package jalview.hmmer;
-import jalview.analysis.SeqsetUtils;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
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;
public class HMMBuildThread extends HmmerCommand implements Runnable
{
- AlignViewport viewport;
+ static final String ARG_AMINO = "--amino";
- boolean multiJob = false;
+ static final String ARG_DNA = "--dna";
- AlignmentI alignment;
-
- SequenceGroup group;
-
- List<ArgumentI> params;
-
- boolean forGroup = false;
-
- File hmmTemp = null;
-
- File stoTemp = null;
+ static final String ARG_RNA = "--rna";
- long barID;
+ AlignmentI alignment;
/**
- * This is used for validation purposes. Do not use!
+ * Constructor
*
- * @param viewport
+ * @param alignFrame
+ * @param args
*/
- public HMMBuildThread(AlignmentI alignment)
- {
- this.alignment = alignment;
- forGroup = false;
- }
-
- public HMMBuildThread(AlignFrame af, List<ArgumentI> args)
+ public HMMBuildThread(AlignFrame alignFrame, List<ArgumentI> args)
{
- this.af = af;
- viewport = af.getViewport();
- params = args;
+ super(alignFrame, args);
}
/**
- * Builds a HMM from an alignment, then imports and adds it to the alignment.
+ * 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();
+ long msgID = System.currentTimeMillis();
if (af != null)
{
af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
- barID);
+ msgID);
}
- List<SequenceGroup> groups = new ArrayList<>();
- if (params != null)
+ AlignViewportI viewport = af.getViewport();
+ try
{
- for (ArgumentI arg : params)
+ if (viewport != null)
+ {
+ alignment = viewport.getAlignment();
+ }
+ List<SequenceGroup> groups = new ArrayList<>();
+ if (params != null)
{
- String name = arg.getName();
- if (MessageManager.getString("label.hmmbuild_for").equals(name))
+ for (ArgumentI arg : params)
{
- String value = arg.getValue();
- if ("Alignment".equals(value))
+ String name = arg.getName();
+ if (MessageManager.getString("label.hmmbuild_for").equals(name))
{
- alignment = viewport.getAlignment();
- break;
- }
- else if ("All groups and alignment".equals(value))
- {
- alignment = viewport.getAlignment();
- groups.addAll(viewport.getAlignment().getGroups());
- if (groups.size() > 0)
+ String value = arg.getValue();
+ if (MessageManager.getString("label.alignment").equals(value))
{
- multiJob = true;
+ alignment = viewport.getAlignment();
}
- break;
- }
- else if ("All groups".equals(value))
- {
- alignment = null;
- groups = viewport.getAlignment().getGroups();
- if (groups.size() > 0)
+ else if (MessageManager.getString("label.groups_and_alignment")
+ .equals(value))
{
- multiJob = true;
+ 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());
}
- 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())
+ else if (MessageManager.getString("label.use_reference")
+ .equals(name))
{
- if (af != null)
+ // todo disable this option if no RF annotation on alignment
+ if (!af.getViewport().hasReferenceAnnotation())
{
- af.setProgressBar(
- MessageManager.getString("status.running_hmmbuild"),
- barID);
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .getString("warn.no_reference_annotation"));
+ // return;
}
- JvOptionPane.showInternalMessageDialog(af, MessageManager
- .getString("warn.no_reference_annotation"));
- return;
}
}
}
- }
- else if (viewport != null)
- {
- alignment = viewport.getAlignment();
- }
- if (alignment != null)
- {
- forGroup = false;
- runHMMBuild();
- }
+ if (alignment != null)
+ {
+ runHMMBuild(null);
+ }
- if (alignment == null)
- {
- alignment = viewport.getAlignment();
- }
+ if (alignment == null)
+ {
+ alignment = viewport.getAlignment();
+ }
- if (groups != null && groups.size() > 0)
- {
for (SequenceGroup grp : groups)
{
- group = grp;
- forGroup = true;
- runHMMBuild();
+ runHMMBuild(grp);
}
- }
-
- if (af != null)
+ } finally
{
- af.setProgressBar("", barID);
+ if (af != null)
+ {
+ af.setProgressBar("", msgID);
+ }
}
}
- private void runHMMBuild()
+ /**
+ * 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
{
- hmmTemp = File.createTempFile("hmm", ".hmm");
- hmmTemp.deleteOnExit();
- stoTemp = File.createTempFile("output", ".sto");
- stoTemp.deleteOnExit();
- } catch (IOException e1)
- {
- e1.printStackTrace();
- }
-
- try
- {
- try
+ hmmFile = createTempFile("hmm", ".hmm");
+ alignmentFile = createTempFile("output", ".sto");
+ SequenceI[] array;
+ List<SequenceI> hmmSeqs = null;
+ if (group != null)
{
- SequenceI[] array;
- List<SequenceI> seqs = null;
- if (forGroup)
+ hmmSeqs = group.getHMMConsensusSequences();
+ array = group.getSelectionAsNewSequences(alignment);
+ }
+ else
+ {
+ hmmSeqs = alignment.getHMMConsensusSequences();
+ // todo pad gaps in an unaligned SequenceGroup as well?
