package jalview.hmmer;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
import jalview.gui.SplitFrame;
import jalview.io.DataSourceType;
import jalview.io.StockholmFile;
import jalview.util.MessageManager;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.ws.params.ArgumentI;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-public class HMMAlignThread implements Runnable
+public class HMMAlignThread extends HmmerCommand implements Runnable
{
+ static final String HMMALIGN = "hmmalign";
- /**
+ /*
* feature settings from view that job was associated with
*/
protected FeatureRendererSettings featureSettings = null;
- /**
- * Object containing frequently used commands.
- */
- HMMERCommands cmds = new HMMERCommands();
-
- AlignFrame af;
-
AlignmentI alignment;
AlignmentI dataset;
HiddenMarkovModel hmm;
+ List<ArgumentI> args;
+
boolean newFrame;
long barID;
- Map<Integer, SequenceI> hmmSeqs;
-
File hmmTemp = null;
File outTemp = null;
* @param af
* @param createNewFrame
*/
- public HMMAlignThread(AlignFrame af, boolean createNewFrame)
+ public HMMAlignThread(AlignFrame af, boolean createNewFrame,
+ List<ArgumentI> args)
{
this.af = af;
alignment = af.getViewport().getAlignment();
}
newFrame = createNewFrame;
featureSettings = af.getFeatureRenderer().getSettings();
+ this.args = args;
}
/**
@Override
public void run()
{
- if (af.getSelectedHMM() == null)
- {
- JOptionPane.showMessageDialog(af,
- MessageManager.getString("warn.no_selected_hmm"));
- return;
- }
- else
- {
- hmm = af.getSelectedHMM();
- }
+
+ hmm = af.getSelectedHMM();
+
barID = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
barID);
- cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
-
- // if (!alignment.isAligned())
- // {
- // alignment.padGaps();
- // }
prepareAlignment();
SequenceI[][] subAlignments = msa.getVisibleContigs('-');
allOrders = new ArrayList<>();
int job = 0;
for (SequenceI[] seqs : subAlignments)
{
- cmds.uniquifySequences(seqs);
+ uniquifySequences(seqs);
try
{
createTemporaryFiles();
}
try
{
- cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
- hmmTemp.getAbsoluteFile());
+ exportData(seqs, outTemp.getAbsoluteFile(), hmm,
+ hmmTemp.getAbsoluteFile(), null);
} catch (IOException e1)
{
e1.printStackTrace();
displayResults(newFrame);
- af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
- barID);
+ af.setProgressBar("", barID);
}
*/
private void createTemporaryFiles() throws IOException
{
- hmmTemp = File.createTempFile("hmm", ".hmm");
- hmmTemp.deleteOnExit();
- outTemp = File.createTempFile("output", ".sto");
- outTemp.deleteOnExit();
+ if (hmmTemp == null)
+ {
+ hmmTemp = File.createTempFile("hmm", ".hmm");
+ hmmTemp.deleteOnExit();
+ }
+ if (outTemp == null)
+ {
+ outTemp = File.createTempFile("output", ".sto");
+ outTemp.deleteOnExit();
+ }
inputTemp = File.createTempFile("input", ".sto");
inputTemp.deleteOnExit();
}
/**
- * Executes the hmmalign command in the command line.
+ * Executes the hmmalign command in the command line
*
* @return
* @throws IOException
*/
private boolean runCommand() throws IOException, InterruptedException
{
- File file = new File(cmds.HMMERFOLDER + "/hmmalign");
- if (!file.canExecute())
- {
- file = new File(cmds.HMMERFOLDER + "/hmmalign.exe");
- {
- if (!file.canExecute())
- {
- return false;
- }
- }
+ String binaryPath = getCommandRoot(HMMALIGN);
+ if (binaryPath == null) {
+ return false;
}
- String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
+ String command = binaryPath + SPACE;
+ // todo parse version from ./hmmerbuild -h
String version = Cache.getProperty("HMMER_VERSION");
if (!"3.1b2".equals(version))
{
- command += cmds.ALLCOL;
- }
- boolean trim = true;
- String bool = Cache.getProperty("TRIM_TERMINI");
- if ("false".equals(bool))
- {
- trim = false;
+ // command += ALLCOL; // todo obsolete option?
}
- if (trim)
+ if (args != null)
{
- command += cmds.TRIM;
+ for (ArgumentI arg : args)
+ {
+ String name = arg.getName();
+ switch (name)
+ {
+ case "Trim Non-Matching Termini":
+ command += "--trim";
+ }
+ }
}
- command += " -o " + inputTemp.getAbsolutePath() + cmds.SPACE
- + hmmTemp.getAbsolutePath() + cmds.SPACE
+ command += " -o " + inputTemp.getAbsolutePath() + SPACE
+ + hmmTemp.getAbsolutePath() + SPACE
+ outTemp.getAbsolutePath();
- return cmds.runCommand(command);
+ return runCommand(command);
}
/**
* Imports the data from the temporary file to which the output of hmmalign is
- * directed.
+ * directed. this is used for an internal job.
*
* @param index
* The index of the 'job' (or region of an alignment).
DataSourceType.FILE);
SequenceI[] result = file.getSeqsAsArray();
AlignmentOrder msaorder = new AlignmentOrder(result);
- jalview.analysis.AlignmentSorter.recoverOrder(result);
- jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, result);
+ AlignmentSorter.recoverOrder(result);
+ SeqsetUtils.deuniquify(hash, result);
allOrders.add(msaorder);
allResults[index] = result;
hmmTemp.delete();
{
AlignmentOrder[] arrOrders = allOrders
.toArray(new AlignmentOrder[allOrders.size()]);
- Object[] newview = msa.getUpdatedView(allResults,
- arrOrders, '-');
+ Object[] newview = msa.getUpdatedView(allResults, arrOrders, '-');
SequenceI[] alignment = (SequenceI[]) newview[0];
HiddenColumns hidden = (HiddenColumns) newview[1];
Alignment al = new Alignment(alignment);
}
}
- }
+ /**
+ * Runs hmmalign, and waits for the results to be imported before continuing
+ */
+ public void hmmalignWaitTillComplete()
+ {
+ Thread loader = new Thread(this);
+ loader.start();
+ while (loader.isAlive())
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff