2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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30 public class APopupMenu
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31 extends java.awt.PopupMenu implements ActionListener, ItemListener
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33 Menu groupMenu = new Menu();
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34 protected MenuItem clustalColour = new MenuItem();
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35 protected MenuItem zappoColour = new MenuItem();
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36 protected MenuItem taylorColour = new MenuItem();
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37 protected MenuItem hydrophobicityColour = new MenuItem();
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38 protected MenuItem helixColour = new MenuItem();
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39 protected MenuItem strandColour = new MenuItem();
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40 protected MenuItem turnColour = new MenuItem();
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41 protected MenuItem buriedColour = new MenuItem();
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42 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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43 protected MenuItem userDefinedColour = new MenuItem();
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44 protected MenuItem PIDColour = new MenuItem();
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45 protected MenuItem BLOSUM62Colour = new MenuItem();
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46 MenuItem noColourmenuItem = new MenuItem();
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47 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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49 final AlignmentPanel ap;
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50 MenuItem unGroupMenuItem = new MenuItem();
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51 MenuItem nucleotideMenuItem = new MenuItem();
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52 Menu colourMenu = new Menu();
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53 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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54 CheckboxMenuItem showText = new CheckboxMenuItem();
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55 CheckboxMenuItem showColourText = new CheckboxMenuItem();
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56 Menu editMenu = new Menu("Edit");
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57 MenuItem copy = new MenuItem("Copy (Jalview Only)");
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58 MenuItem cut = new MenuItem("Cut (Jalview Only)");
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59 MenuItem toUpper = new MenuItem("To Upper Case");
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60 MenuItem toLower = new MenuItem("To Lower Case");
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61 MenuItem toggleCase = new MenuItem("Toggle Case");
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62 Menu outputmenu = new Menu();
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63 Menu seqMenu = new Menu();
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64 MenuItem pdb = new MenuItem();
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65 MenuItem hideSeqs = new MenuItem();
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66 MenuItem repGroup = new MenuItem();
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69 MenuItem revealAll = new MenuItem();
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71 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
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73 ///////////////////////////////////////////////////////////
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74 // If this is activated from the sequence panel, the user may want to
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75 // edit or annotate a particular residue. Therefore display the residue menu
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77 // If from the IDPanel, we must display the sequence menu
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78 //////////////////////////////////////////////////////////
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89 e.printStackTrace();
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92 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-1; i++)
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94 MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
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97 item.addActionListener(this);
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98 outputmenu.add(item);
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101 SequenceGroup sg = ap.av.getSelectionGroup();
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103 if (sg != null && sg.getSize(false)>0)
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105 showText.setState(sg.getDisplayText());
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106 showColourText.setState(sg.getColourText());
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107 showBoxes.setState(sg.getDisplayBoxes());
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108 if (!ap.av.alignment.getGroups().contains(sg))
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110 groupMenu.remove(unGroupMenuItem);
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121 Menu linkMenu = new Menu("Link");
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124 for(int i=0; i<links.size(); i++)
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126 link = links.elementAt(i).toString();
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127 final String target = link.substring(0, link.indexOf("|"));
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128 item = new MenuItem(target);
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132 if (link.indexOf("$SEQUENCE_ID$") > -1)
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134 String id = seq.getName();
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135 if (id.indexOf("|") > -1)
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136 id = id.substring(id.lastIndexOf("|") + 1);
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138 url = link.substring(link.indexOf("|") + 1,
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139 link.indexOf("$SEQUENCE_ID$"))
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141 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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144 url = link.substring(link.lastIndexOf("|")+1);
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146 item.addActionListener(new java.awt.event.ActionListener()
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148 public void actionPerformed(ActionEvent e)
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150 ap.alignFrame.showURL(url, target);
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153 linkMenu.add(item);
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155 seqMenu.add(linkMenu);
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159 seqMenu.setLabel(seq.getName());
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160 repGroup.setLabel("Represent Group with " + seq.getName());
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165 if(!ap.av.hasHiddenRows)
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169 public void itemStateChanged(ItemEvent evt)
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171 if(evt.getSource()==abovePIDColour)
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172 abovePIDColour_itemStateChanged();
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173 else if(evt.getSource()==showColourText)
