args);
if (params.showRunDialog())
{
- new Thread(new HMMAlignThread(this, true, params.getJobParams()))
+ new Thread(new HMMAlignThread(this, params.getJobParams()))
.start();
}
alignPanel.repaint();
args);
if (params.showRunDialog())
{
- new Thread(new HMMSearchThread(this, true, params.getJobParams()))
+ new Thread(new HMMSearchThread(this, params.getJobParams()))
.start();
}
alignPanel.repaint();
{
return;
}
- new Thread(new HMMAlignThread(this, true, null))
- .start();
+ new Thread(new HMMAlignThread(this, null)).start();
}
@Override
{
return;
}
- new Thread(new HMMSearchThread(this, true, null))
- .start();
+ new Thread(new HMMSearchThread(this, null)).start();
}
/**
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.AlignmentOrder;
{
static final String HMMALIGN = "hmmalign";
+ static final String ARG_TRIM = "--trim";
+
/*
* feature settings from view that job was associated with
*/
HiddenMarkovModel hmm;
- List<ArgumentI> args;
-
- boolean newFrame;
-
- long barID;
-
- File hmmTemp = null;
-
- File outTemp = null;
-
- File inputTemp = null;
-
- List<AlignmentOrder> allOrders;
-
SequenceI[][] allResults;
/**
- * Constructor for the HMMAlignThread. If create new frame is set to true, a
- * new frame will be created.
+ * Constructor for the HMMAlignThread
*
* @param af
- * @param createNewFrame
+ * @param args
*/
- public HMMAlignThread(AlignFrame af, boolean createNewFrame,
- List<ArgumentI> args)
+ public HMMAlignThread(AlignFrame af, List<ArgumentI> args)
{
- this.af = af;
+ super(af, args);
alignment = af.getViewport().getAlignment();
if (alignment.getDataset() != null)
{
dataset = alignment.getDataset();
}
- newFrame = createNewFrame;
featureSettings = af.getFeatureRenderer().getSettings();
- this.args = args;
}
/**
@Override
public void run()
{
-
hmm = af.getSelectedHMM();
- barID = System.currentTimeMillis();
+ long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
- barID);
+ msgId);
prepareAlignment();
SequenceI[][] subAlignments = msa.getVisibleContigs('-');
- allOrders = new ArrayList<>();
+
+ List<AlignmentOrder> allOrders = new ArrayList<>();
allResults = new SequenceI[subAlignments.length][];
int job = 0;
for (SequenceI[] seqs : subAlignments)
{
- uniquifySequences(seqs);
+ stashSequences(seqs);
try
{
- createTemporaryFiles();
- } catch (IOException e2)
- {
- e2.printStackTrace();
- }
- try
- {
- exportData(seqs, outTemp.getAbsoluteFile(), hmm,
- hmmTemp.getAbsoluteFile(), null);
- } catch (IOException e1)
- {
- e1.printStackTrace();
- }
- try
- {
- boolean ran = runCommand();
+ File modelFile = createTempFile("hmm", ".hmm");
+ File alignmentFile = createTempFile("output", ".sto");
+ File resultFile = createTempFile("input", ".sto");
+
+ exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null);
+ exportHmm(hmm, modelFile.getAbsoluteFile());
+
+ boolean ran = runCommand(modelFile, alignmentFile, resultFile);
if (!ran)
{
JvOptionPane.showInternalMessageDialog(af,
MessageManager.getString("warn.hmmalign_failed"));
return;
}
- } catch (IOException | InterruptedException e)
- {
- e.printStackTrace();
- }
- try
- {
- importData(job);
- } catch (IOException | InterruptedException e)
+
+ SequenceI[] result = importData(resultFile, allOrders);
+ allResults[job] = result;
+ modelFile.delete();
+ alignmentFile.delete();
+ resultFile.delete();
+ } catch (IOException e)
{
- // TODO Auto-generated catch block
e.printStackTrace();
}
job++;
}
- displayResults(newFrame);
-
- af.setProgressBar("", barID);
-
- }
+ displayResults(allOrders);
- /**
- * Creates temporary files for exporting and importing the data.
