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 javax.swing.*;
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8 import java.awt.event.*;
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12 public class PopupMenu extends JPopupMenu
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14 JMenu groupMenu = new JMenu();
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15 JMenuItem analyze = new JMenuItem();
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16 JMenu defineMenu = new JMenu();
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17 JMenuItem groupName = new JMenuItem();
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18 JMenuItem groupAnnotation = new JMenuItem();
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19 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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20 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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21 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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22 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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23 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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24 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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25 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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26 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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27 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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28 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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29 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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30 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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31 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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32 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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36 JMenu sequenceMenu = new JMenu();
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37 JMenuItem sequenceName = new JMenuItem();
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38 JMenu residueMenu = new JMenu();
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39 JMenuItem annotateResidue = new JMenuItem();
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42 JMenuItem unGroupMenuItem = new JMenuItem();
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43 JMenuItem pdbMenuItem = new JMenuItem();
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44 JMenuItem outline = new JMenuItem();
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45 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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47 public PopupMenu(AlignmentPanel ap, Sequence seq)
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49 ///////////////////////////////////////////////////////////
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50 // If this is activated from the sequence panel, the user may want to
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51 // edit or annotate a particular residue. Therefore display the residue menu
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53 // If from the IDPanel, we must display the sequence menu
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54 //////////////////////////////////////////////////////////
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59 ButtonGroup colours = new ButtonGroup();
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60 colours.add(noColourmenuItem);
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61 colours.add(clustalColour);
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62 colours.add(zappoColour);
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63 colours.add(taylorColour);
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64 colours.add(hydrophobicityColour);
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65 colours.add(helixColour);
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66 colours.add(strandColour);
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67 colours.add(turnColour);
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68 colours.add(buriedColour);
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69 colours.add(abovePIDColour);
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70 colours.add(userDefinedColour);
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71 colours.add(PIDColour);
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72 colours.add(BLOSUM62Colour);
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77 { e.printStackTrace(); }
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79 SequenceGroup sg = ap.av.getSelectionGroup();
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82 groupName.setText(sg.getName());
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83 if(sg.cs instanceof ZappoColourScheme)
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84 zappoColour.setSelected(true);
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85 else if(sg.cs instanceof TaylorColourScheme)
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86 taylorColour.setSelected(true);
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87 else if (sg.cs instanceof PIDColourScheme)
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88 PIDColour.setSelected(true);
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89 else if (sg.cs instanceof Blosum62ColourScheme)
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90 BLOSUM62Colour.setSelected(true);
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91 else if (sg.cs instanceof UserColourScheme)
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92 userDefinedColour.setSelected(true);
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93 else if (sg.cs instanceof HydrophobicColourScheme)
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94 hydrophobicityColour.setSelected(true);
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95 else if (sg.cs instanceof HelixColourScheme)
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96 helixColour.setSelected(true);
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97 else if (sg.cs instanceof StrandColourScheme)
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98 strandColour.setSelected(true);
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99 else if (sg.cs instanceof TurnColourScheme)
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100 turnColour.setSelected(true);
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101 else if (sg.cs instanceof BuriedColourScheme)
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102 buriedColour.setSelected(true);
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103 else if (sg.cs instanceof ClustalxColourScheme)
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104 clustalColour.setSelected(true);
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106 noColourmenuItem.setSelected(true);
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108 if (sg.cs instanceof ConservationColourScheme)
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109 conservationMenuItem.setSelected(true);
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114 residueMenu.setVisible(false);
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116 sequenceMenu.setVisible(false);
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119 private void jbInit() throws Exception
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121 groupMenu.setText("Group");
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122 analyze.setText("Analyze");
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123 analyze.addActionListener(new java.awt.event.ActionListener()
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125 public void actionPerformed(ActionEvent e)
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127 analyze_actionPerformed(e);
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130 defineMenu.setText("Define");
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131 groupName.setText("Name");
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132 groupName.addActionListener(new java.awt.event.ActionListener()
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134 public void actionPerformed(ActionEvent e)
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136 groupName_actionPerformed(e);
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139 groupAnnotation.setEnabled(false);
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140 groupAnnotation.setText("Annotation");
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141 groupAnnotation.addActionListener(new java.awt.event.ActionListener()
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143 public void actionPerformed(ActionEvent e)
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145 groupAnnotation_actionPerformed(e);
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148 sequenceMenu.setText("Sequence");
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149 sequenceName.setText("Edit name");
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150 sequenceName.addActionListener(new java.awt.event.ActionListener()
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152 public void actionPerformed(ActionEvent e)
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154 sequenceName_actionPerformed(e);
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157 residueMenu.setText("Residue");
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158 annotateResidue.setEnabled(false);
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159 annotateResidue.setActionCommand("annotate residue");
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160 annotateResidue.setText("annotate residue???");
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161 PIDColour.setFocusPainted(false);
