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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17 Vector searchResults;
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21 public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
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27 // all a big pain, but we need to wait until the frame is visible before the textfield can
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28 // obtain the focus/////////////////////////
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29 frame.addInternalFrameListener(new InternalFrameAdapter()
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31 public void internalFrameOpened(InternalFrameEvent evt)
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33 SwingUtilities.invokeLater(new Runnable()
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36 { textfield.requestFocus(); }
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40 public void internalFrameClosing(InternalFrameEvent evt)
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42 cancel_actionPerformed(null);
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48 public void textfield_actionPerformed(ActionEvent e)
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53 public void findNext_actionPerformed(ActionEvent e)
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58 public void findAll_actionPerformed(ActionEvent e)
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65 public void cancel_actionPerformed(ActionEvent e)
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68 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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69 ap.highlightSearchResults( null );
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70 ap.idPanel.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 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
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79 Color [] newColors = new Color[24];
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80 for(int i=0; i<24; i++)
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81 newColors[i] = new Color(60,160,115);
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83 ucs.setColourScheme(newColors);
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84 String searchString = textfield.getText();
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86 searchGroup = new SuperGroup(searchString, ucs , true, true, false);
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89 for(int i=0; i<searchResults.size(); i+=3)
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91 // its possible edits may have occurred since search was performed
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92 // account for this here
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94 SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );
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95 int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;
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96 int endRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;
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98 SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes );
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99 sg.addSequence(seq);
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100 av.alignment.addGroup(sg);
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101 searchGroup.addGroup( sg );
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105 ap.av.alignment.addSuperGroup(searchGroup);
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106 ap.highlightSearchResults( null );
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110 void doSearch(boolean findAll)
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112 createNewGroup.setEnabled(false);
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114 String searchString = textfield.getText().toUpperCase();
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116 com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
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118 searchResults = new Vector();
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119 int [] allResults = null;
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123 boolean found = false;
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125 ////// is the searchString a residue number?
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127 int res = Integer.parseInt(searchString);
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130 if(av.getSelectionGroup().getSize()>0)
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131 seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
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133 seq = (Sequence)av.getAlignment().getSequenceAt(0);
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135 searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );
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136 searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
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137 searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
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139 }catch(NumberFormatException ex){}
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140 ///////////////////////////////////////////////
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143 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
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144 Color [] newColors = new Color[24];
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145 for(int i=0; i<24; i++)
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146 newColors[i] = new Color(60,160,115);
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148 ucs.setColourScheme(newColors);
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150 searchGroup = new SuperGroup(searchString, ucs , true, true, false);
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152 int end = av.alignment.getHeight();
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154 SequenceGroup selection = av.getSelectionGroup();
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155 if(selection!=null)
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156 if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
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159 while( !found && seqIndex<end)
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161 seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
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164 if(selection!=null && !selection.sequences.contains(seq))
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171 item = seq.getSequence().toUpperCase();
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173 if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
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174 item = item.substring(0, selection.getEndRes()+1);
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176 ///Shall we ignore gaps????
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177 StringBuffer noGaps = new StringBuffer();
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179 Vector spaces = new Vector();
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181 for (int j=0; j < item.length(); j++)
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184 if(!jalview.util.Comparison.isGap(item.charAt(j)))
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186 noGaps.append(item.charAt(j));
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187 spaces.add(new Integer(insertCount));
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195 for(int r = resIndex; r<noGaps.length(); r++)
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198 if( regex.searchFrom( noGaps.toString(), r ) )
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200 resIndex = regex.matchedFrom();
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201 if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())
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204 searchResults.add( Integer.toString( seqIndex) );
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206 int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );
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207 int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );
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209 searchResults.addElement( sres+"" );
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210 searchResults.addElement( eres+"" );
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214 // thats enough, break and display the result
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231 Vector idMatch = new Vector();
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232 for(int id = 0; id<av.alignment.getHeight(); id++)
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234 if( regex.search( av.alignment.getSequenceAt(id).getName() ) )
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235 idMatch.add( av.alignment.getSequenceAt(id) );
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238 if(searchResults.size()==0 && idMatch.size()>0)
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239 ap.idPanel.highlightSearchResults( idMatch );
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242 if(searchResults.size()>0)
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244 allResults = new int[searchResults.size()];
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245 for(int i=0; i<searchResults.size(); i++)
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246 allResults[i] = Integer.parseInt(searchResults.get(i).toString());
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248 createNewGroup.setEnabled(true);
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252 JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);
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257 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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258 ap.highlightSearchResults( allResults );
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262 String message = (searchResults.size()/3) + " matches found.";
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263 JOptionPane.showInternalMessageDialog(this, message, null,
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264 JOptionPane.INFORMATION_MESSAGE);
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