import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.Preferences;
+import jalview.gui.SplitFrame;
import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileLoader;
+import jalview.io.StockholmFile;
import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import java.io.File;
-import java.io.FileNotFoundException;
import java.io.IOException;
-import java.util.HashMap;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Map;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
public class HMMAlignThread implements Runnable
{
+
+ /**
+ * feature settings from view that job was associated with
+ */
+ protected FeatureRendererSettings featureSettings = null;
+
HMMERCommands cmds = new HMMERCommands();
AlignFrame af;
AlignmentI alignment;
+ AlignmentI dataset;
+
+ List<AlignmentOrder> orders;
+
+ AlignmentView msa;
+
HiddenMarkovModel hmm;
boolean newFrame;
Map<Integer, SequenceI> hmmSeqs;
+ File hmmTemp = null;
+
+ File outTemp = null;
+
+ File inputTemp = null;
+
+ List<AlignmentOrder> allOrders;
+
+ SequenceI[][] allResults;
+
public HMMAlignThread(AlignFrame af, boolean createNewFrame)
{
this.af = af;
alignment = af.getViewport().getAlignment();
- hmm = alignment.getSequenceAt(0).getHMM();
+ if (alignment.getDataset() != null)
+ {
+ dataset = alignment.getDataset();
+ }
newFrame = createNewFrame;
+ featureSettings = af.getFeatureRenderer().getSettings();
}
@Override
public void run()
{
- barID = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
- barID);
- cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
- try
+ if (af.getSelectedHMM() == null)
{
- cmds.HMMBUFFER = File.createTempFile("hmm", ".hmm").getAbsolutePath()
- + cmds.SPACE;
- cmds.ALIGNMENTBUFFER = File.createTempFile("output", ".sto")
- .getAbsolutePath() + cmds.SPACE;
- cmds.ALIGNMENTINPUT = File.createTempFile("input", ".sto")
- .getAbsolutePath() + cmds.SPACE;
- cmds.OUTPUTALIGNMENT = "-o " + cmds.ALIGNMENTINPUT + cmds.SPACE;
- } catch (IOException e1)
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("warn.no_selected_hmm"));
+ return;
+ }
+ else
{
- // TODO Auto-generated catch block
- e1.printStackTrace();
+ hmm = af.getSelectedHMM();
}
+ barID = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
+ barID);
+ cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
- try
+ // if (!alignment.isAligned())
+ // {
+ // alignment.padGaps();
+ // }
+ prepareAlignment();
+ SequenceI[][] subAlignments = msa.getVisibleContigs('-');
+ allOrders = new ArrayList<>();
+ allResults = new SequenceI[subAlignments.length][];
+ int job = 0;
+ for (SequenceI[] seqs : subAlignments)
{
+ cmds.uniquifySequences(seqs);
try
{
- hmmSeqs = alignment.getHMMConsensusSequences(true);
- cmds.exportData(alignment, true, true, hmm);
- } catch (FileNotFoundException e)
+ createTemporaryFiles();
+ } catch (IOException e2)
{
- // TODO Auto-generated catch block
- e.printStackTrace();
-
+ e2.printStackTrace();
}
try
{
- runCommand();
+ cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
+ hmmTemp.getAbsoluteFile());
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ try
+ {
+ boolean ran = runCommand();
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmmalign_failed"));
+ return;
+ }
} catch (IOException | InterruptedException e)
{
- // TODO Auto-generated catch block
e.printStackTrace();
}
try
{
- importData();
+ importData(job);
} catch (IOException | InterruptedException e)
{
// TODO Auto-generated catch block
e.printStackTrace();
}
- } catch (Exception e)
- {
- e.printStackTrace();
- } finally
- {
- af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
- barID);
+ job++;
}
+
+ displayResults(newFrame);
+
+ af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
+ barID);
+
+ }
+
+ private void createTemporaryFiles() throws IOException
+ {
+ hmmTemp = File.createTempFile("hmm", ".hmm");
+ hmmTemp.deleteOnExit();
+ outTemp = File.createTempFile("output", ".sto");
+ outTemp.deleteOnExit();
+ inputTemp = File.createTempFile("input", ".sto");
+ inputTemp.deleteOnExit();
}
- private void runCommand() throws IOException, InterruptedException
+ private boolean runCommand() throws IOException, InterruptedException
{
+ File file = new File(cmds.HMMERFOLDER + "/binaries/hmmalign.exe");
+ if (!file.canExecute())
+ {
+ return false;
+ }
String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
if (!hmm.getFileHeader().contains("HMMER3/f"))
{
command += cmds.ALLCOL;
}
- command += cmds.TRIM + cmds.OUTPUTALIGNMENT + cmds.HMMBUFFER
- + cmds.ALIGNMENTBUFFER;
- cmds.runCommand(command);
+ boolean trim = true;
+ String bool = Cache.getProperty("TRIM_TERMINI");
+ if ("false".equals(bool))
+ {
+ trim = false;
+ }
+ if (trim)
+ {
+ command += cmds.TRIM;
+ }
+ command += " -o" + inputTemp.getAbsolutePath() + cmds.SPACE
+ + hmmTemp.getAbsolutePath() + cmds.SPACE
+ + outTemp.getAbsolutePath();
+ return cmds.runCommand(command);
}