+ if (!alignment.isAligned())
{
- seqs = group.getHMMConsensusSequences(true);
- if (seqs.size() > 0)
- {
- return;
- }
- array = group.getSelectionAsNewSequences(alignment);
+ alignment.padGaps();
}
- else
+ array = alignment.getSequencesArray();
+ }
+
+ if (array.length < 1)
+ {
+ if (af != null)
{
- seqs = alignment.getHMMConsensusSequences(true);
- if (!alignment.isAligned())
- {
- alignment.padGaps();
- }
- array = alignment.getSequencesArray();
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_sequence_data"));
}
+ return;
+ }
- if (array.length < 1)
+ /*
+ * 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())
{
- if (af != null)
- {
- JOptionPane.showMessageDialog(af,
- MessageManager.getString("warn.no_sequence_data"));
- }
- return;
+ alignment.deleteSequence(seq);
}
- SequenceI[] newArr = new SequenceI[array.length];
- int index = 0;
- for (SequenceI seq : array)
+ else
{
newArr[index] = new Sequence(seq);
index++;
}
+ }
- uniquifySequences(newArr);
+ stashSequences(newArr);
- if (forGroup)
- {
- exportData(newArr, stoTemp, null, null, group);
- }
- else
- {
- exportData(newArr, stoTemp, null, null, alignment);
- }
+ exportStockholm(newArr, alignmentFile,
+ group != null ? group : alignment);
- SeqsetUtils.deuniquify(hash, array);
+ recoverSequences(array);
- } catch (FileNotFoundException e)
+ boolean ran = runCommand(alignmentFile, hmmFile, group);
+ if (!ran)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
-
+ return;
}
- try
- {
- boolean ran = runCommand();
- if (!ran)
- {
- return;
- }
- } catch (IOException | InterruptedException e)
+ importData(hmmFile, group);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ } finally
+ {
+ if (hmmFile != null)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ hmmFile.delete();
}
- try
- {
-
- importData();
- } catch (IOException | InterruptedException e)
+ if (alignmentFile != null)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ alignmentFile.delete();
}
- } catch (Exception e)
- {
- e.printStackTrace();
}
}
/**
- * Executes the hmmbuild command in the command line.
+ * 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() throws IOException, InterruptedException
+ private boolean runCommand(File sequences, File hmm, SequenceGroup group)
+ throws IOException, InterruptedException
{
- String binaryPath = getCommandRoot(HMMBUILD);
- if (binaryPath == null)
+
+ String cmd = getCommandPath(HMMBUILD);
+ if (cmd == null)
{
return false;
}
- String command = binaryPath + SPACE;
+ List<String> args = new ArrayList<>();
+ args.add(cmd);
String name = null;
if (params != null)
name = name.trim();
break;
case "Use Reference Annotation":
- command += "--hand ";
+ args.add("--hand");
break;
-
}
}
}
- if (forGroup && multiJob)
+ if (group != null)
{
name = group.getName() + "_HMM";
}
}
- command += "-n " + name.replace(' ', '_') + SPACE;
+ args.add("-n");
+ args.add(name.replace(' ', '_'));
if (!alignment.isNucleotide())
{
- command += FORCEAMINO; // TODO check for rna
+ args.add(ARG_AMINO); // TODO check for rna
}
else
{
- command += FORCEDNA;
+ args.add(ARG_DNA);
}
- command += hmmTemp.getAbsolutePath() + SPACE + stoTemp.getAbsolutePath()
- + SPACE;
- return runCommand(command);
+ args.add(hmm.getAbsolutePath());
+ args.add(sequences.getAbsolutePath());
+
+ return runCommand(args);
}
/**
- * Imports the .hmm file produced by hmmbuild.
+ * 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() throws IOException, InterruptedException
+ private void importData(File hmmFile, SequenceGroup group)
+ throws IOException, InterruptedException
{
HMMFile file = new HMMFile(
- new FileParse(hmmTemp.getAbsolutePath(), DataSourceType.FILE));
+ new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
SequenceI[] seqs = file.getSeqsAsArray();
SequenceI seq = seqs[0];
seq.createDatasetSequence();
alignment.insertSequenceAt(0, seq);
}
+ AlignViewport viewport = af.getViewport();
if (viewport != null)
{
viewport.alignmentChanged(viewport.getAlignPanel());
viewport.getAlignPanel().alignFrame.setSelectedHMMSequence(seq);
}
}
- hmmTemp.delete();
- stoTemp.delete();
}
/**
git://source.jalview.org / jalview.git / blobdiff