1 package jalview.appletgui;
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3 import jalview.datamodel.*;
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4 import jalview.analysis.*;
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5 import jalview.schemes.*;
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7 import java.awt.event.*;
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9 public class APopupMenu extends java.awt.PopupMenu
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11 Menu groupMenu = new Menu();
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12 protected MenuItem clustalColour = new MenuItem();
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13 protected MenuItem zappoColour = new MenuItem();
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14 protected MenuItem taylorColour = new MenuItem();
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15 protected MenuItem hydrophobicityColour = new MenuItem();
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16 protected MenuItem helixColour = new MenuItem();
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17 protected MenuItem strandColour = new MenuItem();
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18 protected MenuItem turnColour = new MenuItem();
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19 protected MenuItem buriedColour = new MenuItem();
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20 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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21 protected MenuItem userDefinedColour = new MenuItem();
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22 protected MenuItem PIDColour = new MenuItem();
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23 protected MenuItem BLOSUM62Colour = new MenuItem();
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24 MenuItem noColourmenuItem = new MenuItem();
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25 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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29 Menu sequenceMenu = new Menu();
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30 MenuItem sequenceName = new MenuItem();
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32 MenuItem unGroupMenuItem = new MenuItem();
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33 MenuItem nucleotideMenuItem = new MenuItem();
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35 public APopupMenu(AlignmentPanel ap, Sequence seq)
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37 ///////////////////////////////////////////////////////////
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38 // If this is activated from the sequence panel, the user may want to
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39 // edit or annotate a particular residue. Therefore display the residue menu
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41 // If from the IDPanel, we must display the sequence menu
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42 //////////////////////////////////////////////////////////
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50 { e.printStackTrace(); }
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53 SequenceGroup sg = ap.av.getSelectionGroup();
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55 if( !ap.av.alignment.getGroups().contains(sg))
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56 groupMenu.remove(unGroupMenuItem);
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59 remove(sequenceMenu);
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63 private void jbInit() throws Exception
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65 groupMenu.setLabel("Group");
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66 groupMenu.setLabel("Define");
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68 sequenceMenu.setLabel("Sequence");
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69 sequenceName.setLabel("Edit name");
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70 unGroupMenuItem.setLabel("Remove Group");
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71 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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73 public void actionPerformed(ActionEvent e)
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75 unGroupMenuItem_actionPerformed(e);
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80 nucleotideMenuItem.setLabel("Nucleotide");
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81 nucleotideMenuItem.addActionListener(new ActionListener()
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83 public void actionPerformed(ActionEvent e)
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85 nucleotideMenuItem_actionPerformed(e);
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90 this.add(sequenceMenu);
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91 groupMenu.add(unGroupMenuItem);
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92 groupMenu.add(noColourmenuItem);
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93 groupMenu.add(clustalColour);
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94 groupMenu.add(BLOSUM62Colour);
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95 groupMenu.add(PIDColour);
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97 groupMenu.add(zappoColour);
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98 groupMenu.add(taylorColour);
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99 groupMenu.add(hydrophobicityColour);
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100 groupMenu.add(helixColour);
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101 groupMenu.add(strandColour);
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102 groupMenu.add(turnColour);
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103 groupMenu.add(buriedColour);
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104 groupMenu.add(nucleotideMenuItem);
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106 groupMenu.add(userDefinedColour);
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108 groupMenu.addSeparator();
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109 groupMenu.add(abovePIDColour);
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110 groupMenu.add(conservationMenuItem);
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112 sequenceMenu.add(sequenceName);
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114 noColourmenuItem.setLabel("None");
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115 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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117 public void actionPerformed(ActionEvent e)
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119 noColourmenuItem_actionPerformed(e);
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123 clustalColour.setLabel("Clustalx colours");
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124 clustalColour.addActionListener(new java.awt.event.ActionListener()
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126 public void actionPerformed(ActionEvent e)
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128 clustalColour_actionPerformed(e);
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131 zappoColour.setLabel("Zappo");
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132 zappoColour.addActionListener(new java.awt.event.ActionListener()
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134 public void actionPerformed(ActionEvent e)
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136 zappoColour_actionPerformed(e);
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139 taylorColour.setLabel("Taylor");
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140 taylorColour.addActionListener(new java.awt.event.ActionListener()
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142 public void actionPerformed(ActionEvent e)
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144 taylorColour_actionPerformed(e);
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147 hydrophobicityColour.setLabel("Hydrophobicity");
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148 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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150 public void actionPerformed(ActionEvent e)
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152 hydrophobicityColour_actionPerformed(e);
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155 helixColour.setLabel("Helix propensity");
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156 helixColour.addActionListener(new java.awt.event.ActionListener()
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158 public void actionPerformed(ActionEvent e)
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160 helixColour_actionPerformed(e);
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163 strandColour.setLabel("Strand propensity");
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164 strandColour.addActionListener(new java.awt.event.ActionListener()
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166 public void actionPerformed(ActionEvent e)
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168 strandColour_actionPerformed(e);
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171 turnColour.setLabel("Turn propensity");
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172 turnColour.addActionListener(new java.awt.event.ActionListener()
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174 public void actionPerformed(ActionEvent e)
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176 turnColour_actionPerformed(e);
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179 buriedColour.setLabel("Buried Index");
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180 buriedColour.addActionListener(new java.awt.event.ActionListener()
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182 public void actionPerformed(ActionEvent e)