- private void importData() throws IOException, InterruptedException
+ private void importData(int index)
+ throws IOException, InterruptedException
{
+ StockholmFile file = new StockholmFile(inputTemp.getAbsolutePath(),
+ DataSourceType.FILE);
+ SequenceI[] result = file.getSeqsAsArray();
+ AlignmentOrder msaorder = new AlignmentOrder(result);
+ jalview.analysis.AlignmentSorter.recoverOrder(result);
+ jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, result);
+ allOrders.add(msaorder);
+ allResults[index] = result;
+ hmmTemp.delete();
+ outTemp.delete();
+ inputTemp.delete();
+ }
+
+ private void prepareAlignment()
+ {
+ // hmmSeqs = alignment.getHMMConsensusSequences(true);
+ msa = af.gatherSequencesForAlignment();
+ }
+
+ private void displayResults(boolean newFrame)
+ {
+ AlignmentOrder[] arrOrders = allOrders
+ .toArray(new AlignmentOrder[allOrders.size()]);
+ Object[] newview = msa.getUpdatedView(allResults,
+ arrOrders, '-');
+ SequenceI[] alignment = (SequenceI[]) newview[0];
+ HiddenColumns hidden = (HiddenColumns) newview[1];
+ Alignment al = new Alignment(alignment);
+ al.setProperty("Alignment Program", "hmmalign");
+ if (dataset != null)
+ {
+ al.setDataset(dataset);
+ }
+
if (newFrame)
{
- FileLoader loader = new FileLoader();
- AlignFrame aFrame = new AlignFrame(new Alignment(new SequenceI[1]),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- Desktop.addInternalFrame(aFrame, aFrame.getTitle(),
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- aFrame.setTitle(
- af.getName() + "Aligned to " + hmm.getName() + "'s HMM");
- af.getViewport().setAlignment(null);
-
- aFrame.loadJalviewDataFile(cmds.ALIGNMENTINPUT,
- DataSourceType.FILE, FileFormat.Stockholm, null);
-
-
-
- Map<Integer, SequenceI> copy = new HashMap<>(
- hmmSeqs);
- addSeqs(aFrame, copy);
- SequenceI seq = aFrame.getViewport().getAlignment()
- .getSequenceAt(0);
- seq.getHMM().mapToReferenceAnnotation(aFrame, seq);
- addSeqs(af, hmmSeqs);
+ displayInNewFrame(al, allOrders, hidden);
}
- else
+ }
+
+ private void displayInNewFrame(AlignmentI al,
+ List<AlignmentOrder> alorders, HiddenColumns hidden)
+ {
+ AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ // initialise with same renderer settings as in parent alignframe.
+ af.getFeatureRenderer().transferSettings(this.featureSettings);
+
+ if (allOrders.size() > 0)
{
- af.getViewport().getAlignment().getSequences().clear();
- af.setIsRecurring(true);
- af.loadJalviewDataFile(cmds.ALIGNMENTBUFFER,
- DataSourceType.FILE, FileFormat.Stockholm, null);
- af.setIsRecurring(false);
- addSeqs(af, hmmSeqs);
+ addSortByMenuItems(af, allOrders);
}
+
+ // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
+ /*
+ * If alignment was requested from one half of a SplitFrame, show in a
+ * SplitFrame with the other pane similarly aligned.
+ */
+ AlignFrame requestedBy = this.af;
+ if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy) != null)
+ {
+ AlignmentI complement = requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy);
+ String complementTitle = requestedBy.getSplitViewContainer()
+ .getComplementTitle(requestedBy);
+ // becomes null if the alignment window was closed before the alignment
+ // job finished.
+ AlignmentI copyComplement = new Alignment(complement);
+ // todo should this be done by copy constructor?
+ copyComplement.setGapCharacter(complement.getGapCharacter());
+ // share the same dataset (and the mappings it holds)
+ copyComplement.setDataset(complement.getDataset());
+ copyComplement.alignAs(al);
+ if (copyComplement.getHeight() > 0)
+ {
+ af.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);
+ 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,
+ AlignFrame.DEFAULT_HEIGHT);
}
- private void addSeqs(AlignFrame alignFrame, Map<Integer, SequenceI> map)
+ /**
+ * Add sort order options to the AlignFrame menus.
+ *
+ * @param af
+ * @param alorders
+ */
+ protected void addSortByMenuItems(AlignFrame af,
+ List<AlignmentOrder> alorders)
{
- for (Map.Entry<Integer, SequenceI> entry : map.entrySet())
+ // update orders
+ if (alorders.size() == 1)
{
- SequenceI seq = entry.getValue();
- Integer pos = entry.getKey();
- cmds.addHMMConsensusSequence(alignFrame, seq, pos);
+ af.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
+ }
+ else
+ {
+ // construct a non-redundant ordering set
+ List<String> names = new ArrayList<>();
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ String orderName = " Region " + i;
+ int j = i + 1;
+
+ while (j < l)
+ {
+ if (alorders.get(i).equals(alorders.get(j)))
+ {
+ alorders.remove(j);
+ l--;
+ orderName += "," + j;
+ }
+ else
+ {
+ j++;
+ }
+ }
+
+ if (i == 0 && j == 1)
+ {
+ names.add("");
+ }
+ else
+ {
+ names.add(orderName);
+ }
+ }
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ af.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
+ alorders.get(i));
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff