3 import jalview.jbgui.GFinder;
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4 import jalview.datamodel.*;
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5 import java.awt.event.*;
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6 import javax.swing.*;
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7 import javax.swing.event.*;
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9 import java.util.regex.*;
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12 public class Finder extends GFinder
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16 JInternalFrame frame;
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17 String searchString;
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18 SuperGroup searchGroup;
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22 public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
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28 // all a big pain, but we need to wait until the frame is visible before the textfield can
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29 // obtain the focus/////////////////////////
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30 frame.addInternalFrameListener(new InternalFrameAdapter()
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32 public void internalFrameOpened(InternalFrameEvent evt)
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34 SwingUtilities.invokeLater(new Runnable()
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37 { textfield.requestFocus(); }
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41 public void internalFrameClosing(InternalFrameEvent evt)
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43 cancel_actionPerformed(null);
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49 public void textfield_actionPerformed(ActionEvent e)
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54 public void findNext_actionPerformed(ActionEvent e)
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59 public void findAll_actionPerformed(ActionEvent e)
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66 public void cancel_actionPerformed(ActionEvent e)
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69 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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70 ap.highlightSearchResults( null );
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71 // frame.setClosed(true);
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72 }catch(Exception ex){ }
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76 public void createNewGroup_actionPerformed(ActionEvent e)
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78 for(int i=0; i<searchGroup.getSize(); i++)
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79 av.alignment.addGroup( searchGroup.getGroupeAt(i));
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81 ap.av.alignment.addSuperGroup(searchGroup);
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82 ap.highlightSearchResults( null );
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86 void doSearch(boolean findAll)
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88 createNewGroup.setEnabled(false);
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89 searchString = textfield.getText().toUpperCase();
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91 ArrayList searchResults = new ArrayList();
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92 int [] allResults = null;
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96 boolean found = false;
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98 /// is the searchString a residue number?
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100 int res = Integer.parseInt(searchString);
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103 if(av.getSelection().size()>0)
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104 seq = (Sequence)(av.getSelection().sequenceAt(0));
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106 seq = (Sequence)av.getAlignment().getSequenceAt(0);
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108 searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );
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109 searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
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110 searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
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113 //av.getAlignment().getSequenceAt(seq).findPosition(res)
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114 }catch(NumberFormatException ex){}
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116 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
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117 Color [] newColors = new Color[24];
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118 for(int i=0; i<24; i++)
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119 newColors[i] = new Color(60,160,115);
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121 ucs.setColourScheme(newColors);
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123 searchGroup = new SuperGroup(searchString, ucs , true, true, false);
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125 while( !found && seqIndex<av.getAlignment().getHeight())
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127 seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
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128 if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
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130 // if a selection has been made, only search within that selection
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136 item = seq.getSequence();
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138 ///Shall we ignore gaps????
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139 StringBuffer noGaps = new StringBuffer();
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141 ArrayList spaces = new ArrayList();
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143 for (int j=0; j < item.length(); j++)
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146 if(!jalview.util.Comparison.isGap(item.charAt(j)))
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148 noGaps.append(item.charAt(j));
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149 spaces.add(new Integer(insertCount));
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156 Pattern pattern = Pattern.compile(searchString);
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157 Matcher matcher = pattern.matcher(noGaps);
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159 for(int r = resIndex; r<noGaps.length(); r++)
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162 if( matcher.find( r ) )
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164 resIndex = matcher.start();
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166 searchResults.add( Integer.toString( seqIndex) );
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167 searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );
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168 searchResults.add( Integer.toString( matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString()) ) );
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170 SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
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171 resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,
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172 matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString())
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174 sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
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175 searchGroup.addGroup( sg );
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179 // thats enough, break and display the result
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195 if(searchResults.size()>0)
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197 allResults = new int[searchResults.size()];
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198 for(int i=0; i<searchResults.size(); i++)
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199 allResults[i] = Integer.parseInt(searchResults.get(i).toString());
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201 createNewGroup.setEnabled(true);
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205 JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);
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210 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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211 ap.highlightSearchResults( allResults );
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215 String message = (searchResults.size()/3) + " matches found.";
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216 JOptionPane.showInternalMessageDialog(this, message, null,
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217 JOptionPane.INFORMATION_MESSAGE);
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