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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11 public class Finder extends GFinder
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15 JInternalFrame frame;
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16 String searchString;
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20 public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
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26 // all a big pain, but we need to wait until the frame is visible before the textfield can
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27 // obtain the focus/////////////////////////
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28 frame.addInternalFrameListener(new InternalFrameAdapter()
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30 public void internalFrameOpened(InternalFrameEvent evt)
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32 SwingUtilities.invokeLater(new Runnable()
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36 textfield.requestFocus();
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44 public void textfield_actionPerformed(ActionEvent e)
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49 public void findNext_actionPerformed(ActionEvent e)
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54 public void findAll_actionPerformed(ActionEvent e)
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61 public void cancel_actionPerformed(ActionEvent e)
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64 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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65 ap.highlightSearchResults( null );
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66 frame.setClosed(true);
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67 }catch(Exception ex){ }
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71 void doSearch(boolean findAll)
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73 searchString = textfield.getText().toUpperCase();
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75 ArrayList searchResults = new ArrayList();
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76 int [] allResults = null;
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80 boolean found = false;
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82 /// is the searchString a residue number?
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84 int res = Integer.parseInt(searchString);
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87 if(av.getSelection().size()>0)
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88 seq = (Sequence)(av.getSelection().sequenceAt(0));
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90 seq = (Sequence)av.getAlignment().getSequenceAt(0);
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92 searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );
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93 searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
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94 searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
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97 //av.getAlignment().getSequenceAt(seq).findPosition(res)
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98 }catch(NumberFormatException ex){}
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101 while( !found && seqIndex<av.getAlignment().getHeight())
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103 seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
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104 if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
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106 // if a selection has been made, only search within that selection
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112 item = seq.getSequence();
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114 ///Shall we ignore gaps????
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115 StringBuffer noGaps = new StringBuffer();
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117 ArrayList spaces = new ArrayList();
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119 for (int j=0; j < item.length(); j++)
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122 if(!jalview.util.Comparison.isGap(item.charAt(j)))
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124 noGaps.append(item.charAt(j));
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125 spaces.add(new Integer(insertCount));
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132 Pattern pattern = Pattern.compile(searchString);
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133 Matcher matcher = pattern.matcher(noGaps);
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135 for(int r = resIndex; r<noGaps.length(); r++)
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138 if( matcher.find( r ) )
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140 resIndex = matcher.start();
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142 searchResults.add( Integer.toString( seqIndex) );
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143 searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );
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144 searchResults.add( Integer.toString( matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString()) ) );
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147 // thats enough, break and display the result
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163 if(searchResults.size()>0)
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165 allResults = new int[searchResults.size()];
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166 for(int i=0; i<searchResults.size(); i++)
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167 allResults[i] = Integer.parseInt(searchResults.get(i).toString());
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172 JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);
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177 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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178 ap.highlightSearchResults( allResults );
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182 String message = (searchResults.size()/3) + " matches found.";
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183 JOptionPane.showInternalMessageDialog(this, message, null,
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184 JOptionPane.INFORMATION_MESSAGE);
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