src/jalview/appletgui/APopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import java.awt.*;\r
  23 import java.awt.event.*;\r
  24 import java.util.Vector;\r
  25 \r
  26 import jalview.analysis.*;\r
  27 import jalview.datamodel.*;\r
  28 import jalview.schemes.*;\r
  29 \r
  30 public class APopupMenu\r
  31     extends java.awt.PopupMenu\r
  32 {\r
  33   Menu groupMenu = new Menu();\r
  34   protected MenuItem clustalColour = new MenuItem();\r
  35   protected MenuItem zappoColour = new MenuItem();\r
  36   protected MenuItem taylorColour = new MenuItem();\r
  37   protected MenuItem hydrophobicityColour = new MenuItem();\r
  38   protected MenuItem helixColour = new MenuItem();\r
  39   protected MenuItem strandColour = new MenuItem();\r
  40   protected MenuItem turnColour = new MenuItem();\r
  41   protected MenuItem buriedColour = new MenuItem();\r
  42   protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();\r
  43   protected MenuItem userDefinedColour = new MenuItem();\r
  44   protected MenuItem PIDColour = new MenuItem();\r
  45   protected MenuItem BLOSUM62Colour = new MenuItem();\r
  46   MenuItem noColourmenuItem = new MenuItem();\r
  47   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
  48 \r
  49   AlignmentPanel ap;\r
  50   MenuItem unGroupMenuItem = new MenuItem();\r
  51   MenuItem nucleotideMenuItem = new MenuItem();\r
  52   Menu colourMenu = new Menu();\r
  53   CheckboxMenuItem showBoxes = new CheckboxMenuItem();\r
  54   CheckboxMenuItem showText = new CheckboxMenuItem();\r
  55   CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
  56 \r
  57   public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\r
  58   {\r
  59     ///////////////////////////////////////////////////////////\r
  60     // If this is activated from the sequence panel, the user may want to\r
  61     // edit or annotate a particular residue. Therefore display the residue menu\r
  62     //\r
  63     // If from the IDPanel, we must display the sequence menu\r
  64     //////////////////////////////////////////////////////////\r
  65 \r
  66     this.ap = ap;\r
  67 \r
  68     try\r
  69     {\r
  70       jbInit();\r
  71     }\r
  72     catch (Exception e)\r
  73     {\r
  74       e.printStackTrace();\r
  75     }\r
  76 \r
  77     SequenceGroup sg = ap.av.getSelectionGroup();\r
  78     if (sg != null)\r
  79     {\r
  80       showText.setState(sg.getDisplayText());\r
  81       showColourText.setState(sg.getColourText());\r
  82       showBoxes.setState(sg.getDisplayBoxes());\r
  83     }\r
  84 \r
  85     if (!ap.av.alignment.getGroups().contains(sg))\r
  86     {\r
  87       groupMenu.remove(unGroupMenuItem);\r
  88     }\r
  89 \r
  90     if (seq != null && links!=null)\r
  91     {\r
  92       Menu linkMenu = new Menu("Link");\r
  93       MenuItem item;\r
  94       String link;\r
  95       for(int i=0; i<links.size(); i++)\r
  96       {\r
  97         link = links.elementAt(i).toString();\r
  98         final String target = link.substring(0, link.indexOf("|"));\r
  99         item = new MenuItem(target);\r
 100         final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
 101                + seq.getName() +\r
 102                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 103 \r
 104            item.addActionListener(new java.awt.event.ActionListener()\r
 105            {\r
 106                public void actionPerformed(ActionEvent e)\r
 107                {\r
 108                   jalview.bin.JalviewLite.showURL(url, target);\r
 109                }\r
 110            });\r
 111           linkMenu.add(item);\r
 112       }\r
 113       add(linkMenu);\r
 114     }\r
 115   }\r
 116 \r
 117   private void jbInit()\r
 118       throws Exception\r
 119   {\r
 120     groupMenu.setLabel("Group");\r
 121     groupMenu.setLabel("Define");\r
 122 \r
 123     unGroupMenuItem.setLabel("Remove Group");\r
 124     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 125     {\r
 126       public void actionPerformed(ActionEvent e)\r
 127       {\r
 128         unGroupMenuItem_actionPerformed(e);\r
 129       }\r
 130     });\r
 131 \r
 132     nucleotideMenuItem.setLabel("Nucleotide");\r
