package jalview.hmmer;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
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.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import java.util.Scanner;
{
static final String HMMSEARCH = "hmmsearch";
+ /*
+ * constants for i18n lookup of passed parameter names
+ */
+ static final String DATABASE_KEY = "label.database";
+
+ static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
+
+ static final String USE_ACCESSIONS_KEY = "label.use_accessions";
+
+ static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
+
+ static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
+
+ static final String TRIM_TERMINI_KEY = "label.trim_termini";
+
+ static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
+
+ static final String CUTOFF_NONE = "None";
+
+ static final String CUTOFF_SCORE = "Score";
+
+ static final String CUTOFF_EVALUE = "E-Value";
+
+ static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+
+ static final String DOM_EVALUE_KEY = "label.dom_evalue";
+
+ static final String SEQ_SCORE_KEY = "label.seq_score";
+
+ static final String DOM_SCORE_KEY = "label.dom_score";
+
boolean realign = false;
boolean trim = false;
@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();// af.getSelectedHMMSequence();
long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
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(getFilePath(searchOutputFile));
args.add("-A");
- args.add(hitsAlignmentFile.getAbsolutePath());
+ args.add(getFilePath(hitsAlignmentFile));
boolean dbFound = false;
String dbPath = "";
File databaseFile = null;
+ boolean useEvalueCutoff = false;
+ boolean useScoreCutoff = false;
+ String seqEvalueCutoff = null;
+ String domEvalueCutoff = null;
+ String seqScoreCutoff = null;
+ String domScoreCutoff = null;
+
if (params != null)
{
for (ArgumentI arg : params)
{
String name = arg.getName();
- if (MessageManager.getString("label.number_of_results")
+ if (MessageManager.getString(NUMBER_OF_RESULTS_KEY)
.equals(name))
{
seqsToReturn = Integer.parseInt(arg.getValue());
}
- else if (MessageManager.getString("label.auto_align_seqs")
+ else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
.equals(name))
{
realign = true; // TODO: not used
}
- else if (MessageManager.getString("label.use_accessions")
+ else if (MessageManager.getString(USE_ACCESSIONS_KEY)
.equals(name))
{
args.add("--acc");
}
- else if (MessageManager.getString("label.seq_e_value").equals(name))
+ else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
+ .equals(name))
+ {
+ if (CUTOFF_EVALUE.equals(arg.getValue()))
+ {
+ useEvalueCutoff = true;
+ }
+ else if (CUTOFF_SCORE.equals(arg.getValue()))
+ {
+ useScoreCutoff = true;
+ }
+ }
+ else if (MessageManager.getString(SEQ_EVALUE_KEY).equals(name))
{
- args.add("--incE");
- args.add(arg.getValue());
+ seqEvalueCutoff = arg.getValue();
}
- else if (MessageManager.getString("label.seq_score").equals(name))
+ else if (MessageManager.getString(SEQ_SCORE_KEY).equals(name))
{
- args.add("-incT");
- args.add(arg.getValue());
+ seqScoreCutoff = arg.getValue();
}
- else if (MessageManager.getString("label.dom_e_value_desc")
+ else if (MessageManager.getString(DOM_EVALUE_KEY)
.equals(name))
{
- args.add("--incdomE");
- args.add(arg.getValue());
+ domEvalueCutoff = arg.getValue();
}
- else if (MessageManager.getString("label.dom_score").equals(name))
+ else if (MessageManager.getString(DOM_SCORE_KEY).equals(name))
{
- args.add("--incdomT");
- args.add(arg.getValue());
+ domScoreCutoff = arg.getValue();
}
- else if (MessageManager.getString("label.trim_termini")
+ else if (MessageManager.getString(TRIM_TERMINI_KEY)
.equals(name))
{
trim = true;
}
- else if (MessageManager.getString("label.database").equals(name))
+ else if (MessageManager.getString(DATABASE_KEY).equals(name))
{
dbFound = true;
dbPath = arg.getValue();
- if (!MessageManager.getString("label.this_alignment")
+ if (!MessageManager.getString(THIS_ALIGNMENT_KEY)
.equals(dbPath))
{
databaseFile = new File(dbPath);
}
}
- if (!dbFound || MessageManager.getString("label.this_alignment")
+ if (useEvalueCutoff)
+ {
+ args.add("-E");
+ args.add(seqEvalueCutoff);
+ args.add("--domE");
+ args.add(domEvalueCutoff);
+ }
+ else if (useScoreCutoff)
+ {
+ args.add("-T");
+ args.add(seqScoreCutoff);
+ args.add("--domT");
+ args.add(domScoreCutoff);
+ }
+
+ if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
.equals(dbPath))
{
/*
* no external database specified for search, so
- * export current alignment as 'database' to search
+ * export current alignment as 'database' to search,
+ * excluding any HMM consensus sequences it contains
*/
- databaseFile = createTempFile("database", ".sto");
+ databaseFile = FileUtils.createTempFile("database", ".sto");
AlignmentI al = af.getViewport().getAlignment();
AlignmentI copy = new Alignment(al);
- SequenceI hmms = copy.getHmmConsensus();
- if (hmms != null)
+ List<SequenceI> hmms = copy.getHmmSequences();
+ for (SequenceI hmmSeq : hmms)
{
- copy.deleteSequence(hmms);
+ copy.deleteSequence(hmmSeq);
}
exportStockholm(copy.getSequencesArray(), databaseFile, null);
- // StockholmFile stoFile = new StockholmFile(copy);
- // stoFile.setSeqs(copy.getSequencesArray());
- // String alignmentString = stoFile.print();
- // PrintWriter writer = new PrintWriter(databaseFile);
- // writer.print(alignmentString);
- // writer.close();
}
- args.add(hmmFile.getAbsolutePath());
- args.add(databaseFile.getAbsolutePath());
+ args.add(getFilePath(hmmFile));
+ args.add(getFilePath(databaseFile));
return runCommand(args);
}
hmmAndSeqs[0] = hmmSeq;
System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
- AlignmentI alignment = new Alignment(hmmAndSeqs);
- AlignFrame frame = new AlignFrame(alignment, 1, 1);
- frame.setSelectedHMMSequence(hmmSeq);
+ /*
+ * 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 defSeq = hmmSeq.getName();
+ List<String> options = Collections.singletonList(defSeq);
+ Option option = new Option(MessageManager.getString("label.use_hmm"),
+ "", true, defSeq, defSeq, options, null);
+ alignArgs.add(option);
if (trim)
{
alignArgs.add(new BooleanOption(
- MessageManager.getString("label.trim_termini"),
+ MessageManager.getString(TRIM_TERMINI_KEY),
MessageManager.getString("label.trim_termini_desc"), true,
true, true, null));
}
- HMMAlign hmmalign = new HMMAlign(frame, alignArgs);
+ HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
hmmalign.run();
frame = null;
hmmTemp.delete();
git://source.jalview.org / jalview.git / blobdiff