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174 showColourText_itemStateChanged();
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175 else if(evt.getSource()==showText)
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176 showText_itemStateChanged();
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177 else if(evt.getSource()==showBoxes)
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178 showBoxes_itemStateChanged() ;
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181 public void actionPerformed(ActionEvent evt)
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183 Object source = evt.getSource();
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184 if(source==clustalColour)
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185 clustalColour_actionPerformed();
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186 else if(source==zappoColour)
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187 zappoColour_actionPerformed();
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188 else if(source==taylorColour)
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189 taylorColour_actionPerformed();
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190 else if(source==hydrophobicityColour)
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191 hydrophobicityColour_actionPerformed();
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192 else if(source==helixColour)
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193 helixColour_actionPerformed();
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194 else if(source==strandColour)
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195 strandColour_actionPerformed();
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196 else if(source==clustalColour)
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197 turnColour_actionPerformed();
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198 else if(source==buriedColour)
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199 buriedColour_actionPerformed();
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200 else if(source==nucleotideMenuItem)
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201 nucleotideMenuItem_actionPerformed();
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203 else if (source == userDefinedColour)
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204 userDefinedColour_actionPerformed();
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205 else if (source == PIDColour)
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206 PIDColour_actionPerformed();
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207 else if (source == BLOSUM62Colour)
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208 BLOSUM62Colour_actionPerformed();
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209 else if (source == noColourmenuItem)
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210 noColourmenuItem_actionPerformed();
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211 else if (source == conservationMenuItem)
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212 conservationMenuItem_itemStateChanged();
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213 else if (source == unGroupMenuItem)
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214 unGroupMenuItem_actionPerformed();
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216 else if(source == pdb)
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218 else if(source == hideSeqs)
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219 hideSequences(false);
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220 else if(source == repGroup)
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221 hideSequences(true);
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222 else if(source == revealAll)
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224 ap.av.showAllHiddenSeqs();
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228 else if(source==copy)
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229 ap.alignFrame.copy_actionPerformed();
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230 else if(source==cut)
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231 ap.alignFrame.cut_actionPerformed();
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232 else if(source==toUpper || source==toLower || source==toggleCase)
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234 SequenceGroup sg = ap.av.getSelectionGroup();
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237 for (int g = 0; g < sg.getSize(true); g++)
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239 if (source == toggleCase)
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240 ((SequenceI) sg.getSequences(true).elementAt(g))
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241 .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
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243 ((SequenceI) sg.getSequences(true).elementAt(g))
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244 .changeCase(source == toUpper, sg.getStartRes(),
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245 sg.getEndRes() + 1);
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247 ap.seqPanel.seqCanvas.repaint();
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255 void outputText(ActionEvent e)
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257 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
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258 Vector vseqs = new Vector();
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260 String [] selection = ap.av.getViewAsString(true);
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261 SequenceI [] seqs = ap.av.getSelectionAsNewSequence();
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262 if (selection != null)
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264 for (int i = 0; i < selection.length; i++)
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266 Sequence seq = new Sequence(
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269 seqs[i].getStart(), seqs[i].getEnd());
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270 seq.setDescription(seqs[i].getDescription());
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271 vseqs.addElement( seq );
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275 Frame frame = new Frame();
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277 jalview.bin.JalviewLite.addFrame(frame,
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278 "Selection output - " + e.getActionCommand(),
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281 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
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282 e.getActionCommand(),
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284 ap.av.showJVSuffix));
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290 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
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291 cap.setText("Paste your PDB file here.");
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292 cap.setPDBImport(seq);
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293 Frame frame = new Frame();
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295 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
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298 private void jbInit()
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301 groupMenu.setLabel("Group");
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302 groupMenu.setLabel("Selection");
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304 unGroupMenuItem.setLabel("Remove Group");
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305 unGroupMenuItem.addActionListener(this);
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307 nucleotideMenuItem.setLabel("Nucleotide");
