@Override
public void actionPerformed(AnActionEvent e) {
Project project = e.getData(PlatformDataKeys.PROJECT);
Editor editor = e.getData(PlatformDataKeys.EDITOR);
if (editor == null) {
return;
}
if (!editor.getDocument().isWritable()) {
return;
}
Document document = editor.getDocument();
SelectionModel selection = editor.getSelectionModel();
String selectedText = selection.getSelectedText();
String autoAlignedText;
int startOffset;
int endOffset;
if (selectedText != null) {
// just align the selected text
autoAlignedText = aligner.align(selectedText);
startOffset = selection.getSelectionStart();
endOffset = selection.getSelectionEnd();
} else {
// auto-align the whole document
autoAlignedText = aligner.align(document.getText());
startOffset = 0;
endOffset = document.getTextLength();
}
replaceString(project, document, autoAlignedText, startOffset, endOffset);
}
public static void main(String[] args) {
try {
String sp1 = "/home/caoc/alterAligner/SCORE_DROP/all_mtx/" + args[0] + ".mtx";
String sp2 = "/home/caoc/alterAligner/SCORE_DROP/all_mtx/" + args[1] + ".mtx";
System.out.println(args[0]);
// String sp1 =
// "/home/caoc/alterAligner/SCORE_DROP/all_fasta/" + args[0] ;
// String sp2 = "/home/caoc/alterAligner/SCORE_DROP/all_fasta/"
// + args[1] ;
Class parserClass = Class.forName("alterAligner.sequenceProfileParsers.PSSMParser");
Class scoreFunctionClass =
Class.forName("alterAligner.scoreFunctionStrategies.WeightedSumStrategy");
SequenceProfileParser aParser = (SequenceProfileParser) parserClass.newInstance();
ScoreFunctionStrategy aStrategy = (ScoreFunctionStrategy) scoreFunctionClass.newInstance();
Aligner aligner = new Aligner(aStrategy, (float) 10, (float) 0.5);
SequenceProfile seqPro1 = aParser.parse(new File(sp1));
SequenceProfile seqPro2 = aParser.parse(new File(sp2));
Alignment alignment = aligner.smithWatermanAlign(seqPro1, seqPro2);
BufferedWriter writer =
new BufferedWriter(
new FileWriter(
"/home/caoc/alterAligner/SCORE_DROP/all_ws_alignment/"
+ args[0]
+ "__"
+ args[1]
+ ".ws.fasta"));
writer.append(
">"
+ alignment.getName1()
+ "\t"
+ alignment.getStart1()
+ "\t"
+ alignment.getEnd1()
+ "\n");
writer.append(alignment.getSequence1AsString() + "\n");
writer.append(
">"
+ alignment.getName2()
+ "\t"
+ alignment.getStart2()
+ "\t"
+ alignment.getEnd2()
+ "\n");
writer.append(alignment.getSequence2AsString() + "\n");
writer.close();
} catch (FileNotFoundException e) {
System.out.println("Failed to open file! " + e.getMessage());
} catch (IOException e) {
System.out.println("Failed to read the file! " + e.getMessage());
} catch (ClassNotFoundException e) {
System.out.println("Failed to find the class! " + e.getMessage());
} catch (Exception e) {
System.out.println("Failed to due to do alignment! " + e.getMessage());
e.printStackTrace();
}
}