- *
- * @throws IOException
- */
- private void createTemporaryFiles() throws IOException
- {
- 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();
+ af.setProgressBar("", msgId);
}
/**
- * Executes the hmmalign command in the command line
+ * Executes the hmmalign command and returns true if successful, false if an
+ * error is detected
*
+ * @param modelFile
+ * the HMM to align to
+ * @param alignmentFile
+ * the sequences to align
+ * @param resultFile
+ * the file to hold the results of alignment
* @return
* @throws IOException
- * @throws InterruptedException
*/
- private boolean runCommand() throws IOException, InterruptedException
+ private boolean runCommand(File modelFile, File alignmentFile,
+ File resultFile)
+ throws IOException
{
- 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))
+ String command = getCommandPath(HMMALIGN);
+ if (command == null)
{
- // command += ALLCOL; // todo obsolete option?
+ return false;
}
- if (args != null)
+ List<String> args = new ArrayList<>();
+ args.add(command);
+
+ if (params != null)
{
- for (ArgumentI arg : args)
+ for (ArgumentI arg : params)
{
String name = arg.getName();
- switch (name)
+ if (MessageManager.getString("label.trim_termini").equals(name))
{
- case "Trim Non-Matching Termini":
- command += "--trim";
+ args.add(ARG_TRIM);
}
}
}
- command += " -o " + inputTemp.getAbsolutePath() + SPACE
- + hmmTemp.getAbsolutePath() + SPACE
- + outTemp.getAbsolutePath();
- return runCommand(command);
+ args.add("-o");
+ args.add(resultFile.getAbsolutePath());
+ args.add(modelFile.getAbsolutePath());
+ args.add(alignmentFile.getAbsolutePath());
+
+ return runCommand(args);
}
/**
- * Imports the data from the temporary file to which the output of hmmalign is
- * directed. this is used for an internal job.
+ * Imports the data from the file holding the output of hmmalign
+ *
+ * @param resultFile
+ * @param allOrders
+ * a list of alignment orders to add to
*
- * @param index
- * The index of the 'job' (or region of an alignment).
+ * @return
* @throws IOException
- * @throws InterruptedException
*/
- private void importData(int index)
- throws IOException, InterruptedException
+ private SequenceI[] importData(File resultFile,
+ List<AlignmentOrder> allOrders) throws IOException
{
- StockholmFile file = new StockholmFile(inputTemp.getAbsolutePath(),
+ StockholmFile file = new StockholmFile(resultFile.getAbsolutePath(),
DataSourceType.FILE);
SequenceI[] result = file.getSeqsAsArray();
AlignmentOrder msaorder = new AlignmentOrder(result);
AlignmentSorter.recoverOrder(result);
- SeqsetUtils.deuniquify(hash, result);
+ recoverSequences(result);
allOrders.add(msaorder);
- allResults[index] = result;
- hmmTemp.delete();
- outTemp.delete();
- inputTemp.delete();
+
+ return result;
}
/**
*/
private void prepareAlignment()
{
- // hmmSeqs = alignment.getHMMConsensusSequences(true);
msa = af.gatherSequencesForAlignment();
}
/**
- * Displays the results of all 'jobs'.
+ * Displays the results of all 'jobs' in a new frame
*
- * @param newFrame
+ * @param allOrders
*/
- private void displayResults(boolean newFrame)
+ private void displayResults(List<AlignmentOrder> allOrders)
{
AlignmentOrder[] arrOrders = allOrders
.toArray(new AlignmentOrder[allOrders.size()]);
Object[] newview = msa.getUpdatedView(allResults, arrOrders, '-');
- SequenceI[] alignment = (SequenceI[]) newview[0];
+ SequenceI[] seqs = (SequenceI[]) newview[0];
HiddenColumns hidden = (HiddenColumns) newview[1];
- Alignment al = new Alignment(alignment);
+ Alignment al = new Alignment(seqs);
al.setProperty("Alignment Program", "hmmalign");
if (dataset != null)
{
al.setDataset(dataset);
}
- if (newFrame)
- {
- displayInNewFrame(al, allOrders, hidden);
- }
+ displayInNewFrame(al, allOrders, hidden);
}
/**
- * Displays the results in a new frame.
