--- /dev/null
+package jalview.hmmer;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.util.FileUtils;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Scanner;
+
+public abstract class Search extends HmmerCommand
+{
+
+ static final String JACKHMMER = "jackhmmer";
+
+ static final String HMMSEARCH = "hmmsearch";
+
+ boolean realign = false;
+
+ boolean trim = false;
+
+ SequenceI[] seqs;
+
+ String databaseName;
+
+ boolean searchAlignment = true;
+
+ Hashtable sequencesHash;
+
+ public Search(AlignFrame alignFrame, List<ArgumentI> args)
+ {
+ super(alignFrame, args);
+ }
+
+ @Override
+ public void run()
+ {
+ }
+
+ /*
+ void readOutputFile(File inputTableTemp) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
+
+
+ String line = "";
+ while (!line.startsWith("//"))
+ {
+
+ while (!line.startsWith(">> ") && !line.startsWith("//"))
+ {
+ line = br.readLine();
+ }
+
+ if (line.startsWith("//"))
+ {
+ break;
+ }
+
+ Scanner scanner = new Scanner(line);
+ String name = scanner.next();
+ name = scanner.next();
+
+ br.readLine();
+ br.readLine();
+
+ List<SequenceI> domains = new ArrayList<>();
+
+ for (SequenceI seq : seqs)
+ {
+ if (seq.getName().contains(name))
+ {
+ domains.add(seq);
+ }
+ }
+
+ if (domains.contains(getSequence()))
+ {
+ domains.remove(getSequence());
+ }
+
+ if (domains.size() > 0)
+ {
+ readOutputTable(br, domains);
+ }
+
+ line = br.readLine();
+ }
+
+ }
+
+
+ /**
+ * Reads in the scores table output by jackhmmer and adds annotation to
+ * sequences for E-value and bit score
+ *
+ * @param inputTableTemp
+ * @throws IOException
+ */
+ /*
+ void readOutputTable(BufferedReader br, List<SequenceI> seqs) throws IOException
+ {
+ String line = br.readLine();
+
+ while (!"".equals(line) && line != null)
+ {
+ if (" ------ inclusion threshold ------".equals(line))
+ {
+ line = br.readLine();
+ continue;
+ }
+
+ Scanner scanner = new Scanner(line);
+ scanner.next();
+ scanner.next();
+ String score = scanner.next();
+
+ scanner.next();
+
+ String evalue = scanner.next();
+
+ scanner.next();
+ scanner.next();
+ scanner.next();
+ scanner.next();
+
+ int start = scanner.nextInt();
+ int end = scanner.nextInt();
+
+ SequenceI seq = null;
+ for (SequenceI sequence : seqs)
+ {
+ if (sequence.getStart() >= start && sequence.getEnd() <= end)
+ {
+ seq = sequence;
+ break;
+ }
+ }
+
+ if (seq != null)
+ {
+ addScoreAnnotations(evalue, score, seq);
+ }
+
+ scanner.close();
+ line = br.readLine();
+ }
+ }
+ */
+
+ void readDomainTable(File inputTableTemp, boolean includesQuery)
+ throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
+
+ String line = br.readLine();
+ br.readLine();
+ br.readLine();
+ line = br.readLine();
+
+ int index;
+
+ if (includesQuery)
+ {
+ index = 1;
+ }
+ else
+ {
+ index = 0;
+ }
+ while (!line.startsWith("#"))
+ {
+ if (line.contains("inclusion threshold"))
+ {
+ line = br.readLine();
+ continue;
+ }
+
+ Scanner scanner = new Scanner(line);
+ String name = scanner.next();
+
+ for (int i = 0; i < 10; i++)
+ {
+ scanner.next();
+ }
+
+ String evalue = scanner.next();
+ scanner.next();
+ String score = scanner.next();
+
+ addScoreAnnotations(evalue, score, seqs[index]);
+ index++;
+
+ scanner.close();
+ line = br.readLine();
+ }
+ br.close();
+ }
+
+
+
+
+ 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);
+ }
+ }
+
+ void buildArguments(List<String> args, File searchOutputFile,
+ File hitsAlignmentFile, File queryFile) throws IOException
+ {
+ args.add("--domtblout");
+ args.add(getFilePath(searchOutputFile, true));
+ args.add("-A");
+ args.add(getFilePath(hitsAlignmentFile, true));
+
+ File databaseFile = null;
+
+ boolean useEvalueCutoff = false;
+ boolean useScoreCutoff = false;
+ String seqReportingEvalueCutoff = null;
+ String domReportingEvalueCutoff = null;
+ String seqReportingScoreCutoff = null;
+ String domReportingScoreCutoff = null;
+ String seqInclusionEvalueCutoff = null;
+ String domInclusionEvalueCutoff = null;
+ String seqInclusionScoreCutoff = null;
+ String domInclusionScoreCutoff = 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(REPORTING_SEQ_EVALUE_KEY)
+ .equals(name))
+ {
+ seqReportingEvalueCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(REPORTING_SEQ_SCORE_KEY)
+ .equals(name))
+ {
+ seqReportingScoreCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(REPORTING_DOM_EVALUE_KEY)
+ .equals(name))
+ {
+ domReportingEvalueCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(REPORTING_DOM_SCORE_KEY)
+ .equals(name))
+ {
+ domReportingScoreCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(INCLUSION_SEQ_EVALUE_KEY)
+ .equals(name))
+ {
+ seqInclusionEvalueCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(INCLUSION_SEQ_SCORE_KEY)
+ .equals(name))
+ {
+ seqInclusionScoreCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(INCLUSION_DOM_EVALUE_KEY)
+ .equals(name))
+ {
+ domInclusionEvalueCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(INCLUSION_DOM_SCORE_KEY)
+ .equals(name))
+ {
+ domInclusionScoreCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(DATABASE_KEY).equals(name))
+ {
+ databaseFile = new File(arg.getValue());
+ if (!arg.getValue().isEmpty())
+ {
+ searchAlignment = false;
+ }
+ }
+ else if (MessageManager.getString(NUMBER_OF_ITERATIONS)
+ .equals(name))
+ {
+ if (!arg.getValue().isEmpty())
+ {
+ args.add("-N");
+ args.add(arg.getValue());
+ }
+ }
+ }
+ }
+
+ if (useEvalueCutoff)
+ {
+ args.add("-E");
+ args.add(seqReportingEvalueCutoff);
+ args.add("--domE");
+ args.add(domReportingEvalueCutoff);
+
+ args.add("--incE");
+ args.add(seqInclusionEvalueCutoff);
+ args.add("--incdomE");
+ args.add(domInclusionEvalueCutoff);
+ }
+ else if (useScoreCutoff)
+ {
+ args.add("-T");
+ args.add(seqReportingScoreCutoff);
+ args.add("--domT");
+ args.add(domReportingScoreCutoff);
+
+ args.add("--incT");
+ args.add(seqInclusionEvalueCutoff);
+ args.add("--incdomT");
+ args.add(domInclusionEvalueCutoff);
+ }
+
+ // 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(queryFile, true));
+ args.add(getFilePath(databaseFile, true));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff