Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
DTASelect2mzIdentML version 1.1 release
- Loading branch information
Showing
6 changed files
with
714 additions
and
14 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -17,3 +17,4 @@ hs_err_pid* | |
| /build/ | ||
| /src/test | ||
| /releases/ | ||
| .classpath | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
97 changes: 97 additions & 0 deletions
97
src/main/java/edu/scripps/yates/dtaselect2mzid/skyline/MzXMLFixer.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,97 @@ | ||
| package edu.scripps.yates.dtaselect2mzid.skyline; | ||
|
|
||
| import java.io.BufferedReader; | ||
| import java.io.File; | ||
| import java.io.FileReader; | ||
| import java.io.FileWriter; | ||
| import java.io.IOException; | ||
|
|
||
| import javax.swing.SwingWorker; | ||
|
|
||
| import org.apache.commons.io.FilenameUtils; | ||
|
|
||
| import edu.scripps.yates.utilities.util.Pair; | ||
|
|
||
| /** | ||
| * This class reads an input mzXML file and outputs the same file correcting | ||
| * mz-int tag by m/z-int | ||
| * | ||
| * @author Salva | ||
| * | ||
| */ | ||
| public class MzXMLFixer extends SwingWorker<Void, Void> { | ||
| private final File mzXMLFile; | ||
| private final File outputFolder; | ||
| public final static String STARTING = "MzXMLFixerSTARTING"; | ||
| public final static String CANCELED = "MzXMLFixerCANCELED"; | ||
| public final static String DONE = "MzXMLFixerDONE"; | ||
| public static final String ERROR = "MzXMLFixerERROR"; | ||
| public static final String NUM_LINES = "MzXMLFixerNUM_LINES"; | ||
|
|
||
| public MzXMLFixer(File mzXMLFile, File outputFolder) { | ||
| if (mzXMLFile.getParentFile().getAbsolutePath().equals(outputFolder.getAbsolutePath())) { | ||
| throw new IllegalArgumentException( | ||
| "Output folder has to be different than the one containing the input mzXML file"); | ||
| } | ||
| this.mzXMLFile = mzXMLFile; | ||
| this.outputFolder = outputFolder; | ||
| } | ||
|
|
||
| public void fixMZXML() throws IOException { | ||
| firePropertyChange(STARTING, null, this.mzXMLFile); | ||
| File mzXML = this.mzXMLFile; | ||
| File output = new File( | ||
| this.outputFolder + File.separator + FilenameUtils.getName(this.mzXMLFile.getAbsolutePath())); | ||
| FileWriter fw = null; | ||
| BufferedReader br = null; | ||
| try { | ||
| long numLinesFixed = 0; | ||
| fw = new FileWriter(output); | ||
| br = new BufferedReader(new FileReader(mzXML)); | ||
| String line = br.readLine(); | ||
| while (line != null) { | ||
|
|
||
| Thread.sleep(0); | ||
| if (line.contains("\"mz-int\"")) { | ||
| line = line.replace("\"mz-int\"", "\"m/z-int\""); | ||
| numLinesFixed++; | ||
| firePropertyChange(NUM_LINES, null, new Pair<File, Long>(this.mzXMLFile, numLinesFixed)); | ||
| } | ||
| fw.write(line); | ||
| fw.write("\n"); | ||
| line = br.readLine(); | ||
| } | ||
| } catch (InterruptedException e) { | ||
|
|
||
| } finally { | ||
| try { | ||
| fw.close(); | ||
| br.close(); | ||
| } catch (IOException e) { | ||
| e.printStackTrace(); | ||
| } | ||
|
|
||
| } | ||
| } | ||
|
|
||
| @Override | ||
| protected Void doInBackground() throws Exception { | ||
| try { | ||
| fixMZXML(); | ||
| } catch (Exception e) { | ||
| e.printStackTrace(); | ||
| firePropertyChange(ERROR, null, e); | ||
| } | ||
| return null; | ||
| } | ||
|
|
||
| @Override | ||
| protected void done() { | ||
| if (isCancelled()) { | ||
| firePropertyChange(CANCELED, null, this.mzXMLFile); | ||
| } else { | ||
| firePropertyChange(DONE, null, this.mzXMLFile); | ||
| } | ||
| super.done(); | ||
| } | ||
| } |
Oops, something went wrong.