+ * Displays the results in a new frame
*
* @param al
- * The alignment containing the results.
+ * The alignment containing the results
* @param alorders
* The order of the sequences in the alignment on which the jobs were
- * run.
+ * run
* @param hidden
- * Hidden columns in the previous alignment.
+ * Hidden columns in the previous alignment
*/
private void displayInNewFrame(AlignmentI al,
List<AlignmentOrder> alorders, HiddenColumns hidden)
{
- AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame alignFrame = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
// initialise with same renderer settings as in parent alignframe.
- af.getFeatureRenderer().transferSettings(this.featureSettings);
+ alignFrame.getFeatureRenderer().transferSettings(this.featureSettings);
- if (allOrders.size() > 0)
- {
- addSortByMenuItems(af, allOrders);
- }
+ addSortByMenuItems(alignFrame, alorders);
// TODO: refactor retrieve and show as new splitFrame as Desktop method
copyComplement.alignAs(al);
if (copyComplement.getHeight() > 0)
{
- af.setTitle(this.af.getTitle());
+ alignFrame.setTitle(this.af.getTitle());
AlignFrame af2 = new AlignFrame(copyComplement,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af2.setTitle(complementTitle);
String linkedTitle = MessageManager
.getString("label.linked_view_title");
JInternalFrame splitFrame = new SplitFrame(
- al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
+ al.isNucleotide() ? alignFrame : af2, al.isNucleotide() ? af2 : alignFrame);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
return;
}
/*
* Not from SplitFrame, or failed to created a complementary alignment
*/
- Desktop.addInternalFrame(af, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ Desktop.addInternalFrame(alignFrame, alignFrame.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
/**
- * Add sort order options to the AlignFrame menus.
+ * Adds sort order options to the AlignFrame menus
*
- * @param af
+ * @param alignFrame
* @param alorders
*/
- protected void addSortByMenuItems(AlignFrame af,
+ protected void addSortByMenuItems(AlignFrame alignFrame,
List<AlignmentOrder> alorders)
{
// update orders
if (alorders.size() == 1)
{
- af.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
+ alignFrame.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
}
else
{
}
for (int i = 0, l = alorders.size(); i < l; i++)
{
- af.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
+ alignFrame.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
alorders.get(i));
}
}
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)
+ 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))
- {
- alignment = viewport.getAlignment();
- break;
- }
- else if ("All groups and alignment".equals(value))
+ String name = arg.getName();
+ if (MessageManager.getString("label.hmmbuild_for").equals(name))
{
- 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();
- }
+ 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> hmmSeqs = null;
- if (forGroup)
- {
- hmmSeqs = group.getHMMConsensusSequences();
- if (hmmSeqs.size() > 0)
- {
- // todo why this test? means can't re-run hmmbuild on a group?
- return;
- }
- array = group.getSelectionAsNewSequences(alignment);
- }
- else
- {
- hmmSeqs = alignment.getHMMConsensusSequences();
- if (!alignment.isAligned())
- {
- alignment.padGaps();
- }
- array = alignment.getSequencesArray();
- }
-
- if (array.length < 1)
+ hmmSeqs = group.getHMMConsensusSequences();
+ array = group.getSelectionAsNewSequences(alignment);
+ }
+ else
+ {
+ hmmSeqs = alignment.getHMMConsensusSequences();
+ // todo pad gaps in an unaligned SequenceGroup as well?
