package jalview.hmmer;
+
import jalview.bin.Cache;
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.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.gui.Preferences;
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.File;
import java.io.FileNotFoundException;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.List;
import javax.swing.JOptionPane;
{
HMMERCommands cmds = new HMMERCommands();
AlignFrame af;
- AlignmentI alignment;
+ AlignViewport viewport;
+
+ boolean multiJob = false;
+ AlignmentI alignment;
SequenceGroup group;
+ List<ArgumentI> params;
- boolean canRun = true;
+
+ boolean forGroup = false;
File hmmTemp = null;
long barID;
- public HMMBuildThread(AlignFrame af)
+ /**
+ * This is used for validation purposes. Do not use!
+ *
+ * @param viewport
+ */
+ public HMMBuildThread(AlignmentI alignment)
{
- this.af = af;
- if (af.getViewport().getSelectionGroup() != null)
- {
- group = af.getViewport().getSelectionGroup();
- }
- alignment = af.getViewport().getAlignment();
+ this.alignment = alignment;
+ forGroup = false;
+ }
+ public HMMBuildThread(AlignFrame af, List<ArgumentI> args)
+ {
+ this.af = af;
+ viewport = af.getViewport();
+ params = args;
}
+ /**
+ * Builds a HMM from an alignment, then imports and adds it to the alignment.
+ */
@Override
public void run()
{
barID = System.currentTimeMillis();
+ if (af != null)
+ {
af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
barID);
+ }
cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
- if (alignment == null && group == null)
+
+ List<SequenceGroup> groups = new ArrayList<>();
+ if (params != null)
{
- JOptionPane.showMessageDialog(af,
- MessageManager.getString("label.no_sequence_data"));
- return;
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (MessageManager.getString("label.hmmbuild_for").equals(name))
+ {
+ String value = arg.getValue();
+ if ("Alignment".equals(value))
+ {
+ alignment = viewport.getAlignment();
+ break;
+ }
+ else if ("All groups and alignment".equals(value))
+ {
+ alignment = viewport.getAlignment();
+ groups.addAll(viewport.getAlignment().getGroups());
+ if (groups.size() > 0)
+ {
+ multiJob = true;
+ }
+ break;
+ }
+ else if ("All groups".equals(value))
+ {
+ alignment = null;
+ groups = viewport.getAlignment().getGroups();
+ if (groups.size() > 0)
+ {
+ multiJob = true;
+ }
+ break;
+ }
+ else if ("Selected group".equals(value))
+ {
+ alignment = null;
+ groups.add(viewport.getSelectionGroup());
+ break;
+ }
+ }
+ else if (MessageManager.getString("label.use_reference")
+ .equals(name))
+ {
+ if (!af.getViewport().hasReferenceAnnotation())
+ {
+ if (af != null)
+ {
+ af.setProgressBar(
+ MessageManager.getString("status.running_hmmbuild"),
+ barID);
+ }
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .getString("warn.no_reference_annotation"));
+ return;
+ }
+ }
+ }
}
- try
+ else if (viewport != null)
+ {
+ alignment = viewport.getAlignment();
+ }
+
+ if (alignment != null)
+ {
+ forGroup = false;
+ runHMMBuild();
+ }
+
+ if (alignment == null)
{
- hmmTemp = File.createTempFile("hmm", ".hmm");
- hmmTemp.deleteOnExit();
- stoTemp = File.createTempFile("output", ".sto");
- stoTemp.deleteOnExit();
- } catch (IOException e1)
+ alignment = viewport.getAlignment();
+ }
+
+ if (groups != null && groups.size() > 0)
{
- e1.printStackTrace();
+ for (SequenceGroup grp : groups)
+ {
+ group = grp;
+ forGroup = true;
+ runHMMBuild();
+ }
}
- try
+
+ if (af != null)
{
+ af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+ barID);
+ }
+ }
+
+ private void runHMMBuild()
+ {
+ if (alignment == null && group == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_sequence_data"));
+ }
+ try
+ {
+ hmmTemp = File.createTempFile("hmm", ".hmm");
+ hmmTemp.deleteOnExit();
+ stoTemp = File.createTempFile("output", ".sto");
+ stoTemp.deleteOnExit();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+
try
{
- List<SequenceI> seqs = alignment
- .getHMMConsensusSequences(true);
- cmds.setHmmSeqs(seqs);
- if (group != null)
+ try
+ {
+ SequenceI[] array;
+ List<SequenceI> seqs = null;
+ if (forGroup)
{
- SequenceI[] array = group.getSelectionAsNewSequences(alignment);
-
- cmds.exportData(array, stoTemp, null, null);
+ seqs = group.getHMMConsensusSequences(true);
+ if (seqs.size() > 0)
+ {
+ return;
+ }
+ array = group.getSelectionAsNewSequences(alignment);
}
else
{
+ seqs = alignment.getHMMConsensusSequences(true);
if (!alignment.isAligned())
{
alignment.padGaps();
}
- cmds.exportData(alignment.getSequencesArray(), stoTemp, null,
- null);
+ array = alignment.getSequencesArray();
}
- } catch (FileNotFoundException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ cmds.setHmmSeqs(seqs);
+
+ if (array.length < 1)
+ {
+ if (af != null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_sequence_data"));
+ }
+ return;
+ }
+ SequenceI[] newArr = new SequenceI[array.length];
+ int index = 0;
+ for (SequenceI seq : array)
+ {
+ newArr[index] = new Sequence(seq);
+ index++;
+ }
+
+ cmds.uniquifySequences(newArr);
+
+ if (forGroup)
+ {
+ cmds.exportData(newArr, stoTemp, null, null, group);
+ }
+ else
+ {
+ cmds.exportData(newArr, stoTemp, null, null, alignment);
+ }
+
+ jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
+
+ } catch (FileNotFoundException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+
+ }
+ try
+ {
+ boolean ran = runCommand();
+ if (!ran)
+ {
+ return;
+ }
+ } catch (IOException | InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ try
+ {
+
+ importData();
+ } catch (IOException | InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
- try
+ }
+
+
+
+ /**
+ * Executes the hmmbuild command in the command line.