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308 nucleotideMenuItem.addActionListener(this);
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309 conservationMenuItem.addItemListener(this);
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310 abovePIDColour.addItemListener(this);
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311 colourMenu.setLabel("Group Colour");
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312 showBoxes.setLabel("Boxes");
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313 showBoxes.setState(true);
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314 showBoxes.addItemListener(this);
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316 showText.setLabel("Text");
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317 showText.addItemListener(this);
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318 showColourText.setLabel("Colour Text");
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319 showColourText.addItemListener(this);
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320 outputmenu.setLabel("Output to Textbox...");
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321 seqMenu.setLabel("Sequence");
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322 pdb.setLabel("View PDB Structure");
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323 hideSeqs.setLabel("Hide Sequences");
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324 repGroup.setLabel("Represent Group with");
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325 revealAll.setLabel("Reveal All");
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329 this.add(hideSeqs);
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330 this.add(revealAll);
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331 groupMenu.add(editMenu);
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332 groupMenu.add(outputmenu);
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333 groupMenu.addSeparator();
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334 groupMenu.add(unGroupMenuItem);
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335 groupMenu.add(colourMenu);
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336 groupMenu.add(showBoxes);
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337 groupMenu.add(showText);
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338 groupMenu.add(showColourText);
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339 colourMenu.add(noColourmenuItem);
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340 colourMenu.add(clustalColour);
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341 colourMenu.add(BLOSUM62Colour);
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342 colourMenu.add(PIDColour);
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343 colourMenu.add(zappoColour);
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344 colourMenu.add(taylorColour);
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345 colourMenu.add(hydrophobicityColour);
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346 colourMenu.add(helixColour);
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347 colourMenu.add(strandColour);
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348 colourMenu.add(turnColour);
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349 colourMenu.add(buriedColour);
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350 colourMenu.add(nucleotideMenuItem);
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351 colourMenu.add(userDefinedColour);
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352 colourMenu.addSeparator();
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353 colourMenu.add(abovePIDColour);
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354 colourMenu.add(conservationMenuItem);
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356 noColourmenuItem.setLabel("None");
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357 noColourmenuItem.addActionListener(this);
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359 clustalColour.setLabel("Clustalx colours");
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360 clustalColour.addActionListener(this);
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361 zappoColour.setLabel("Zappo");
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362 zappoColour.addActionListener(this);
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363 taylorColour.setLabel("Taylor");
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364 taylorColour.addActionListener(this);
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365 hydrophobicityColour.setLabel("Hydrophobicity");
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366 hydrophobicityColour.addActionListener(this);
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367 helixColour.setLabel("Helix propensity");
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368 helixColour.addActionListener(this);
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369 strandColour.setLabel("Strand propensity");
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370 strandColour.addActionListener(this);
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371 turnColour.setLabel("Turn propensity");
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372 turnColour.addActionListener(this);
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373 buriedColour.setLabel("Buried Index");
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374 buriedColour.addActionListener(this);
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375 abovePIDColour.setLabel("Above % Identity");
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377 userDefinedColour.setLabel("User Defined");
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378 userDefinedColour.addActionListener(this);
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379 PIDColour.setLabel("Percentage Identity");
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380 PIDColour.addActionListener(this);
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381 BLOSUM62Colour.setLabel("BLOSUM62");
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382 BLOSUM62Colour.addActionListener(this);
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383 conservationMenuItem.setLabel("Conservation");
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385 editMenu.add(copy);
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386 copy.addActionListener(this);
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388 cut.addActionListener(this);
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389 editMenu.add(toUpper);
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390 toUpper.addActionListener(this);
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391 editMenu.add(toLower);
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392 toLower.addActionListener(this);
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393 editMenu.add(toggleCase);
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395 seqMenu.add(repGroup);
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396 toggleCase.addActionListener(this);
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397 pdb.addActionListener(this);
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398 hideSeqs.addActionListener(this);
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399 repGroup.addActionListener(this);
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400 revealAll.addActionListener(this);
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406 ap.seqPanel.seqCanvas.repaint();
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407 if(ap.overviewPanel!=null)
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408 ap.overviewPanel.updateOverviewImage();
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411 protected void clustalColour_actionPerformed()