+ if (!alignment.isAligned())
{
- if (af != null)
- {
- JOptionPane.showMessageDialog(af,
- MessageManager.getString("warn.no_sequence_data"));
- }
- return;
+ alignment.padGaps();
}
+ array = alignment.getSequencesArray();
+ }
- /*
- * copy over sequences excluding hmm consensus sequences
- */
- SequenceI[] newArr = new SequenceI[array.length - hmmSeqs.size()];
- int index = 0;
- for (SequenceI seq : array)
+ if (array.length < 1)
+ {
+ if (af != null)
{
- if (!seq.isHMMConsensusSequence())
- {
- newArr[index] = new Sequence(seq);
- index++;
- }
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_sequence_data"));
}
+ return;
+ }
- uniquifySequences(newArr);
-
- if (forGroup)
+ /*
+ * 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())
{
- exportData(newArr, stoTemp, null, null, group);
+ alignment.deleteSequence(seq);
}
else
{
- exportData(newArr, stoTemp, null, null, alignment);
+ newArr[index] = new Sequence(seq);
+ index++;
}
+ }
- SeqsetUtils.deuniquify(hash, array);
+ stashSequences(newArr);
- } catch (FileNotFoundException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ exportStockholm(newArr, alignmentFile,
+ group != null ? group : alignment);
- }
- try
- {
- boolean ran = runCommand();
- if (!ran)
- {
- return;
- }
- } catch (IOException | InterruptedException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- try
- {
+ recoverSequences(array);
- importData();
- } catch (IOException | InterruptedException e)
+ boolean ran = runCommand(alignmentFile, hmmFile, group);
+ if (!ran)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ return;
}
+ importData(hmmFile, group);
} catch (Exception e)
{
e.printStackTrace();
+ } finally
+ {
+ if (hmmFile != null)
+ {
+ hmmFile.delete();
+ }
+ if (alignmentFile != null)
+ {
+ alignmentFile.delete();
+ }
}
}
/**
- * 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();
}
/**
public class HMMERParamStore implements ParamDatastoreI
{
-
String name;
List<WsParamSetI> presets = new ArrayList<>();
- public HMMERParamStore(String name)
+ public HMMERParamStore(String nam)
{
- this.name = name;
+ this.name = nam;
}
@Override
public List<WsParamSetI> getPresets()
{
- // TODO Auto-generated method stub
return presets;
}
@Override
- public WsParamSetI getPreset(String name)
+ public WsParamSetI getPreset(String nam)
{
- // TODO Auto-generated method stub
return null;
}
{
args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
MessageManager.getString("label.hmm_name_desc"), true, ""));
+ // todo only enable Use Reference Annotation if RF is present
args.add(new BooleanOption(
MessageManager.getString("label.use_reference"),
MessageManager.getString("label.use_reference_desc"), true,
@Override
public boolean presetExists(String name)
{
- // TODO Auto-generated method stub
return false;
}
@Override
public void deletePreset(String name)
{
- // TODO Auto-generated method stub
-
}
@Override
public void updatePreset(String oldName, String presetName, String text,
List<ArgumentI> jobParams)
{
- // TODO Auto-generated method stub
-
}
@Override
String description, String[] serviceURL, String parameters)
throws IOException
{
- // TODO Auto-generated method stub
return null;
}
public String generateServiceParameterFile(WsParamSetI pset)
throws IOException
{
- // TODO Auto-generated method stub
return null;
}
import jalview.io.FileParse;
import jalview.io.StockholmFile;
import jalview.util.MessageManager;
-import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.simple.BooleanOption;
{
static final String HMMSEARCH = "hmmsearch";
- /*
- * feature settings from view that job was associated with
- */
- protected FeatureRendererSettings featureSettings = null;
-
- HiddenMarkovModel hmm;
-
- boolean newFrame;
-
boolean realign = false;
boolean trim = false;
- Integer numberOfSequences = null;
-
- long barID;
-
- List<ArgumentI> params;
-
- File hmmTemp = null;
-
- File inputAlignmentTemp = null;
-
- File inputTableTemp = null;
-
- File databaseFile = null;
+ int seqsToReturn = Integer.MAX_VALUE;
SequenceI[] seqs;
/**
- * Constructor for the HMMSearchThread. If create new frame is set to true, a
- * new frame will be created.