 133     nucleotideMenuItem.addActionListener(new ActionListener()\r
 134     {\r
 135       public void actionPerformed(ActionEvent e)\r
 136       {\r
 137         nucleotideMenuItem_actionPerformed(e);\r
 138       }\r
 139     });\r
 140     conservationMenuItem.addItemListener(new ItemListener()\r
 141     {\r
 142       public void itemStateChanged(ItemEvent itemEvent)\r
 143       {\r
 144         conservationMenuItem_itemStateChanged(itemEvent);\r
 145       }\r
 146     });\r
 147     abovePIDColour.addItemListener(new ItemListener()\r
 148     {\r
 149       public void itemStateChanged(ItemEvent itemEvent)\r
 150       {\r
 151         abovePIDColour_itemStateChanged(itemEvent);\r
 152       }\r
 153     });\r
 154     colourMenu.setLabel("Group Colour");\r
 155     showBoxes.setLabel("Boxes");\r
 156     showBoxes.setState(true);\r
 157     showBoxes.addItemListener(new ItemListener()\r
 158     {\r
 159       public void itemStateChanged(ItemEvent itemEvent)\r
 160       {\r
 161         showBoxes_itemStateChanged(itemEvent);\r
 162       }\r
 163     });\r
 164 \r
 165     showText.setLabel("Text");\r
 166     showText.addItemListener(new ItemListener()\r
 167     {\r
 168       public void itemStateChanged(ItemEvent itemEvent)\r
 169       {\r
 170         showText_itemStateChanged(itemEvent);\r
 171       }\r
 172     });\r
 173     showColourText.setLabel("Colour Text");\r
 174     showColourText.addItemListener(new ItemListener()\r
 175     {\r
 176       public void itemStateChanged(ItemEvent itemEvent)\r
 177       {\r
 178         showColourText_itemStateChanged(itemEvent);\r
 179       }\r
 180     });\r
 181 \r
 182     add(groupMenu);\r
 183     groupMenu.add(unGroupMenuItem);\r
 184     groupMenu.add(colourMenu);\r
 185     groupMenu.addSeparator();\r
 186     groupMenu.add(showBoxes);\r
 187     groupMenu.add(showText);\r
 188     groupMenu.add(showColourText);\r
 189     colourMenu.add(noColourmenuItem);\r
 190     colourMenu.add(clustalColour);\r
 191     colourMenu.add(BLOSUM62Colour);\r
 192     colourMenu.add(PIDColour);\r
 193     colourMenu.add(zappoColour);\r
 194     colourMenu.add(taylorColour);\r
 195     colourMenu.add(hydrophobicityColour);\r
 196     colourMenu.add(helixColour);\r
 197     colourMenu.add(strandColour);\r
 198     colourMenu.add(turnColour);\r
 199     colourMenu.add(buriedColour);\r
 200     colourMenu.add(nucleotideMenuItem);\r
 201     colourMenu.add(userDefinedColour);\r
 202     colourMenu.addSeparator();\r
 203     colourMenu.add(abovePIDColour);\r
 204     colourMenu.add(conservationMenuItem);\r
 205 \r
 206     noColourmenuItem.setLabel("None");\r
 207     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 208     {\r
 209       public void actionPerformed(ActionEvent e)\r
 210       {\r
 211         noColourmenuItem_actionPerformed(e);\r
 212       }\r
 213     });\r
 214 \r
 215     clustalColour.setLabel("Clustalx colours");\r
 216     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 217     {\r
 218       public void actionPerformed(ActionEvent e)\r
 219       {\r
 220         clustalColour_actionPerformed(e);\r
 221       }\r
 222     });\r
 223     zappoColour.setLabel("Zappo");\r
 224     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 225     {\r
 226       public void actionPerformed(ActionEvent e)\r
 227       {\r
 228         zappoColour_actionPerformed(e);\r
 229       }\r
 230     });\r
 231     taylorColour.setLabel("Taylor");\r
 232     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 233     {\r
 234       public void actionPerformed(ActionEvent e)\r
 235       {\r
 236         taylorColour_actionPerformed(e);\r
 237       }\r
 238     });\r
 239     hydrophobicityColour.setLabel("Hydrophobicity");\r
 240     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 241     {\r
 242       public void actionPerformed(ActionEvent e)\r
 243       {\r
 244         hydrophobicityColour_actionPerformed(e);\r
 245       }\r
 246     });\r
 247     helixColour.setLabel("Helix propensity");\r
 248     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 249     {\r
 250       public void actionPerformed(ActionEvent e)\r
 251       {\r
 252         helixColour_actionPerformed(e);\r
