package jalview.hmmer;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
-import java.util.Scanner;
import javax.swing.JOptionPane;
-public class JackHMMER extends HmmerCommand
+public class JackHMMER extends Search
{
- static final String JACKHMMER = "jackhmmer";
- boolean realign = false;
-
- boolean trim = false;
-
- int seqsToReturn = Integer.MAX_VALUE;
-
- SequenceI[] seqs;
-
- private String databaseName;
-
- boolean searchAlignment = true;
-
- Hashtable sequencesHash;
+ SequenceI seq = null;
/**
* Constructor for the JackhmmerThread
@Override
public void run()
{
- SequenceI seq = getSequence();
+ seq = getSequence();
if (seq == null)
{
// shouldn't happen if we got this far
- Cache.log.error("Error: no sequence for jackhmmer");
+ Console.error("Error: no sequence for jackhmmer");
return;
}
}
/**
- * Appends command line arguments to the given list, to specify input and output
- * files for the search, and any additional options that may have been passed
- * from the parameters dialog
- *
- * @param args
- * @param searchOutputFile
- * @param hitsAlignmentFile
- * @param seqFile
- * @throws IOException
- */
- protected void buildArguments(List<String> args, File searchOutputFile,
- File hitsAlignmentFile, File seqFile) throws IOException
- {
- args.add("-o");
- args.add(getFilePath(searchOutputFile, true));
- args.add("-A");
- args.add(getFilePath(hitsAlignmentFile, true));
-
- File databaseFile = null;
-
- boolean useEvalueCutoff = false;
- boolean useScoreCutoff = false;
- String seqEvalueCutoff = null;
- String domEvalueCutoff = null;
- String seqScoreCutoff = null;
- String domScoreCutoff = null;
- databaseName = "Alignment";
-
- if (params != null)
- {
- for (ArgumentI arg : params)
- {
- String name = arg.getName();
-
- if (MessageManager.getString(REPORTING_CUTOFF_KEY)
- .equals(name))
- {
- if (MessageManager.getString(CUTOFF_EVALUE)
- .equals(arg.getValue()))
- {
- useEvalueCutoff = true;
- }
- else if (MessageManager.getString(CUTOFF_SCORE)
- .equals(arg.getValue()))
- {
- useScoreCutoff = true;
- }
- }
- else if (MessageManager.getString(SEQ_EVALUE_KEY).equals(name))
- {
- seqEvalueCutoff = arg.getValue();
- }
- else if (MessageManager.getString(SEQ_SCORE_KEY).equals(name))
- {
- seqScoreCutoff = arg.getValue();
- }
- else if (MessageManager.getString(DOM_EVALUE_KEY).equals(name))
- {
- domEvalueCutoff = arg.getValue();
- }
- else if (MessageManager.getString(DOM_SCORE_KEY).equals(name))
- {
- domScoreCutoff = arg.getValue();
- }
- else if (MessageManager.getString(DATABASE_KEY).equals(name))
- {
- databaseFile = new File(arg.getValue());
- if (!arg.getValue().isEmpty())
- {
- searchAlignment = false;
- }
- }
- }
- }
-
- 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))
- if (searchAlignment)
- {
- /*
- * no external database specified for search, so
- * export current alignment as 'database' to search
- */
- databaseFile = FileUtils.createTempFile("database", ".sto");
- AlignmentI al = af.getViewport().getAlignment();
- AlignmentI copy = new Alignment(al);
-
- deleteHmmSequences(copy);
-
- if (searchAlignment)
- {
- sequencesHash = stashSequences(copy.getSequencesArray());
- }
-
- exportStockholm(copy.getSequencesArray(), databaseFile, null);
- }
-
- args.add(getFilePath(seqFile, true));
- args.add(getFilePath(databaseFile, true));
- }
-
- /**
* Imports the data from the temporary file to which the output of jackhmmer was
* directed.
*/
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
+ readDomainTable(searchOutputFile, true);
+
if (searchAlignment)
{
recoverSequences(sequencesHash, seqs);
}
- readTable(searchOutputFile);
- int seqCount = Math.min(seqs.length, seqsToReturn);
+
+ int seqCount = seqs.length;
+
AlignmentI al = new Alignment(seqs);
}
}
- /**
- * Reads in the scores table output by jackhmmer and adds annotation to
- * sequences for E-value and bit score
- *
- * @param inputTableTemp
- * @throws IOException
- */
- void readTable(File inputTableTemp) throws IOException
- {
- BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
- String line = "";
- while (!line.startsWith("Query:"))
- {
- line = br.readLine();
- }
- while (!line.contains("-------"))
- {
- line = br.readLine();
- }
- line = br.readLine();
-
- int index = 0;
- while (!" ------ inclusion threshold ------".equals(line)
- && !"".equals(line))
- {
-
- Scanner scanner = new Scanner(line);
- String evalue = scanner.next();
- evalue = scanner.next();
- checkSequenceOrder(index, scanner);
- SequenceI seq = seqs[index];
- String score = scanner.next();
- addScoreAnnotations(evalue, score, seq);
- scanner.close();
- line = br.readLine();
- index++;
- }
-
- br.close();
- }
-
- private void checkSequenceOrder(int index, Scanner scanner)
- {
- String seqName = null;
-
- for (int i = 0; i < 8; i++)
- {
- seqName = scanner.next();
- }
-
- if (!seqs[index + 1].getName().equals(seqName))
- {
- SequenceI temp = seqs[index + 1];
-
- for (int j = 0; j < seqs.length; j++)
- {
- if (seqs[j].getName().equals(seqName))
- {
- seqs[index + 1] = seqs[j];
- seqs[j] = temp;
- break;
- }
- }
- }
- }
-
- protected void addScoreAnnotations(String eValue, String bitScore,
- SequenceI seq)
- {
- String label = "Search Scores";
- String description = "Full sequence bit score and E-Value";
-
- try
- {
- AlignmentAnnotation annot = new AlignmentAnnotation(label,
- description, null);
-
- annot.label = label;
- annot.description = description;
-
- annot.setCalcId(JACKHMMER);
-
- double dEValue = Double.parseDouble(eValue);
- annot.setEValue(dEValue);
-
- double dBitScore = Double.parseDouble(bitScore);
- annot.setBitScore(dBitScore);
-
- annot.setSequenceRef(seq);
- seq.addAlignmentAnnotation(annot);
-
- } catch (NumberFormatException e)
- {
- System.err.println("Error parsing " + label + " from " + eValue
- + " & " + bitScore);
- }
- }
git://source.jalview.org / jalview.git / blobdiff