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413 SequenceGroup sg = getGroup();
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414 sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
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418 protected void zappoColour_actionPerformed()
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420 getGroup().cs = new ZappoColourScheme();
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424 protected void taylorColour_actionPerformed()
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426 getGroup().cs = new TaylorColourScheme();
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430 protected void hydrophobicityColour_actionPerformed()
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432 getGroup().cs = new HydrophobicColourScheme();
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436 protected void helixColour_actionPerformed()
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438 getGroup().cs = new HelixColourScheme();
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442 protected void strandColour_actionPerformed()
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444 getGroup().cs = new StrandColourScheme();
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448 protected void turnColour_actionPerformed()
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450 getGroup().cs = new TurnColourScheme();
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454 protected void buriedColour_actionPerformed()
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456 getGroup().cs = new BuriedColourScheme();
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460 public void nucleotideMenuItem_actionPerformed()
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462 getGroup().cs = new NucleotideColourScheme();
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466 protected void abovePIDColour_itemStateChanged()
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468 SequenceGroup sg = getGroup();
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472 if (abovePIDColour.getState())
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474 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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475 ap.av.alignment.getWidth()));
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476 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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477 getGroup().getName());
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479 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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481 SliderPanel.showPIDSlider();
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484 else // remove PIDColouring
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486 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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493 protected void userDefinedColour_actionPerformed()
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495 new UserDefinedColours(ap, getGroup());
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498 protected void PIDColour_actionPerformed()
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500 SequenceGroup sg = getGroup();
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501 sg.cs = new PIDColourScheme();
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502 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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503 ap.av.alignment.getWidth()));
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507 protected void BLOSUM62Colour_actionPerformed()
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509 SequenceGroup sg = getGroup();
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511 sg.cs = new Blosum62ColourScheme();
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513 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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514 ap.av.alignment.getWidth()));
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519 protected void noColourmenuItem_actionPerformed()
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521 getGroup().cs = null;
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525 protected void conservationMenuItem_itemStateChanged()
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527 SequenceGroup sg = getGroup();
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531 if (conservationMenuItem.getState())
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534 Conservation c = new Conservation("Group",
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535 ResidueProperties.propHash, 3,
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536 sg.getSequences(true), 0,
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537 ap.av.alignment.getWidth());
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540 c.verdict(false, ap.av.ConsPercGaps);
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542 sg.cs.setConservation(c);
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544 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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545 SliderPanel.showConservationSlider();
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547 else // remove ConservationColouring
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549 sg.cs.setConservation(null);
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556 SequenceGroup getGroup()
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558 SequenceGroup sg = ap.av.getSelectionGroup();
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560 // this method won't add a new group if it already exists
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562 ap.av.alignment.addGroup(sg);
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567 void unGroupMenuItem_actionPerformed()
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569 SequenceGroup sg = ap.av.getSelectionGroup();
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570 ap.av.alignment.deleteGroup(sg);
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571 ap.av.setSelectionGroup(null);
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575 public void showColourText_itemStateChanged()
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577 getGroup().setColourText(showColourText.getState());
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581 public void showText_itemStateChanged()
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583 getGroup().setDisplayText(showText.getState());
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587 public void showBoxes_itemStateChanged()
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589 getGroup().setDisplayBoxes(showBoxes.getState());
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593 void hideSequences(boolean representGroup)
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595 SequenceGroup sg = ap.av.getSelectionGroup();
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596 if(sg==null || sg.getSize(false)<1)
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598 ap.av.hideSequence(seq);
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603 while(index < sg.getSize(false))
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605 if(representGroup && sg.getSequenceAt(index)!=seq)
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607 seq.addHiddenSequence(sg.getSequenceAt(index));
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608 ap.av.hideSequence(sg.getSequenceAt(index));
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610 else if(!representGroup)
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612 ap.av.hideSequence(sg.getSequenceAt(index));
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617 ap.av.setSelectionGroup(null);
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