 253       }\r
 254     });\r
 255     strandColour.setLabel("Strand propensity");\r
 256     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 257     {\r
 258       public void actionPerformed(ActionEvent e)\r
 259       {\r
 260         strandColour_actionPerformed(e);\r
 261       }\r
 262     });\r
 263     turnColour.setLabel("Turn propensity");\r
 264     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 265     {\r
 266       public void actionPerformed(ActionEvent e)\r
 267       {\r
 268         turnColour_actionPerformed(e);\r
 269       }\r
 270     });\r
 271     buriedColour.setLabel("Buried Index");\r
 272     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 273     {\r
 274       public void actionPerformed(ActionEvent e)\r
 275       {\r
 276         buriedColour_actionPerformed(e);\r
 277       }\r
 278     });\r
 279     abovePIDColour.setLabel("Above % Identity");\r
 280 \r
 281     userDefinedColour.setLabel("User Defined");\r
 282     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 283     {\r
 284       public void actionPerformed(ActionEvent e)\r
 285       {\r
 286         userDefinedColour_actionPerformed(e);\r
 287       }\r
 288     });\r
 289     PIDColour.setLabel("Percentage Identity");\r
 290     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 291     {\r
 292       public void actionPerformed(ActionEvent e)\r
 293       {\r
 294         PIDColour_actionPerformed(e);\r
 295       }\r
 296     });\r
 297     BLOSUM62Colour.setLabel("BLOSUM62");\r
 298     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 299     {\r
 300       public void actionPerformed(ActionEvent e)\r
 301       {\r
 302         BLOSUM62Colour_actionPerformed(e);\r
 303       }\r
 304     });\r
 305     conservationMenuItem.setLabel("Conservation");\r
 306 \r
 307   }\r
 308 \r
 309   void refresh()\r
 310   {\r
 311     SequenceGroup sg = getGroup();\r
 312     if(sg!=null)\r
 313     {\r
 314       SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
 315 \r
 316       if (superG != null)\r
 317       {\r
 318         superG.setSuperGroupProperties(sg);\r
 319       }\r
 320         }\r
 321     ap.seqPanel.seqCanvas.repaint();\r
 322   }\r
 323 \r
 324   protected void clustalColour_actionPerformed(ActionEvent e)\r
 325   {\r
 326     SequenceGroup sg = getGroup();\r
 327     sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
 328     refresh();\r
 329   }\r
 330 \r
 331   protected void zappoColour_actionPerformed(ActionEvent e)\r
 332   {\r
 333     getGroup().cs = new ZappoColourScheme();\r
 334     refresh();\r
 335   }\r
 336 \r
 337   protected void taylorColour_actionPerformed(ActionEvent e)\r
 338   {\r
 339     getGroup().cs = new TaylorColourScheme();\r
 340     refresh();\r
 341   }\r
 342 \r
 343   protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 344   {\r
 345     getGroup().cs = new HydrophobicColourScheme();\r
 346     refresh();\r
 347   }\r
 348 \r
 349   protected void helixColour_actionPerformed(ActionEvent e)\r
 350   {\r
 351     getGroup().cs = new HelixColourScheme();\r
 352     refresh();\r
 353   }\r
 354 \r
 355   protected void strandColour_actionPerformed(ActionEvent e)\r
 356   {\r
 357     getGroup().cs = new StrandColourScheme();\r
 358     refresh();\r
 359   }\r
 360 \r
 361   protected void turnColour_actionPerformed(ActionEvent e)\r
 362   {\r
 363     getGroup().cs = new TurnColourScheme();\r
 364     refresh();\r
 365   }\r
 366 \r
 367   protected void buriedColour_actionPerformed(ActionEvent e)\r
 368   {\r
 369     getGroup().cs = new BuriedColourScheme();\r
 370     refresh();\r
 371   }\r
 372 \r
 373   public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
 374   {\r
 375     getGroup().cs = new NucleotideColourScheme();\r
 376     refresh();\r
 377   }\r
 378 \r
 379   protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
 380   {\r
 381     SequenceGroup sg = getGroup();\r
 382     if(sg.cs==null)\r
 383           return;\r
 384 \r
 385     if (abovePIDColour.getState())\r
 386     {\r
 387       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 388                                                ap.av.alignment.getWidth()));\r
