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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18 public Finder(final AlignmentPanel ap)
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22 frame = new Frame();
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24 jalview.bin.JalviewLite.addFrame(frame, "Find", 340,120);
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26 frame.addWindowListener(new WindowAdapter()
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27 {public void windowClosing(WindowEvent evt)
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28 { ap.highlightSearchResults( null ); }
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32 public void textfield_actionPerformed(ActionEvent e)
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37 public void findNext_actionPerformed(ActionEvent e)
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42 public void findAll_actionPerformed(ActionEvent e)
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49 public void cancel_actionPerformed(ActionEvent e)
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52 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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53 ap.highlightSearchResults( null );
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54 ap.idPanel.highlightSearchResults( null );
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55 // frame.setClosed(true);
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56 }catch(Exception ex){ }
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60 public void createNewGroup_actionPerformed(ActionEvent e)
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62 for(int i=0; i<searchGroup.getSize(); i++)
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63 av.alignment.addGroup( searchGroup.getGroupeAt(i));
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65 ap.av.alignment.addSuperGroup(searchGroup);
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66 ap.highlightSearchResults( null );
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70 void doSearch(boolean findAll)
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72 createNewGroup.setEnabled(false);
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74 String searchString = textfield.getText().toUpperCase();
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76 com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
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78 Vector searchResults = new Vector();
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79 int [] allResults = null;
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83 boolean found = false;
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85 ////// is the searchString a residue number?
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87 int res = Integer.parseInt(searchString);
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90 if(av.getSelectionGroup().getSize()>0)
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91 seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));
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93 seq = (Sequence)av.getAlignment().getSequenceAt(0);
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95 searchResults.addElement( Integer.toString( av.getAlignment().findIndex(seq) ) );
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96 searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
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97 searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );
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99 }catch(NumberFormatException ex){}
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100 ///////////////////////////////////////////////
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103 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
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104 Color [] newColors = new Color[24];
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105 for(int i=0; i<24; i++)
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106 newColors[i] = new Color(60,160,115);
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108 ucs.setColourScheme(newColors);
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110 searchGroup = new SuperGroup(searchString, ucs , true, true, false);
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112 int end = av.alignment.getHeight();
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114 SequenceGroup selection = av.getSelectionGroup();
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115 if(selection!=null)
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116 if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))
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119 while( !found && seqIndex<end)
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121 seq = (Sequence)av.alignment.getSequenceAt(seqIndex);
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124 if(selection!=null && !selection.sequences.contains(seq))
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131 item = seq.getSequence().toUpperCase();
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133 if(selection!=null && selection.getEndRes()<av.alignment.getWidth())
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134 item = item.substring(0, selection.getEndRes()+1);
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136 ///Shall we ignore gaps????
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137 StringBuffer noGaps = new StringBuffer();
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139 Vector spaces = new Vector();
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141 for (int j=0; j < item.length(); j++)
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144 if(!jalview.util.Comparison.isGap(item.charAt(j)))
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146 noGaps.append(item.charAt(j));
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147 spaces.addElement(new Integer(insertCount));
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155 for(int r = resIndex; r<noGaps.length(); r++)
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158 if( regex.searchFrom( noGaps.toString(), r ) )
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160 resIndex = regex.matchedFrom();
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161 if(selection!=null && ( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) )<selection.getStartRes())
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164 searchResults.addElement( Integer.toString( seqIndex) );
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165 searchResults.addElement( Integer.toString( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) ) );
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166 searchResults.addElement( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) ) );
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168 SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
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169 resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) ,
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170 regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString())
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172 sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));
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173 searchGroup.addGroup( sg );
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177 // thats enough, break and display the result
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194 Vector idMatch = new Vector();
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195 for(int id = 0; id<av.alignment.getHeight(); id++)
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197 if( regex.search( av.alignment.getSequenceAt(id).getName() ) )
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198 idMatch.addElement( av.alignment.getSequenceAt(id) );
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201 if(searchResults.size()==0 && idMatch.size()>0)
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202 ap.idPanel.highlightSearchResults( idMatch );
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205 if(searchResults.size()>0)
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207 allResults = new int[searchResults.size()];
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208 for(int i=0; i<searchResults.size(); i++)
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209 allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());
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211 createNewGroup.setEnabled(true);
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219 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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220 ap.highlightSearchResults( allResults );
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224 String message = (searchResults.size()/3) + " matches found.";
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225 System.out.println(message);
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