From e91b3faae4cde4e18a2965af05248dd3eebe578e Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 19 Feb 2018 10:19:19 +0000 Subject: [PATCH] JAL-2629 formatting only --- src/jalview/hmmer/HMMAlignThread.java | 90 +++++++++++++-------------- src/jalview/hmmer/HMMBuildThread.java | 107 ++++++++++++++++---------------- src/jalview/hmmer/HMMERCommands.java | 44 +++++++------ src/jalview/hmmer/HMMERParamStore.java | 11 ++-- src/jalview/hmmer/HMMSearchThread.java | 10 +-- 5 files changed, 123 insertions(+), 139 deletions(-) diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java index 5eec1c4..168e3f9 100644 --- a/src/jalview/hmmer/HMMAlignThread.java +++ b/src/jalview/hmmer/HMMAlignThread.java @@ -107,53 +107,52 @@ public class HMMAlignThread implements Runnable af.setProgressBar(MessageManager.getString("status.running_hmmalign"), barID); cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH); - prepareAlignment(); - SequenceI[][] subAlignments = msa.getVisibleContigs('-'); - allOrders = new ArrayList<>(); - allResults = new SequenceI[subAlignments.length][]; - int job = 0; - for (SequenceI[] seqs : subAlignments) + prepareAlignment(); + SequenceI[][] subAlignments = msa.getVisibleContigs('-'); + allOrders = new ArrayList<>(); + allResults = new SequenceI[subAlignments.length][]; + int job = 0; + for (SequenceI[] seqs : subAlignments) + { + cmds.uniquifySequences(seqs); + try { - cmds.uniquifySequences(seqs); - try - { - createTemporaryFiles(); - } catch (IOException e2) - { - e2.printStackTrace(); - } - try - { - cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm, + createTemporaryFiles(); + } catch (IOException e2) + { + e2.printStackTrace(); + } + try + { + cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm, hmmTemp.getAbsoluteFile(), null); - } catch (IOException e1) - { - e1.printStackTrace(); - } - try - { - boolean ran = runCommand(); - if (!ran) - { - JvOptionPane.showInternalMessageDialog(af, - MessageManager.getString("warn.hmmalign_failed")); - return; - } - } catch (IOException | InterruptedException e) - { - e.printStackTrace(); - } - try - { - importData(job); - } catch (IOException | InterruptedException e) + } catch (IOException e1) + { + e1.printStackTrace(); + } + try + { + boolean ran = runCommand(); + if (!ran) { - // TODO Auto-generated catch block - e.printStackTrace(); + JvOptionPane.showInternalMessageDialog(af, + MessageManager.getString("warn.hmmalign_failed")); + return; } - job++; + } catch (IOException | InterruptedException e) + { + e.printStackTrace(); } - + try + { + importData(job); + } catch (IOException | InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + job++; + } displayResults(newFrame); @@ -270,8 +269,7 @@ public class HMMAlignThread implements Runnable { AlignmentOrder[] arrOrders = allOrders .toArray(new AlignmentOrder[allOrders.size()]); - Object[] newview = msa.getUpdatedView(allResults, - arrOrders, '-'); + Object[] newview = msa.getUpdatedView(allResults, arrOrders, '-'); SequenceI[] alignment = (SequenceI[]) newview[0]; HiddenColumns hidden = (HiddenColumns) newview[1]; Alignment al = new Alignment(alignment); @@ -430,6 +428,4 @@ public class HMMAlignThread implements Runnable } } - } - - +} diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java index 346bcbd..2262bae 100644 --- a/src/jalview/hmmer/HMMBuildThread.java +++ b/src/jalview/hmmer/HMMBuildThread.java @@ -1,6 +1,5 @@ package jalview.hmmer; - import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenMarkovModel; @@ -28,15 +27,18 @@ import javax.swing.JOptionPane; public class HMMBuildThread 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 +47,7 @@ public class HMMBuildThread implements Runnable File stoTemp = null; long barID; - + /** * This is used for validation purposes. Do not use! * @@ -73,8 +75,8 @@ 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); @@ -163,7 +165,6 @@ public class HMMBuildThread implements Runnable } } - if (af != null) { af.setProgressBar(MessageManager.getString("status.running_hmmbuild"), @@ -174,20 +175,20 @@ public class HMMBuildThread implements Runnable 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 { @@ -214,26 +215,26 @@ public class HMMBuildThread implements Runnable array = alignment.getSequencesArray(); } - cmds.setHmmSeqs(seqs); + 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++; - } + } + SequenceI[] newArr = new SequenceI[array.length]; + int index = 0; + for (SequenceI seq : array) + { + newArr[index] = new Sequence(seq); + index++; + } - cmds.uniquifySequences(newArr); + cmds.uniquifySequences(newArr); if (forGroup) { @@ -244,7 +245,7 @@ public class HMMBuildThread implements Runnable cmds.exportData(newArr, stoTemp, null, null, alignment); } - jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array); + jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array); } catch (FileNotFoundException e) { @@ -254,11 +255,11 @@ 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 @@ -273,14 +274,12 @@ 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. * @@ -333,20 +332,19 @@ 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"; + } } @@ -360,11 +358,11 @@ public class HMMBuildThread