 389       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 390           getGroup().getName());\r
 391 \r
 392       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 393 \r
 394       SliderPanel.showPIDSlider();\r
 395 \r
 396     }\r
 397     else // remove PIDColouring\r
 398     {\r
 399       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 400     }\r
 401 \r
 402     refresh();\r
 403 \r
 404   }\r
 405 \r
 406   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 407   {\r
 408     new UserDefinedColours(ap, getGroup());\r
 409   }\r
 410 \r
 411   protected void PIDColour_actionPerformed(ActionEvent e)\r
 412   {\r
 413     SequenceGroup sg = getGroup();\r
 414     sg.cs = new PIDColourScheme();\r
 415     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 416                                              ap.av.alignment.getWidth()));\r
 417     refresh();\r
 418   }\r
 419 \r
 420   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 421   {\r
 422     SequenceGroup sg = getGroup();\r
 423 \r
 424     sg.cs = new Blosum62ColourScheme();\r
 425 \r
 426     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
 427                                              ap.av.alignment.getWidth()));\r
 428 \r
 429     refresh();\r
 430   }\r
 431 \r
 432   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 433   {\r
 434     getGroup().cs = null;\r
 435     refresh();\r
 436   }\r
 437 \r
 438   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
 439   {\r
 440     SequenceGroup sg = getGroup();\r
 441     if(sg.cs==null)\r
 442           return;\r
 443 \r
 444     if (conservationMenuItem.getState())\r
 445     {\r
 446 \r
 447       Conservation c = new Conservation("Group",\r
 448                                         ResidueProperties.propHash, 3,\r
 449                                         sg.sequences, 0,\r
 450                                         ap.av.alignment.getWidth());\r
 451 \r
 452       c.calculate();\r
 453       c.verdict(false, ap.av.ConsPercGaps);\r
 454 \r
 455       sg.cs.setConservation(c);\r
 456 \r
 457       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
 458       SliderPanel.showConservationSlider();\r
 459     }\r
 460     else // remove ConservationColouring\r
 461     {\r
 462       sg.cs.setConservation(null);\r
 463     }\r
 464 \r
 465     refresh();\r
 466   }\r
 467 \r
 468   protected void analyze_actionPerformed(ActionEvent e)\r
 469   {\r
 470     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 471     Frame frame = new Frame();\r
 472     frame.add(cap);\r
 473     jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
 474     SequenceGroup sg = getGroup();\r
 475     StringBuffer sb = new StringBuffer();\r
 476 \r
 477     for (int i = 0; i < sg.sequences.size(); i++)\r
 478     {\r
 479       Sequence tmp = (Sequence) sg.sequences.elementAt(i);\r
 480       sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
 481       sb.append("\n");\r
 482     }\r
 483 \r
 484     sb.append("Something amazing will happen soon");\r
 485     cap.setText(sb.toString());\r
 486 \r
 487   }\r
 488 \r
 489   SequenceGroup getGroup()\r
 490   {\r
 491     SequenceGroup sg = ap.av.getSelectionGroup();\r
 492 \r
 493     // this method won't add a new group if it already exists\r
 494     if(sg!=null)\r
 495       ap.av.alignment.addGroup(sg);\r
 496 \r
 497     return sg;\r
 498   }\r
 499 \r
 500   void unGroupMenuItem_actionPerformed(ActionEvent e)\r
 501   {\r
 502     SequenceGroup sg = ap.av.getSelectionGroup();\r
 503     ap.av.alignment.deleteGroup(sg);\r
 504     ap.av.setSelectionGroup(null);\r
 505     ap.repaint();\r
 506   }\r
 507 \r
 508   public void showColourText_itemStateChanged(ItemEvent itemEvent)\r
 509   {\r
 510     getGroup().setColourText(showColourText.getState());\r
 511     refresh();\r
 512   }\r
 513 \r
 514   public void showText_itemStateChanged(ItemEvent itemEvent)\r
 515   {\r
 516     getGroup().setDisplayText(showText.getState());\r
 517     refresh();\r
 518   }\r
 519 \r
 520   public void showBoxes_itemStateChanged(ItemEvent itemEvent)\r
 521   {\r
 522     getGroup().setDisplayBoxes(showBoxes.getState());\r
 523     refresh();\r
 524   }\r
 525 \r
 526 }\r