package jalview.hmmer;
-import jalview.bin.Cache;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.Preferences;
+import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
-import java.io.FileNotFoundException;
+import java.io.File;
import java.io.IOException;
-import java.util.Map;
+import java.util.ArrayList;
+import java.util.List;
-public class HMMBuildThread implements Runnable
+import javax.swing.JOptionPane;
+
+public class HMMBuildThread extends HmmerCommand implements Runnable
{
+ static final String ARG_AMINO = "--amino";
- AlignFrame af;
- AlignmentI alignment;
+ static final String ARG_DNA = "--dna";
- long barID;
+ static final String ARG_RNA = "--rna";
+
+ AlignmentI alignment;
- Map<Integer, SequenceI> hmmSeqs;
-
- public HMMBuildThread(AlignFrame af)
+ /**
+ * Constructor
+ *
+ * @param alignFrame
+ * @param args
+ */
+ public HMMBuildThread(AlignFrame alignFrame, List<ArgumentI> args)
{
- this.af = af;
- alignment = af.getViewport().getAlignment();
+ super(alignFrame, args);
}
+ /**
+ * Builds a HMM from an alignment (and/or groups), then imports and adds it to
+ * the alignment (and/or groups)
+ */
@Override
public void run()
{
- barID = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
- barID);
- HMMERCommands.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
-
- try
+ long msgID = System.currentTimeMillis();
+ if (af != null)
{
+ af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+ msgID);
+ }
+
+ AlignViewportI viewport = af.getViewport();
try
{
- hmmSeqs = alignment.getHMMConsensusSequences(true);
- HMMERCommands.exportData(alignment, true, false,
- new HiddenMarkovModel());
- } catch (FileNotFoundException e)
+ if (viewport != null)
+ {
+ alignment = viewport.getAlignment();
+ }
+ List<SequenceGroup> groups = new ArrayList<>();
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString("label.hmmbuild_for").equals(name))
+ {
+ String value = arg.getValue();
+ if (MessageManager.getString("label.alignment").equals(value))
+ {
+ alignment = viewport.getAlignment();
+ }
+ else if (MessageManager.getString("label.groups_and_alignment")
+ .equals(value))
+ {
+ alignment = viewport.getAlignment();
+ groups.addAll(viewport.getAlignment().getGroups());
+ }
+ else if (MessageManager.getString("label.groups").equals(value))
+ {
+ alignment = null;
+ groups = viewport.getAlignment().getGroups();
+ }
+ else if ("label.selected_group".equals(value))
+ {
+ alignment = null;
+ groups.add(viewport.getSelectionGroup());
+ }
+ }
+ else if (MessageManager.getString("label.use_reference")
+ .equals(name))
+ {
+ // todo disable this option if no RF annotation on alignment
+ if (!af.getViewport().hasReferenceAnnotation())
+ {
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .getString("warn.no_reference_annotation"));
+ // return;
+ }
+ }
+ }
+ }
+
+ if (alignment != null)
+ {
+ runHMMBuild(null);
+ }
+
+ if (alignment == null)
+ {
+ alignment = viewport.getAlignment();
+ }
+
+ for (SequenceGroup grp : groups)
+ {
+ runHMMBuild(grp);
+ }
+ } finally
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ if (af != null)
+ {
+ af.setProgressBar("", msgID);
+ }
+ }
+ }
+ /**
+ * Runs hmmbuild on the alignment, or on the group if one is specified
+ *
+ * @param grp
+ */
+ private void runHMMBuild(SequenceGroup group)
+ {
+ if (alignment == null && group == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_sequence_data"));
}
+ File hmmFile = null;
+ File alignmentFile = null;
try
{
- runCommand();
- } catch (IOException | InterruptedException e)
+ hmmFile = createTempFile("hmm", ".hmm");
+ alignmentFile = createTempFile("output", ".sto");
+ SequenceI[] array;
+ List<SequenceI> hmmSeqs = null;
+ if (group != null)
+ {
+ hmmSeqs = group.getHMMConsensusSequences();
+ array = group.getSelectionAsNewSequences(alignment);
+ }
+ else
+ {
+ hmmSeqs = alignment.getHMMConsensusSequences();
+ // todo pad gaps in an unaligned SequenceGroup as well?