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184 buriedColour_actionPerformed(e);
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187 abovePIDColour.setLabel("Above % Identity");
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188 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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190 public void actionPerformed(ActionEvent e)
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192 abovePIDColour_actionPerformed(e);
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195 userDefinedColour.setLabel("User Defined");
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196 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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198 public void actionPerformed(ActionEvent e)
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200 userDefinedColour_actionPerformed(e);
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203 PIDColour.setLabel("Percentage Identity");
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204 PIDColour.addActionListener(new java.awt.event.ActionListener()
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206 public void actionPerformed(ActionEvent e)
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208 PIDColour_actionPerformed(e);
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211 BLOSUM62Colour.setLabel("BLOSUM62");
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212 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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214 public void actionPerformed(ActionEvent e)
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216 BLOSUM62Colour_actionPerformed(e);
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219 conservationMenuItem.setLabel("Conservation");
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220 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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222 public void actionPerformed(ActionEvent e)
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224 conservationMenuItem_actionPerformed(e);
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234 SequenceGroup sg = getGroup();
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235 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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237 superG.setSuperGroupProperties( sg );
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239 ap.seqPanel.seqCanvas.repaint();
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242 protected void clustalColour_actionPerformed(ActionEvent e)
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244 SequenceGroup sg = getGroup();
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245 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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249 protected void zappoColour_actionPerformed(ActionEvent e)
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251 getGroup().cs = new ZappoColourScheme();
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255 protected void taylorColour_actionPerformed(ActionEvent e)
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257 getGroup().cs = new TaylorColourScheme();
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262 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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264 getGroup().cs = new HydrophobicColourScheme();
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268 protected void helixColour_actionPerformed(ActionEvent e)
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270 getGroup().cs = new HelixColourScheme();
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274 protected void strandColour_actionPerformed(ActionEvent e)
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276 getGroup().cs = new StrandColourScheme();
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280 protected void turnColour_actionPerformed(ActionEvent e)
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282 getGroup().cs = new TurnColourScheme();
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286 protected void buriedColour_actionPerformed(ActionEvent e)
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288 getGroup().cs = new BuriedColourScheme();
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292 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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294 getGroup().cs = new NucleotideColourScheme();
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300 protected void abovePIDColour_actionPerformed(ActionEvent e)
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302 SequenceGroup sg = getGroup();
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303 if (abovePIDColour.getState())
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305 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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306 ap.av.alignment.getWidth()));
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307 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
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308 if (sg.cs instanceof ResidueColourScheme)
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309 ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
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310 else if (sg.cs instanceof ScoreColourScheme)
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311 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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313 SliderPanel.showPIDSlider();
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317 else // remove PIDColouring
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319 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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320 rcs.setThreshold(0);
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329 protected void userDefinedColour_actionPerformed(ActionEvent e)
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331 UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());
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334 protected void PIDColour_actionPerformed(ActionEvent e)
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339 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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341 SequenceGroup sg = getGroup();
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343 sg.cs = new Blosum62ColourScheme();
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345 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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346 ap.av.alignment.getWidth()));
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352 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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354 getGroup().cs = null;
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358 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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360 SequenceGroup sg = getGroup();
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362 if(conservationMenuItem.getState())
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365 Conservation c = new Conservation("Group",
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366 ResidueProperties.propHash, 3,
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368 ap.av.alignment.getWidth());
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371 c.verdict(false, ap.av.ConsPercGaps);
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372 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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377 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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378 SliderPanel.showConservationSlider();
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380 else // remove ConservationColouring
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382 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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390 protected void analyze_actionPerformed(ActionEvent e)
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392 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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393 Frame frame = new Frame();
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395 jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
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396 SequenceGroup sg = getGroup();
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397 StringBuffer sb = new StringBuffer();
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399 for(int i=0; i<sg.sequences.size(); i++)
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401 Sequence tmp = (Sequence)sg.sequences.elementAt(i);
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402 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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406 sb.append("Something amazing will happen soon");
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407 cap.setText( sb.toString() );
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411 SequenceGroup getGroup()
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413 SequenceGroup sg = ap.av.getSelectionGroup();
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415 // this method won't add a new group if it already exists
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416 ap.av.alignment.addGroup(sg);
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421 void unGroupMenuItem_actionPerformed(ActionEvent e)
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423 SequenceGroup sg = ap.av.getSelectionGroup();
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424 ap.av.alignment.deleteGroup(sg);
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425 ap.av.setSelectionGroup(null);
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