+ *
+ * @return
+ * @throws IOException
+ * @throws InterruptedException
+ */
+ private boolean runCommand() throws IOException, InterruptedException
+ {
+ File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
+ if (!file.canExecute())
{
- boolean ran = runCommand();
- if (!ran)
+ file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
+ {
+ if (!file.canExecute())
{
- JvOptionPane.showInternalMessageDialog(af,
- MessageManager.getString("warn.hmmbuild_failed"));
- return;
+ if (af != null)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmbuild_failed"));
+ }
+ return false;
}
- } catch (IOException | InterruptedException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ }
}
- try
- {
+ String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.SPACE;
+ String name = null;
- importData();
- } catch (IOException | InterruptedException e)
+ 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":
+ command += "--hand ";
+ break;
+
+ }
+
+ }
}
- } catch (Exception e)
- {
- e.printStackTrace();
- } finally
+
+ if (forGroup && multiJob)
{
- af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
- barID);
+ name = group.getName() + "_HMM";
}
- }
-
-
- private boolean runCommand() throws IOException, InterruptedException
- {
- File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild.exe");
- if (!file.canExecute())
+ if (name == null || "".equals(name))
{
- return false;
+ if (af != null)
+ {
+ if (af.getTitle().length() < 15)
+ {
+ name = af.getTitle();
+ }
+ }
+ if (name == null || "".equals(name))
+ {
+ name = "Alignment";
+ }
+
}
- String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
- + af.getName() + cmds.SPACE;
+
+ command += "-n " + name.replace(' ', '_') + cmds.SPACE;
if (!alignment.isNucleotide())
{
command += cmds.FORCEAMINO; // TODO check for rna
return cmds.runCommand(command);
}
+ /**
+ * Imports the .hmm file produced by hmmbuild.
+ *
+ * @throws IOException
+ * @throws InterruptedException
+ */
private void importData() throws IOException, InterruptedException
{
- cmds.addHMMConsensusSequences(af);
- af.loadJalviewDataFile(hmmTemp.getAbsolutePath(), DataSourceType.FILE,
- FileFormat.HMMER3, null);
+ HMMFile file = new HMMFile(
+ new FileParse(hmmTemp.getAbsolutePath(),
+ DataSourceType.FILE));
+ SequenceI[] seqs = file.getSeqsAsArray();
+ SequenceI seq = seqs[0];
+ seq.createDatasetSequence();
+ HiddenMarkovModel hmm = file.getHMM();
+ 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);
+ }
+
+ if (viewport != null)
+ {
+ viewport.alignmentChanged(viewport.getAlignPanel());
+ viewport.getAlignPanel().adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+
+ if (viewport.getAlignPanel().alignFrame.getSelectedHMM() == null)
+ {
+ viewport.getAlignPanel().alignFrame.setSelectedHMMSequence(seq);
+ }
+ }
hmmTemp.delete();
stoTemp.delete();
}
- public boolean canRun()
+ /**
+ * Runs hmmbuild, and waits for the results to be imported before continuing
+ */
+ public void hmmbuildWaitTillComplete()
{
- return canRun;
+ Thread loader = new Thread(this);
+ loader.start();
+
+ while (loader.isAlive())
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (Exception ex)
+ {
+ }
+ }
}
-
-
-
}
git://source.jalview.org / jalview.git / blobdiff