+ * Constructor for the HMMSearchThread
*
* @param af
- * @param createNewFrame
*/
- public HMMSearchThread(AlignFrame af, boolean createNewFrame,
- List<ArgumentI> args)
+ public HMMSearchThread(AlignFrame af, List<ArgumentI> args)
{
- this.af = af;
- newFrame = createNewFrame;
- featureSettings = af.getFeatureRenderer().getSettings();
- params = args;
+ super(af, args);
}
/**
* Runs the HMMSearchThread: 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).
+ * imported and displayed in a new frame
*/
@Override
public void run()
{
- if (af.getSelectedHMM() == null)
+ HiddenMarkovModel hmm = af.getSelectedHMM();
+ if (hmm == null)
{
JOptionPane.showMessageDialog(af,
MessageManager.getString("warn.no_selected_hmm"));
return;
}
- else
- {
- hmm = af.getSelectedHMM();
- }
SequenceI hmmSeq = af.getSelectedHMMSequence();
- barID = System.currentTimeMillis();
+ long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
- barID);
+ msgId);
try
{
- createTemporaryFiles();
- } catch (IOException e2)
- {
- e2.printStackTrace();
- }
- try
- {
- exportData(null, null, hmm, hmmTemp.getAbsoluteFile(), null);
- } catch (IOException e1)
- {
- e1.printStackTrace();
- }
- try
- {
- boolean ran = runCommand();
+ File hmmFile = createTempFile("hmm", ".hmm");
+ File hitsAlignmentFile = createTempFile("hitAlignment", ".sto");
+ File searchOutputFile = createTempFile("searchOutput", ".sto");
+
+ exportHmm(hmm, hmmFile.getAbsoluteFile());
+
+ boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
if (!ran)
{
JvOptionPane.showInternalMessageDialog(af,
MessageManager.getString("warn.hmmsearch_failed"));
return;
}
+
+ importData(hmmSeq, hitsAlignmentFile, hmmFile, searchOutputFile);
+ // TODO make realignment of search results a step at this level
+ // and make it conditional on this.realign
} catch (IOException | InterruptedException e)
{
e.printStackTrace();
}
- try
- {
- importData(hmmSeq);
- } catch (IOException | InterruptedException e)
+ finally
{
- // TODO Auto-generated catch block
- e.printStackTrace();
+ af.setProgressBar("", msgId);
}
-
- af.setProgressBar("", barID);
-
}
/**
- * Creates temporary files for exporting and importing the data.
+ * Executes an hmmsearch with the given hmm as input. The database to be
+ * searched is a local file as specified by the 'Database' parameter, or the
+ * current alignment (written to file) if none is specified.
*
- * @throws IOException
- */
- private void createTemporaryFiles() throws IOException
- {
- hmmTemp = File.createTempFile("hmm", ".hmm");
- hmmTemp.deleteOnExit();
- inputAlignmentTemp = File.createTempFile("inputAl", ".sto");
- inputAlignmentTemp.deleteOnExit();
- inputTableTemp = File.createTempFile("buffer", ".sto");
- inputTableTemp.deleteOnExit();
- }
-
- /**
- * Executes the hmmsearch command in the command line.
