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