package jalview.hmmer;
import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.util.List;
+import java.util.Map;
import javax.swing.JOptionPane;
// Path of hmmer binaries directory
private static final String HMMERFOLDER = "H:/Documents/";
- private static final String HMMALIGN = HMMERFOLDER + "hmmalign";
+ private static final String HMMALIGN = HMMERFOLDER + "hmmalign ";
- private static final String HMMBUILD = HMMERFOLDER + "hmmbuild";
+ private static final String HMMBUILD = HMMERFOLDER + "hmmbuild ";
- private static final String HMMSEARCH = HMMERFOLDER + "hmmsearch";
+ private static final String HMMSEARCH = HMMERFOLDER + "hmmsearch ";
private static final String JALVIEWDIRECTORY = "C:/Users/TZVanaalten/git/jalview/";
- private static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm";
+ private static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm ";
- private static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto";
+ private static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto ";
- private static final String ALIGNMENTINPUT = "src/jalview/hmmer/alignment_input.sto";
+ private static final String ALIGNMENTINPUT = "src/jalview/hmmer/alignment_input.sto ";
- private static final String OUTPUTALIGNMENT = " -o " + JALVIEWDIRECTORY
+ private static final String OUTPUTALIGNMENT = "-o " + JALVIEWDIRECTORY
+ ALIGNMENTINPUT;
+ private static final String NAME = "-n ";
+
private static final String SPACE = " ";
- private static final String ALLCOL = " --allcol";
+ private static final String ALLCOL = "--allcol ";
- private static final String TRIM = " --trim";
+ private static final String TRIM = "--trim ";
public static void hmmBuild(AlignFrame af)
throws IOException, InterruptedException
{
- HiddenMarkovModel hmm = null;
+
+ PrintWriter clearer = new PrintWriter(HMMBUFFER);
+ clearer.print("");
+ clearer.close();
AlignmentI alignment = af.getViewport().getAlignment();
+ Map<Integer, SequenceI> seqs = alignment.getHMMConsensusSequences(true);
exportAlignment(alignment);
- final String command = HMMBUILD + SPACE + JALVIEWDIRECTORY + HMMBUFFER
- + SPACE
+ final String command = HMMBUILD + NAME + af.getName() + SPACE
+ + JALVIEWDIRECTORY + HMMBUFFER
+ JALVIEWDIRECTORY + ALIGNMENTBUFFER;
- removeHMMData(alignment);
runCommand(command);
af.loadJalviewDataFile(HMMBUFFER, DataSourceType.FILE,
FileFormat.HMMER3, null);
+ for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
+ {
+ SequenceI seq = entry.getValue();
+ Integer pos = entry.getKey();
+ addHMMConsensusSequence(af, seq, pos);
+ }
+ af.alignPanel.alignmentChanged();
}
- public static void hmmAlign(AlignFrame af)
+ public static void hmmAlign(AlignFrame af, boolean createNewFrame,
+ HiddenMarkovModel hmm)
throws IOException, InterruptedException
{
+
+ PrintWriter clearer = new PrintWriter(ALIGNMENTINPUT);
+ clearer.print("");
+ clearer.close();
+
AlignmentI al = af.getViewport().getAlignment();
- List<SequenceI> seqs = al.getSequences();
- HiddenMarkovModel hmm = null;
+ Map<Integer, SequenceI> seqs = al.getHMMConsensusSequences(true);
int index = 0;
- for (SequenceI seq : seqs)
- {
- if (seq.getHMM() != null)
- {
- hmm = seq.getHMM();
- seqs.remove(index);
- break;
- }
- index++;
- }
if (hmm == null)
{
JOptionPane.showMessageDialog(af,
MessageManager.getString("warn.null_hmm"));
return;
}
-
exportAlignment(al);
- addHMM(af, hmm);
+
HMMFile file = new HMMFile(hmm);
file.exportFile(HMMBUFFER);
- final String command = HMMALIGN + ALLCOL + TRIM
- + OUTPUTALIGNMENT + SPACE + JALVIEWDIRECTORY + HMMBUFFER + SPACE
+ String command = HMMALIGN;
+ if (!hmm.getFileHeader().contains("HMMER3/f"))
+ {
+ command += ALLCOL;
+ }
+ command += TRIM + OUTPUTALIGNMENT + JALVIEWDIRECTORY + HMMBUFFER
+ JALVIEWDIRECTORY + ALIGNMENTBUFFER;
runCommand(command);
- FileLoader loader = new FileLoader();
- AlignFrame newFrame = loader.LoadFileWaitTillLoaded(ALIGNMENTINPUT,
- DataSourceType.FILE);
- HiddenMarkovModel copy = new HiddenMarkovModel(hmm);
- addHMM(newFrame, copy);
-
- // addHMMData(newFrame, tempHMM);
-
-
-
-
- //af.loadJalviewDataFile(ALIGNMENTINPUT, DataSourceType.FILE,
- // FileFormat.Stockholm, null);
- //addHMMData(af, tempHMM);
+ if (createNewFrame)
+ {
+ FileLoader loader = new FileLoader();
+ AlignFrame newFrame = loader.LoadFileWaitTillLoaded(ALIGNMENTINPUT,
+ DataSourceType.FILE);
+ for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
+ {
+ SequenceI seq = entry.getValue();
+ Integer pos = entry.getKey();
+ addHMMConsensusSequence(newFrame, seq, pos);
+ }
+ newFrame.alignPanel.alignmentChanged();
+ }
+ else
+ {
+ af.getViewport().getAlignment().getSequences().clear();
+ af.loadJalviewDataFile(ALIGNMENTBUFFER, DataSourceType.FILE,
+ FileFormat.Stockholm, null);
+ for (Map.Entry<Integer, SequenceI> entry : seqs.entrySet())
+ {
+ SequenceI seq = entry.getValue();
+ Integer pos = entry.getKey();
+ addHMMConsensusSequence(af, seq, pos);
+ }
-
+ }
}
+
/**
* Runs a command in the terminal.
*
writer.close();
}
- /**
- * Removes the HMM sequence and information annotation from the alignment and
- * stores it in a temporary container while the alignment is operated on.
- *
- * @param alignment
- * @return
- */
- private static SequenceI removeHMMData(AlignmentI alignment)
- {
- SequenceI seq = null;
-
- List<SequenceI> list = alignment.getSequences();
- for (int i = 0; i < list.size(); i++)
- {
- if (list.get(i).getName().contains("HMM CONSENSUS"))
- {
- seq = list.get(i);
- list.remove(i);
- }
- }
-
- AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
- AlignmentAnnotation[] newAnnots = new AlignmentAnnotation[annots.length
- - 1];
- int index = 0;
- for (AlignmentAnnotation annot : annots)
- {
- if (annot.label.contains("Information"))
- {
- alignment.deleteAnnotation(annot);
- }
- }
-
-
- return seq;
- }
-
- private static void addHMM(AlignFrame af, HiddenMarkovModel hmm)
+ private static void addHMMConsensusSequence(AlignFrame af, SequenceI seq,
+ Integer position)
{
- hmm.mapToReferenceAnnotation(af);
- hmm.initPlaceholder(af);
+ seq.getHMM().initHMMSequence(af, position);
AlignmentI al = af.getViewport().getAlignment();
- AlignmentAnnotation annot = hmm.createAnnotation(al.getWidth());
- al.addAnnotation(annot);
af.getViewport().setAlignment(al);
af.alignPanel.adjustAnnotationHeight();
af.getViewport().updateSequenceIdColours();
af.buildSortByAnnotationScoresMenu();
-
}
+
}
git://source.jalview.org / jalview.git / blobdiff