+ * @param searchOutputFile
+ * @param hitsAlignmentFile
+ * @param hmmFile
*
* @return
* @throws IOException
- * @throws InterruptedException
*/
- private boolean runCommand() throws IOException, InterruptedException
+ private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,
+ File hmmFile) throws IOException
{
- String binaryPath = getCommandRoot(HMMSEARCH);
- if (binaryPath == null)
+ String command = getCommandPath(HMMSEARCH);
+ if (command == null)
{
return false;
}
- String command = binaryPath + " -o "
- + inputTableTemp.getAbsolutePath() + " -A "
- + inputAlignmentTemp.getAbsolutePath() + SPACE;
+ List<String> args = new ArrayList<>();
+ args.add(command);
+ args.add("-o");
+ args.add(searchOutputFile.getAbsolutePath());
+ args.add("-A");
+ args.add(hitsAlignmentFile.getAbsolutePath());
boolean dbFound = false;
String dbPath = "";
+ File databaseFile = null;
+
if (params != null)
{
for (ArgumentI arg : params)
{
String name = arg.getName();
- switch (name)
+ if (MessageManager.getString("label.number_of_results")
+ .equals(name))
+ {
+ seqsToReturn = Integer.parseInt(arg.getValue());
+ }
+ else if (MessageManager.getString("label.auto_align_seqs")
+ .equals(name))
+ {
+ realign = true; // TODO: not used
+ }
+ else if (MessageManager.getString("label.use_accessions")
+ .equals(name))
+ {
+ args.add("--acc");
+ }
+ else if (MessageManager.getString("label.seq_e_value").equals(name))
+ {
+ args.add("--incE");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.seq_score").equals(name))
+ {
+ args.add("-incT");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.dom_e_value_desc")
+ .equals(name))
+ {
+ args.add("--incdomE");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.dom_score").equals(name))
+ {
+ args.add("--incdomT");
+ args.add(arg.getValue());
+ }
+ else if (MessageManager.getString("label.trim_termini")
+ .equals(name))
{
- case "Number of Results to Return":
- numberOfSequences = Integer.parseInt(arg.getValue());
- break;
- case "Automatically Align Fetched Sequences":
- if ("Automatically Align Fetched Sequences"
- .equals(arg.getValue()))
- {
- realign = true;
- }
- break;
- case "Return Accessions":
- if ("Return Accessions".equals(arg.getValue()))
- {
- command += "--acc ";
- }
- break;
- case "Sequence E-value Cutoff":
- command += "--incE " + arg.getValue() + SPACE;
- break;
- case "Sequence Score Threshold":
- command += "-incT " + arg.getValue() + SPACE;
- break;
- case "Domain E-value Threshold":
- command += "--incdomE " + arg.getValue() + SPACE;
- break;
- case "Domain Score Threshold":
- command += "--incdomT " + arg.getValue() + SPACE;
- break;
- case "Trim Non-Matching Termini":
trim = true;
- break;
- case "Database":
+ }
+ else if (MessageManager.getString("label.database").equals(name))
+ {
dbFound = true;
dbPath = arg.getValue();
if (!MessageManager.getString("label.this_alignment")
databaseFile = new File(dbPath);
}
}
-
}
}
StockholmFile stoFile = new StockholmFile(copy);
stoFile.setSeqs(copy.getSequencesArray());
String alignmentString = stoFile.print();
- databaseFile = File.createTempFile("database", ".sto");
- databaseFile.deleteOnExit();
+ databaseFile = createTempFile("database", ".sto");
PrintWriter writer = new PrintWriter(databaseFile);
writer.print(alignmentString);
writer.close();
}
- command += hmmTemp.getAbsolutePath() + SPACE
- + databaseFile.getAbsolutePath();
- return runCommand(command);
+ args.add(hmmFile.getAbsolutePath());
+ args.add(databaseFile.getAbsolutePath());
