package jalview.hmmer;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StockholmFile;
+import jalview.util.FileUtils;
import jalview.util.MessageManager;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.Option;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
-import java.io.PrintWriter;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
-import java.util.Scanner;
import javax.swing.JOptionPane;
-public class HMMSearch extends HmmerCommand
+public class HMMSearch extends Search
{
- static final String HMMSEARCH = "hmmsearch";
boolean realign = false;
boolean trim = false;
+ boolean returnNoOfNewSeqs = false;
+
int seqsToReturn = Integer.MAX_VALUE;
- SequenceI[] seqs;
/**
* Constructor for the HMMSearchThread
@Override
public void run()
{
- HiddenMarkovModel hmm = af.getSelectedHMM();
+ HiddenMarkovModel hmm = getHmmProfile();
if (hmm == null)
{
- JOptionPane.showMessageDialog(af,
- MessageManager.getString("warn.no_selected_hmm"));
+ // shouldn't happen if we got this far
+ Cache.log.error("Error: no hmm for hmmsearch");
return;
}
- SequenceI hmmSeq = af.getSelectedHMMSequence();
+ SequenceI hmmSeq = hmm.getConsensusSequence();
long msgId = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+ af.setProgressBar(MessageManager.getString("status.running_search"),
msgId);
try
{
- File hmmFile = createTempFile("hmm", ".hmm");
- File hitsAlignmentFile = createTempFile("hitAlignment", ".sto");
- File searchOutputFile = createTempFile("searchOutput", ".sto");
+ File hmmFile = FileUtils.createTempFile("hmm", ".hmm");
+ File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
+ ".sto");
+ File searchOutputFile = FileUtils.createTempFile("searchOutput",
+ ".sto");
exportHmm(hmm, hmmFile.getAbsoluteFile());
boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
if (!ran)
{
- JvOptionPane.showInternalMessageDialog(af,
- MessageManager.getString("warn.hmmsearch_failed"));
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "hmmsearch"));
return;
}
List<String> args = new ArrayList<>();
args.add(command);
- args.add("-o");
- args.add(searchOutputFile.getAbsolutePath());
- args.add("-A");
- args.add(hitsAlignmentFile.getAbsolutePath());
-
- boolean dbFound = false;
- String dbPath = "";
- File databaseFile = null;
-
- if (params != null)
- {
- for (ArgumentI arg : params)
- {
- String name = arg.getName();
- if (MessageManager.getString("label.number_of_results")
- .equals(name))
- {
- seqsToReturn = Integer.parseInt(arg.getValue());
- }
- else if (MessageManager.getString("label.auto_align_seqs")
- .equals(name))
- {
- realign = true; // TODO: not used
- }
- else if (MessageManager.getString("label.use_accessions")
- .equals(name))
- {
- args.add("--acc");
- }
- else if (MessageManager.getString("label.seq_e_value").equals(name))
- {
- args.add("--incE");
- args.add(arg.getValue());
- }
- else if (MessageManager.getString("label.seq_score").equals(name))
- {
- args.add("-incT");
- args.add(arg.getValue());
- }
- else if (MessageManager.getString("label.dom_e_value_desc")
- .equals(name))
- {
- args.add("--incdomE");
- args.add(arg.getValue());
- }
- else if (MessageManager.getString("label.dom_score").equals(name))
- {
- args.add("--incdomT");
- args.add(arg.getValue());
- }
- else if (MessageManager.getString("label.trim_termini")
- .equals(name))
- {
- trim = true;
- }
- else if (MessageManager.getString("label.database").equals(name))
- {
- dbFound = true;
- dbPath = arg.getValue();
- if (!MessageManager.getString("label.this_alignment")
- .equals(dbPath))
- {
- databaseFile = new File(dbPath);
- }
- }
- }
- }
-
- if (!dbFound || MessageManager.getString("label.this_alignment")
- .equals(dbPath))
- {
- AlignmentI alignment = af.getViewport().getAlignment();
- AlignmentI copy = new Alignment(alignment);
- SequenceI hmms = copy.getHmmConsensus();
- if (hmms != null)
- {
- copy.deleteSequence(hmms);
- }
- StockholmFile stoFile = new StockholmFile(copy);
- stoFile.setSeqs(copy.getSequencesArray());
- String alignmentString = stoFile.print();
- databaseFile = createTempFile("database", ".sto");
- PrintWriter writer = new PrintWriter(databaseFile);
- writer.print(alignmentString);
- writer.close();
- }
-
- args.add(hmmFile.getAbsolutePath());
- args.add(databaseFile.getAbsolutePath());
+ buildArguments(args, searchOutputFile, hitsAlignmentFile, hmmFile);
return runCommand(args);
}
+
/**
* Imports the data from the temporary file to which the output of hmmsearch
- * is directed.
+ * was directed. The results are optionally realigned using hmmalign.