+ if (!alignment.isAligned())
+ {
+ alignment.padGaps();
+ }
+ array = alignment.getSequencesArray();
+ }
+
+ if (array.length < 1)
+ {
+ if (af != null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_sequence_data"));
+ }
+ return;
+ }
+
+ /*
+ * copy over sequences excluding hmm consensus sequences
+ */
+ SequenceI[] newArr = new SequenceI[array.length - hmmSeqs.size()];
+ int index = 0;
+ for (SequenceI seq : array)
+ {
+ if (seq.isHMMConsensusSequence())
+ {
+ alignment.deleteSequence(seq);
+ }
+ else
+ {
+ newArr[index] = new Sequence(seq);
+ index++;
+ }
+ }
+
+ stashSequences(newArr);
+
+ exportStockholm(newArr, alignmentFile,
+ group != null ? group : alignment);
+
+ recoverSequences(array);
+
+ boolean ran = runCommand(alignmentFile, hmmFile, group);
+ if (!ran)
+ {
+ return;
+ }
+ importData(hmmFile, group);
+ } catch (Exception e)
{
- // TODO Auto-generated catch block
e.printStackTrace();
+ } finally
+ {
+ if (hmmFile != null)
+ {
+ hmmFile.delete();
+ }
+ if (alignmentFile != null)
+ {
+ alignmentFile.delete();
+ }
}
- try
+ }
+
+ /**
+ * Constructs and executes the hmmbuild command as a separate process
+ *
+ * @param sequences
+ * the alignment from which the HMM is built
+ * @param hmm
+ * the output file to which the HMM is written
+ * @param group
+ * (optional) group for which the hmm is generated
+ *
+ * @return
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private boolean runCommand(File sequences, File hmm, SequenceGroup group)
+ throws IOException, InterruptedException
+ {
+
+ String cmd = getCommandPath(HMMBUILD);
+ if (cmd == null)
{
- importData();
- } catch (IOException | InterruptedException e)
+ return false;
+ }
+ List<String> args = new ArrayList<>();
+ args.add(cmd);
+ String name = null;
+
+ if (params != null)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ for (ArgumentI arg : params)
+ {
+ String argName = arg.getName();
+ switch (argName)
+ {
+ case "HMM Name":
+ name = arg.getValue();
+ name = name.trim();
+ break;
+ case "Use Reference Annotation":
+ args.add("--hand");
+ break;
+ }
+ }
}
- } catch (Exception e)
+
+ if (group != null)
{
+ name = group.getName() + "_HMM";
+ }
- } finally
+ if (name == null || "".equals(name))
{
- af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
- barID);
+ if (af != null)
+ {
+ if (af.getTitle().length() < 15)
+ {
+ name = af.getTitle();
+ }
+ }
+ if (name == null || "".equals(name))
+ {
+ name = "Alignment";
+ }
+
}
- }
-
+ args.add("-n");
+ args.add(name.replace(' ', '_'));
+ if (!alignment.isNucleotide())
+ {
+ args.add(ARG_AMINO); // TODO check for rna
+ }
+ else
+ {
+ args.add(ARG_DNA);
+ }
+
+ args.add(hmm.getAbsolutePath());
+ args.add(sequences.getAbsolutePath());
+
+ return runCommand(args);
+ }
-
- private void runCommand() throws IOException, InterruptedException
+ /**
+ * Imports the .hmm file produced by hmmbuild, and inserts the HMM consensus
+ * sequence (with attached HMM profile) as the first sequence in the alignment
+ * or group for which it was generated
+ *
+ * @param hmmFile
+ * @oparam group (optional) the group for which the hmm was generated
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private void importData(File hmmFile, SequenceGroup group)
+ throws IOException, InterruptedException
{
- final String command = HMMERCommands.HMMERFOLDER
- + HMMERCommands.HMMBUILD + HMMERCommands.NAME
- + af.getName() + HMMERCommands.SPACE
- + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
- + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER;
- HMMERCommands.runCommand(command);
+ HMMFile file = new HMMFile(
+ new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
+ SequenceI[] seqs = file.getSeqsAsArray();
+ SequenceI seq = seqs[0];
+ seq.createDatasetSequence();
+ if (group != null)
+ {
+ seq.insertCharAt(0, group.getStartRes(), '-');
+ seq.insertCharAt(group.getEndRes() + 1,
+ alignment.getWidth() - group.getEndRes() - 1, '-');
+ seq.updateHMMMapping();
+ SequenceI topSeq = group.getSequencesInOrder(alignment)[0];
+ int topIndex = alignment.findIndex(topSeq);
+ alignment.insertSequenceAt(topIndex, seq);
+ group.setSeqrep(seq);
+ group.addSequence(seq, false);
+ }
+ else
+ {
+ alignment.insertSequenceAt(0, seq);
+ }
+
+ AlignViewport viewport = af.getViewport();
+ if (viewport != null)
+ {
+ viewport.alignmentChanged(viewport.getAlignPanel());
+ viewport.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+
+ if (viewport.getAlignPanel().alignFrame.getSelectedHMM() == null)
+ {
+ viewport.getAlignPanel().alignFrame.setSelectedHMMSequence(seq);
+ }
+ }
}
-
- private void importData() throws IOException, InterruptedException
+
+ /**
+ * Runs hmmbuild, and waits for the results to be imported before continuing
+ */
+ public void hmmbuildWaitTillComplete()
{
- af.loadJalviewDataFile(HMMERCommands.HMMBUFFER, DataSourceType.FILE,
- FileFormat.HMMER3, null);
- for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
+ Thread loader = new Thread(this);
+ loader.start();
+
+ while (loader.isAlive())
{
- SequenceI seq = entry.getValue();
- Integer pos = entry.getKey();
- HMMERCommands.addHMMConsensusSequence(af, seq, pos);
+ try
+ {
+ Thread.sleep(500);
+ } catch (Exception ex)
+ {
+ }
}
- af.alignPanel.alignmentChanged();
}
-
-
-
-
}
git://source.jalview.org / jalview.git / blobdiff