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162 unGroupMenuItem.setText("Remove Group");
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163 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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165 public void actionPerformed(ActionEvent e)
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167 unGroupMenuItem_actionPerformed(e);
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170 pdbMenuItem.setText("View PDB structure");
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171 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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173 public void actionPerformed(ActionEvent e)
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175 pdbMenuItem_actionPerformed(e);
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178 outline.setText("Border colour");
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179 outline.addActionListener(new java.awt.event.ActionListener()
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181 public void actionPerformed(ActionEvent e)
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183 outline_actionPerformed(e);
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186 nucleotideMenuItem.setText("Nucleotide");
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187 nucleotideMenuItem.addActionListener(new ActionListener()
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189 public void actionPerformed(ActionEvent e)
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191 nucleotideMenuItem_actionPerformed(e);
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195 this.add(sequenceMenu);
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196 this.add(residueMenu);
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197 groupMenu.add(defineMenu);
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198 groupMenu.add(unGroupMenuItem);
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199 groupMenu.addSeparator();
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200 groupMenu.add(analyze);
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201 defineMenu.add(groupName);
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202 defineMenu.add(groupAnnotation);
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203 defineMenu.addSeparator();
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204 defineMenu.add(outline);
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205 defineMenu.addSeparator();
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206 defineMenu.add(noColourmenuItem);
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207 defineMenu.add(clustalColour);
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208 defineMenu.add(BLOSUM62Colour);
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209 defineMenu.add(PIDColour);
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211 defineMenu.add(zappoColour);
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212 defineMenu.add(taylorColour);
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213 defineMenu.add(hydrophobicityColour);
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214 defineMenu.add(helixColour);
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215 defineMenu.add(strandColour);
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216 defineMenu.add(turnColour);
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217 defineMenu.add(buriedColour);
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218 defineMenu.add(nucleotideMenuItem);
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220 defineMenu.add(userDefinedColour);
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222 defineMenu.addSeparator();
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223 defineMenu.add(abovePIDColour);
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224 defineMenu.add(conservationMenuItem);
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226 sequenceMenu.add(sequenceName);
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227 sequenceMenu.add(pdbMenuItem);
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228 residueMenu.add(annotateResidue);
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230 noColourmenuItem.setText("None");
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231 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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233 public void actionPerformed(ActionEvent e)
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235 noColourmenuItem_actionPerformed(e);
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239 clustalColour.setText("Clustalx colours");
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240 clustalColour.addActionListener(new java.awt.event.ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 clustalColour_actionPerformed(e);
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247 zappoColour.setText("Zappo");
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248 zappoColour.addActionListener(new java.awt.event.ActionListener()
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250 public void actionPerformed(ActionEvent e)
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252 zappoColour_actionPerformed(e);
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255 taylorColour.setText("Taylor");
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256 taylorColour.addActionListener(new java.awt.event.ActionListener()
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258 public void actionPerformed(ActionEvent e)
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260 taylorColour_actionPerformed(e);
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263 hydrophobicityColour.setText("Hydrophobicity");
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264 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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266 public void actionPerformed(ActionEvent e)
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268 hydrophobicityColour_actionPerformed(e);
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271 helixColour.setText("Helix propensity");
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272 helixColour.addActionListener(new java.awt.event.ActionListener()
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274 public void actionPerformed(ActionEvent e)
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276 helixColour_actionPerformed(e);
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279 strandColour.setText("Strand propensity");
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280 strandColour.addActionListener(new java.awt.event.ActionListener()
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282 public void actionPerformed(ActionEvent e)
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284 strandColour_actionPerformed(e);
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287 turnColour.setText("Turn propensity");
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288 turnColour.addActionListener(new java.awt.event.ActionListener()
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290 public void actionPerformed(ActionEvent e)
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292 turnColour_actionPerformed(e);
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295 buriedColour.setText("Buried Index");
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296 buriedColour.addActionListener(new java.awt.event.ActionListener()
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298 public void actionPerformed(ActionEvent e)
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300 buriedColour_actionPerformed(e);
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303 abovePIDColour.setText("Above % Identity");
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304 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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306 public void actionPerformed(ActionEvent e)
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308 abovePIDColour_actionPerformed(e);
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311 userDefinedColour.setText("User Defined");
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312 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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314 public void actionPerformed(ActionEvent e)
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316 userDefinedColour_actionPerformed(e);
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319 PIDColour.setText("Percentage Identity");
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320 PIDColour.addActionListener(new java.awt.event.ActionListener()
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322 public void actionPerformed(ActionEvent e)
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324 PIDColour_actionPerformed(e);
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327 BLOSUM62Colour.setText("BLOSUM62");
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328 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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330 public void actionPerformed(ActionEvent e)
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332 BLOSUM62Colour_actionPerformed(e);
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335 conservationMenuItem.setText("Conservation");
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336 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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338 public void actionPerformed(ActionEvent e)
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340 conservationMenuItem_actionPerformed(e);
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350 SequenceGroup sg = getGroup();
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351 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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353 superG.setSuperGroupProperties( sg );
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355 ap.seqPanel.repaint();
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358 protected void clustalColour_actionPerformed(ActionEvent e)
