X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fhmmer%2FHMMBuildThread.java;h=24106d60e62801865f1ef599bb8087b91d95cf55;hb=6dda78dd65a8f6f25356d9fe95078afbba4eadcd;hp=48796e4b75680a45c8e1f2a355132fcb8305472c;hpb=d9a5e7ac4957e98089c082e629d6e79dd5d30199;p=jalview.git diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java index 48796e4..24106d6 100644 --- a/src/jalview/hmmer/HMMBuildThread.java +++ b/src/jalview/hmmer/HMMBuildThread.java @@ -1,62 +1,175 @@ package jalview.hmmer; -import jalview.bin.Cache; +import jalview.analysis.SeqsetUtils; import jalview.datamodel.AlignmentI; +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; -public class HMMBuildThread implements Runnable +public class HMMBuildThread extends HmmerCommand implements Runnable { - HMMERCommands cmds = new HMMERCommands(); - AlignFrame af; + AlignViewport viewport; + + boolean multiJob = false; + AlignmentI alignment; SequenceGroup group; - boolean canRun = true; + List params; + + boolean forGroup = false; File hmmTemp = null; File stoTemp = 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 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(); - af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), - barID); - cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH); + if (af != null) + { + af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), + barID); + } + + List 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 ("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; + } + } + } + } + else if (viewport != null) + { + alignment = viewport.getAlignment(); + } + + if (alignment != null) + { + forGroup = false; + runHMMBuild(); + } + + if (alignment == null) + { + alignment = viewport.getAlignment(); + } + + if (groups != null && groups.size() > 0) + { + for (SequenceGroup grp : groups) + { + group = grp; + forGroup = true; + runHMMBuild(); + } + } + + if (af != null) + { + af.setProgressBar("", barID); + } + } + + private void runHMMBuild() + { if (alignment == null && group == null) { JOptionPane.showMessageDialog(af, - MessageManager.getString("label.no_sequence_data")); - return; + MessageManager.getString("warn.no_sequence_data")); } try { @@ -71,107 +184,233 @@ public class HMMBuildThread implements Runnable try { - try - { + try + { SequenceI[] array; - List seqs = alignment - .getHMMConsensusSequences(true); - cmds.setHmmSeqs(seqs); - if (group != null) + List 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(); } - cmds.uniquifySequences(array); - cmds.exportData(array, stoTemp, null, null); - jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array); - } catch (FileNotFoundException e) - { - // TODO Auto-generated catch block - e.printStackTrace(); + if (array.length < 1) + { + if (af != null) + { + JOptionPane.showMessageDialog(af, + MessageManager.getString("warn.no_sequence_data")); + } + return; + } - } - try - { + /* + * 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()) + { + newArr[index] = new Sequence(seq); + index++; + } + } + + uniquifySequences(newArr); + + if (forGroup) + { + exportData(newArr, stoTemp, null, null, group); + } + else + { + exportData(newArr, stoTemp, null, null, alignment); + } + + SeqsetUtils.deuniquify(hash, array); + + } catch (FileNotFoundException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + + } + try + { boolean ran = runCommand(); if (!ran) { - JvOptionPane.showInternalMessageDialog(af, - MessageManager.getString("warn.hmmbuild_failed")); return; } - } catch (IOException | InterruptedException e) - { - // TODO Auto-generated catch block - e.printStackTrace(); - } - try - { + } catch (IOException | InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + try + { - importData(); - } catch (IOException | InterruptedException e) - { - // TODO Auto-generated catch block - e.printStackTrace(); - } + importData(); + } catch (IOException | InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } } catch (Exception e) { e.printStackTrace(); - } finally - { - af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), - barID); } } - - - + /** + * 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 + "/binaries/hmmbuild.exe"); - if (!file.canExecute()) + String binaryPath = getCommandRoot(HMMBUILD); + if (binaryPath == null) { return false; } - String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME - + af.getName() + cmds.SPACE; + String command = binaryPath + SPACE; + String name = null; + + if (params != null) + { + 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; + + } + } + } + + if (forGroup && multiJob) + { + name = group.getName() + "_HMM"; + } + + if (name == null || "".equals(name)) + { + if (af != null) + { + if (af.getTitle().length() < 15) + { + name = af.getTitle(); + } + } + if (name == null || "".equals(name)) + { + name = "Alignment"; + } + + } + + command += "-n " + name.replace(' ', '_') + SPACE; if (!alignment.isNucleotide()) { - command += cmds.FORCEAMINO; // TODO check for rna + command += FORCEAMINO; // TODO check for rna } else { - command += cmds.FORCEDNA; + command += FORCEDNA; } - command += hmmTemp.getAbsolutePath() - + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE; - return cmds.runCommand(command); + command += hmmTemp.getAbsolutePath() + SPACE + stoTemp.getAbsolutePath() + + SPACE; + return 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(); + 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) + { + } + } } - - - }