1 package jalview.appletgui;
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3 import jalview.jbappletgui.GFinder;
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4 import jalview.datamodel.*;
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5 import java.awt.event.*;
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9 public class Finder extends GFinder
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14 SuperGroup searchGroup;
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15 Vector searchResults;
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19 public Finder(final AlignmentPanel ap)
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23 frame = new Frame();
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25 jalview.bin.JalviewLite.addFrame(frame, "Find", 340,120);
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27 frame.addWindowListener(new WindowAdapter()
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28 {public void windowClosing(WindowEvent evt)
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29 { ap.highlightSearchResults( null ); }
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33 public void textfield_actionPerformed(ActionEvent e)
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38 public void findNext_actionPerformed(ActionEvent e)
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43 public void findAll_actionPerformed(ActionEvent e)
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50 public void cancel_actionPerformed(ActionEvent e)
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53 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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54 ap.highlightSearchResults( null );
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55 ap.idPanel.highlightSearchResults( null );
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56 // frame.setClosed(true);
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57 }catch(Exception ex){ }
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61 public void createNewGroup_actionPerformed(ActionEvent e)
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63 Color [] newColors = new Color[24];
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64 for(int i=0; i<24; i++)
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65 newColors[i] = new Color(60,160,115);
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67 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
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68 String searchString = textfield.getText();
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70 searchGroup = new SuperGroup(searchString, ucs , true, true, false);
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73 for(int i=0; i<searchResults.size(); i+=3)
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75 // its possible edits may have occurred since search was performed
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76 // account for this here
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78 SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );
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79 int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;
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80 int endRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;
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82 SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes );
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83 sg.addSequence(seq);
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84 av.alignment.addGroup(sg);
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85 searchGroup.addGroup( sg );
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89 ap.av.alignment.addSuperGroup(searchGroup);
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90 ap.highlightSearchResults( null );
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94 void doSearch(boolean findAll)
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96 createNewGroup.setEnabled(false);
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98 String searchString = textfield.getText().toUpperCase();
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100 com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
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102 searchResults = new Vector();
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103 int [] allResults = null;
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107 boolean found = false;
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109 ////// is the searchString a residue number?
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111 int res = Integer.parseInt(searchString);
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114 if(av.getSelectionGroup().getSize()>0)
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115 seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
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117 seq = (Sequence)av.getAlignment().getSequenceAt(0);
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119 searchResults.addElement( Integer.toString( av.getAlignment().findIndex(seq) ) );
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120 searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
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121 searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
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123 }catch(NumberFormatException ex){}
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124 ///////////////////////////////////////////////
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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 Vector spaces = new Vector();
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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.addElement(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.elementAt(resIndex).toString()) )<selection.getStartRes())
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179 searchResults.addElement( Integer.toString( seqIndex) );
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180 int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );
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181 int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );
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182 searchResults.addElement( sres+"" );
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183 searchResults.addElement( eres+"" );
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188 // thats enough, break and display the result
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205 Vector idMatch = new Vector();
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206 for(int id = 0; id<av.alignment.getHeight(); id++)
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208 if( regex.search( av.alignment.getSequenceAt(id).getName() ) )
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209 idMatch.addElement( av.alignment.getSequenceAt(id) );
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212 if(searchResults.size()==0 && idMatch.size()>0)
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213 ap.idPanel.highlightSearchResults( idMatch );
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216 if(searchResults.size()>0)
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218 allResults = new int[searchResults.size()];
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219 for(int i=0; i<searchResults.size(); i++)
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220 allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());
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222 createNewGroup.setEnabled(true);
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230 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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231 ap.highlightSearchResults( allResults );
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235 String message = (searchResults.size()/3) + " matches found.";
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236 System.out.println(message);
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