalx colours");
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470 clustalColour.addActionListener(this);
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471 zappoColour.setLabel("Zappo");
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472 zappoColour.addActionListener(this);
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473 taylorColour.setLabel("Taylor");
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474 taylorColour.addActionListener(this);
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475 hydrophobicityColour.setLabel("Hydrophobicity");
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476 hydrophobicityColour.addActionListener(this);
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477 helixColour.setLabel("Helix propensity");
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478 helixColour.addActionListener(this);
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479 strandColour.setLabel("Strand propensity");
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480 strandColour.addActionListener(this);
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481 turnColour.setLabel("Turn propensity");
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482 turnColour.addActionListener(this);
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483 buriedColour.setLabel("Buried Index");
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484 buriedColour.addActionListener(this);
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485 abovePIDColour.setLabel("Above % Identity");
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487 userDefinedColour.setLabel("User Defined");
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488 userDefinedColour.addActionListener(this);
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489 PIDColour.setLabel("Percentage Identity");
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490 PIDColour.addActionListener(this);
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491 BLOSUM62Colour.setLabel("BLOSUM62");
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492 BLOSUM62Colour.addActionListener(this);
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493 conservationMenuItem.setLabel("Conservation");
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495 editMenu.add(copy);
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496 copy.addActionListener(this);
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498 cut.addActionListener(this);
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499 editMenu.add(toUpper);
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500 toUpper.addActionListener(this);
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501 editMenu.add(toLower);
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502 toLower.addActionListener(this);
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503 editMenu.add(toggleCase);
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504 seqMenu.add(sequenceName);
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506 seqMenu.add(repGroup);
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507 menu1.add(unGroupMenuItem);
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508 menu1.add(colourMenu);
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509 menu1.add(showBoxes);
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510 menu1.add(showText);
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511 menu1.add(showColourText);
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512 toggleCase.addActionListener(this);
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513 pdb.addActionListener(this);
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514 hideSeqs.addActionListener(this);
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515 repGroup.addActionListener(this);
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516 revealAll.addActionListener(this);
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517 okDialog.addActionListener(this);
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518 cancelDialog.addActionListener(this);
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524 ap.seqPanel.seqCanvas.repaint();
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525 if(ap.overviewPanel!=null)
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526 ap.overviewPanel.updateOverviewImage();
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529 protected void clustalColour_actionPerformed()
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531 SequenceGroup sg = getGroup();
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532 sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
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536 protected void zappoColour_actionPerformed()
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538 getGroup().cs = new ZappoColourScheme();
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542 protected void taylorColour_actionPerformed()
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544 getGroup().cs = new TaylorColourScheme();
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548 protected void hydrophobicityColour_actionPerformed()
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550 getGroup().cs = new HydrophobicColourScheme();
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554 protected void helixColour_actionPerformed()
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556 getGroup().cs = new HelixColourScheme();
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560 protected void strandColour_actionPerformed()
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562 getGroup().cs = new StrandColourScheme();
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566 protected void turnColour_actionPerformed()
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568 getGroup().cs = new TurnColourScheme();
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572 protected void buriedColour_actionPerformed()
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574 getGroup().cs = new BuriedColourScheme();
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578 public void nucleotideMenuItem_actionPerformed()
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580 getGroup().cs = new NucleotideColourScheme();
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584 protected void abovePIDColour_itemStateChanged()
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586 SequenceGroup sg = getGroup();
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590 if (abovePIDColour.getState())
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592 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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593 ap.av.alignment.getWidth()));
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594 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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595 getGroup().getName());
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597 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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599 SliderPanel.showPIDSlider();
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602 else // remove PIDColouring
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604 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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611 protected void userDefinedColour_actionPerformed()
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613 new UserDefinedColours(ap, getGroup());
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616 protected void PIDColour_actionPerformed()
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618 SequenceGroup sg = getGroup();
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619 sg.cs = new PIDColourScheme();
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620 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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621 ap.av.alignment.getWidth()));
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625 protected void BLOSUM62Colour_actionPerformed()
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627 SequenceGroup sg = getGroup();
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629 sg.cs = new Blosum62ColourScheme();
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631 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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632 ap.av.alignment.getWidth()));
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637 protected void noColourmenuItem_actionPerformed()
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639 getGroup().cs = null;
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643 protected void conservationMenuItem_itemStateChanged()
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645 SequenceGroup sg = getGroup();
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649 if (conservationMenuItem.getState())
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652 Conservation c = new Conservation("Group",
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653 ResidueProperties.propHash, 3,
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654 sg.getSequences(true), 0,
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655 ap.av.alignment.getWidth());
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658 c.verdict(false, ap.av.ConsPercGaps);
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660 sg.cs.setConservation(c);
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662 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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663 SliderPanel.showConservationSlider();
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665 else // remove ConservationColouring
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667 sg.cs.setConservation(null);
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674 SequenceGroup getGroup()
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676 SequenceGroup sg = ap.av.getSelectionGroup();
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678 // this method won't add a new group if it already exists
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680 ap.av.alignment.addGroup(sg);
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685 void unGroupMenuItem_actionPerformed()
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687 SequenceGroup sg = ap.av.getSelectionGroup();
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688 ap.av.alignment.deleteGroup(sg);
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689 ap.av.setSelectionGroup(null);
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693 public void showColourText_itemStateChanged()
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695 getGroup().setColourText(showColourText.getState());
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699 public void showText_itemStateChanged()
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701 getGroup().setDisplayText(showText.getState());
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705 public void showBoxes_itemStateChanged()
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707 getGroup().setDisplayBoxes(showBoxes.getState());
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711 void hideSequences(boolean representGroup)
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713 SequenceGroup sg = ap.av.getSelectionGroup();
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714 if(sg==null || sg.getSize(false)<1)
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716 ap.av.hideSequence(new SequenceI[]{seq});
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720 int gsize = sg.getSize(false);
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721 SequenceI [] hseqs;
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723 hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
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726 for(int i=0; i<gsize; i++)
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728 if(representGroup && sg.getSequenceAt(i)!=seq)
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730 seq.addHiddenSequence(sg.getSequenceAt(i));
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731 hseqs[index++] = sg.getSequenceAt(i);
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733 else if(!representGroup)
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735 hseqs[index++] = sg.getSequenceAt(i);
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739 ap.av.hideSequence(hseqs);
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741 ap.av.setSelectionGroup(null);
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