+
+ return runCommand(args);
}
/**
*
* @param hmmSeq
*/
- private void importData(SequenceI hmmSeq)
+ private void importData(SequenceI hmmSeq, File inputAlignmentTemp,
+ File hmmTemp, File searchOutputFile)
throws IOException, InterruptedException
{
BufferedReader br = new BufferedReader(
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
- readTable();
+ readTable(searchOutputFile);
- SequenceI[] hmmAndSeqs;
- if (numberOfSequences != null && numberOfSequences < seqs.length)
- {
- hmmAndSeqs = new SequenceI[numberOfSequences + 1];
- }
- else
- {
- hmmAndSeqs = new SequenceI[seqs.length + 1];
- }
+ int seqCount = Math.min(seqs.length, seqsToReturn);
+ SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
hmmAndSeqs[0] = hmmSeq;
-
- if (numberOfSequences != null && seqs.length > numberOfSequences)
- {
- System.arraycopy(seqs, 0, hmmAndSeqs, 1, numberOfSequences);
- }
- else
- {
- System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqs.length);
- }
+ System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
AlignmentI alignment = new Alignment(hmmAndSeqs);
AlignFrame frame = new AlignFrame(alignment, 1, 1);
MessageManager.getString("label.trim_termini_desc"), true,
true, true, null));
}
- HMMAlignThread hmmalign = new HMMAlignThread(frame, true, alignArgs);
+ HMMAlignThread hmmalign = new HMMAlignThread(frame, alignArgs);
hmmalign.hmmalignWaitTillComplete();
frame = null;
hmmTemp.delete();
inputAlignmentTemp.delete();
- inputTableTemp.delete();
+ searchOutputFile.delete();
} finally
{
if (br != null)
}
- void readTable() throws IOException
+ void readTable(File inputTableTemp) throws IOException
{
BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
String line = "";
package jalview.hmmer;
+import jalview.analysis.SeqsetUtils;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.io.HMMFile;
import jalview.io.StockholmFile;
import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
import java.io.BufferedReader;
import java.io.File;
{
public static final String HMMBUILD = "hmmbuild";
- public String JALVIEWDIRECTORY = System.getProperty("user.dir")
- + File.separator;
+ private Hashtable hash = new Hashtable();
- public String OUTPUTALIGNMENT;
-
- public final String SPACE = " ";
-
- public final String ALLCOL = "--allcol ";
-
- public final String TRIM = "--trim ";
-
- public final String FORCEAMINO = "--amino ";
-
- public final String FORCEDNA = "--dna ";
-
- public final String FORCERNA = "--rna ";
-
- Hashtable hash = new Hashtable();
+ protected AlignFrame af;
- List<SequenceI> hmmSeqs;
+ protected List<ArgumentI> params;
- protected AlignFrame af;
+ public HmmerCommand(AlignFrame alignFrame, List<ArgumentI> args)
+ {
+ af = alignFrame;
+ params = args;
+ }
public static boolean isHmmerAvailable()
{
/**
* Uniquifies the sequences when exporting and stores their details in a
- * hashtable.
+ * hashtable
*
* @param seqs
*/
- public void uniquifySequences(SequenceI[] seqs)
+ protected void stashSequences(SequenceI[] seqs)
{
- hash = jalview.analysis.SeqsetUtils.uniquify(seqs, true);
+ hash = SeqsetUtils.uniquify(seqs, true);
}
/**
- * Recover the sequence data lost by uniquifying.
+ * Restores the sequence data lost by uniquifying
*
* @param seqs
*/
- public void recoverSequenceNames(SequenceI[] seqs)
+ protected void recoverSequences(SequenceI[] seqs)
{
- jalview.analysis.SeqsetUtils.deuniquify(hash, seqs);
+ SeqsetUtils.deuniquify(hash, seqs);
}
/**
- * Runs a command in the command line.