*
* @param hmmSeq
*/
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
- readTable(searchOutputFile);
+ readDomainTable(searchOutputFile, false);
+
+ if (searchAlignment)
+ {
+ recoverSequences(sequencesHash, seqs);
+ }
+
+ // look for PP cons and ref seq in alignment only annotation
+ AlignmentAnnotation modelpos = null, ppcons = null;
+ for (AlignmentAnnotation aa : file.getAnnotations())
+ {
+ if (aa.sequenceRef == null)
+ {
+ if (aa.label.equals("Reference Positions")) // RF feature type in
+ // stockholm parser
+ {
+ modelpos = aa;
+ }
+ if (aa.label.equals("Posterior Probability"))
+ {
+ ppcons = aa;
+ }
+ }
+ }
+
int seqCount = Math.min(seqs.length, seqsToReturn);
SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
+ hmmSeq = hmmSeq.deriveSequence(); // otherwise all bad things happen
hmmAndSeqs[0] = hmmSeq;
System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
+ if (modelpos != null)
+ {
+ // TODO need - get ungapped sequence method
+ hmmSeq.setSequence(
+ hmmSeq.getDatasetSequence().getSequenceAsString());
+ Annotation[] refpos = modelpos.annotations;
+ // insert gaps to match with refseq positions
+ int gc = 0, lcol = 0;
+ for (int c = 0; c < refpos.length; c++)
+ {
+ if (refpos[c] != null && ("x".equals(refpos[c].displayCharacter)))
+ {
+ if (gc > 0)
+ {
+ hmmSeq.insertCharAt(lcol + 1, gc, '-');
+ }
+ gc = 0;
+ lcol = c;
+ }
+ else
+ {
+ gc++;
+ }
+ }
+ }
- AlignmentI alignment = new Alignment(hmmAndSeqs);
- AlignFrame frame = new AlignFrame(alignment, 1, 1);
- frame.setSelectedHMMSequence(hmmSeq);
- List<ArgumentI> alignArgs = new ArrayList<>();
- if (trim)
+ if (realign)
{
- alignArgs.add(new BooleanOption(
- MessageManager.getString("label.trim_termini"),
- MessageManager.getString("label.trim_termini_desc"), true,
- true, true, null));
+ realignResults(hmmAndSeqs);
}
- HMMAlign hmmalign = new HMMAlign(frame, alignArgs);
- hmmalign.run();
- frame = null;
+ else
+ {
+ AlignmentI al = new Alignment(hmmAndSeqs);
+ if (ppcons != null)
+ {
+ al.addAnnotation(ppcons);
+ }
+ if (modelpos != null)
+ {
+ al.addAnnotation(modelpos);
+ }
+ AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ String ttl = "hmmSearch of " + databaseName + " using "
+ + hmmSeq.getName();
+ Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ if (returnNoOfNewSeqs)
+ {
+ int nNew = checkForNewSequences();
+ JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
+ + MessageManager.getString("label.new_returned"));
+ }
+
+ }
+
+
hmmTemp.delete();
inputAlignmentTemp.delete();
searchOutputFile.delete();
}
}
- void readTable(File inputTableTemp) throws IOException
+ private int checkForNewSequences()
{
- BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
- String line = "";
- while (!line.startsWith("Query:"))
+ int nNew = seqs.length;
+
+ for (SequenceI resultSeq : seqs)
{
- line = br.readLine();
+ for (SequenceI aliSeq : alignment.getSequencesArray())
+ {
+ if (resultSeq.getName().equals(aliSeq.getName()))
+ {
+ nNew--;
+ break;
+ }
+ }
}
- for (int i = 0; i < 5; i++)
+
+ return nNew;
+
+ }
+
+ /**
+ * Realigns the given sequences using hmmalign, to the HMM profile sequence
+ * which is the first in the array, and opens the results in a new frame
+ *
+ * @param hmmAndSeqs
+ */
+ protected void realignResults(SequenceI[] hmmAndSeqs)
+ {
+ /*
+ * and align the search results to the HMM profile
+ */
+ AlignmentI al = new Alignment(hmmAndSeqs);
+ AlignFrame frame = new AlignFrame(al, 1, 1);
+ List<ArgumentI> alignArgs = new ArrayList<>();
+ String alignTo = hmmAndSeqs[0].getName();
+ List<String> options = Collections.singletonList(alignTo);
+ Option option = new Option(MessageManager.getString("label.use_hmm"),
+ "", true, alignTo, alignTo, options, null);
+ alignArgs.add(option);
+ if (trim)
{
- line = br.readLine();
+ alignArgs.add(new BooleanOption(
+ MessageManager.getString(TRIM_TERMINI_KEY),
+ MessageManager.getString("label.trim_termini_desc"), true,
+ true, true, null));
}
+ HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
+ hmmalign.run();
- int index = 0;
- while (!" ------ inclusion threshold ------".equals(line)
- && !"".equals(line))
+ if (returnNoOfNewSeqs)
{
- Scanner scanner = new Scanner(line);
-
- String str = scanner.next(); // full sequence eValue score
- float eValue = Float.parseFloat(str);
- int seqLength = seqs[index].getLength();
- Annotation[] annots = new Annotation[seqLength];
- for (int j = 0; j < seqLength; j++)
- {
- annots[j] = new Annotation(eValue);
- }
- AlignmentAnnotation annot = new AlignmentAnnotation("E-value",
- "Score", annots);
- annot.setScore(Double.parseDouble(str));
- annot.setSequenceRef(seqs[index]);
- seqs[index].addAlignmentAnnotation(annot);
-
- scanner.close();
- line = br.readLine();
- index++;
+ int nNew = checkForNewSequences();
+ JvOptionPane.showMessageDialog(frame.alignPanel,
+ nNew + " " + MessageManager.getString("label.new_returned"));
}
-
- br.close();
}
}
git://source.jalview.org / jalview.git / blobdiff