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.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
-import jalview.gui.Preferences;
+import jalview.gui.JvOptionPane;
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;
-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;
- 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;
SequenceI[][] allResults;
- public HMMAlignThread(AlignFrame af, boolean createNewFrame)
+ /**
+ * Constructor for the HMMAlignThread. If create new frame is set to true, a
+ * new frame will be created.
+ *
+ * @param af
+ * @param createNewFrame
+ */
+ public HMMAlignThread(AlignFrame af, boolean createNewFrame,
+ List<ArgumentI> args)
{
this.af = af;
alignment = af.getViewport().getAlignment();
{
dataset = alignment.getDataset();
}
- hmm = alignment.getSequenceAt(0).getHMM();
newFrame = createNewFrame;
featureSettings = af.getFeatureRenderer().getSettings();
+ this.args = args;
}
+ /**
+ * Runs the HMMAlignThread: the data on the alignment or group is exported,
+ * then the command is executed in the command line and then the data is
+ * imported and displayed in a new frame (if true). The command is executed
+ * for each segemtn of the alignment.
+ */
@Override
public void run()
{
+
+ hmm = af.getSelectedHMM();
+
barID = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+ 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();
}
try
{
- runCommand();
+ boolean ran = runCommand();
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmalign_failed"));
+ return;
+ }
} catch (IOException | InterruptedException e)
{
e.printStackTrace();
displayResults(newFrame);
- af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
- barID);
+ af.setProgressBar("", barID);
}
+ /**
+ * Creates temporary files for exporting and importing the data.
+ *
+ * @throws IOException
+ */
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();
}
- private void runCommand() throws IOException, InterruptedException
+ /**
+ * Executes the hmmalign command in the command line
+ *
+ * @return
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private boolean runCommand() throws IOException, InterruptedException
{
- String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
- if (!hmm.getFileHeader().contains("HMMER3/f"))
+ String binaryPath = getCommandRoot(HMMALIGN);
+ if (binaryPath == null) {
+ return false;
+ }
+ String command = binaryPath + SPACE;
+ // todo parse version from ./hmmerbuild -h
+ String version = Cache.getProperty("HMMER_VERSION");
+ if (!"3.1b2".equals(version))
+ {
+ // command += ALLCOL; // todo obsolete option?
+ }
+ if (args != null)
{
- command += cmds.ALLCOL;
+ for (ArgumentI arg : args)
+ {
+ String name = arg.getName();
+ switch (name)
+ {
+ case "Trim Non-Matching Termini":
+ command += "--trim";
+ }
+ }
}
- command += cmds.TRIM + " -o" + inputTemp.getAbsolutePath() + cmds.SPACE
- + hmmTemp.getAbsolutePath() + cmds.SPACE
+ command += " -o " + inputTemp.getAbsolutePath() + SPACE
+ + hmmTemp.getAbsolutePath() + SPACE
+ outTemp.getAbsolutePath();
- cmds.runCommand(command);
+ return runCommand(command);
}
+ /**
+ * Imports the data from the temporary file to which the output of hmmalign is
+ * directed. this is used for an internal job.
+ *
+ * @param index
+ * The index of the 'job' (or region of an alignment).
+ * @throws IOException
+ * @throws InterruptedException
+ */
private void importData(int index)
throws IOException, InterruptedException
{
DataSourceType.FILE);
SequenceI[] result = file.getSeqsAsArray();
AlignmentOrder msaorder = new AlignmentOrder(result);
- // always recover the order - makes parseResult()'s life easier.
- 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;
-
- /*
- if (newFrame)
- {
- FileLoader loader = new FileLoader();
- AlignFrame aFrame = new AlignFrame(new Alignment(new SequenceI[1]),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- Desktop.addInternalFrame(aFrame, aFrame.getTitle(),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- aFrame.setTitle(
- af.getName() + "Aligned to " + hmm.getName() + "'s HMM");
- af.getViewport().setAlignment(null);
-
- aFrame.loadJalviewDataFile(inputTemp.getAbsolutePath(),
- DataSourceType.FILE, FileFormat.Stockholm, null);
-
-
-
- Map<Integer, SequenceI> copy = new HashMap<>(
- hmmSeqs);
- addSeqs(aFrame, copy);
- SequenceI seq = aFrame.getViewport().getAlignment()
- .getSequenceAt(0);
- seq.getHMM().mapToReferenceAnnotation(aFrame, seq);
- addSeqs(af, hmmSeqs);
- }
- else
- {
- af.getViewport().getAlignment().getSequences().clear();
- af.setIsRecurring(true);
- af.loadJalviewDataFile(inputTemp.getAbsolutePath(),
- DataSourceType.FILE, FileFormat.Stockholm, null);
- af.setIsRecurring(false);
- addSeqs(af, hmmSeqs);
- }
- */
hmmTemp.delete();
outTemp.delete();
inputTemp.delete();
}
- private void addSeqs(AlignFrame alignFrame, Map<Integer, SequenceI> map)
- {
- for (Map.Entry<Integer, SequenceI> entry : map.entrySet())
- {
- SequenceI seq = entry.getValue();
- Integer pos = entry.getKey();
- cmds.addHMMConsensusSequence(alignFrame, seq, pos);
- }
- }
-
+ /**
+ * Gathers the sequences in preparation for the alignment.
+ */
private void prepareAlignment()
{
// hmmSeqs = alignment.getHMMConsensusSequences(true);
msa = af.gatherSequencesForAlignment();
}
+ /**
+ * Displays the results of all 'jobs'.
+ *
+ * @param newFrame
+ */
private void displayResults(boolean newFrame)
{
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);
}
}
+ /**
+ * Displays the results in a new frame.
+ *
+ * @param al
+ * The alignment containing the results.
+ * @param alorders
+ * The order of the sequences in the alignment on which the jobs were
+ * run.
+ * @param hidden
+ * Hidden columns in the previous alignment.
+ */
private void displayInNewFrame(AlignmentI al,
List<AlignmentOrder> alorders, HiddenColumns hidden)
{
}
}
- }
+ /**
+ * 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