+ * Runs a command as a separate process
*
* @param command
+ * the executable command and any arguments to it
* @throws IOException
- * @throws InterruptedException
*/
- public boolean runCommand(String command)
- throws IOException, InterruptedException
+ public boolean runCommand(List<String> command)
+ throws IOException
{
try
{
- final Process p = Runtime.getRuntime().exec(command);
-
+ ProcessBuilder pb = new ProcessBuilder(command);
+ pb.redirectErrorStream(true); // send syserr to sysout
+ final Process p = pb.start();
new Thread(new Runnable()
{
@Override
{
BufferedReader input = new BufferedReader(
new InputStreamReader(p.getInputStream()));
- String line = null;
-
try
{
- while ((line = input.readLine()) != null)
+ String line = input.readLine();
+ while (line != null)
{
System.out.println(line);
+ line = input.readLine();
}
} catch (IOException e)
{
}).start();
p.waitFor();
+ return p.exitValue() == 0; // 0 is success, by convention
} catch (Exception e)
{
e.printStackTrace();
return false;
}
- return true;
}
/**
- * Exports an alignment and/or HMM to the specified file.
+ * Exports an alignment (and possibly annotation) to the specified file, in
+ * Stockholm format
*
- * @param alignment
+ * @param seqs
+ * @param toFile
+ * @param annotated
* @throws IOException
*/
- public void exportData(SequenceI[] seqs, File stoLocation,
- HiddenMarkovModel hmm, File hmmLocation, AnnotatedCollectionI al)
+ public void exportStockholm(SequenceI[] seqs, File toFile,
+ AnnotatedCollectionI annotated)
throws IOException
{
if (seqs != null)
{
AlignmentI newAl = new Alignment(seqs);
- if (stoLocation != null && al != null)
+ if (toFile != null && annotated != null)
{
- for (AlignmentAnnotation annot : al.getAlignmentAnnotation())
+ for (AlignmentAnnotation annot : annotated.getAlignmentAnnotation())
{
if (annot.label.contains("Reference") || "RF".equals(annot.label))
{
StockholmFile file = new StockholmFile(newAl);
String output = file.print(seqs, false);
- PrintWriter writer = new PrintWriter(stoLocation);
+ PrintWriter writer = new PrintWriter(toFile);
writer.println(output);
writer.close();
}
-
- if (hmm != null)
- {
- HMMFile file = new HMMFile(hmm);
- PrintWriter writer = new PrintWriter(hmmLocation);
- writer.print(file.print());
- writer.close();
- }
- }
-
- /**
- * Returns the list of HMM sequences removed
- *
- * @return
- */
- public List<SequenceI> getHmmSeqs()
- {
- return hmmSeqs;
- }
-
- /**
- * Sets the list of removed HMM sequences
- *
- * @param hmmSeqs
- */
- public void setHmmSeqs(List<SequenceI> hmmSeqs)
- {
- this.hmmSeqs = hmmSeqs;
}
/**
* command short name e.g. hmmalign
* @return
*/
- protected String getCommandRoot(String cmd)
+ protected String getCommandPath(String cmd)
{
String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
File file = getExecutable(cmd, binariesFolder);
}
return file;
}
+
+ /**
+ * A convenience method to create a temporary file that is deleted on exit of
+ * the JVM
+ *
+ * @param prefix
+ * @param suffix
+ * @return
+ * @throws IOException
+ */
+ protected File createTempFile(String prefix, String suffix)
+ throws IOException
+ {
+ File f = File.createTempFile(prefix, suffix);
+ f.deleteOnExit();
+ return f;
+
+ }
+
+ /**
+ * Exports an HMM to the specified file
+ *
+ * @param hmm
+ * @param hmmFile
+ * @throws IOException
+ */
+ public void exportHmm(HiddenMarkovModel hmm, File hmmFile)
+ throws IOException
+ {
+ if (hmm != null)
+ {
+ HMMFile file = new HMMFile(hmm);
+ PrintWriter writer = new PrintWriter(hmmFile);
+ writer.print(file.print());
+ writer.close();
+ }
+ }
}
@Test(priority = 1)
public void testHMMAlign() throws MalformedURLException, IOException
{
- HMMAlignThread thread = new HMMAlignThread(frame, true,
+ HMMAlignThread thread = new HMMAlignThread(frame,
new ArrayList<ArgumentI>());
try
{
git://source.jalview.org / jalview.git / commitdiff