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360 SequenceGroup sg = getGroup();
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361 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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365 protected void zappoColour_actionPerformed(ActionEvent e)
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367 getGroup().cs = new ZappoColourScheme();
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371 protected void taylorColour_actionPerformed(ActionEvent e)
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373 getGroup().cs = new TaylorColourScheme();
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378 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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380 getGroup().cs = new HydrophobicColourScheme();
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384 protected void helixColour_actionPerformed(ActionEvent e)
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386 getGroup().cs = new HelixColourScheme();
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390 protected void strandColour_actionPerformed(ActionEvent e)
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392 getGroup().cs = new StrandColourScheme();
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396 protected void turnColour_actionPerformed(ActionEvent e)
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398 getGroup().cs = new TurnColourScheme();
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402 protected void buriedColour_actionPerformed(ActionEvent e)
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404 getGroup().cs = new BuriedColourScheme();
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408 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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410 getGroup().cs = new NucleotideColourScheme();
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416 protected void abovePIDColour_actionPerformed(ActionEvent e)
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418 SequenceGroup sg = getGroup();
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419 if (abovePIDColour.isSelected())
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421 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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422 ap.av.alignment.getWidth()));
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423 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
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424 if (sg.cs instanceof ResidueColourScheme)
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425 ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
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426 else if (sg.cs instanceof ScoreColourScheme)
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427 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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429 SliderPanel.showPIDSlider();
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433 else // remove PIDColouring
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435 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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436 rcs.setThreshold(0);
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445 protected void userDefinedColour_actionPerformed(ActionEvent e)
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447 UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());
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450 protected void PIDColour_actionPerformed(ActionEvent e)
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455 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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457 SequenceGroup sg = getGroup();
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459 sg.cs = new Blosum62ColourScheme();
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461 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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462 ap.av.alignment.getWidth()));
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468 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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470 getGroup().cs = null;
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474 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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476 SequenceGroup sg = getGroup();
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478 if(conservationMenuItem.isSelected())
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481 Conservation c = new Conservation("Group",
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482 ResidueProperties.propHash, 3,
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484 ap.av.alignment.getWidth());
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487 c.verdict(false, ap.av.ConsPercGaps);
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488 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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493 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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494 SliderPanel.showConservationSlider();
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496 else // remove ConservationColouring
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498 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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505 protected void groupAnnotation_actionPerformed(ActionEvent e)
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510 protected void groupName_actionPerformed(ActionEvent e)
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512 SequenceGroup sg = getGroup();
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513 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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518 groupName.setText(reply);
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522 protected void analyze_actionPerformed(ActionEvent e)
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524 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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525 JInternalFrame frame = new JInternalFrame();
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526 cap.formatForOutput();
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527 frame.setContentPane(cap);
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528 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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529 SequenceGroup sg = getGroup();
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530 StringBuffer sb = new StringBuffer();
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532 for(int i=0; i<sg.sequences.size(); i++)
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534 Sequence tmp = (Sequence)sg.sequences.get(i);
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535 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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539 sb.append("Something amazing will happen soon");
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540 cap.setText( sb.toString() );
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544 SequenceGroup getGroup()
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546 SequenceGroup sg = ap.av.getSelectionGroup();
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548 // this method won't add a new group if it already exists
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549 ap.av.alignment.addGroup(sg);
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554 void sequenceName_actionPerformed(ActionEvent e)
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556 String id = sequence.getName();
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557 String s = (String)JOptionPane.showInternalInputDialog(
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559 "Edit sequence name",
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560 "Edit sequence name ("+sequence.getName()+")",
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561 JOptionPane.PLAIN_MESSAGE,
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568 sequence.setName(s);
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574 void unGroupMenuItem_actionPerformed(ActionEvent e)
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576 SequenceGroup sg = ap.av.getSelectionGroup();
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577 ap.av.alignment.deleteGroup(sg);
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578 ap.av.setSelectionGroup(null);
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582 void pdbMenuItem_actionPerformed(ActionEvent e)
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584 if(sequence.getPDBId()==null)
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589 EBIFetchClient ebi = new EBIFetchClient();
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590 String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
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592 System.out.println("Got "+ sequence.getPDBId() );
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593 PDBfile pdb = new PDBfile(result);
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595 rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
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596 JInternalFrame frame = new JInternalFrame();
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597 frame.setContentPane(rc);
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598 Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
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600 catch (Exception ex)
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602 ex.printStackTrace();
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606 protected void outline_actionPerformed(ActionEvent e)
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608 SequenceGroup sg = getGroup();
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609 Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
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611 sg.setOutlineColour(col);
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