implements Runnable command += cmds.FORCEDNA; } - command += hmmTemp.getAbsolutePath() - + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE; + command += hmmTemp.getAbsolutePath() + cmds.SPACE + + stoTemp.getAbsolutePath() + cmds.SPACE; return cmds.runCommand(command); } - + /** * Imports the .hmm file produced by hmmbuild. * @@ -374,8 +372,7 @@ public class HMMBuildThread implements Runnable private void importData() throws IOException, InterruptedException { HMMFile file = new HMMFile( - new FileParse(hmmTemp.getAbsolutePath(), - DataSourceType.FILE)); + new FileParse(hmmTemp.getAbsolutePath(), DataSourceType.FILE)); SequenceI[] seqs = file.getSeqsAsArray(); SequenceI seq = seqs[0]; seq.createDatasetSequence(); @@ -411,7 +408,7 @@ public class HMMBuildThread implements Runnable hmmTemp.delete(); stoTemp.delete(); } - + /** * Runs hmmbuild, and waits for the results to be imported before continuing */ diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java index ea795dd..854f0c5 100644 --- a/src/jalview/hmmer/HMMERCommands.java +++ b/src/jalview/hmmer/HMMERCommands.java @@ -31,8 +31,7 @@ public class HMMERCommands // Path of hmmer binaries directory String HMMERFOLDER = "/Documents/"; - public String JALVIEWDIRECTORY = System.getProperty("user.dir") - + "/"; + public String JALVIEWDIRECTORY = System.getProperty("user.dir") + "/"; public final String HMMALIGN = "/hmmalign "; @@ -91,31 +90,31 @@ public class HMMERCommands { try { - final Process p = Runtime.getRuntime().exec(command); + final Process p = Runtime.getRuntime().exec(command); - new Thread(new Runnable() - { - @Override - public void run() + new Thread(new Runnable() { - BufferedReader input = new BufferedReader( - new InputStreamReader(p.getInputStream())); - String line = null; - - try + @Override + public void run() { - while ((line = input.readLine()) != null) + BufferedReader input = new BufferedReader( + new InputStreamReader(p.getInputStream())); + String line = null; + + try + { + while ((line = input.readLine()) != null) + { + System.out.println(line); + } + } catch (IOException e) { - System.out.println(line); + e.printStackTrace(); } - } catch (IOException e) - { - e.printStackTrace(); } - } - }).start(); + }).start(); - p.waitFor(); + p.waitFor(); } catch (Exception e) { e.printStackTrace(); @@ -130,9 +129,8 @@ public class HMMERCommands * @param alignment * @throws IOException */ - public void exportData(SequenceI[] seqs, - File stoLocation, HiddenMarkovModel hmm, File hmmLocation, - AnnotatedCollectionI al) + public void exportData(SequenceI[] seqs, File stoLocation, + HiddenMarkovModel hmm, File hmmLocation, AnnotatedCollectionI al) throws IOException { if (seqs != null) diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java index 11cde90..c23fe02 100644 --- a/src/jalview/hmmer/HMMERParamStore.java +++ b/src/jalview/hmmer/HMMERParamStore.java @@ -1,6 +1,5 @@ package jalview.hmmer; - import jalview.bin.Cache; import jalview.gui.Preferences; import jalview.util.MessageManager; @@ -19,7 +18,6 @@ import java.util.Collection; import java.util.List; import java.util.Scanner; - public class HMMERParamStore implements ParamDatastoreI { @@ -117,8 +115,8 @@ public class HMMERParamStore implements ParamDatastoreI false, true, null)); args.add(new LogarithmicParameter( MessageManager.getString("label.seq_e_value"), - MessageManager.getString("label.seq_e_value_desc"), false, - -3d, -37.92977945, 1d, 10d)); + MessageManager.getString("label.seq_e_value_desc"), false, -3d, + -37.92977945, 1d, 10d)); /* args.add(new DoubleParameter( MessageManager.getString("label.seq_score"), @@ -127,8 +125,8 @@ public class HMMERParamStore implements ParamDatastoreI */ args.add(new LogarithmicParameter( MessageManager.getString("label.dom_e_value_desc"), - MessageManager.getString("label.dom_e_value_desc"), false, - -3d, -37.92977945, 1d, 10d)); + MessageManager.getString("label.dom_e_value_desc"), false, -3d, + -37.92977945, 1d, 10d)); /* args.add(new DoubleParameter( MessageManager.getString("label.dom_score"), @@ -138,7 +136,6 @@ public class HMMERParamStore implements ParamDatastoreI */ } - private void getHMMAlignParams(List args) { args.add(new BooleanOption( diff --git a/src/jalview/hmmer/HMMSearchThread.java b/src/jalview/hmmer/HMMSearchThread.java index 8adeb22..d5baedf 100644 --- a/src/jalview/hmmer/HMMSearchThread.java +++ b/src/jalview/hmmer/HMMSearchThread.java @@ -63,11 +63,8 @@ public class HMMSearchThread implements Runnable File databaseFile = null; - - SequenceI[] seqs; - /** * Constructor for the HMMSearchThread. If create new frame is set to true, a * new frame will be created. @@ -360,7 +357,7 @@ public class HMMSearchThread implements Runnable && !"".equals(line)) { Scanner scanner = new Scanner(line); - + String str = scanner.next(); Annotation[] annots = new Annotation[seqs[index].getLength()]; for (Annotation an : annots) @@ -372,14 +369,13 @@ public class HMMSearchThread implements Runnable annot.setScore(Double.parseDouble(str)); annot.setSequenceRef(seqs[index]); seqs[index].addAlignmentAnnotation(annot); - + scanner.close(); line = br.readLine(); index++; } - + br.close(); } - } -- 1.7.10.2