X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMBuildThread.java;h=24106d60e62801865f1ef599bb8087b91d95cf55;hb=6dda78dd65a8f6f25356d9fe95078afbba4eadcd;hp=2ff89c1bfd271cce112d459c173ce06d77f89839;hpb=eea8fd41febcec44a0e098ddfbea74545561f473;p=jalview.git diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java index 2ff89c1..24106d6 100644 --- a/src/jalview/hmmer/HMMBuildThread.java +++ b/src/jalview/hmmer/HMMBuildThread.java @@ -1,16 +1,13 @@ package jalview.hmmer; - -import jalview.bin.Cache; +import jalview.analysis.SeqsetUtils; 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.FileParse; import jalview.io.HMMFile; @@ -25,18 +22,17 @@ 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; - List params; + List params; boolean forGroup = false; @@ -45,7 +41,7 @@ public class HMMBuildThread implements Runnable File stoTemp = null; long barID; - + /** * This is used for validation purposes. Do not use! * @@ -73,10 +69,9 @@ public class HMMBuildThread implements Runnable barID = System.currentTimeMillis(); if (af != null) { - af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), - barID); + af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), + barID); } - cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH); List groups = new ArrayList<>(); if (params != null) @@ -163,50 +158,49 @@ public class HMMBuildThread implements Runnable } } - if (af != null) { - af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), - barID); + af.setProgressBar("", barID); } } private void runHMMBuild() { if (alignment == null && group == null) - { - JOptionPane.showMessageDialog(af, + { + 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 + { + hmmTemp = File.createTempFile("hmm", ".hmm"); + hmmTemp.deleteOnExit(); + stoTemp = File.createTempFile("output", ".sto"); + stoTemp.deleteOnExit(); + } catch (IOException e1) + { + e1.printStackTrace(); + } try { try { SequenceI[] array; - List seqs = null; + List hmmSeqs = null; if (forGroup) { - seqs = group.getHMMConsensusSequences(true); - if (seqs.size() > 0) + 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 { - seqs = alignment.getHMMConsensusSequences(true); + hmmSeqs = alignment.getHMMConsensusSequences(); if (!alignment.isAligned()) { alignment.padGaps(); @@ -214,28 +208,42 @@ public class HMMBuildThread implements Runnable array = alignment.getSequencesArray(); } - 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) + } + + /* + * 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++; } + } - cmds.uniquifySequences(newArr); - cmds.exportData(newArr, stoTemp, null, null); - jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array); + uniquifySequences(newArr); + + if (forGroup) + { + exportData(newArr, stoTemp, null, null, group); + } + else + { + exportData(newArr, stoTemp, null, null, alignment); + } + + SeqsetUtils.deuniquify(hash, array); } catch (FileNotFoundException e) { @@ -245,11 +253,11 @@ public class HMMBuildThread implements Runnable } try { - boolean ran = runCommand(); - if (!ran) - { - return; - } + boolean ran = runCommand(); + if (!ran) + { + return; + } } catch (IOException | InterruptedException e) { // TODO Auto-generated catch block @@ -264,14 +272,12 @@ public class HMMBuildThread implements Runnable // TODO Auto-generated catch block e.printStackTrace(); } - } catch (Exception e) - { - e.printStackTrace(); + } catch (Exception e) + { + e.printStackTrace(); } } - - /** * Executes the hmmbuild command in the command line. * @@ -281,23 +287,12 @@ public class HMMBuildThread implements Runnable */ private boolean runCommand() throws IOException, InterruptedException { - File file = new File(cmds.HMMERFOLDER + "/hmmbuild"); - if (!file.canExecute()) + String binaryPath = getCommandRoot(HMMBUILD); + if (binaryPath == null) { - file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe"); - { - if (!file.canExecute()) - { - if (af != null) - { - JvOptionPane.showInternalMessageDialog(af, - MessageManager.getString("warn.hmmbuild_failed")); - } - return false; - } - } + return false; } - String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.SPACE; + String command = binaryPath + SPACE; String name = null; if (params != null) @@ -316,7 +311,6 @@ public class HMMBuildThread implements Runnable break; } - } } @@ -325,35 +319,37 @@ public class HMMBuildThread implements Runnable name = group.getName() + "_HMM"; } - if (name == null || "".equals(name)) { - if (af != null) + if (af != null) + { + if (af.getTitle().length() < 15) { name = af.getTitle(); } - if (name == null || "".equals(name)) - { - name = "Alignment"; - } + } + if (name == null || "".equals(name)) + { + name = "Alignment"; + } } - command += "-n " + name.replace(' ', '_') + cmds.SPACE; + 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. * @@ -362,17 +358,16 @@ public class HMMBuildThread implements Runnable */ private void importData() throws IOException, InterruptedException { - HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(), - DataSourceType.FILE)); + 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(), '-'); + alignment.getWidth() - group.getEndRes() - 1, '-'); seq.updateHMMMapping(); SequenceI topSeq = group.getSequencesInOrder(alignment)[0]; int topIndex = alignment.findIndex(topSeq); @@ -399,7 +394,7 @@ public class HMMBuildThread implements Runnable hmmTemp.delete(); stoTemp.delete(); } - + /** * Runs hmmbuild, and waits for the results to be imported before continuing */