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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11 public class Finder extends GFinder
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15 JInternalFrame frame;
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16 SuperGroup searchGroup;
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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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35 { textfield.requestFocus(); }
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39 public void internalFrameClosing(InternalFrameEvent evt)
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41 cancel_actionPerformed(null);
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47 public void textfield_actionPerformed(ActionEvent e)
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52 public void findNext_actionPerformed(ActionEvent e)
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57 public void findAll_actionPerformed(ActionEvent e)
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64 public void cancel_actionPerformed(ActionEvent e)
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67 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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68 ap.highlightSearchResults( null );
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69 ap.idPanel.highlightSearchResults( null );
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70 // frame.setClosed(true);
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71 }catch(Exception ex){ }
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75 public void createNewGroup_actionPerformed(ActionEvent e)
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77 for(int i=0; i<searchGroup.getSize(); i++)
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78 av.alignment.addGroup( searchGroup.getGroupeAt(i));
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80 ap.av.alignment.addSuperGroup(searchGroup);
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81 ap.highlightSearchResults( null );
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85 void doSearch(boolean findAll)
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87 createNewGroup.setEnabled(false);
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89 String searchString = textfield.getText().toUpperCase();
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91 com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
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93 ArrayList searchResults = new ArrayList();
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94 int [] allResults = null;
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98 boolean found = false;
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100 ////// is the searchString a residue number?
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102 int res = Integer.parseInt(searchString);
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105 if(av.getSelectionGroup().getSize()>0)
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106 seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
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108 seq = (Sequence)av.getAlignment().getSequenceAt(0);
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110 searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );
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111 searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
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112 searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
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114 }catch(NumberFormatException ex){}
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115 ///////////////////////////////////////////////
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118 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
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119 Color [] newColors = new Color[24];
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120 for(int i=0; i<24; i++)
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121 newColors[i] = new Color(60,160,115);
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123 ucs.setColourScheme(newColors);
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125 searchGroup = new SuperGroup(searchString, ucs , true, true, false);
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127 int end = av.alignment.getHeight();
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129 SequenceGroup selection = av.getSelectionGroup();
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130 if(selection!=null)
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131 if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
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134 while( !found && seqIndex<end)
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136 seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
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139 if(selection!=null && !selection.sequences.contains(seq))
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146 item = seq.getSequence().toUpperCase();
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148 if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
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149 item = item.substring(0, selection.getEndRes()+1);
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151 ///Shall we ignore gaps????
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152 StringBuffer noGaps = new StringBuffer();
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154 ArrayList spaces = new ArrayList();
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156 for (int j=0; j < item.length(); j++)
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159 if(!jalview.util.Comparison.isGap(item.charAt(j)))
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161 noGaps.append(item.charAt(j));
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162 spaces.add(new Integer(insertCount));
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170 for(int r = resIndex; r<noGaps.length(); r++)
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173 if( regex.searchFrom( noGaps.toString(), r ) )
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175 resIndex = regex.matchedFrom();
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176 if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())
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179 searchResults.add( Integer.toString( seqIndex) );
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180 searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );
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181 searchResults.add( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString()) ) );
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183 SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
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184 resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,
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185 regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())
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187 sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
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188 searchGroup.addGroup( sg );
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192 // thats enough, break and display the result
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209 ArrayList idMatch = new ArrayList();
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210 for(int id = 0; id<av.alignment.getHeight(); id++)
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212 if( regex.search( av.alignment.getSequenceAt(id).getName() ) )
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213 idMatch.add( av.alignment.getSequenceAt(id) );
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216 if(searchResults.size()==0 && idMatch.size()>0)
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217 ap.idPanel.highlightSearchResults( idMatch );
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220 if(searchResults.size()>0)
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222 allResults = new int[searchResults.size()];
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223 for(int i=0; i<searchResults.size(); i++)
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224 allResults[i] = Integer.parseInt(searchResults.get(i).toString());
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226 createNewGroup.setEnabled(true);
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230 JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);
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235 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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236 ap.highlightSearchResults( allResults );
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240 String message = (searchResults.size()/3) + " matches found.";
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241 JOptionPane.showInternalMessageDialog(this, message, null,
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242 JOptionPane.INFORMATION_MESSAGE);
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